tag:blogger.com,1999:blog-68218407587560750482024-03-13T19:21:29.629-07:00Evolutionary NoveltiesA blog mainly about evolution. But sometimes linguistics or baseball.Unknownnoreply@blogger.comBlogger110125tag:blogger.com,1999:blog-6821840758756075048.post-29258590228942594842017-07-29T09:03:00.003-07:002017-07-29T09:03:52.416-07:00How many manuscripts to review?<div dir="ltr" style="text-align: left;" trbidi="on">
Question from a colleague about how many manuscripts to review:<br />
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<span style="font-family: Helvetica; font-size: 12px;">I saw your note about being awash with review requests on Twitter. </span><br />
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<span style="font-family: Helvetica;"><span style="font-size: 12px;">I'm just curious what your opinion is on the number of papers we should agree to review per month; i.e. What is professionally responsible?</span></span><br />
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<span style="font-family: Helvetica;"><span style="font-size: 12px;">I still learning the rules here on when is OK to say no to things.</span></span><br />
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My fairly off-the-cuff response (although it is something I've thought about over the years):<span style="-webkit-text-stroke: rgb(0, 0, 0);"> </span><br />
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<span class="s1">Well, I don’t think there is any rule at all against saying ’no’; especially to review a paper.<span class="Apple-converted-space"> </span></span></div>
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<span class="s1">Before agreeing to review, I must:</span></div>
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<span class="s1">1. Be very interested to read the manuscript</span></div>
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<span class="s1">2. Confident I am qualified to critique at least 1 major aspect of the paper</span></div>
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<span class="s1">3. Not be reviewing more than 2 other manuscripts already at the time (unless REALLY interested in it)</span></div>
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<span class="s1">4. Feel I have a reasonable chance to be able to complete it in the timeframe they request (ie not too swamped with other stuff at the time).<span class="Apple-converted-space"> </span></span></div>
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<span class="s1">I suppose my rule of thumb-calculus is that every paper requires 2-3 reviewers (although more if submitted more than once), so to break even, we’d need to review 2-3 manuscripts for every publication — but don’t forget to divide by the number of co-authors of all your publications. So, for me, my papers have at least 2-3 co-authors almost always. Therefore, reviewing 1 paper for every publication feels fair to me. I’ve never discussed this with anyone before, so there could be some flaws in my logic.</span></div>
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<span class="s1">But honestly, I don’t think about the quota, I think about #1-4. I get enough requests that agreeing to the interesting ones leads to enough (based on my rule-of-thumb calculus; which others may disagree with, of course).</span></div>
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<span class="s1">If declining, I try to do so quickly, and recommend someone else. </span></div>
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<span class="s1">Also, I sometimes ask grad students to review papers that I”m asked to do. If they are new at it, I read their review, and let the editor know about that. It is good training for them, and can save a little time for me doing the full review. A few journals now have a formal process for that, I think it might be common in molecular biology.</span></div>
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Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-6821840758756075048.post-54762036528498277572017-02-14T09:35:00.000-08:002017-02-14T09:35:00.228-08:00Exaptation vs Neo-functionalization vs Co-option<div dir="ltr" style="text-align: left;" trbidi="on">
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<span><span style="vertical-align: baseline;"><span style="font-family: Arial;"><span style="white-space: pre-wrap;">I just reviewed a paper that equated Neo-functionaliztion, exaptation, and co-option - using the terms </span><span style="white-space: pre-wrap;">interchangeably</span><span style="white-space: pre-wrap;">. My first instinct was that this was a problem, but it took me a while to work through my thoughts on it; including influential twitter discussion with Vincent Lynch. I thought I would put my thoughts here, in case they are useful or objectionable to anyone.</span></span></span></span><br />
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<span id="docs-internal-guid-8a30ec1e-3d88-4e36-e0c8-b25f7a12693a"><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">In my understanding of the terms, “</span><span style="font-family: Arial; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Neo-functionalization</span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">” implies that a *</span><span style="font-family: Arial; font-style: italic; vertical-align: baseline; white-space: pre-wrap;">duplicated</span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">* structure (usually a gene, but not always) gains a new function. As Vinny puts it:</span></span><br />
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<span style="background-color: white; color: #292f33; font-family: Arial, sans-serif; font-size: 26px; letter-spacing: 0.26px; white-space: pre-wrap;">"b/c neofunc is a process in which a homologous character maintains ancestral function"</span></div>
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<a href="https://twitter.com/VinJLynch/status/829763433721655296" target="_blank">https://twitter.com/VinJLynch/status/829763433721655296</a><br />
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<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">“</span><span style="font-family: Arial; font-weight: 700; vertical-align: baseline; white-space: pre-wrap;">Exaptation</span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">” implies no such duplication. A classic example is feathers - their original function was probably insulation, and their exapted function is flight. Here, there is no substantive change in the exapted structure (or at least that is not the point) - instead, exaptation is a change in function at one level of biological organization. The point is that selection can fix a structure with one function that is later exapted for another function.</span></span><br />
<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span>
<span style="font-family: Arial; white-space: pre-wrap;"><b>Co-option</b> is a bit similar to both neo-functionalization and exaptation; but I think there are subtle differences. C</span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">o-option has become a dominant term in gene expression, and I think even in other contexts (unlike co-option and neo-functionalization) usually examines two levels of structural organization at once. For example, co-option </span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">of a gene is inferred when we discover expression in a new place (or perhaps time). Co-option is a copying of expression, but not a duplication of the gene’s structure. Expression is an element of function, but not really the same as the organismal functions usually in play in exaptation. I think people use co-option similarly in morphology where a structure is moved to a new place to become part of another structure that was already there.</span><br />
<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span>
<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">Unfortunately, co-option is a very vague and diffuse term in general, and I think is used in ways more extensively than I suggested in the previous paragraph.</span></span><br />
<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;"><br /></span></span>
<span><span style="font-family: Arial; vertical-align: baseline; white-space: pre-wrap;">For one thing, co-option is sometimes used to describe a duplicated element (see Ganfornina et al 1999 for some examples). For another thing, co-option refers to both pattern and process (mentioned in Oakley, 2007). It is used both to describe a pattern where a gene seems to be expressed in unrelated places, and to describe the mechanism that causes such gene expression. It's like the early days of "species", where species meant both the elements and the process.</span></span><br />
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Ganfornina M.D., Sánchez D. 1999. Generation of evolutionary novelty by functional shift. Bioessays. 21:432–439.<br />
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Oakley T.H. 2007. A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evol. Dev. 9:514–516.</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-91703499829650602712016-12-22T11:31:00.001-08:002016-12-22T11:31:27.423-08:00tsujii abounds<div dir="ltr" style="text-align: left;" trbidi="on">
For the first time ever, I was able to collect all at once hundreds of Vargula tsujii, the California Sea Firefly. Here is the story.<br />
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I've collected <i>V. tsujii</i> at Catalina Island and in San Pedro Los Angeles in the past. But never before have I trapped more that a few 10's of them at a time.<br />
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But on Sunday December 18, we got nearly 1000 in our traps at San Pedro. Cabrillo Beach is just in front of the public aquarium by the same name. There is a boat launch there. In past years, I collected <i>tsujii </i>there by trapping. On the pier next to the boat launch, I would get a few animals in the traps. There used to be a jetty extending out perpindicular to the beach. I'd walk out to the end of that and was able to get more animals in each trap, perhaps up to 50 at a time. But for several years, I was not getting any at all in traps, and folks from our lab also tried, to no avail. The disappearance seemed to correspond to with beach dredging that I saw going on several years ago. This might be the project listed in 2013 <a href="https://www.portoflosangeles.org/history/timeline.asp" target="_blank">here</a>. A colleague told me she'd gotten some animals recently, so I decided to try again, when high seas foiled a trip to Catalina to get tsujii.<br />
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I set 5 PVC traps in just a couple feet of water, maybe 20 feet out on the pier next to the boat launch. I always try to drop the traps in dark places, because I think many ostracods are negatively phototactic. I set the traps at about 5:30 pm and brought them in around 10:00 pm. When I looked at the traps later in the hotel, I couldn't believe my eyes. The mesh funnels were caked with 'cods. I had never seen this many <i>tsujii</i>. I've seen <i>hilgendorfii </i>in this abundance and <i>Photeros annecohenae</i>, but never <i>tsujii</i>.<br />
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The habitat does look cleaner to me now, compared to before the dredging. The Port of LA was required by law to clean up the area, according to this <a href="http://www.ocregister.com/articles/schaadt-602108-open-marsh.html" target="_blank">link</a>. I can't be certain, but it sure seems like this has improved the tsujii in the area. I used to see weedy algae and thousands of caprellid amphipods in that algae. Now there is sea grass and kelp, and the water looks much clearer. The salt marsh is also restored (news story link above) and it might allow more fish to survive, food for the ostracods. Of course, we also had warmer seas last year from El Nino, so that might have contributed, too.<br />
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Back at UCSB, I sorted the tsujii from the remaining bait, sand, and algae. I counted roughly 800 animals alive, plus some that died during transit. All in all, perhaps pushing 1000.<br />
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After a couple days in the flowing sea water at UCSB, in various containers (some of which may have leaked), we sorted and counted all the stages. These are the results:<br />
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Adult males: 49<br />
Adult females: 228<br />
Brooding females: 3<br />
Juveniles: 348<br />
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for a total of 628. This is less than the 800 of my rough count, some were lost out of one container, and I may have counted wrong. But as a BARE minimum, we got over 600 healthy animals to UCSB from San Pedro!<br />
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We also sorted a sample of the juveniles to get an idea of the demographics, with these results:<br />
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A-1: 121<br />
A-2: 153<br />
A-3: 75<br />
A-4: 12<br />
A-5: 1<br />
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I am keeping these is sea water at UCSB. Since they are local (small populations live here, we've trapped a few of them), we can use flowing sea water, which makes care easier. I'm keeping them in small mesh boxes made for breeding fish. Water flows through them to keep the water fresh, but the ostracods cannot swim through the mesh.<br />
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Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-20111701805344553112016-11-16T12:39:00.001-08:002016-11-16T12:39:16.753-08:00Drafting Sisters or Public Goods - how tree-like is evolution?<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="font-family: Arial;"><span style="font-size: 14.6667px; white-space: pre-wrap;">I am drafting a paper exploring how tree like evolution is. A prime focus will be on "cell type trees" and "organ trees" - phylogenetic trees of those entities using gene expression data.</span></span></div>
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<span style="font-family: Arial;"><span style="font-size: 14.6667px; white-space: pre-wrap;">I want to set the stage for that discussion in the context of similar questions for gene trees and species trees.</span></span></div>
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<span style="font-family: Arial;"><span style="font-size: 14.6667px; white-space: pre-wrap;">Here is a draft of 8 paragraphs starting in that direction. Note, these are not yet referenced fully, and are a hastily written draft. Any feedback, comments, omissions, disagreements, etc are most welcome.....</span></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 21.333333333333332px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 21.333333333333332px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Sisters or Public Goods? How tree-like is the evolution of genes, modules, cell types, organs, or species?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 18.666666666666664px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Introduction</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The metaphor of a tree of life occupies a central place in our understanding of evolution, but how often do features evolve strictly by bifurcation? Is there an alternative metaphor to the tree of life? At the level of species, horizontal transfer, hybridization, and incomplete lineage sorting often interrupt strict bifurcation (or “treeness” </span><a href="https://paperpile.com/c/znBhhd/dWwv" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Cavalli-Sforza and Piazza 1975)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">), causing incongruence between the history of genes and the species that contain them. Therefore, the history of all species cannot accurately be visualized as a single bifurcating tree. Instead, that history is a network. What about other levels of biological organization? Protein domains, genes, modules, cell types, and organs may also evolve by furcation </span><a href="https://paperpile.com/c/znBhhd/hGnI" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Oakley et al. 2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, and if so, their history could be visualized as phylogenetic trees. However, at each of these levels, processes analogous to horizontal transfer, including domain shuffling and co-option, also interrupt strict treeness. Therefore, those histories are also often networks rather than trees. An alternative to strict tree-thinking may be a public goods metaphor </span><a href="https://paperpile.com/c/znBhhd/U3y8" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(McInerney et al. 2011)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, borrowed from economics, where biological entities are ‘non-excludable’. In the context of species phylogeny, ‘non-excludable’ means that the the parts of species (e.g. genetic material) can be transferred horizontally from species to distantly related species. What, if any, are the implications for our understanding of evolution if we adopt a public goods metaphor instead of the tree of life?</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 18.666666666666664px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Thinking about evolutionary history at multiple levels</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">If evolutionary history is treelike, or if we can determine subsets of life’s history that are treelike, we can use the statistical machinery of phylogenetics, developed over decades, to analyze the rising deluge of RNA-seq data and address questions of homology, convergent evolution, cell-type evolution, and more. If evolution is usually not treelike, we may need a fundamental shift in how we analyze comparative data sets. Before exploring whether evolution is treelike, I use this section to explain some background, introducing how we might think about evolutionary history at levels of organization that include protein domains, cell-types, organs, and morphological characters.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">All of life shares common descent and biologists use tree thinking </span><a href="https://paperpile.com/c/znBhhd/bijX" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Plachetzki and Oakley 2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> to organize patterns of common descent. Patterns of common descent result from mechanisms that split lineages. I’ve previously termed lineage splitting at any level “furcation” </span><a href="https://paperpile.com/c/znBhhd/hGnI" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Oakley et al. 2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. The mechanisms that split species and genes are speciation and gene duplication, respectively. In addition, mechanisms may split lineages at other levels. Parts of genes, like protein domains furcate through “exon shuffling”. Developmental fields furcate by field splitting </span><a href="https://paperpile.com/c/znBhhd/XV27+aESW+hGnI+3EWj" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Friedrich 2006; Oakley et al. 2007; Buschbeck and Friedrich 2008; Oakley and Rivera 2008)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> and cell types furcate to become sister cells, perhaps often by subdividing functions of the ancestral cell </span><a href="https://paperpile.com/c/znBhhd/GkPB+YAVY" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Arendt 2008; Arendt et al. 2009)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. If new biological entities arise strictly by furcation, then a bifurcating tree, the tree of life metaphor, is the result. Biologists are used to thinking about bifurcating gene trees and species trees. In addition, some scientists have begun to explore the idea of phylogenetic trees of protein networks </span><a href="https://paperpile.com/c/znBhhd/bijX" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Plachetzki and Oakley 2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, morphological features, tissues, and organs </span><a href="https://paperpile.com/c/znBhhd/hGnI+XV27+VYJU" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Geeta 2003; Oakley et al. 2007; Buschbeck and Friedrich 2008)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, and cell types </span><a href="https://paperpile.com/c/znBhhd/GkPB" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Arendt 2008)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The tree of life metaphor makes a strict assumption that during lineage splitting, all components are inherited vertically, from direct ancestor to descendant, and are never passed horizontally, from evolutionary cousin to cousin. We know this assumption is often violated through mechanisms that vary by level of organization. The components of genes (protein domains) are often exchanged between distantly related genes </span><a href="https://paperpile.com/c/znBhhd/ApS2" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Haggerty et al. 2013)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> by duplicating domains independently of full genes. Therefore, a gene tree may not be strictly bifurcating, forming a network. Multiple mechanisms can cause incongruence of species tree and gene trees, such that genes are sometimes exchanged horizontally. Horizontal transfer occurs routinely through various copying mechanisms in prokaryotes, but is also important in animals (refs). Hybridization and introgression are being recognized as a common mechanism </span><a href="https://paperpile.com/c/znBhhd/EF0m+lb4R" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Hahn and Nakhleh 2016; Pease et al. 2016)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> that we might call horizontal transfer, even though close relatives are involved. In cell type and tissue phylogenies, the components also may not be inherited from direct ancestors, as in the sister-cell model, but rather could be co-opted from distant cell-type or tissue-cousins. When the assumption of vertical descent holds, there is great potential to use existing phylogenetic methods to understand evolution. However, given that strict bifurcation is commonly violated, we may want to explore other models and metaphors for macroevolution. One of those metaphors is a public goods model.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 18.666666666666664px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Economic classification of goods</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In economics, “goods” may be classified into a 2x2 matrix, forming four categories. In practice, the categories are usually not discrete alternatives, but instead form axes with continuous variation. One axis asks how “excludable” and the other axis asks how “rival” is a particular good. Non-excludable goods can be ubiquitously accessed, whereas excludable goods have restricted access. For example, the air we breath has low excludability because we cannot prevent anyone from breathing the atmosphere. However, a theme park is quite excludable; only those with a ticket may enter. On the other axis, highly rivalrous goods are exhaustible, but non-rival goods are unlimited. A parking space is rivalrous because if I park there, no one else can. In contrast, a public radio signal is non-rivalrous. My listening to 92.9 KJEE does not prevent someone else from also listening. “Public goods” are defined as both nonrivalrous and nonexcludable. The extreme corners of these two axes form four named categories and there are many everyday examples for each category (Table 1).</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Table 1</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. The classification of goods</span></div>
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<table style="border-collapse: collapse; border: none;"><colgroup><col width="148"></col><col width="227"></col><col width="249"></col></colgroup><tbody>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Excludable (high)</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Excludable (low)</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Rivalrous (high)</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Private Goods</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Car, apple, parking spot</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Common Pool Goods</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Fish stock, public park bench</span></div>
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<tr style="height: 0px;"><td style="border-bottom: solid #000000 1px; border-left: solid #000000 1px; border-right: solid #000000 1px; border-top: solid #000000 1px; padding: 7px 7px 7px 7px; vertical-align: top;"><div dir="ltr" style="line-height: 1.2; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Rivalrous (low)</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Club Goods</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Private golf course,</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">satellite TV</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Public Goods</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Air, public radio signal, </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 18.666666666666664px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Public Goods in Macroevolution</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Recent papers applied the concept of public goods to macroevolutionary topics like the tree of life and novelties. McInerney et al </span><a href="https://paperpile.com/c/znBhhd/U3y8/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2011)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> considered genetic material (“genes” for short) to be a public good and considered biological species to be the consumers in this economic metaphor. McInerney et al </span><a href="https://paperpile.com/c/znBhhd/U3y8/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2011)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> contrast their public good hypothesis of genes with the traditional idea of a universally bifurcating ‘tree of life’, with vertical transmission from ancestor to descendant species. With only vertical transmission, genes are highly excludable between species because they can only be present in a genome if inherited from a direct ancestor. Genes also have low rivalrousness because no matter how many descendents evolve, they all can have those genes in their genome. Non-rivalrous, excludable goods of the tree of life model are “club goods”. Instead, McInerney et al </span><a href="https://paperpile.com/c/znBhhd/U3y8/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2011)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> argue that genes should be considered “public goods” because horizontal transfer is very common. Horizontal transfer makes genes much less excludable because they could be transferred from any clade to any other clade.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Erwin </span><a href="https://paperpile.com/c/znBhhd/jVua/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2015)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> applied the concept of public goods to major innovations during evolution. He extends public goods thinking in macroevolution beyond genes to include environmental and ecological goods. In particular, he suggests that the origins of particular public goods were associated with major transitions in evolution. A prime example is the production of oxygen, first as a waste product of photosynthetic cyanobacteria. Once oxygen accumulated in the Great Oxygenation Event, it became both non-excludable and non-rivalrous, a public good that was exploited by other organisms. </span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The macroevolutionary applications above differ from public goods applications to microevolution, especially by ignoring costs. Frank </span><a href="https://paperpile.com/c/znBhhd/JQTx/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2010)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> defined a public good as “An individually </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">costly </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">act that benefits all group members”. The conflict between cost and benefit is central to microevolutionary topics like altruism or cooperation, kin and group selection </span><a href="https://paperpile.com/c/znBhhd/fAIV" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Hamilton 1975)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, parasite virulence </span><a href="https://paperpile.com/c/znBhhd/prVr" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Frank 1996)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, ‘tragedy of the commons’ scenarios, and cases where microbes produce public goods like nitrogen </span><a href="https://paperpile.com/c/znBhhd/632D" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(West et al. 2002)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> or iron-scavenging molecules </span><a href="https://paperpile.com/c/znBhhd/peyn" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Kümmerli et al. 2009)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. One link of these microevolutionary topics to macroevolution posits that cooperation between units led to changes in the level of selection that precipitated major transitions in evolution </span><a href="https://paperpile.com/c/znBhhd/HFgq" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Smith and Szathmary 1997)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. Unlike the microevolutionary applications, where a cost is incurred by individuals producing the good, the macroevolutionary applications discussed above are not concerned with costs to the producers. The production of oxygen is presumably cost-free waste for the photosynthetic organisms that produce it and only a benefit to some organisms that do not produce it, like animals. Oxygen production does not then set the stage for conflict between producers and benefactors that are so central to the microevolutionary topics listed above. Similarly, if genes are public goods for all species through horizontal transfer, the costs to producers again are not apparent. There would seem to be no direct cost to a species if one its genes are copied into a distant relative. Perhaps because of this explicit absence of costs (and any quantification of benefits), very little research in macroevolution uses the mathematical framework of public goods that is so prevalent in microevolution. Instead, the macroevolutionary research simply points out that some critical elements of evolution are nonrivalrous and nonexcludable.</span></div>
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<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 700; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Measuring Excludability with Treeness</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<br /></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 11pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/GkPB" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Arendt D. 2008. The evolution of cell types in animals: emerging principles from molecular studies. Nat. Rev. Genet. 9:868–882.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/YAVY" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Arendt D., Hausen H., Purschke G. 2009. The “division of labour” model of eye evolution. Philosophical Transactions of the Royal Society B-Biological Sciences. 364:2809–2817.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/XV27" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Buschbeck E.K., Friedrich M. 2008. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling. Evo Edu Outreach. 1:448–462.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/dWwv" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Cavalli-Sforza L.L., Piazza A. 1975. Analysis of evolution: evolutionary rates, independence and treeness. Theor. Popul. Biol. 8:127–165.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/jVua" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Erwin D.H. 2015. A public goods approach to major evolutionary innovations. Geobiology. 13:308–315.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/bveQ" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Ferrer R.P., Zimmer R.K. 2012. Community ecology and the evolution of molecules of keystone significance. Biol. Bull. 223:167–177.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/prVr" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Frank S.A. 1996. Models of parasite virulence. Q. Rev. Biol. 71:37–78.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/JQTx" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Frank S.A. 2010. A general model of the public goods dilemma. J. Evol. Biol. 23:1245–1250.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/aESW" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Friedrich M. 2006. Continuity versus split and reconstitution: exploring the molecular developmental corollaries of insect eye primordium evolution. Dev. Biol. 299:310–329.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/VYJU" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Geeta R. 2003. Structure trees and species trees: what they say about morphological development and evolution. Evol. Dev. 5:609–621.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/ApS2" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Haggerty L.S., Jachiet P.-A., Hanage W.P., Fitzpatrick D., Lopez P., O’Connell M.J., Pisani D., Wilkinson M., Bapteste E., McInerney J.O. 2013. A pluralistic account of homology: adapting the models to the data. Mol. Biol. Evol.:mst228.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/EF0m" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Hahn M.W., Nakhleh L. 2016. Irrational exuberance for resolved species trees. Evolution. 70:7–17.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/fAIV" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Hamilton W.D. 1975. Innate social aptitudes of man: an approach from evolutionary genetics. Biosocial anthropology. 133:155.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/peyn" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Kümmerli R., Jiricny N., Clarke L.S., West S.A., Griffin A.S. 2009. Phenotypic plasticity of a cooperative behaviour in bacteria. J. Evol. Biol. 22:589–598.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/U3y8" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">McInerney J.O., Pisani D., Bapteste E., O’Connell M.J. 2011. The Public Goods Hypothesis for the evolution of life on Earth. Biol. Direct. 6:41.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/hGnI" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Oakley T.H., Plachetzki D.C., Rivera A.S. 2007. Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod Struct. Dev. 36:386–400.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/3EWj" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Oakley T.H., Rivera A.S. 2008. Genomics and the evolutionary origins of nervous system complexity. Curr. Opin. Genet. Dev. 18:479–492.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/lb4R" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Pease J.B., Haak D.C., Hahn M.W., Moyle L.C. 2016. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation. PLoS Biol. 14:e1002379.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/bijX" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Plachetzki D.C., Oakley T.H. 2007. Key transitions during the evolution of animal phototransduction: novelty,“tree-thinking,” co-option, and co-duplication. Integr. Comp. Biol.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/D6G1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Serb J.M., Oakley T.H. 2005. Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology. Bioessays. 27:1158–1166.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/HFgq" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Smith J.M., Szathmary E. 1997. The Major Transitions in Evolution. OUP Oxford.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/632D" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">West S.A., Kiers E.T., Simms E.L., Denison R.F. 2002. Sanctions and mutualism stability: why do rhizobia fix nitrogen? Proc. Biol. Sci. 269:685–694.</span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 11pt; margin-left: 22pt; margin-top: 0pt; text-indent: -22pt;">
<a href="http://paperpile.com/b/znBhhd/2BZh" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Whitehead A., Crawford D.L. 2006. Variation within and among species in gene expression: raw material for evolution. Mol. Ecol. 15:1197–1211.</span></a></div>
<span id="docs-internal-guid-d809ee73-6ed9-52cb-b432-f2e798ac8f03"><a href="http://paperpile.com/b/znBhhd/4j8l" style="text-decoration: none;"><span style="color: black; font-family: Arial; font-size: 14.6667px; vertical-align: baseline; white-space: pre-wrap;">Wray G.A., Hahn M.W., Abouheif E., Balhoff J.P., Pizer M., Rockman M.V., Romano L.A. 2003. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20:1377–1419.</span></a></span></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-62220996248948202292016-10-15T11:57:00.000-07:002016-10-15T11:57:01.747-07:00What grad students need to know about submitting a grant proposal<div dir="ltr" style="text-align: left;" trbidi="on">
Our lab just submitted two Doctoral Dissertation Improvement Grants (DDIGs). Each time I've been involved in similar such submissions - including when I first submitted a grant to NASA as a grad student in the late 1990s - I find that graduate students encounter a number of misunderstandings. These can cause obstacles to submitting the grants that could be lessened or avoided if they knew about this in advance.<br />
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I hope I will remember to show this post to my future students, and I hope others can find it useful too.<br />
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1. <b>The Institution (e.g. The University) </b><b>officially submits m</b><b>any grants, NOT the individual student.</b> I think this is the root cause of most of the misunderstandings. While some student grants are submitted by an individual (especially local departmental grants or grants to scientific societies) - <i>most are submitted by the institution</i>. So, here at UCSB, The University Office of Research submits a DDIG, as with any full proposal to NSF or NIH. Since the grants that students submit early in their careers are smaller grants to smaller agencies, the students might think that all proposals are submitted by individuals, but they are not.<br />
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The fact that the institution submits grants has several important downstream effects.<br />
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2. <b>Your practical deadline will be earlier than the final proposal deadline.</b> Since The University has to make sure that the proposal does not break any rules, staff need to read your proposal and approve it before it is submitted. At UCSB, our Office of Research (OR) requests us to give them the full proposal 1 week before the deadline. NOTE: They still allow some changes to the proposal after their screening, as long as they don't affect things that OR is looking to approve. So, you can fix typos, change hypotheses, rewrite a section. As long as you do not do things like: Add a new experiment that now requires IACUC (animal welfare) approval, add a new experiment on human subjects, add a new experiment that requires SCUBA, or other activities that are regulated by the institution. The OR will also check the grant for compliance, and may give feedback about things that don't comply.<br />
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3. <b>There are other forms and signatures needed, besides those required by the grant. </b>Again because The Institution submits the grant, they want assurances about the activities proposed in the grant. The forms at UCSB ask whether we propose to use human or vertebrate subjects, whether we will use SCUBA, whether we will use recombinant/genetically engineered organisms, whether we are up to date on chemical safety plans, and other things. Note that these activities of course do not prevent us from submitting a grant. Instead, they will trigger other actions that we need to take - like completing an IACUC or SCUBA plan.<br />
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4. <b>You need to contact your grant administrator early. </b>Institutions vary in how they handle grants. But I believe that usually, a department will have a grant administrator or team. My lab submits grants through UCSB's Marine Science Institute (MSI). My lab is assigned a grant administrator in MSI. She acts as a liaison with the UCSB Office of Research, and helps us get everything done that we need to do. In MSI, the grant administrator uploads files to Fastlane, and will create a formal budget (in a spreadsheet) based on the budget that we sketch. The budget can be complicated because there are a lot of rules (that change yearly) about overhead, salaries, and benefits. Overhead is a "tax" that the university charges on grants, that is used for institutional infrastructure that allows the research to be done.<br />
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Based on the above considerations, I recommend the following timeline:<br />
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<b>About 1-2 months in advance:</b><br />
A. Read the call for proposals to get an idea of whether your idea fits with the call. If you are unsure, call the program officer. You should also make a note of all the forms you will need to do, maybe make a To-Do list. This might include things like: A Data Management Plan, Your advisor's Biosketch (a specifically formatted CV), Collaborator Letters, Evidence of Permits, Evidence of your Advance to Candidacy, etc, etc<br />
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<b>About 1 month in advance of deadline:</b><br />
B. Contact your departmental grant administrator. Tell him or her that you will submit a grant in one month, and ask what the first steps are for you. For me, I usually provide the following:<br />
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<ol style="text-align: left;">
<li>The Title of the Grant Proposal</li>
<li>The projected start date of the proposed work</li>
<li>The duration of the proposed work</li>
<li>A sketch of the budget</li>
</ol>
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It seems counterintuitive and difficult to know what the budget and title will be so early. But these are the things the grant admin needs first. This is why I now focus on the big idea and the budgetary pieces first. What salary do I need to complete the work? What equipment? What supplies and services like sequencing services? (I usually estimate a yearly budget for supplies, and then fit details to that later)</div>
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C. For NSF, get your fastlane ID, or for other agencies, make sure you have any accounts that you need.</div>
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D. Write the actual the proposal. If you can complete a draft with several weeks to spare, you can get comments from colleagues. In our lab, I try to go back and forth on drafts with the student, making incremental improvements. I estimate I go through 5-10 drafts with each student. Often it is easier to focus on one section at a time. </div>
<div>
<br /></div>
<div>
I won't go into writing strategies here, this is about the administrative hurdles.</div>
<div>
<br /></div>
<div>
<br /></div>
<div>
<b>About 2 weeks before the deadline</b>. </div>
<div>
<br /></div>
<div>
E. Complete all forms and administrative paperwork. Check with your departmental grants administrator to make sure all is done. Re-read the call for propoposals carefully to make sure you have everything done.</div>
<div>
<br /></div>
<div>
F. Finalize the proposal, incorporating comments from colleagues.</div>
<br />
<br />
<br />
<b>About 1 week before the deadline</b>.<br />
<br />
G. Have your grant administrator contact the Office of Research to review your full proposal.<br />
<br />
<b>Just before the deadline</b><br />
<b><br /></b>
H. Make any final changes to your proposal. Some may be indicated by OR.<br />
I. When you are ready, tell your grant administrator they can submit the grant. Remember, the Institution applies for the grant, so they submit it too. Grants administrators like to submit a day early to avoid any unforeseen difficulties, like server traffic, or who-knows-what. Your grant administrator probably works 9-5 or maybe 9-12 that day for an appointment. Make sure to communicate about exactly when they will ask OR to submit the grant.<br />
<br />
<br />
And remember, "A grant is never done, the deadline just arrives."<br />
<br />
<b>After the deadline</b><br />
J. If you go back and re-read your proposal, you will find mistakes and typos. There is nothing you can do about it now. I know it's hard, but the best you can do is try to forget you ever submitted the proposal, until you get the email from the organization.<br />
<br />
<br />
This is based on my experience, mainly at UCSB. Specifics will vary from institute to institute. Specifics may also change from year to year. If I forgot some things, please add a comment and let everyone know!<br />
<br />
<br /></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-16540872057448062792016-03-07T10:13:00.002-08:002016-03-07T10:13:40.892-08:00Why is English - and biology - so Complicated?<div dir="ltr" style="text-align: left;" trbidi="on">
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">On the evening his sixtieth birthday, Kelly Sutton lay on the floor of his living room, barely alive and gasping for air. On the other side of town, his friends had planned a surprise party and they crouched in the darkness of their office space; in cubicles, behind desks and chairs, gripping confetti and streamers. They anxiously awaited Kelly’s arrival to celebrate his milestone. Earlier in the day, Kelly begrudgingly agreed to come back to the office to fix a computer. But Kelly did not return that evening. His friends would never get the chance to surprise him. As the night pressed on, Kelly’s friend Angus stared off into the darkened spaces of the office and began to put the pieces of a puzzle together. Not long before, Kelly had given Angus a prized possession, Kelly’s trusted pool cue. Angus hadn’t thought much about it at the time, but this was a clue. This was a cry for help.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Angus rushed to Kelly’s apartment. He burst out of the elevator across from Kelly’s door, only to find it locked and dead-bolted shut. Angus smelled the distinctly putrid odor of mercaptan, found in blood and brains, and excreted in animal feces. But because humans can detect it very easily, mercaptan is also added to natural gas so that we can quickly detect a leak of an otherwise colorless, odorless gas. Although his his tight acid washed jeans made bending difficult, Angus kneeled down, and quickly traced the odor to the crack under Kelly’s apartment door. Angus knew immediately he had to act quickly. He knew his friend was in grave, grave danger.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Angus spied a glass cabinet with a fire hose in the wall just next to Kelly’s apartment. He opened the cabinet door and hastily unravelled the hose, stringing the nozzle through Kelly’s door handle and tying the hose quickly but securely. Angus yanked a length of hose and pulled a Swiss Army knife from his pocket to cut the hose from the cabinet. Just then, the elevator door opened spontaneously, and Angus pulled the freshly cut hose into the back of the elevator, and tied it to the metal railing. He pushed the round plastic “1” button before jumping back out into the hall outside Kelly’s apartment. Then Angus flattened the hose on the floor, just as the elevator door closed above it. As the elevator went down, the slack came out of the hose, and pressure built on the door handle before the wood gave way with a smashing sound. Triumphant horns blared, reminiscent of the movie soundtrack of</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> Back to the Future</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> on a tight budget. Angus reached through the newly breached gap to open the door and find Kelly passed out on the floor. Angus fought through the stench, holding the front of his grey blazer over his face, while keeping its sleeves pushed up to his elbows. He closed the nozzle of the gas fireplace, before rushing to open a nearby window. Angus returned for his friend, hoisting Kelly’s limp body off the ground to the window for fresh air. After a pregnant pause, Kelly finally let out a cough. Angus’ shoulders dropped in relief and he put his hand on his friend’s shoulder as Kelly looked up at him sheepishly. “Happy Birthday”, was all Angus could say.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Kelly’s suicide attempt, prompted by his getting hustled out of his life’s savings, would alter the course of history by leaving an indelible mark on the English language. Once Kelly’s friends knew the reason for the attempted suicide, they brought an important visitor to the office by the name of Joanne Remmings (she happened to have just written a major research paper on bunko scams). Remmings was bookish and undeniably beautiful, with fine features beneath pulled-back blonde hair and behind impossibly large, impossibly round, and impossibly red, plastic-framed glasses. She was unashamedly excited to meet Angus and it was precisely that moment when history was made. She reached out to shake Angus’ hand.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">“Hi, Joanne Remmings”, she said.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">“MacGyver”, Angus replied, shaking her hand.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">“Oh I’ve heard about you”, her eyes widening, “you’re the guy that does the ‘whatchamacallits’, you know, ‘macgyverisms’.”</span></div>
<b id="docs-internal-guid-04fb9200-5242-92c5-a15c-d43d088095d4" style="font-weight: normal;"><br /></b>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">“Macgyverisms?”, Mac asked, with a touch of smugness.</span></div>
<b style="font-weight: normal;"><br /></b>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">And so a word was born. And so too did the English language increase - if ever so slightly - in complexity. A neologism - a new word - was born of and on the 1980’s television show </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MacGyver</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> as one of many quixotic eponyms to enter the English language. From that point forward, macgyver came to mean using materials at hand to quickly engineer an ad hoc solution to a problem.</span></div>
<b style="font-weight: normal;"><br /></b>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Some thirty years later, on Thanksgiving in 2014, sixty-seven year old fisherman Ron Ingraham was convinced he was going to die. He left Kaunakakai in his sailboat that day, aiming for the nearby port of Manele Bay, a short jaunt from one Hawaiian Island to another. This was not the sort of trip Ingraham, a seasoned seaman, would think twice about. But history tells us that the seas must be respected. After a rogue wave slammed into his 25-foot sailboat </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Malia</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, Ingraham was in trouble. Both Malia’s masts were broken, and she was taking on water. Ingraham got off a distress call that set into action a Coast Guard search. But after two days’ time and thousands of square miles searched, the rescue attempt was called off.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">People have survived at sea for extended periods of time. Although he doesn’t remember details, a fisherman from Mexico is thought to have survived 13 months at sea, before he was rescued some 6500 miles away in the Marshall Islands. In another incident, three teenagers from the tiny remote Pacific Islands of Tokelau once got drunk and mischievously stole a dinghy and tried to drive it to the next island. But they ran out of fuel and drifted for 41 days before a tuna-fishing boat happened to discover them, naked, blistered, and barely alive. The biggest challenge to surviving at sea is staying hydrated. Even though castaways are floating on an ocean, drinking sea water is like drinking poison. The Mexican fisherman says he ate small fish and drank birds’ blood. The Tokalauan boys collected just enough rain water on a tarp in their boat. But had the tuna-boat not seen them, they probably would have perished - mainly from dehydration - within a few days of when they were rescued.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Ron Ingraham’s ordeal was a 12-day drift, comfortable compared to the Tokalauan boys’ plight, yet it easily could have been much longer. Ingraham lives on his boat, so he had some supplies, including fishing gear. After his rescue, he told reporters he hydrated with fish. There is just enough hydration in fish eyes and fish bones for a person to survive. But Ingraham’s real break is the point of this story. According to his son’s interview, the elder Ingraham “</span><span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">managed to </span><span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">macgyver</span><span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> a way to make that last call.” Ron Ingraham’s radio had taken water and stopped working after the second day. When the Coast Guard could not find him, and did not hear any more signals, they gave up the search. But using material at hand (Angus MacGyver himself often used duct tape or a Swiss Army knife), Ingraham was able to fix his radio just enough to get off a mayday signal that saved his life. Some thirty years after the character Joanne Remmings first uttered the word ‘macgyverisms’ on network television, Ron Ingraham’s son found ‘macgyver’ to be the perfect word to describe his father’s life-saving improvisation.</span></div>
<br />
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">The Ingraham story has some irony. To describe his father’s nautical improvisation, Ingraham’s son actually eschewed a synonym with nautical origins: jury rig. The elder Ingraham not only macgyvered a fix for his radio, one might have said he jury rigged one. And here lies the irony: ‘jury rig’ originated as a term for a makeshift, often improvised mast, after the original mast of a ship breaks. This term is at least as old as 1616, according to the Oxford English Dictionary. And although originally a nautical term describing an improvised mast, it later came to mean any improvised solution, not only a nautical one. In fact, Ron Ingraham did lose both masts on his sailboat, but it was not a jury rig - in the original sense of the word at least - that saved him, it was a macgyvered radio that carried his cry for help to the Coast Guard. In the thirty years since Joanne Remmings, the word macgyverism and its variants (macgyver and macgyvered) had become enough of a part of the English language that Ingraham’s son had no qualms about using it in a formal interview with the press.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">So then, why is language so complicated? For that matter, why did organs like eyes evolve to be so complex? And why are most human systems - like governments, companies, computer programs, and sports leagues - so filled with complicated rules, traditions, and procedures?</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt; text-indent: 36pt;">
<span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span id="docs-internal-guid-04fb9200-5246-0ba0-386a-90e777ae62b2"><br /><span style="font-size: 14.6667px; vertical-align: baseline;">All of these entities are so complicated because they are </span><span style="font-size: 14.6667px; font-style: italic; vertical-align: baseline;">evolved</span><span style="font-size: 14.6667px; vertical-align: baseline;">. Because they have </span><span style="font-size: 14.6667px; font-style: italic; vertical-align: baseline;">history</span><span style="font-size: 14.6667px; vertical-align: baseline;">. Above all, these entities are complicated because they are governed by compromises, in many different ways. Language, biology, and human systems are giant collections of macgyverisms - one-off solutions to immediate needs: patches and retrofits that use whatever is at hand to meet a need. Once patches and retrofits become useful and integrated, they cannot be easily erased. Just as it would be ludicrous to ban new words like macgyver in the first place (even though a group called ‘The Immortals’ try to do just this for French), it would be impractical, even impossible to go back and erase “jury rig” from peoples’ consciousness and from literary history, just because the new word “macgyver” came along. And so the new solutions stay, often alongside the old. Jury rig remains alongside macgyver (and MacGyver), and remains alongside bricolage and kluge. If people use these words, they are useful. Biology is not much different. Mutations cause new combinations of parts, jury rigged and macgyvered together. If they are useful, an organism will pass the new combination along to its offspring. Once useful and integrated, these biological traits will not easily be erased. The complexity of human systems provide many other examples to illustrate the same principles. Rules, laws, and ways of doing things become institutionalized. Complexity increases as complexity evolves.</span></span></span></div>
<div>
<span style="background-color: white; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-18399804320529543222016-02-24T21:12:00.000-08:002016-02-24T23:56:19.950-08:00Response to Judge Starling on Novelty<div dir="ltr" style="text-align: left;" trbidi="on">
I've just experienced an interesting scientific exchange through social media. I believe much of the exchange boils down to "novelty" - an obsession of mine.<br />
<br />
Here is my version of what happened:<br />
<br />
1. I saw Dan Graur's post on "All of Evolutionary Biology in 12 Paragraphs" <a href="https://www.dropbox.com/s/5aqbuc7s46h48ht/All%20of%20evolutionary%20biology.pdf?dl=0" target="_blank">linked here</a>, a provocative claim to distill all of evolutionary biology into 237 words. Very interesting! Do I agree?<br />
<br />
Well, #10 stood out to me as false, especially the claim that "there is no true novelty in evolution"<br />
<br />
Update: The full statement is here "<i>10. Evolution cannot create something out of nothing; there is no true novelty in evolution.</i>"<br />
<br />
I am confident that Professor Graur is not a creationist, but this sounds like the creationist logic that goes, "there is only microevolution, but no macroevolution". I am sensitive to these things, having been quoted out of context by creationists. I could imagine creationists using this quote to argue things like 'evolutionists agree that evolution cannot produce new information - only destroy it'. Well, to my mind all of this is about equating processes that occur in populations with macroevolution. Macroevolution and microevolution are not the same -- even if microevolution is involved in every step along the way.<br />
<br />
My first response to the 12 paragraphs was this tweet:<br />
<blockquote class="twitter-tweet" data-conversation="none" data-lang="en">
<div dir="ltr" lang="en">
<a href="https://twitter.com/DanGraur"><br class="Apple-interchange-newline" />@DanGraur</a> #10 (no true novelty) must be struck from the list. Macroevolution made all of biodiversity - even if #10 is true in populations.</div>
— Todd Oakley (@UCSB_OakleyLab) <a href="https://twitter.com/UCSB_OakleyLab/status/701774329567010816">February 22, 2016</a><br />
<div>
<br /></div>
</blockquote>
If there is no true novelty, evolution cannot happen. Life could not evolve, photosynthesis could not evolve, eyes could not evolve. As I tweeted, macroevolution made ALL of biodiversity. Every species, every trait, every gene of every species. It simply does not follow that evolution could even occur without novelty. Evolution is a tinkerer, and biological entities get copied (at all levels of organization) and they diverge from each other. This is the source of novelty. True novelty. Before the origin of Pax genes, there may have been Paired domains, and there may have been Hox domains. But these domains came together anew (yes, by a single mutation in a single individual, originally, Prof Graur's #5) - but that WAS a novelty, a true novelty. Once that first Pax gene was fixed in that first population by (say) natural selection, evolution created a novelty. Evolution creates novelty like this every day, and has for billions of years to give us slime molds and sloths.<br />
<br />
As far as I can tell, my original tweet went mainly unnoticed. I think because I replied to a particular tweet in a thread discussing the "12 paragraphs" tweet.<br />
<br />
Next, someone else had the same critique I did about #10 of the 12 paragraphs. Here is what bluebear tweeted:<br />
<br />
<blockquote class="twitter-tweet" data-conversation="none" data-lang="en">
<div dir="ltr" lang="en">
<a href="https://twitter.com/toxicpath">@toxicpath</a> <a href="https://twitter.com/DanGraur">@DanGraur</a> Just because a famous authority says it, doesn't make it so. I think point 10) is nonsense. Evolution makes new things.</div>
— Blue Bear (@bluebearsoup) <a href="https://twitter.com/bluebearsoup/status/701840819037327360">February 22, 2016</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
<br />
<br />
Dan responded, and I replied to that response as follows:<br />
<br />
<blockquote class="twitter-tweet" data-conversation="none" data-lang="en">
<div dir="ltr" lang="en">
No novelty (creatio ex nihilo) in nature. Venoms from from digestive enzymes, fly halteres from wings. <a href="https://twitter.com/bluebearsoup">@bluebearsoup</a> <a href="https://twitter.com/toxicpath">@toxicpath</a></div>
— Dan Graur (@DanGraur) <a href="https://twitter.com/DanGraur/status/701844943258521600">February 22, 2016</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
<br />
<blockquote class="twitter-tweet" data-lang="en">
<div dir="ltr" lang="en">
<a href="https://twitter.com/DanGraur">@DanGraur</a> <a href="https://twitter.com/bluebearsoup">@bluebearsoup</a> <a href="https://twitter.com/toxicpath">@toxicpath</a> where did digestive enzymes & wings come from? &back &back. Don't submit to popgen hubris of no macroevo</div>
— Todd Oakley (@UCSB_OakleyLab) <a href="https://twitter.com/UCSB_OakleyLab/status/702003056825626624">February 23, 2016</a></blockquote>
<br />
Well, there is the source of the disagreement/argument. Dan says there is no creation from nothing (creatio ex nihilo) in nature. I agree this is true IN POPULATIONS but as stated above, I do not agree this can be true for evolution AS A WHOLE. In the tweet, I alluded to this difference by writing "don't submit to popgen hubris of no macroevo".<br />
<br />
By that I meant I think there are aspects of macroevolution that are not explained by population genetics alone. For example, I believe the evolution of complexity and diversity are not understood by thinking only about populations. Eyes and species and photosynthesis cannot originate within a single population (usually). These are composites of multiple changes that happen across time, in multiple different populations/generations. Sure, populations change at every step by processes like natural selection. But we can't know about natural selection in that population way back that first had a Pax gene, or that first added a pigment to a photoreceptor cell in the early evolution of eyes. But we still can ask questions about the timing and order of these macroevolutionary events. These are questions outside the scope of population genetics, and within the realm of macroevolution. I personally am not that interested in documenting some change in allele frequencies. But how did complex features, like eyes evolve? How did animals come to be able to *produce* light. These are the big questions that interest me, so I am sensitive to people dismissing these questions by equating microevolution and macroevolution. Such as this tweet:<br />
<blockquote class="twitter-tweet" data-conversation="none" data-lang="en">
<div dir="ltr" lang="en">
Evolution = a popgen process. Macroevolution = microevolution + time. Ergo, no macro evolution. <a href="https://twitter.com/UCSB_OakleyLab">@UCSB_OakleyLab</a> <a href="https://twitter.com/bluebearsoup">@bluebearsoup</a> <a href="https://twitter.com/toxicpath">@toxicpath</a></div>
— Dan Graur (@DanGraur) <a href="https://twitter.com/DanGraur/status/702016876876988416">February 23, 2016</a></blockquote>
Dan then tweeted:<br />
<blockquote class="twitter-tweet" data-conversation="none" data-lang="en">
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If I am wrong about macroevolution, what are the rules of macroevolution? <a href="https://twitter.com/UCSB_OakleyLab">@UCSB_OakleyLab</a> <a href="https://twitter.com/bluebearsoup">@bluebearsoup</a> <a href="https://twitter.com/toxicpath">@toxicpath</a></div>
— Dan Graur (@DanGraur) <a href="https://twitter.com/DanGraur/status/702017492810510336">February 23, 2016</a></blockquote>
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It is true that study of macroevolution is a lot about studies of patterns. I am fine with that - we can learn a lot from pattern. But it is an interesting question - what are the rules of macroevolution. To the question, I fairly quickly responded:<br />
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<a href="https://twitter.com/DanGraur">@DanGraur</a> Rule (Law) #1 of macroevolution: complexity (=diversity) increases unless opposed.</div>
— Todd Oakley (@UCSB_OakleyLab) <a href="https://twitter.com/UCSB_OakleyLab/status/702019794032263168">February 23, 2016</a></blockquote>
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Professor Graur then asked to what I was referring, and I answered as follows:<br />
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<a href="https://twitter.com/DanGraur">@DanGraur</a> McShea and Brandon. Book called Biology's First Law. Very happy to discuss it. It resonates with me, so challenges most welcome.</div>
— Todd Oakley (@UCSB_OakleyLab) <a href="https://twitter.com/UCSB_OakleyLab/status/702029890271342592">February 23, 2016</a></blockquote>
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This led to his reading the book in an impressively fast amount of time. He just as quickly dismissed the book, writing:<br />
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Kindle. Read ~25 pages. Unclear, self-contradictory, false, pretentious. I'll summarize at the end. You may owe me $14.04. <a href="https://twitter.com/UCSB_OakleyLab">@UCSB_OakleyLab</a></div>
— Dan Graur (@DanGraur) <a href="https://twitter.com/DanGraur/status/702123413498793984">February 23, 2016</a></blockquote>
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A bit later, he wrote a longer critique of the book on tumblr, linked <a href="http://judgestarling.tumblr.com/post/139925176456/biologys-first-law-by-mcshea-brandon" target="_blank">here</a>.<br />
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Now things get a bit complicated, because the tumblr post is a critique of the book, and a statement that I suck at judging books because the book sucks.<br />
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I will discuss a few of the critiques of the book, where I can. But most of the statements are just subjective, so I cannot really comment on opinions of "pretentious" or even "self-contradictory" when no specific instances are stated.<br />
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But first, I reiterate that my main reason for citing the book is that I think thesis of McShea and Brandon IS in fact a rule of macroevolution. In macroevolution, duplication happens. After duplication** happens - at all levels (protein domains, genes, networks, genomes, cell types, organs, modules, populations). After biological entities duplicate, they go their own way. This is the source of evolutionary novelty, biodiversity, and complexity. I see nothing in the tumblr post that argues against this. The tumblr post says very little of substance, in my opinion (although perhaps there is substance behind the comments; but that is not stated in the post). <span style="color: red;">Even though it is a side track from the reason I cited McShea and Brandon, below, I respond to some of the critiques of the book that are written in the tumblr post.</span><br />
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**duplication is not a very precise word here, but it is easily understood by people who study molecular evolution because of gene duplication. What I really mean is "furcation", a word I have coined to include splitting of lineages at any level of organization. Splitting could be duplication, but it also could be fission.<br />
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Below, I respond in line (in black text) to Dan Graur's tumblr post about Biology's First Law... The text from the tumblr post is in in blue.<br />
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<span style="color: blue;">Todd Oakley recommended the book. I became intrigued. Now, that I finished reading it, I’m not impressed.<span style="background-color: transparent;"> </span>It is a very pompous philosophical treatise</span></div>
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Pompousness is a rather subjective critique that is unrelated to the content of the arguments in the book.<br />
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<span style="color: blue;"> that attempts to explain everything from the evolution of organisms to the fate of unattended picket fences by using a single law. </span></div>
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The unattended picket fence is just an analogy. The authors are not trying to explain the fate of the pickets with their law, which is a biological law.<br />
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<span style="color: blue;">It’s a law whose purpose is to find an answer to Life, the Universe, and Everything, </span></div>
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I don't recall that the book claims to answer Life, the Universe, and Everything. But it has been a few years since I read the book.<br />
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<span style="color: blue;">but as opposed to number 42 in <i>The Hitchhiker’s Guide to the Galaxy</i> by Douglas Adams, McShea & Brandon’s First Law is neither amusing nor original. </span></div>
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<span style="color: blue;">Their “First Law” states “In any evolutionary system in which there is variation and heredity, there is, in the absence of constraint, a tendency for diversity and complexity to increase.”</span></div>
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Yes, I believe this to be a rule, or law, of macroevolution. This is the reason I cited the book - because Dan Graur asked for a rule of macroevolution after claiming that macroevolution is nothing but microevolution.<br />
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<span style="color: blue;">The mere fact that for these two authors “diversity” and “complexity” are synonymous should have been a warning. (This synonymization was referred to as asinine in several reviews.)</span></div>
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I believe under the definition that McShea and Brandon use for "complexity" -- which I believe is more clearly communicated as "structural complexity" -- that biodiversity is usefully lumped with complexity. More biodiversity is more different kinds of species; more structural complexity is more different kinds of parts (I like to call them components).<br />
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Professor Graur does not state WHY this line of thought is asinine, so I cannot argue against assertions, nor calls to the "authority" of "several reviews".<br />
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<span style="color: blue;"> However, it took me a while to understand that the two authors are either talking about entropy without mentioning the term entropy,</span></div>
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The authors do distinguish their ideas from entropy. I did a quick Google books search, and they mention the similarity on Page 12. There they refer to another chapter where they discuss the difference. My memory is that the biological law (the ZFEL) varies across levels of biological organization in a way that entropy does not. For example, in animals (with multi-cellular bodies) the complexity within each cell goes down (because of specialization) - even while the complexity of the wholes organisms increases.<br />
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In any event, I agree it is a useful analogy to think about entropy - after furcation, shit happens, and biological entities diverge. When divergent copies are maintained, complexity or diversity goes up.<br />
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<span style="color: blue;"> or about variance in a random genetic drift process without saying so.</span></div>
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I believe the authors also equate the ZFEL to increasing variance in drift processes. I think they discussed Brownian Motion, a drift model I know about from phylogenetics.<br />
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<span style="color: blue;">After deciding for myself that the book is shit, I looked for opinions about the book in the literature. Professionals, it seems were not impressed.</span></div>
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<span style="color: blue;">As <a href="http://t.umblr.com/redirect?z=https%3A%2F%2Fndpr.nd.edu%2Fnews%2F24573-biology-s-first-law-the-tendency-for-diversity-and-complexity-to-increase-in-evolutionary-systems%2F&t=NzkwZjEyYjQxZDNjODExYThlNmQ3MTI3OTk3YjkxOTljNjlkNGNlMCx1MTlITnZwZg%3D%3D" style="border: 0px; font-family: inherit; font-style: inherit; font-weight: inherit; margin: 0px; outline: 0px; padding: 0px 1px; text-decoration: none; vertical-align: baseline;">noted</a> by Mohan Matthen from the University of Toronto, the two parts of the law are equally problematic.</span></div>
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<span style="color: blue;">The first part “In any evolutionary system in which there is variation and heredity, there is a tendency for diversity and complexity to increase” can be easily shown to be false.</span></div>
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Ummm, so if this can be easily shown to be false, has it been shown false?<br />
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<span style="color: blue;">The additional clause “in the absence of constraint,” in which “constraint” is undefined, is untestable and hence unscientific.</span></div>
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Constraint is defined. McShea and Brandon point out that selection can constrain the ZFEL, such that complexity will not increase. The idea is that often, selection will oppose increases in complexity because more complexity will reduce fitness.<br />
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In molecular evolution, one process that constrains the ZFEL is concerted evolution. After duplication, we expect genes to go there own way - we expect the complexity of that gene family to increase. But concerted evolution keeps them similar or the same.<br />
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<span style="color: blue;">Other reviews, such as by <a href="http://t.umblr.com/redirect?z=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fqjzh2jab40u2jut%2FA+Review+of+Biology+s+First+Law+The+Tendency+for+Diversity+and+Complexity+to+Increase+in+Evolutionary+Systems+by+Daniel+W+McShea+and+Robert+N+Brandon.pdf%3Fdl%3D0&t=MjQ4NmI4MTFkZTc1NGZkNGI4MDczODM3YTIzZjY3YmQyZTc4YmUwNCx1MTlITnZwZg%3D%3D" style="border: 0px; font-family: inherit; font-style: inherit; font-weight: inherit; margin: 0px; outline: 0px; padding: 0px 1px; text-decoration: none; vertical-align: baseline;">Noël Bonneuil</a> from the Institut National d'Etudes Demographiques and <a href="http://t.umblr.com/redirect?z=https%3A%2F%2Fphylogenous.wordpress.com%2F2011%2F08%2F17%2Fbook-review-biologys-first-law-by-mcshea-and-brandon-2010%2F&t=MjEwMDE1NjIzMzcxODA3YjlkNTMwZWU5MDFiNWIyOWEzMTllYWZhNSx1MTlITnZwZg%3D%3D" style="border: 0px; font-family: inherit; font-style: inherit; font-weight: inherit; margin: 0px; outline: 0px; padding: 0px 1px; text-decoration: none; vertical-align: baseline;">Kele Cable</a> from the University of Minnesota were also quite lethal in their verdicts on the merits of the book. </span></div>
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<span style="color: blue;">“Biology’s First Law” is clearly neither a first nor a law.</span></div>
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Okay, why?<br />
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<span style="color: blue;">Following Samuel Johnson, I can state with confidence that McShea & Brandon book is both good and original. Unfortunately, the part that is good is not original, and the part that is original is not good.</span><span style="background-color: transparent;"> </span></div>
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<span style="color: blue;">If you don’t believe me that none of the ideas in McShea & Brandon’s book are original, kindly read Brooks & Wiley’s 1986 <i>Evolution as Entropy</i> to judge for yourself. As noted <a href="http://judgestarling.tumblr.com/post/139465521326/switzerland-is-a-flat-country-the-importance-of" style="border: 0px; font-family: inherit; font-style: inherit; font-weight: inherit; margin: 0px; outline: 0px; padding: 0px 1px; text-decoration: none; vertical-align: baseline;">previously</a>, before making extravagant claims, kindly read the literature. </span></div>
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I think this request to read Brooks and Wiley (it's actually 1988) is directed at McShea and Brandon. From a Google book search, here are a few times that M&B cite B&W:<br />
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page 11 "based on what we have said so far, some will be poised and ready to make the leap from the notion of the accumulation of accidents to the second law of thermodynamics (... Brooks and Wiley, 1988).<br />
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page 12 - " some work in the past few decades on the application of the second law to biology has been inspirational (especially Wicken, 1987; Brooks and Wiley, 1988; Salthe, 1993), and <span style="color: red;">we gratefully acknowledge the intellectual debt</span>. "<br />
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There are other citations too.<br />
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So, who needs to kindly read the literature before making extravagant claims?<br />
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And back to my reason for citing McShea and Brandon in the first place. A rule of macroevolution is that complexity increases. Perhaps this is in fact quite related to the idea of entropy. So, by stating that M&B is not original, I assume that Prof. Graur accepts the thesis of Brooks and Wiley, 1988. Does that mean he accepts my "rule" of macroevolution, that complexity and diversity happen?<br />
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<span style="color: blue;">I’ll finish by quoting an anonymous critic on Amazon, <i>“The authors’ shocking ignorance of (or willful disregard of) the history of evolutionary thought is the only surprising thing in this book. I can only hope that they are as embarrassed by their own poor scholarship as they deserve to be.”</i></span></div>
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Simply asserting and accusing, without backing up those assertions or accusations is the epitome of poor scholarship. The one specific example of poor scholarship above (Brooks and Wiley) did not hold. It was cited multiple times by McShea and Brandon.<br />
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<span style="color: blue;">There are amazing scientists out there that I don’t trust with books, movie, or restaurant recommendations. Yes, it is difficult to reconcile the Todd Oakley, who conducted such groundbreaking studies in molecular evolution, as his “The origins of novel protein interactions during animal opsin evolution,” with the Todd Oakley who was greatly impressed by a very bad book. </span></div>
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Thank you for the back handed compliment.<br />
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I will say in response that I very much respect Professor Graur. I learned molecular evolution from his text book! Once I asked him via Twitter about radical amino acid changes. A couple days later (or less maybe) he responded with a detailed review on his tumblr page. That was an amazingly collegial and scholarly thing to do! I was greatly impressed.<br />
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Today, it is hard for me to reconcile that Dan Graur with the Dan Graur who wrote this mainly content free, yet still blustery, critique of a book that I respect, written by authors whom I respect.<br />
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<span style="color: blue;">Anyway, the latter Todd Oakley owes me $14.04 and half a pound of candy as compensation for his book recommendation. </span></div>
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I'd rather use my $14.04 to buy each of us a beverage (and a pound of candy), and discuss all this the next time we meet in person.<br />
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In the end, I think it ironic that all our disagreement comes down to our view of what 'novelty' means. I believe that novelty must be rampant in evolution - even true novelty. Novelty can come from new combinations of existing biological elements. So to can novelty and originality in scholarship come from new combinations of existing ideas. This is how I read McShea and Brandon. Many of the ideas I had seen or heard before - partly because M&B are professors where I was a graduate student. But by putting many ideas together in a new way, namely by being bravely and ambitiously general, I found the book Biology's First Law to be a novelty. A true novelty.<br />
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true novelty in </div>
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Unknownnoreply@blogger.com6tag:blogger.com,1999:blog-6821840758756075048.post-23909353105870848302016-01-01T19:53:00.000-08:002016-01-01T19:53:02.701-08:00SICB 2016 Schedule<div dir="ltr" style="text-align: left;" trbidi="on">
Here are some #SICB2016 presentations I have marked after key word searches. What great ones am I missing?<br />
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<tr style="border: 0px; margin: 0px; padding: 0px;"><th align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top" width="50"><a href="http://www.sicb.org/meetings/2016/schedule/personal/personalschedule-view.php?myschedule=:41:48:59:62:77:87:142:167:170:173:178:221:246:260:261:337:357:388:420:460:542:548:631:635:751:769:787:824:841:851:878:920:921:945:984:1007:1229:1275:1312:1352:1378:1403:1483:1559:1566:1570:1660:1666:1673:1675:1679:1723&ordered=ORDER+BY+sday" style="border: 0px; color: #666666; margin: 0px; padding: 0px;"><br class="Apple-interchange-newline" />Day</a></th><th align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top" width="45"><a href="http://www.sicb.org/meetings/2016/schedule/personal/personalschedule-view.php?ordered=ORDER+BY+abstracts2016.sessionnumber,paperno" style="border: 0px; color: #666666; margin: 0px; padding: 0px;">Session/Paper#</a></th><th align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top" width="65"><a href="http://www.sicb.org/meetings/2016/schedule/personal/personalschedule-view.php?myschedule=:41:48:59:62:77:87:142:167:170:173:178:221:246:260:261:337:357:388:420:460:542:548:631:635:751:769:787:824:841:851:878:920:921:945:984:1007:1229:1275:1312:1352:1378:1403:1483:1559:1566:1570:1660:1666:1673:1675:1679:1723&ordered=ORDER+BY+sday,+time" style="border: 0px; color: #666666; margin: 0px; padding: 0px;">Time</a></th><th align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top" width="65">Room</th><th align="left" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/personal/personalschedule-view.php?myschedule=:41:48:59:62:77:87:142:167:170:173:178:221:246:260:261:337:357:388:420:460:542:548:631:635:751:769:787:824:841:851:878:920:921:945:984:1007:1229:1275:1312:1352:1378:1403:1483:1559:1566:1570:1660:1666:1673:1675:1679:1723&ordered=ORDER+BY+author1" style="border: 0px; color: #666666; margin: 0px; padding: 0px;">Author 1</a></th><th align="left" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/personal/personalschedule-view.php?myschedule=:41:48:59:62:77:87:142:167:170:173:178:221:246:260:261:337:357:388:420:460:542:548:631:635:751:769:787:824:841:851:878:920:921:945:984:1007:1229:1275:1312:1352:1378:1403:1483:1559:1566:1570:1660:1666:1673:1675:1679:1723&ordered=ORDER+BY+title" style="border: 0px; color: #666666; margin: 0px; padding: 0px;">Title</a></th></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="167" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">22-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C125/126 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SCHNITZLER, CE</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=167" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Genomics of <i style="border: 0px; margin: 0px; padding: 0px;">Hydractinia</i>: A Cnidarian Model for Regeneration, Allorecognition, and Developmental Biology </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1559" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">33-5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C125/126 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">VON DASSOW, M</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1559" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">The echinoid blastula: linking biomechanics to development-environment interactions </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="824" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">33-6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C125/126 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SERVETNICK, MD</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=824" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">CRISPR/Cas9-mediated excision of the <i style="border: 0px; margin: 0px; padding: 0px;">brachyury</i> gene disrupts endoderm development in the sea anemone <i style="border: 0px; margin: 0px; padding: 0px;">Nematostella vectensis</i>. </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="77" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-143 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">DONOHUE, M.W.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=77" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Behavioral and molecular evidence for opsin-based extraocular photoreception in stomatopod crustaceans </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="337" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-157 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">ARUL NAMBI RAJAN, A</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=337" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Neural Determinants of Behavior in an Organism without a Nervous System </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="548" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-162 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">PRICE, C.L.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=548" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">The genetics of the visual system of two species of pupfishes (genus Cyprinodon) </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="635" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-147 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">PICCIANI, N.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=635" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Light modulated cnidocyte firing predates the evolution of eyes in Cnidaria (Metazoa) </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="751" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-144 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">NOTAR, JC</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=751" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">A Comparative Study of Sea Urchin Visual Ecology </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="945" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-145 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MILLER, H.V.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=945" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Pupillary responses in scallops </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1312" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-78 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SIMMONS, S</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1312" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Mesoglea and Muscle in Cubozoan Jellyfish <i style="border: 0px; margin: 0px; padding: 0px;">Carybdea marsupialis</i> and <i style="border: 0px; margin: 0px; padding: 0px;">Tripedalia cystophora</i> </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1570" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-22 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MUNRO, C</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1570" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Exploring the evolution of functional specialization in siphonophores using RNAseq </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1675" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Monday, Jan. 4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P1-148 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SWAFFORD, A.J.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1675" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new"><b style="border: 0px; margin: 0px; padding: 0px;">Gain and Loss of Sensory Modalities Alter Guidance of <i style="border: 0px; margin: 0px; padding: 0px;">Allomyces</i> Zoospores</b> </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="460" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-2 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">PORTER, M.L.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=460" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Beyond the eye: extraocular opsin evolution </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="173" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-3 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">COLLEY, N.J.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=173" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Photoreception in Phytoplankton </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="420" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">40-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B114 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">DALTON, B E</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=420" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Coexpression of opsins in each cone class spectrally tunes regions of the retina to distinct parts of the visual field </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1660" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">09:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">OAKLEY, TH</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1660" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Opsins without eyes – precursors or derivatives? </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="41" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">40-6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">09:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B114 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">FAULKES, Z.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=41" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Eyes under the beach: the visual system of sand crabs (<i style="border: 0px; margin: 0px; padding: 0px;">Lepidopa benedicti</i>) </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="59" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">KINGSTON, ACN</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=59" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Extraocular opsins in skin and nervous systems of aquatic animals </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="170" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-7 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">11:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">BATTELLE, B-A</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=170" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Ocular and extraocular photosensitivity and opsin expression in the American horseshoe crab<i style="border: 0px; margin: 0px; padding: 0px;">Limulus polyphemus</i>, a chelicerate arthropod. </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1723" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-8 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">11:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">BOK, M.J.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1723" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Looking with gills: The function and evolution of fan worm branchial photoreceptors </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="769" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-9 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">13:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">WALKER, Marquis T.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=769" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">A mouse homolog of Drosophila RDGB functions in ipRGC dim light activation </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="178" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">68-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">13:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B118/119 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">DALY, M</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=178" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">The tree’s the thing: phylogeny as a way of understanding the diversity of venom in sea anemones </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="542" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">67-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B117 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">LARSON, P.G.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=542" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Evaluating taxonomic characters of <i style="border: 0px; margin: 0px; padding: 0px;">Anthopleura</i> and other sea anemones in a molecular phylogenetic context </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="920" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-10 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SCHMIDT, T.M.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=920" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">New roles for ganglion cell photoreceptors </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="357" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">67-2 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B117 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MACRANDER, J</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=357" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">A High-Throughput Investigation into the Tissue Specific Venom Composition and Differential Gene Expression in Three Species of Sea Anemone </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="62" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">67-3 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B117 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">GOODHEART, J.A.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=62" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Phylogenomics of Cladobranchia (Mollusca: Gastropoda: Heterobranchia) </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1378" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-11 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SPEISER, D.I.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1378" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Eyes most numerous: extracephalic visual systems in molluscs </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1679" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">67-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B117 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">CHANG, J.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1679" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">The tempo of body shape evolution in ray-finned fishes: bringing morphology into the “phenomic era” with crowdsourced morphometrics </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="142" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S4-12 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C123 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">JOHNSEN, S.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=142" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">What Next? Unanswered questions about extraocular photoreception and how we might answer them </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="787" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P2-136 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">STABILE, F. A.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=787" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Identification of four genes involved in the development of feathers but not scales in birds </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1229" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Tuesday, Jan. 5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P2-156 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MURPHY, P.J.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1229" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Regional Genetic Variation of Two Ephemeral Pool Crustacean Species: Implications for Visual System Plasticity or Local Adaptation </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="841" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">74-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">BABONIS, L.S.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=841" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Seeing without eyes: Opsins and the evolution of photodetection in basal metazoans </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1403" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">79-2 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B118/119 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MCCULLOCH, KJ</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1403" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Photoreceptor Cell Sensitivity and Sexual Dimorphism in the Compound Eye of the Butterfly<i style="border: 0px; margin: 0px; padding: 0px;">Heliconius erato</i> </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1673" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">74-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">08:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MASON, B.M.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1673" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Coral opsins: photosensitivity and partial characterization of five opsins from <i style="border: 0px; margin: 0px; padding: 0px;">Acropora millepora</i> </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="631" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">74-5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">09:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">SERB, J.M.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=631" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Expression and spectral analysis of two Gq-opsins from the mantle and the eyes of the scallop <i style="border: 0px; margin: 0px; padding: 0px;">Placopecten magellanicus</i> </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="851" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">74-6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">09:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">FAGGIONATO, D.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=851" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Spectra analysis of Gq-opsins from four scallop species </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="388" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">74-7 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">09:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">BRANDLEY, N</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=388" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Do warning signals exploit an evolutionary constraint on insect visual acuity? </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="921" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">85-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">THOMAS, K.N.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=921" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">The perks of being cock-eyed: Orientation and visual characteristics of histioteuthid squids </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1007" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">85-2 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">HOLT, A.L.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1007" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Light guides and open water camouflage in <i style="border: 0px; margin: 0px; padding: 0px;">Galiteuthis</i> </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="221" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">85-3 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">CAVES, EM</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=221" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Visual acuity in fish: the effects of eye morphology, environment, and ecology </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="87" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">85-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">11:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">JOHNSEN, S.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=87" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Another beautiful hypothesis slain by an ugly fact: Polarization vision does not increase the sighting distance of silvery fish </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="878" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">85-5 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">11:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">DODSON, T</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=878" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Origins of Polydispersity In Cephalopod Photonic Systems - Are Squids Masters of RNA Editing? </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="246" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">96-2 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">13:45 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B112 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">EMERLING, C.A.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=246" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Spectral shifts of mammalian ultraviolet-sensitive pigments (SWS1) are associated with eye length and photic niche evolution </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1666" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">92-3 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">A104 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">CORYELL, R.L.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1666" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Phylogeographic patterns in the Philippine archipelago drive symbiont diversity in the bobtail squid-<i style="border: 0px; margin: 0px; padding: 0px;">Vibrio</i> mutualism </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="984" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">101-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">B118/119 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">MOROZ, LL</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=984" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Can Synapses Evolve Independently? </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="261" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">S8-10 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">14:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">C124 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">LEWIS, C.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=261" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Differential expression of genes implicated in venom, vision and sex in the aggregating box jellyfish <i style="border: 0px; margin: 0px; padding: 0px;">Alatina alata</i> </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="260" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P3-198 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">LIN, C.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=260" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Neural organization of the optic lobes in the two midband-row stomatopod <i style="border: 0px; margin: 0px; padding: 0px;">Squilla empusa</i> </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1352" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Wednesday, Jan. 6 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">P3-16 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">15:30 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Exhibit Hall A </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">STERN, D.B.</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1352" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Comparative Vision Gene Expression in Cave Adapted Crayfish </a></td></tr>
<tr bgcolor="#ccddcc" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1483" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Thursday, Jan. 7 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">115-1 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">10:15 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">A107-109 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">ADAMS, DK</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1483" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Evolution of the neurosensory system mediates gain and loss of phenotypic plasticity </a></td></tr>
<tr bgcolor="#ddeedd" style="border: 0px; margin: 0px; padding: 0px;"><td align="center" bgcolor="#ff8888" style="border: 0px; margin: 0px; padding: 0px;" valign="top"><input name="1566" style="border-color: rgb(152, 152, 152) rgb(195, 195, 195) rgb(221, 221, 221) !important; border-style: solid !important; border-width: 2px 2px 1px !important; font-size: small !important; margin: 0px; padding: 1px 3px !important;" type="checkbox" /></td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">Thursday, Jan. 7 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">114-4 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">11:00 </td><td align="center" style="border: 0px; margin: 0px; padding: 0px;" valign="top">A105 </td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top">KELLY, MW</td><td style="border: 0px; margin: 0px; padding: 0px;" valign="top"><a href="http://www.sicb.org/meetings/2016/schedule/abstractdetails.php?id=1566" style="border: 0px; color: #666666; margin: 0px; padding: 0px;" target="new">Adaptation to heat stress reduces phenotypic and gene expression plasticity in a marine copepod </a></td></tr>
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Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-65910997627340651162015-11-06T06:40:00.000-08:002015-11-06T06:40:13.417-08:00Postdoctoral Position in Ecological Genomics at UCSB<div dir="ltr" style="text-align: left;" trbidi="on">
Postdoctoral Researcher in Ecological and Evolutionary Genomics<br />
<br />
We seek a researcher to lead the genomics aspects of an interdisciplinary research program on algal ecology and biofuels. The candidate will work at UCSB in the lab of Todd Oakley and collaborate with ecologists and engineers at the University of Michigan. This project was awarded by the National Science Foundation through its Emerging Frontiers in Research and Innovation (EFRI) initiative. The team is testing the hypothesis that certain naturally diverse groups of algae have complementary traits that enhance the efficiency and stability of biofuel yield beyond what any single species can achieve alone. The UCSB members of the team are testing whether gene expression differences under different ecological conditions correlate with measures biofuel yield.<br />
<br />
The minimum requirement is a PhD in bioinformatics, genomics or a related field. Applicant should also be comfortable working in a collaborative, interdisciplinary environment, which requires excellent written and oral communication skills. The applicant should be able to handle large transcriptomic and genomic data sets, and be adept at coding (Python, PERL, or similar) and at using and implementing bioinformatics software.<br />
<br />
Applicants should submit a cover letter, curriculum vitae, research statement, summary of research experience, publications. In addition, supply contact information for 3 colleagues willing to provide letters of recommendation (we will contact the letter writers for a short list of candidates).<br />
<br />
We will begin to review applications immediately, but apply by Dec 1, 2015 for full consideration. Please direct questions or informal inquiries to Todd Oakley (oakley@lifesci.ucsb.edu).<br />
<br />
The department is interested in candidates who can contribute to the diversity and excellence of the academic community through research, teaching and service. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, or any other characteristic protected by law including protected Veterans and individuals with disabilities.</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-19068828266446556302015-10-28T16:56:00.003-07:002015-10-28T16:56:55.606-07:00How old are fireflies?<div dir="ltr" style="text-align: left;" trbidi="on">
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">This is an "open lab notebook" detailing an analysis I did trying to figure out how old are fireflies.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Are fireflies - beetles who use light for courtship - more diverse than expected from the age of their lineage? Answering this question in part depends on knowing the age of the clades.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b id="docs-internal-guid-3349aa7f-b0df-bf8c-da64-f26371749e93" style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In this analysis, I come up with a very rough estimate that one firefly clade is 145 MY and another is 128 MY. Divergence time estimation is notoriously error-prone and these estimates are based on a number of assumptions. They should therefore be taken with a (large) grain of salt, ie be skeptical.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I began with the phylogeny of Martin et al. </span><a href="https://paperpile.com/c/4OVKQa/KiCE/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2015)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. They concluded adult bioluminescence was originated twice in fireflies. One clade contains Lampyrinae+Photurinae, which I call ‘firefly1’. The other clade contains Pterotinae+Luciolinae - I call this the “firefly2” clade. This tree is based on 18S, 16S, </span><span style="font-family: Arial; font-size: 14.6667px; line-height: 20.24px; white-space: pre-wrap;">and CO1, but did not do any divergence time analyses.</span></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br /></span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span><img height="433px;" src="https://lh3.googleusercontent.com/jNR60FpYXEVzqu0jmVEtCxuXCQ_iD2gjj5IDfouWbvvJlRSqBmKG6pKuWCUnEqhHt0RrtecSy8eiKTCrlEK9Zn88jK1WPHkD7-bYgDdjIXJwuU3iDmxOcVJL6-KAc53vLWjmA-Q3" style="-webkit-transform: rotate(0.00rad); border: none; transform: rotate(0.00rad);" width="304px;" /></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">In order to estimate divergence times, I needed to include clades that could be constrained with fossils. I consulted Hunt et al. </span><a href="https://paperpile.com/c/4OVKQa/enTc/?locator_label=book&noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">, a phylogeny of all beetles, with divergence times. The closest clade to fireflies with a fossil constraint is their constraint “e”. This is </span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: italic; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Elaterophanes</span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> from 196.5 MY, used as a minimum age for the Elateridae. Hunt et al. </span><a href="https://paperpile.com/c/4OVKQa/enTc/?locator_label=book&noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> used the same genes as Martin et al. </span><a href="https://paperpile.com/c/4OVKQa/KiCE/?noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2015)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> (MEA), so I concatenated the MEA data set with elaterids from HEA. I also fixed beetles to be 285 MY, after Hunt et al. </span><a href="https://paperpile.com/c/4OVKQa/enTc/?locator_label=book&noauthor=1" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(2007)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">. This is their estimate of divergence time for beetles. Using the fossil record could lead to a ‘maximum’ age of beetles as 411 (Rhynie Chert). But if I use 285 as a minimum and 411 as a maximum, the age gets pushed up to 411, which does not seem particularly realistic. Doing that raises the age estimates by some 40 MY- for FF1 and FF2 to 186 and 164 MY, respectively.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I also included some other outgroups. First, I used a Hydroscaphidae because the MRCA of that clade and Lampyridae is the MRCA of all beetles. In addition, I used a non-beetle, Chrysopidae. These two taxa were the only species in HEA that had all 3 genes. For divtime analyses in r8s, I pruned the Chrysopidae to leave a rooted, fully resolved tree.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I required all 3 genes to be present for each species (using phylocatenator of Osiris </span><a href="https://paperpile.com/c/4OVKQa/POpL" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Oakley et al. 2014)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">). My tree had some differences with HEA and MEA:</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /><br /><br /><img height="536px;" src="https://lh5.googleusercontent.com/I0sqwz7h-mxUrn4hKJ5fLEMmJD2LNy3NmwACiMNo9l8NsLJU43Glate6xg6tyZG9eXpiR-Dj88-TljD8b8ly2t-8QLxv-zIDIaOvgUahfoNQiLp2KAzvbt40DLgcDDai1xFlR8DY" style="border: none; transform: rotate(0rad);" width="276px;" /><br /></b></div>
<ol style="margin-bottom: 0pt; margin-top: 0pt;">
<li dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; list-style-type: decimal; text-decoration: none; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Elateridae are not monophyletic. With some different outgroups, I did get monophyly. HEA also consistently got monophyly. Perhaps adding Cantheridae (a closer sister to Lampyridae) would allow recovery of the expected monyphyly of elateridae. As a result, the divtime constraint is at the base of Elateridae AND Lampyridae, and could influence final results.</span></div>
</li>
<li dir="ltr" style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; list-style-type: decimal; text-decoration: none; vertical-align: baseline;"><div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Firefly 2 (red taxa) is not monophyletic as in MEA. Instead, I get Pollaclasis and Cyphonocerus within the Firefly2 clade. This could influence the time estimate for this clade. I could perhaps constrain monophyly here. Also other outgroups also could influence monophyly because Pterotus is the taxon changing places, and it is fairly long branch, and may be influenced by outgroups.</span></div>
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<b style="font-weight: normal;"><br /><br /><br /><br /><br /><br /><br /><br /></b></div>
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<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> </span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Data Files:</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I used Osiris </span><a href="https://paperpile.com/c/4OVKQa/POpL" style="text-decoration: none;"><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">(Oakley et al. 2014)</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"> to build the phylogeny, which uses phytab format. That file is </span><a href="https://docs.google.com/spreadsheets/d/1Vlvteg5c8RmFvIOPzC1DSAXVCVEddn5QLDDGOXE7ihk/edit?usp=sharing" style="text-decoration: none;"><span style="background-color: transparent; color: #1155cc; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here</span></a><span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">.</span></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<b style="font-weight: normal;"><br /></b></div>
<div dir="ltr" style="line-height: 1.38; margin-bottom: 0pt; margin-top: 0pt;">
<span style="background-color: transparent; color: black; font-family: Arial; font-size: 14.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">I used r8s for the divergence time analysis, and that file is here:</span></div>
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<b style="font-weight: normal;"><br /></b></div>
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<span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">#NEXUS</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Begin TREES;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">TREE 'Tree1' = ((((Oxynopterus_sp.:463.5249944,Agrypnus_murinus:526.2532825):58.07102708,(Panspaeus_guttatus:460.2987223,(Stenagostus_rhombeus:490.0649111,(Denticollis_linearis:345.0885786,Athous_haemorrhoidalis:348.234297):128.0768835):72.63022263):60.96422013):35.09443673,((((Phausis_reticulata:1662.289658,((((Lamprohiza_splendidula:544.0746241,Phosphaenus_hemipterus:229.7443014):285.1154906,Lucidota_atra:437.7055071):401.9635656,((((Photinus_australis:253.4245299,Photinus_tanytoxus:505.5902659):83.13503158,((Photinus_punctulatus:528.7843213,Photinus_pyralis:301.5064629):50.68180427,(Photinus_floridanus:473.4079674,(Ellychnia_californica:135.4824287,Ellychnia_aff._corrusca_KSH611:25.24849269):286.7912686):70.99285141):18.53357795):329.2700252,((Aspisoma_sp.:283.3096828,(Pyractomena_dispersa:29.67243287,(Pyractomena_palustris:31.23178185,(Pyractomena_angulata:517.0946069,Pyractomena_borealis:67.81801332):70.86493904):110.1146049):238.5808725):339.3010688,((Pleotomodes_needhami:426.6510094,Pleotomus_pallens:389.0211618):76.84583685,(Lampyris_noctiluca:477.2948781,((Diaphanes_formosus:371.9065228,Lychnuris_formosana:449.5272741):90.09984008,(Microphotus_angustus:406.2856534,Paraphausis_eximius:395.3158416):117.5049772):29.6282204):72.85630302):111.0228766):116.0625074):59.48984988,Micronaspis_floridana:558.9615698):107.7999852):229.3020886,(Vesta_sp.:561.4644596,(Bicellonycha_wickershamorum:491.2011309,((Photuris_tremulans:49.09336296,Photuris_aff._lucicrescens_KSH1:100.1688104):15.59686292,Photuris_quadrifulgens:50.11517938):457.7292255):121.0831356):150.8011019):163.8652632):66.19287172,((Brachylampis_blaisdelli:759.3860187,((Drilaster_axillaris:123.8337303,(Flabellotreta_sp.:171.4133031,Flabellotreta_obscuricollis:146.3672477):242.4682661):163.5674534,(Ceylonidrilus_sp.:422.4286714,(Drilaster_sp.:354.6668547,Drilaster_borneensis:394.0848821):241.6799973):72.15723681):351.5818484):270.4748514,((Luciola_sp.:326.8593145,((Luciola_parvula:576.0213995,(Curtos_okinawanus:182.2933313,Curtos_costipennis:220.7797732):214.4995191):130.4914738,Curtos_sp.:346.5873752):104.5451147):267.9094037,(Pterotus_obscuripennis:672.2005806,(Pollaclasis_bifaria:627.4316177,Cyphonocerus_ruficollis:348.7937363):198.7861435):41.84871305):52.94860049):62.12407915):680.5789337,Plateros_sp.:1002.688879):111.8242026,((Rhagophthalmus_ohbai:539.4926404,(Cebrioninae_sp.:547.7782899,Ampedus_balteatus:478.7696559):125.5329304):66.72017755,Cardiophorinae_sp.:883.3299248):39.872645):47.59526361):1043.317628,Hydroscaphidae:1499.20604);</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">End;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">[** Beginning of the rates block containing commands for r8s **]</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">begin r8s;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">blformat lengths=persite nsites=6417 ultrametric=no;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MRCA beetles</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span class="Apple-tab-span" style="white-space: pre;"> </span></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">Hydroscaphidae Drilaster_borneensis;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MRCA elateridae Cardiophorinae_sp. Panspaeus_guttatus;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MRCA firefly1 Phausis_reticulata Pleotomus_pallens;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">MRCA firefly2 Pterotus_obscuripennis Luciola_parvula;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">fixage taxon=beetles age=285;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">#constrain taxon=beetles min_age=280 max_age=411;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">constrain taxon=elateridae min_age=196.5;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">divtime method=pl algorithm=tn [cvStart=0 cvInc=0.2 cvNum=8 crossv=yes];</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">describe plot=chrono_description;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">showage shownamed=yes;</span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><br class="kix-line-break" /></span><span style="background-color: transparent; color: black; font-family: 'Courier New'; font-size: 10.666666666666666px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;">end;</span></div>
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<b>References</b></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 12pt; margin-left: 24pt; margin-top: 12pt; text-indent: -24pt;">
<span style="background-color: transparent; font-family: Arial; font-size: 14.6667px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><a href="http://paperpile.com/b/4OVKQa/enTc" style="text-decoration: none;">Hunt T., Bergsten J., Levkanicova Z., Papadopoulou A., John O.S., Wild R., Hammond P.M., Ahrens D., Balke M., Caterino M.S., Gómez-Zurita J., Ribera I., Barraclough T.G., Bocakova M., Bocak L., Vogler A.P. 2007. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science. 318:1913–1916.</a></span></div>
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<a href="http://paperpile.com/b/4OVKQa/KiCE" style="text-decoration: none;"><span style="background-color: transparent; font-family: Arial; font-size: 14.6667px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="color: black;">Martin G.J., Lord N.P., Branham M.A., Bybee S.M. 2015. Review of the firefly visual system (Coleoptera: Lampyridae) and evolution of the opsin genes underlying color vision. Org. Divers. Evol.:1–14.</span></span></a></div>
<div dir="ltr" style="line-height: 1.2; margin-bottom: 12pt; margin-left: 24pt; margin-top: 0pt; text-indent: -24pt;">
<a href="http://paperpile.com/b/4OVKQa/POpL" style="text-decoration: none;"><span style="background-color: transparent; font-family: Arial; font-size: 14.6667px; font-style: normal; font-variant: normal; font-weight: 400; text-decoration: none; vertical-align: baseline; white-space: pre-wrap;"><span style="color: black;">Oakley T.H., Alexandrou M.A., Ngo R., Pankey M.S., Churchill C.K., Chen W., Lopker K.B. 2014. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics. 15:230.</span></span></a></div>
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Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-84012177094852087052015-07-26T21:11:00.000-07:002017-07-29T10:43:09.273-07:00Graduating Little League<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="margin-bottom: 0in;">
Before the actual day, I worried about
the arrival of my 40<sup>th</sup> birthday. But when that day came,
it felt like any other day. I was still me, just a day older. I
felt the same for “Y2K”, the year 2000. After months of doomsday
scenarios, January 1, 2000 was just like any other day that saw the
sun rise and saw the sun set. All our computers still turned on.
Partly because these were so normal, I am caught off-guard that today
does not feel like any other day. As strange as it may sound, the end
of my son's 12-year-old Little League year feels like I thought age
40 or Y2K might feel; like the end of an era. In many ways, my son
and his baseball buddies are no longer children. Today, our boys have
graduated Little League.</div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in;">
It is true that Little League goes on
past age 12. But the 12-year-old year is the privileged year. The
name of the 12U division is simply “Little League”, as if to
assert the 12-year-old division <i>is</i> Little League. In our town,
the 12 year-old division is top dog. It's considered first in
scheduling games and practices and batting cage time. It's the only
division without a time limit on games. At 12, Little Leaguers
traditionally play their final year on the small field, where
T-ballers and mini-minor kids also learn the game. Next comes a big
transition to a full, major-league-sized field. Many kids do not
make the transition to the more demanding field and they leave
baseball behind. There are other reasons to stop Little League after
12. Some of the best players leave to focus only on more competitive
club teams. And so the 12-year old year is the peak of Little League
participation and competition. The kids fortunate enough to be
selected to represent their league as All-Stars extend their regular
seasons with summer tournaments against other leagues. For the 12U
Little League division, the tournament is truly world-wide,
culminating in The Little League World Series in Williamsport, PA,
watched by millions each year on television.</div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in;">
This year, my son's 12-year-old Little
League year, he and I were especially fortunate. He represented his
league as an All-Star, with me as a coach. It was a special team that
exceeded expectations and got significant
contributions from every single player. It was a special team because the
whole was greater than the sum of the parts, with strong leadership and strong families. Most of all, it was a team of great boys who worked hard, who played hard to win,
who never gave up, and who had fun. Had these boys lost in their
district (the first tournament), not many people would have been surprised. Defying
expectations, these boys breezed to the District championship, even winning that game 11-0. Then
they went even farther. They won a Sectional championship with two
comeback, walk-off victories in a row. One of the Sectional victories
was against a power house team, last year's 11U state champions. In
so doing, our team became only the third in our league's 47-year
history to be Section champions as 12-year-olds. As Section champions, they were one
of ten teams to remain alive in all of Southern California, usually one of the very strongest regions of Little League baseball in the world.
</div>
<div style="margin-bottom: 0in;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-jPOlyoNDCDc/VbWt2oy6edI/AAAAAAAAASo/J7Lekc1iBrU/s1600/SectionWalkoffMob.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="212" src="https://2.bp.blogspot.com/-jPOlyoNDCDc/VbWt2oy6edI/AAAAAAAAASo/J7Lekc1iBrU/s320/SectionWalkoffMob.png" width="320" /></a></div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in; text-align: center;">
<span style="font-size: x-small;">Our team celebrates their walk-off Sectional Championship.</span></div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in;">
For all but a handful of players and
coaches, the Little League tournament ends in defeat. We know all
along that the odds of reaching a Williamsport dream are very long,
and we assume that defeat will come eventually. Yet with every win,
the dream stays alive. Why couldn't it be us? Why shouldn't it be us?
We could be the team of destiny. These boys <i>deserve</i> to be the
team of destiny. With every win we keep working, every day. We keep
practicing and we keep playing hard. We do not give up and we focus
on getting better. In every game, we expect to win. In every game, we
plan to win. And so we do not mentally prepare for losing. Until we
lose. Then it all changes in an instant.</div>
<div style="margin-bottom: 0in;">
<br /></div>
<div style="margin-bottom: 0in;">
It is not the loss of a game that is so
difficult. Perhaps it is the loss of an opportunity. Maybe it is the
loss of our summertime family, with whom we cheered and celebrated.
When players finish their season at age 10, they look forward to
moving up to the Little League Majors division. When they finish at
age 11, they look forward to their privileged year, when their
Williamsport dreams become most vivid. But when they are 12, and
their season comes to its inevitable end, they will never again be
little boys playing on a little diamond. My son is someone I can
still play catch with, but no longer can I play catch with my little
boy. Today, our little boys have graduated.</div>
<div style="margin-bottom: 0in;">
<br /></div>
<br />
<div style="margin-bottom: 0in;">
Even though I will miss the days of
playing baseball with a great group of boys on a perfect Santa
Barbara summer afternoon, I know that graduations are also a time to
be proud. We are so proud of what these boys accomplished. We know
they will become strong young men. These will be young men who strive
to win. These will be young men who will always do their best, and who never give up. These
will be young men who support each other and who contribute to
communities and teams in ways that maximize their individual
strengths and gifts. These will be young men who know that sometimes,
a whole can be greater than the sum of its parts. These are young men
who today graduated Little League.</div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-89002738483656253482015-04-06T17:05:00.000-07:002015-04-06T17:29:24.414-07:00Everything's comin up peropsin<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoTitle">
(Or maybe coming up RGR). My research activities on opsin have lately led me to peropsin and RGR. These are opsins in the RGR/Go superfamily (a la Plachetzki et al 2007) [Note Porter et al 2012 named this superfamily Group IV, but I don't like that name as much because it is not clear there are actually four superfamily groups].</div>
<div class="MsoTitle">
<br /></div>
<div class="MsoTitle">
Below is a report I sent to the first author of a paper that just came out. The paper is here:
<b><br />
<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Journal+of+Experimental+Biology&rft_id=info%3Adoi%2F10.1242%2Fjeb.116087&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Opsins+in+Limulus+eyes%3A+characterization+of+three+visible+light-sensitive+opsins+unique+to+and+co-expressed+in+median+eye+photoreceptors+and+a+peropsin%2FRGR+that+is+expressed+in+all+eyes&rft.issn=0022-0949&rft.date=2014&rft.volume=218&rft.issue=3&rft.spage=466&rft.epage=479&rft.artnum=http%3A%2F%2Fjeb.biologists.org%2Fcgi%2Fdoi%2F10.1242%2Fjeb.116087&rft.au=Battelle%2C+B.&rft.au=Kempler%2C+K.&rft.au=Saraf%2C+S.&rft.au=Marten%2C+C.&rft.au=Dugger%2C+D.&rft.au=Speiser%2C+D.&rft.au=Oakley%2C+T.&rfe_dat=bpr3.included=1;bpr3.tags=Biology">Battelle, B., Kempler, K., Saraf, S., Marten, C., Dugger, D., Speiser, D., & Oakley, T. (2014). Opsins in Limulus eyes: characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes <span style="font-style: italic;">Journal of Experimental Biology, 218</span> (3), 466-479 DOI: <a href="http://dx.doi.org/10.1242/jeb.116087" rev="review">10.1242/jeb.116087</a></span>
<b><br />
<b><br /></b></b></b></div>
<div class="MsoTitle">
I've taken to writing reports for collaborations, as it focuses me to get done the work, and to share it with collaborators in a way where they can easily extract information for the publication. Below is such a report that I created for the above-cited paper:</div>
<div class="MsoTitle">
<br /></div>
<div class="MsoTitle">
<br /></div>
<div class="MsoTitle">
<b><br /></b></div>
<div class="MsoTitle">
<b><a href="https://www.blogger.com/null" name="h.u001f9rcis9n"></a>Limulus Peropsin-like gene
phylogeny report</b><o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b>Introduction</b><o:p></o:p></div>
<div class="MsoNormal">
In 1997, <a href="https://paperpile.com/c/MlL5sI/jLXw"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Sun et al.
1997)</span></a> reported a new opsin, found in cDNA libraries of human eyes,
and shown by immunohistochemistry to be expressed in Retinal Pigment
Epithelium. Another name for peropsin is RRH (retinal pigment
epithelium-derived rhodopsin homologue). The most closely related gene to
peropsin in the human genome is RGR (RPE−retinal G protein−coupled receptor),
first discovered in 1993 <a href="https://paperpile.com/c/MlL5sI/pFwC"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Jiang,
Pandey, and Fong 1993)</span></a>. Based on mouse knockout experiments, RGR is
a photoisomerase involved in the generation of 11-cis-retinal <a href="https://paperpile.com/c/MlL5sI/gFCS"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Chen et al. 2001)</span></a>. Both
of these vertebrate genes belong to a large clade of opsins called “RGR/Go” <a href="https://paperpile.com/c/MlL5sI/ina4+quO3"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Plachetzki, Degnan, and Oakley 2007;
Feuda et al. 2012)</span></a> or “Group-IV” opsins <a href="https://paperpile.com/c/MlL5sI/J8bg"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Porter et al. 2012)</span></a>.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Nagata et al <a href="https://paperpile.com/c/MlL5sI/s1FI/?noauthor=1"><span style="color: windowtext; text-decoration: none; text-underline: none;">(2010)</span></a> claimed to find the
first peropsin from a protostome, a jumping spider, <i>Hasarius adansoni</i>. However, their phylogenetic analysis showed only
weak support (77%) for the spider gene as the sister to peropsins and was based
on overly simplistic phylogenetic techniques (neighbor-joining based on an
unspecified distance model). Eriksson et al <a href="https://paperpile.com/c/MlL5sI/ZZ4e/?locator_label=book&noauthor=1"><span style="color: windowtext; text-decoration: none; text-underline: none;">(2013)</span></a>
discovered a gene from the spider <i>Cupiennius
salei</i> that is very similar to the jumping spider gene. While their
phylogenetic analysis shows good support for these spider genes in the Group IV
clade (1.0 posterior probability in Bayesian Inference), their placement with
peropsin is again tenuous (0.62). Hering and Mayer <a href="https://paperpile.com/c/MlL5sI/gZWT/?noauthor=1"><span style="color: windowtext; text-decoration: none; text-underline: none;">(2014)</span></a> reported a third
chelicerate peropsin-like gene from the genome of the spider mite <i>Tetranychus urticae</i>. The three
chelicerate genes form a well-supported clade within Group IV opsins, but their
phylogenetic position was again uncertain with respect to peropsin and RGR. In
some analysis of Hering and Mayer <a href="https://paperpile.com/c/MlL5sI/gZWT/?noauthor=1"><span style="color: windowtext; text-decoration: none; text-underline: none;">(2014)</span></a>, the chelicerate
genes are weakly supported as sister to all other RGR and peropsin genes and in
one analysis they are weakly supported as sister to RGR.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b>Methods</b><o:p></o:p></div>
<div class="MsoNormal">
I conducted phylogenetic analyses on 30 opsin sequences,
including our putative Limulus peropsin/RGR-like gene, 27 genes of the
RGR/peropsin (=RPE/peropsin) clade of Hering and Mayer <a href="https://paperpile.com/c/MlL5sI/gZWT/?noauthor=1"><span style="color: windowtext; text-decoration: none; text-underline: none;">(2014)</span></a>, plus two outgroup
opsins with solved crystal structures (<i>Bos
taurus</i> c-opsin <a href="https://paperpile.com/c/MlL5sI/5OIL"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Palczewski
et al. 2000)</span></a> and <i>Todarodes </i>r-opsin
<a href="https://paperpile.com/c/MlL5sI/hqCt"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Murakami and Kouyama 2008)</span></a>).
I conducted all phylogenetic analyses using the Osiris phylogenetics package <a href="https://paperpile.com/c/MlL5sI/aHHD"><span style="color: windowtext; text-decoration: none; text-underline: none;">(Oakley et al. 2014)</span></a>
within Galaxy <a href="https://paperpile.com/c/MlL5sI/j90D"><span style="color: #1155cc;">(Blankenberg et al. 2005)</span></a>. I first aligned all
30 sequences using MUSCLE <a href="https://paperpile.com/c/MlL5sI/z5jk"><span style="color: #1155cc;">(Edgar 2004)</span></a>. I next used RAxML version 7.4 <a href="https://paperpile.com/c/MlL5sI/nJIA"><span style="color: #1155cc;">(Stamatakis
2006)</span></a>, assuming a GTR+G model to search for the Maximum Likelihood
phylogeny, and conducted 100 bootstrap pseudoreplications to gauge node
stability.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b>Results</b><o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
The new <i>Limulus </i>peropsin/RGR-like
gene forms a clade with the three “peropsins” previously described from
chelicerates (100%), and is sister to the two spider “peropsins” (93%). The
relationships within chelicerates are not consistent with taxonomy, which would
predict that <i>Limulus</i>, as the only
non-arachnid, should fall as the sister gene to the other three chelicerate
genes. Our results are similar to previous analyses that cannot confidently
place the chelicerate genes in a specific position between RGR and peropsin.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="http://1.bp.blogspot.com/--UCbNw0n-0c/VSMe4_l6X9I/AAAAAAAAARE/ZsbFqZpXjwI/s1600/PeropsinRPE%2BFigure%2BWeb%2Bresolution.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/--UCbNw0n-0c/VSMe4_l6X9I/AAAAAAAAARE/ZsbFqZpXjwI/s1600/PeropsinRPE%2BFigure%2BWeb%2Bresolution.jpg" height="400" width="292" /></a></div>
<br />
<div class="MsoNormal">
<b>Discussion</b><o:p></o:p></div>
<div class="MsoNormal">
We found a gene in <i>Limulus
</i>that is very similar to other chelicerate genes known in the literature as
protostome “peropsins”. However, a careful examination of previous studes, and
our own results, indicate that the chelicerate genes may orthologs of peropsins
or RGR genes, or that vertebrate RGR and peropsins are in paralogs compared to
the chelicerate genes. The inability of phylogenetic analyses to unequivocally
place the chelicerate genes could be caused by sparse sampling of invertebrate
genomes. In addition, many of the peropsin/RGR sequences found in invertebrate
full genome sequences have not been experimentally verified, nor has function
been demonstrated for them. Clearly, there is much to learn about this clade of
opsins.<o:p></o:p></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b>References</b><o:p></o:p></div>
<div class="MsoNormal" style="margin: 12pt 0in 0.0001pt 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/gFCS"><span style="color: windowtext;">Chen, P, W
Hao, L Rife, X P Wang, D Shen, J Chen, T Ogden, et al. 2001. “A Photic Visual
Cycle of Rhodopsin Regeneration Is Dependent on Rgr.” </span></a><a href="http://paperpile.com/b/MlL5sI/gFCS"><i><span style="color: windowtext;">Nature
Genetics</span></i></a><a href="http://paperpile.com/b/MlL5sI/gFCS"><span style="color: windowtext;"> 28 (3):
256–60.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/ZZ4e"><span style="color: windowtext;">Eriksson, Bo
Joakim, David Fredman, Gerhard Steiner, and Axel Schmid. 2013.
“Characterisation and Localisation of the Opsin Protein Repertoire in the Brain
and Retinas of a Spider and an Onychophoran.” </span></a><a href="http://paperpile.com/b/MlL5sI/ZZ4e"><i><span style="color: windowtext;">BMC
Evolutionary Biology</span></i></a><a href="http://paperpile.com/b/MlL5sI/ZZ4e"><span style="color: windowtext;"> 13
(September): 186.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/quO3"><span style="color: windowtext;">Feuda,
Roberto, Sinead C Hamilton, James O McInerney, and Davide Pisani. 2012.
“Metazoan Opsin Evolution Reveals a Simple Route to Animal Vision.” </span></a><a href="http://paperpile.com/b/MlL5sI/quO3"><i><span style="color: windowtext;">Proceedings
of the National Academy of Sciences of the United States of America</span></i></a><a href="http://paperpile.com/b/MlL5sI/quO3"><span style="color: windowtext;"> 109 (46): 18868–72.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/gZWT"><span style="color: windowtext;">Hering, Lars,
and Georg Mayer. 2014. “Analysis of the Opsin Repertoire in the Tardigrade
Hypsibius Dujardini Provides Insights into the Evolution of Opsin Genes in
Panarthropoda.” </span></a><a href="http://paperpile.com/b/MlL5sI/gZWT"><i><span style="color: windowtext;">Genome Biology and Evolution</span></i></a><a href="http://paperpile.com/b/MlL5sI/gZWT"><span style="color: windowtext;">, September. doi:</span></a><a href="http://dx.doi.org/10.1093/gbe/evu193"><span style="color: windowtext;">10.1093/gbe/evu193</span></a><a href="http://paperpile.com/b/MlL5sI/gZWT"><span style="color: windowtext;">.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/pFwC"><span style="color: windowtext;">Jiang, M, S
Pandey, and H K Fong. 1993. “An Opsin Homologue in the Retina and Pigment
Epithelium.” </span></a><a href="http://paperpile.com/b/MlL5sI/pFwC"><i><span style="color: windowtext;">Investigative Ophthalmology & Visual Science</span></i></a><a href="http://paperpile.com/b/MlL5sI/pFwC"><span style="color: windowtext;"> 34 (13): 3669–78.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/hqCt"><span style="color: windowtext;">Murakami,
Midori, and Tsutomu Kouyama. 2008. “Crystal Structure of Squid Rhodopsin.” </span></a><a href="http://paperpile.com/b/MlL5sI/hqCt"><i><span style="color: windowtext;">Nature</span></i></a><a href="http://paperpile.com/b/MlL5sI/hqCt"><span style="color: windowtext;"> 453 (7193): 363–67.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/s1FI"><span style="color: windowtext;">Nagata,
Takashi, Mitsumasa Koyanagi, Hisao Tsukamoto, and Akihisa Terakita. 2010.
“Identification and Characterization of a Protostome Homologue of Peropsin from
a Jumping Spider.” </span></a><a href="http://paperpile.com/b/MlL5sI/s1FI"><i><span style="color: windowtext;">Journal of Comparative Physiology. A, Neuroethology,
Sensory, Neural, and Behavioral Physiology</span></i></a><a href="http://paperpile.com/b/MlL5sI/s1FI"><span style="color: windowtext;"> 196 (1): 51–59.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/aHHD"><span style="color: windowtext;">Oakley, Todd
H, Markos A Alexandrou, Roger Ngo, M Sabrina Pankey, Celia K C Churchill,
William Chen, and Karl B Lopker. 2014. “Osiris: Accessible and Reproducible
Phylogenetic and Phylogenomic Analyses within the Galaxy Workflow Management
System.” </span></a><a href="http://paperpile.com/b/MlL5sI/aHHD"><i><span style="color: windowtext;">BMC Bioinformatics</span></i></a><a href="http://paperpile.com/b/MlL5sI/aHHD"><span style="color: windowtext;"> 15 (July): 230.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/5OIL"><span style="color: windowtext;">Palczewski,
K, T Kumasaka, T Hori, C A Behnke, H Motoshima, B A Fox, I Le Trong, et al.
2000. “Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor.” </span></a><a href="http://paperpile.com/b/MlL5sI/5OIL"><i><span style="color: windowtext;">Science</span></i></a><a href="http://paperpile.com/b/MlL5sI/5OIL"><span style="color: windowtext;"> 289 (5480): 739–45.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/ina4"><span style="color: windowtext;">Plachetzki,
David C, Bernard M Degnan, and Todd H Oakley. 2007. “The Origins of Novel
Protein Interactions during Animal Opsin Evolution.” </span></a><a href="http://paperpile.com/b/MlL5sI/ina4"><i><span style="color: windowtext;">PloS One</span></i></a><a href="http://paperpile.com/b/MlL5sI/ina4"><span style="color: windowtext;"> 2 (10): e1054.</span></a><o:p></o:p></div>
<div class="MsoNormal" style="margin-left: 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/J8bg"><span style="color: windowtext;">Porter, Megan
L, Joseph R Blasic, Michael J Bok, Evan G Cameron, Thomas Pringle, Thomas W
Cronin, and Phyllis R Robinson. 2012. “Shedding New Light on Opsin Evolution.” </span></a><a href="http://paperpile.com/b/MlL5sI/J8bg"><i><span style="color: windowtext;">Proceedings.
Biological Sciences / The Royal Society</span></i></a><a href="http://paperpile.com/b/MlL5sI/J8bg"><span style="color: windowtext;"> 279 (1726): 3–14.</span></a><o:p></o:p></div>
<br />
<div class="MsoNormal" style="margin: 0in 0in 12pt 24pt; text-indent: -23.95pt;">
<a href="http://paperpile.com/b/MlL5sI/jLXw"><span style="color: windowtext;">Sun, H, D J Gilbert, N G Copeland, N
A Jenkins, and J Nathans. 1997. “Peropsin, a Novel Visual Pigment-like Protein
Located in the Apical Microvilli of the Retinal Pigment Epithelium.” </span></a><a href="http://paperpile.com/b/MlL5sI/jLXw"><i><span style="color: windowtext;">Proceedings
of the National Academy of Sciences of the United States of America</span></i></a><a href="http://paperpile.com/b/MlL5sI/jLXw"><span style="color: windowtext;"> 94 (18): 9893–98.</span></a><o:p></o:p></div>
</div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-23129863230775335062015-03-20T02:52:00.000-07:002015-03-20T02:52:12.633-07:00Little League Ethics<div dir="ltr" style="text-align: left;" trbidi="on">
<div style="margin-bottom: 0in; text-align: justify;">
<span style="text-align: left;"><br /></span></div>
<div style="margin-bottom: 0in; text-align: justify;">
<span style="text-align: left;">Our local Little League does not have
lights to play night games. Because baseball cannot be played in the
dark, the lack of stadium lights imposes a highly unnatural rule on
some of our baseball games: a time limit.</span></div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
One of the truly beautiful things about
baseball (besides that the defense has the ball!) is there is not
normally natural time limit. It's what led Yogi Berra to say “It
ain't over til it's over”. In typical Yogi style, his famous quote
makes no sense and perfect sense, all at the same time. A team always
has a chance in baseball, even when down by a huge margin, if they
can just score enough before their final out.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
It truly ain't over til it's over.
</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
Until there is a time limit.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
A time limit in baseball changes
everything. It raises strategic and ethical dilemmas: Is it ethical
to stall to try to reach the time limit and preserve a win? Is it
ethical to purposely speed up the game to reach the time limit and
preserve a win?</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
I have encountered these ethical
questions forced by Little League time limits, and these ethical
questions to me are critical. In my life, I strive for excellence.
One goal is to achieve excellence in sportsmanship and ethics –
especially in Little League. By definition, excellence is not easy to
achieve. Excellence requires dedication. Excellence requires plain
old fashioned hard work. Excellence requires a lot of thought and
discipline. Excellence is the highest achievement for which I can
strive, and I can think of fewer more important goals than setting an
example of excellence in sportsmanship and ethics for our youth. This
is serious.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
In a baseball game with a time limit,
the visiting team can take the lead in the final inning – only to
have the game revert back to penultimate inning – resulting in a
loss – if the time limit is reached. This is highly unnatural in
baseball, but it does come up. Many tournaments must be on a time
limit. Rain storms sometimes even impose time limits in Major League
Baseball.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
After much thought, I believe that
speeding up a game intentionally under the rules, even in Little
League, is ethical. I believe that slowing down the game
intentionally is less clearly ethical, but can mainly be moderated by
the umpire anyway.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
Here is an example. My team will be the
visiting Brewers, the home team will be the Giants. Going into the
last inning, the home Giants are winning 8-6. The sun is going down,
and the rule is that when the ambient light gets low enough, an
automatic light goes on. When that light is on, there is one more
batter. If the game's final inning is not complete, the score reverts
back to the last complete inning.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
On this night, the Brewers stage a
valiant comeback. There was a walk or two, but our Brewers were
hitting and running and scoring. They were jubilant. They had taken
back the lead in dramatic fashion. Yogi was right, it wasn't over!
Life lesson speeches on not giving up write themselves after
comebacks like this one. This kind of come back is beautiful. It is
powerful.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
The Brewers went up 11-8, with only 1
out in the last inning! But now the ethical dilemmas start. If time
runs out, the Brewers lose. Once that light goes on and the umpire
calls the game, the score reverts back to last final inning. The
comeback – officially – is erased. But it is not erased from the
minds of the Brewers. It is not erased from the minds of the Giants.
The rule is for safety, so there are no games after dark, and so
umpires don't push it. But tell that to Alex when his game winning
hit is nullified. Tell that to Andre, when his game-tying run no
longer counts. Let the games begin!</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
It's the final inning. The Giants'
coach takes a leisurely stroll to the mound to talk to his pitcher.
And most of the defense. While infuriating to the opponents, a
coaches' visit is well within the rules. It might even be advisable
to calm down the pitcher and the defense. I conclude such a visit is
ethical. However, the umpire MUST keep a tight leash on how long such
a visit can last. Stalling must be controlled by the umpire, but I do
think it is actually ethical for the team with that advantage to slow
down a little bit: within the rules and within reason. What if a
coach tells a kid to tie his shoe 4 times? This is pushing the limits
dramatically now. But here again, I believe the umpire can have some
control on the stalling. He can yell “play ball”. If the kid is
tying his shoe on the base, that is his team's disadvantage. If a
batter will not get in the batters box, the umpire can allow a pitch,
and call a strike for each one. Soon, pitch timers will be part of
the major leagues, like shot clocks in basketball. So, I don't
believe there is strong ability for a team to stall the game with a
strong umpire who keeps a lid on it. Of course, a stalling team could
purposely try very hard to get no outs and prolong an inning
indefinitely. Although the other team could counter, I think this
would now cross the line for me into unethical. The stalling team
would be purposely failing in order to salvage a win on a
technicality: a time limit.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
Now, what about the team that went
ahead with a fight to the end and a dramatic come back, our visiting
Brewers? Can those Brewers ethically speed up the game to bring the
end more quickly? I believe this is ethical. After taking the lead by
three, can they purposely make their final two offensive outs to get
on to the field faster, and try to get their final three defensive
outs in time? Can they purposely steal a base when they think there
is a VERY strong chance they will be thrown out? Can they purposely
strike out, no matter where the pitch is thrown? Or is asking kids to
do that for the team going too far?</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
My instinct tells me rushing to outs
is, in fact, an ethical tactic. Unlike excessive stalling, it is
striving to finish the game to AVOID the technicality. It's striving
to finish the game naturally, before getting to the time limit. In
the words of the Little League pledge, it is “Striving to Win” –
and I believe it is also “Playing Fair”.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
I read an interesting story on Little
League ethics that parallels my thoughts. I won't recount the whole
story, but the link is here
</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
http://www.ethicsscoreboard.com/list/littleleague2.html</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
Without retelling the entire story, one
quote is particularly apropos, edited slightly to fit this current
situation</div>
<div style="margin-bottom: 0in;">
“True, [running into an out or
striking out purposely] was superficially a violation of the
League's "strive to win" ethic, but in this odd instance
it was really the opposite: only by [quickly making outs] could his
team win.”</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
Of course trying to win cannot dictate
everything. It has to be within the rules. But clearly, trying to
steal a base is within the rules, and striking out is also.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
The link to the ethics story also
points out an interesting parallel. When we ask a player to perform a
sacrifice bunt, s/he is purposely (probably) making an out for the
betterment of the team. I maintain that getting outs quickly to
finish a game before a time limit is in fact directly akin to a
sacrifice bunt. I'd like to award Jack a sacrifice steal, and Justin
a sacrifice strike out.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<div style="margin-bottom: 0in;">
This is important to me. I want to do
the right thing. I believe sacrificing for the good of the team is
noble. I believe striving to win is critical to sport. I believe
fighting to avoid the nullification of a brave and jubilant comeback
is itself noble and ethical. I believe in running into an out. I
believe in a quick strike out. I believe in the sacrifice bunt.</div>
<div style="margin-bottom: 0in;">
<br />
</div>
<br />
<div style="margin-bottom: 0in;">
And I would fight that fight again.</div>
</div>
Unknownnoreply@blogger.com6tag:blogger.com,1999:blog-6821840758756075048.post-62565806764963490942014-11-07T08:46:00.001-08:002014-11-07T08:46:22.424-08:00Question on Independent Origins Test<div dir="ltr" style="text-align: left;" trbidi="on">
We just <a href="http://www.pnas.org/content/111/44/E4736.abstract" target="_blank">published a paper on convergent evolution</a>, which uses a new test of convergence called the "Independent Origins Test". In the main text, the description of the test is limited (however see the supplement).<br />
<br />
Just now, I received a question about this test, and I paste my answer below, in case others might benefit from the answer.<br />
<br />
<pre wrap="">THE QUESTION: Dear Dr Oakley I read you article: Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid (great!)
I do not undestand the logic behind this
The observed data are approximately and conservatively 5,000 times less likely to have arisen from an evolutionary history with less than three gains of photophores than from an evolutionary history with three or more photophore gains
we should compared 1 gain (ancestral) follow by 8 losses versus 2 independent gains here you compare less than 3 gain (1 or 2 (which is the case here)
versus 4 ,5 ,6
could please tell me what am I missing</pre>
<br />
<br />
THE ANSWER<br />
Yes, the traditionally more common way to frame alternative hypotheses
to test independent origins is to compare the likelihood of X gains
versus Y losses. This is what we did for example in <a href="http://www.pnas.org/content/99/3/1426.full.pdf" target="_blank">Oakley and Cunningham (2002) </a><br />
<br />
However, the "independent origins" test in this 2014 paper frames
the alternative hypotheses in a different way. The alternatives are: 1
gain of the trait (= homology) versus more than one gain (=independent
origins). The test calculates probabilities (assuming the model of trait
evolution, the phylogeny, and the distribution of traits on the tree)
of these alternative hypotheses.<br />
<br />
Why, you might ask then, did we compare the probabilities of "1 or 2
gains" to "3 or more gains"? The general reason is to be conservative.
More specifically, in the case of these squid, there is a clade where
photophore might have evolved more than once within that clade itself.
This was not the focus of the paper, and we were really interested in
whether two distantly related clades (loliginids and sepiolids) evolved
photophores separately. Since the independent origins test counts total
number of gains on the entire tree, it was not distinguishing between
two gains in those distant clades versus a separate gain within
sepiolids. To be conservative then, we reported the probability of at
least 3 gains. Examining "at least 2 gains" would yield even higher
differences between alternative models.<br />
<br />
I believe the easiest critique of this approach is the simplicity of
the model, which assumes the same rate of character gain and loss for
the entire tree. In simulations I have done (a la Simmap), a little bit
of homoplasy on a tree leads to estimated rates of trait evolution that
require HUGE numbers of gains and losses on a tree, to the point of
being biologically very unrealistic. I believe that models that allow
different rates of evolution on different parts of the tree could do
better at yielding biologically realistic rates of trait evolution. See for example <a href="http://sysbio.oxfordjournals.org/content/59/6/723.short" target="_blank">Skinner (2010) </a></div>
Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-26708817403866847392013-12-27T01:14:00.001-08:002013-12-27T01:14:32.497-08:00Starting a lingustic foray into evolution - cray cray?<div dir="ltr" style="text-align: left;" trbidi="on">
This holiday season, I've learned a new word from my nephews, and that word is 'cray-cray'*. According to my nephews, and the <a href="http://www.urbandictionary.com/define.php?term=cray%20cray" target="_blank">Urban Dictionary</a>, cray-cray means 'really crazy'.<br />
<br />
Researching this word has led me - yet again - to some parallels between evolution and linguistics. I want to start documenting these parallels more formally, because I think it could be important. My biology research is focused on how new traits originate during evolution, sometimes called 'evolutionary novelty'. How did eyes originate in evolution? How about <a href="http://evolutionarynovelty.blogspot.com/2008/11/evolutionary-novelty-hair.html" target="_blank">hair</a> or <a href="http://evolutionarynovelty.blogspot.com/2009/05/evolutionary-novelty-get-milk.html" target="_blank">milk</a>? Although I could be cray-cray, I believe this area of evolution has received less attention than other areas, and the theory and concepts are underdeveloped. Yet in linguistics, it seems novelty is a central area of theory.<br />
<br />
Cray-cray is a new word, a novelty. Languages change so fast, with such full documentation, it seems as though linguists have a richer theory for explaining how novelties arise. One aspect of novelty in linguistics is called Word Formation, and there are several ways in which word formation occurs. I believe many of these have parallels in organic evolution, although they may not generally be differentiated or articulated. I want to explore that on future posts.<br />
<br />
Craycray seems to be due to a particular type of word formation that is not particularly common in English, called reduplication. Actually, as I read and understand further, it seems reduplication is considered to be a change in grammar, and not as a mechanism of word formation. From this perspective, cray cray is not a new word, but is rather a grammatical change to convey a new meaning. In both evolution and linguistics, it seems challenging to think clearly and consistently about structure (word) and function (meaning) and their relationship to each other.<br />
<br />
Reduplication is quite common in many languages, and is used in several different ways. Our cray cray example seems to be reduplication for the purpose of intensifying a noun. I don't think this is common in English. Wikipedia gives an example from Hebrew, where Gever means 'man' and 'Gever Gever' seems to mean something like a man's man or a manly man, or perhaps a macho man. A man, intensified, just as cray cray means crazy, intensified.<br />
<br />
According to the same Wikipedia site on <a href="http://en.wikipedia.org/wiki/Reduplication" target="_blank">reduplication</a>, there are some English examples of reduplication. We mimic baby talk, as in 'bye-bye'; use rhyming reduplication, as in super-duper; or sometimes change the vowel sounds in the reduplication, like zig-zag. An interesting example is the 'schm' reduplication - adding 'schm' to belittle something, or to indicate irony: 'craycray, schmacray - I can just say lunatic'. Schm-reduplication is said to be 'productive', because it can be used with most any word. We also use reduplication to clarify a literal meaning versus a figurative meaning. An example that comes to mind is to clarify hot - 'do you mean spicy-hot or HOT-hot'? HOT-hot is clarifying the meaning as temperature. By the way, I think we should adopt the Spanish word picante to mean spicy-hot, a word we need in English!<br />
<br />
Besides cray cray, I can't think of any other examples in English of intensifying reduplication. From that perspective, it might not actually be reduplication, since reduplication refers to grammar. In English, our grammar doesn't usually <i>intensify</i> using reduplication, so cray cray perhaps really does fit more into Word Formation. But I also cannot fit it into established modes of Word Formation, either, such as those explained on Wikipedia or a <a href="http://www.ruf.rice.edu/~kemmer/Words/wordtypes.html" target="_blank">Rice site</a> (by the way the Rice site counted zig-zag as compound word formation, not as reduplication). Instead, cray cray is part clipping - taking just part of a longer word, like ad for advertisement, or dis for disrespect - and part compounding - putting two words together, like phone booth. Crazy clipped is cray and compounded is cray cray.<br />
<br />
My purpose here is to understand novelty in linguistics to draw parallels to evolution. For example, thinking genetically, I know that protein domains are often 'reduplicated' within the same gene. It will be interesting to think this through and research it. What types of function can protein domain reduplication provide? Are the biological-functional implications similar to linguistic-grammatical implications? I believe intensification of biological function does happen by domain reduplication (I can think of some examples, that I won't go into). But what about other parallels? That will perhaps be the subject of a future post.<br />
<br />
I should end now before this post is so long as to be cray cray.<br />
<br />
<br />
<br />
<br />
<br />
<br />
* I believe this is mainly a spoken word, such that the spelling is not yet standard. It could be craycray, cray-cray, or cray cray. </div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-6821840758756075048.post-32575395733010900152013-12-26T22:46:00.002-08:002013-12-26T22:46:42.083-08:00The resurrection of Evolutionary Novelties<div dir="ltr" style="text-align: left;" trbidi="on">
I've decided to resurrect the Evolutionary Novelties blog. While I wrote fairly regularly from late 2007 until 2009, I stopped writing any blog posts after that. Although I didn't specifically plan the regular writing sessions or the hiatus, I've felt lately that I would like again to use this forum to share some ideas.<br />
<br />
<h2 style="text-align: left;">
Why the hiatus? Blogging changed my brain</h2>
<div>
Late in 2009, I began to feel that blogging changed my brain in ways that I did not like at the time. Namely I felt like I was thinking too much about blog posts. Blog posts - at least good ones - are short, punchy and catchy - like a quick sprint. Yet conducting research and writing scientific papers takes dedication and persistence - like a marathon. When writing Evolutionary Novelties posts regularly, I began thinking about posts a lot; so much I felt like it was taking 'thinking time' and writing time away from my research. Professional research takes a huge amount of thinking time, from brainstorming to problem solving to deciding how to pitch grant proposals and publications.</div>
<div>
<br /></div>
<div>
There are also two more mechanistic reasons I took a hiatus from writing blog posts. First, I got my first smart phone around that time. Instead of doing a lot of reading (email, news, papers, other blogs) on a computer with a keyboard at the ready - I began reading on a mobile device. Without a keyboard under-finger, the possibility of a response became less immediate, and my habits changed. The second mechanistic reason is personal. My son grew to genuinely love playing sports and following professional sports. This rekindled my childhood love of sports, and I've come to spend much more time coaching, playing, and following sports. Following and participating in sports also competes for my online time, and my 'thinking time', so writing blog posts fell away.</div>
<div>
<br /></div>
<div>
<br /></div>
<h2 style="text-align: left;">
Why the resurrection? I have things to say</h2>
<div>
Writing blog posts can be a great outlet for certain topics, and some such topics have become priorities for me.</div>
<div>
<ol style="text-align: left;">
<li>I feel I am becoming a good mentor, and <b>I would like to share more broadly mentoring advice</b>. Well, actually, I think I've always been pretty good at mentoring because I genuinely care about the people I mentor, I care about their careers, and I generally have good instincts about career decisions (it's something I think a lot about). I also sometimes worry that with more students and postdocs in my lab, that there is not enough time for me to be effective at mentoring everyone all the time. Pointing to a blog post with career advice might sometimes be effective, and might help people outside my lab. In this regard, I've been inspired by <a href="http://sociobiology.wordpress.com/" target="_blank">Sociobiology</a>.</li>
<li>I've lately focused my research efforts and ideas more squarely on my '<b>home group' ostracods, and I'd like to share more about their amazing biology</b>. During the golden era of Evolutionary Novelties, I wrote about these animals in a series I called '<a href="http://evolutionarynovelty.blogspot.com/search?q=ostra-blog" target="_blank">ostra-blogs</a>'. I'd like to continue this part-travellogue, part nature writing series because we've had some fun adventures lately. My students have also expressed interest in writing ostra-blogs, and they make a good vehicle for possibly telling the public about ostracods (or is it <a href="http://evolutionarynovelty.blogspot.com/2008/08/ostra-blog-2-to-e-or-not-to-e.html" target="_blank">ostracodes</a>?).</li>
<li><b>I want to document ideas about parallels between Evolutionary Novelties and the linguistic novelties. </b>I have a long-term goal to write a book that teaches concepts of how new things evolve, using examples from linguistics. I need to learn and remember a lot about linguistics before that can happen.</li>
</ol>
<div>
So, I am going to try to find the time to contribute to Evolutionary Novelties more regularly. At least until I want my brain back again for other things...</div>
</div>
</div>
Unknownnoreply@blogger.com1tag:blogger.com,1999:blog-6821840758756075048.post-73720710660645501072013-11-21T11:17:00.000-08:002013-11-26T13:02:03.804-08:00Unfortunate arbitrariness at NSF costs our graduate students<div dir="ltr" style="text-align: left;" trbidi="on">
Last week, a student in <a href="https://labs.eemb.ucsb.edu/oakley/todd/">our lab</a> had an NSF DDIG (Doctoral Dissertation Improvement Grant) returned without review. The reason is the proposal did not fit the goals of the panel, according to the program officer. Unfortunately, the PO thought the proposal fit more squarely in a different panel, which does not accept DDIG proposals. To me, this points to a very unfortunate difficulty at NSF, which is that in the IOS (Integrative Organismal Systems) division, only one panel - Animal Behavior - accepts DDIG proposals. This puts the Animal Behavior Program Officers in a difficult position: They are forced to define discrete boundaries to a scientific field. While all fields are a continuum, defining discrete fields within the division of "Integrative" biology seems particularly arbitrary because the very definition of the division is to use multidisciplinary perspectives.<br />
<br />
This week, I learned through social media that the students of multiple colleagues experienced the same rejection without review. I know how hard students work on these proposals, and to have them returned without review is a disservice to the students who are the future of our disciplines. On one hand, it reinforces a mantra that NSF promotes - "always contact your program officer". Yes, I certainly should have checked that we were within the scope of the panel. That said, my excuse is that I really didn't imagine, as I will describe briefly below, that our proposal on the evolutionary and genetic basis of behavior would not be considered animal behavior. But this points to the challenge - the current structure forces an arbitrarily discrete definition of a field. According to<a href="http://www.nsf.gov/pubs/2013/nsf13568/nsf13568.htm"> the call</a> "<i>In the Division of Integrative Organismal Systems (IOS) only proposals within the scientific area of animal behavior supported by the Behavioral Systems Cluster are eligible.</i>"<br />
<br />
<h3 style="text-align: left;">
<b>What is (Animal) Behavior?</b></h3>
Since I am a newcomer to behavior (through training in evolution and phylogenetics), I've actually been wondering a lot about the question of what is behavior. What about bacteria that follow chemical cues? Is that behavior? Do plants or slime molds behave? Viruses? I think they do. The NSF panel has the word "animal" in it, which would rule out these questions (even that seems arbitrary to me). But still there are ambiguities. Do light-following, swimming sponge larvae that lack nervous systems behave? What about annelid worm larvae or box jelly larvae that have ciliated cells that respond to light? In these animals, a single cell acts as a sensor (light) and a motor (cilium) to cause swimming. Is that behavior, or is that physiology? To ask interesting questions about these systems, we don't need to classify it into a field. But to get a DDIG proposal funded, a student is restricted in the questions she can ask.<br />
<br />
My student's proposal walks the line between behavior and physiology, a little bit. But the student and I both feel very strongly that we are studying behavior (even <i>animal </i>behavior, since these are cephalopods). Here are the first few lines from the project description:<br />
<br />
<blockquote class="tr_bq">
"Cephalopods dazzle prey, woo mates and seamlessly blend into the background using skin that changes in both color and texture (Hanlon and Messenger, 1998). These diverse behaviors in cephalopods and countless others found throughout animals inspire the question of how new behaviors evolve to produce the riotous variety we see today (Tinbergen, 1963). Do novel behaviors stem from evolved mechanisms? Or do new behaviors primarily arise through evolutionary “tinkering”, which may co-opt, retool and recombine existing mechanisms and modules? Answering these questions is fundamental to understanding how behaviors evolve."</blockquote>
<br />
Our goal really is to understand how behaviors evolve, especially at the genetic level. Yet the program officers write:<br />
<blockquote class="tr_bq">
"... As written, this proposal does not address questions or theory in the field of Animal Behavior. Thus it is not appropriate for this competition and is being returned without review."</blockquote>
and yet, here is how the NSF Behavioral Systems Cluster describes its goals (<b>my emphasis</b>):<br />
<blockquote class="tr_bq">
The Behavioral Systems Cluster supports research on the development, function, <b>mechanisms</b>, and <b>evolutionary history</b> of behavior, with emphasis on a vertically integrated understanding of the behavioral phenotype in nature. To foster this integrative goal, the Cluster specifically encourages projects that seek to understand how combinations of <b>neural</b>, hormonal, <b>physiological</b>, and developmental mechanisms act synergistically as a system from which behavior emerges. Laboratory work or the study of animals in captivity is encouraged, to the extent that it contributes to the understanding of behavior in natural systems.</blockquote>
I still feel our proposal addresses questions in the field of Animal Behavior. Yet, I recognize the root of the problem is that only one area in IOS accepts DDIG proposals. This forces a line to be drawn somewhere, and even if our proposal is animal behavior, there must be discrete decisions about where animal behavior ends that will affect someone.<br />
<br />
<h3 style="text-align: left;">
<b>A broader view</b></h3>
National Academy Member, David Hillis of the University of Texas, astutely pointed out that the current difficulty points to a fundamental decision about funding many small grants or funding fewer larger grants:<br />
<br />
<span data-reactid=".r[4txns].[1][3][1]{comment10152052125455767_30118046}.[0].{right}.[0].{left}.[0].[0].[0][3].[0].[0]" style="background-color: #edeff4; color: #333333; font-family: 'lucida grande', tahoma, verdana, arial, sans-serif; font-size: 11px; line-height: 14px;"><span data-reactid=".r[4txns].[1][3][1]{comment10152052125455767_30118046}.[0].{right}.[0].{left}.[0].[0].[0][3].[0].[0].[0]">"The problem, as I understand it, is that only DEB and part of IOS make the case that DDIGs are worthwhile. To me, they are perhaps the best use of NSF funds, and result in the highest return for the buck of any federal funding. But the science communit</span></span><span data-reactid=".r[4txns].[1][3][1]{comment10152052125455767_30118046}.[0].{right}.[0].{left}.[0].[0].[0][3].[0].[3]" style="background-color: #edeff4; color: #333333; font-family: 'lucida grande', tahoma, verdana, arial, sans-serif; font-size: 11px; line-height: 14px;"><span data-reactid=".r[4txns].[1][3][1]{comment10152052125455767_30118046}.[0].{right}.[0].{left}.[0].[0].[0][3].[0].[3].[0]"><span data-reactid=".r[4txns].[1][3][1]{comment10152052125455767_30118046}.[0].{right}.[0].{left}.[0].[0].[0][3].[0].[3].[0].[0]">ies (outside of DEB) need to make this case to NSF, if they agree. There is much more of a tradition of independent research by graduate students in the fields represented by DEB, compared to many other areas. I've heard that some other programs resist DDIGs because they disperse a small amount of money per proposal, so they have a relatively high administrative cost per dollar of research funds dispersed, and graduate students are much less likely to be doing truly independent research outside of DEB. But I think any increase in admin costs is more than made up by the high return in each dollar used, which I think is far more efficient for DDIGs than most other programs. The trend at NSF is actually in the opposite direction: funding of very large, multi-institutional grants and centers. I think these probably result in the least efficient use of research dollars (certainly far less efficient than DDIGs, in my experience). But that balance may differ among fields, which is why DEB makes the argument for DDIGs, but most other programs don't. "</span></span></span><br />
<br />
I wholeheartedly agree with those comments. Supporting DDIG proposals is a very wise investment, not only to fund up-and-coming researchers, but to provide a platform to learn how to write grants, to learn about the NSF funding system, and to promote early independence in scientists. As such, I very much advocate expanding the DDIG call to all of IOS.<br />
<br />
<h2 style="text-align: left;">
<span style="color: red;">Action</span></h2>
<div>
So, what can I/we do besides complain about the situation on an obscure blog? I propose to organize anonymous peer reviews for those students whose DDIG proposals were returned without review. For the students in this situation to whom I've spoken, this is their biggest regret: They worked hard and cannot even get feedback. I propose to facilitate obtaining that feedback. Hey, maybe we could get really creative and start a Kickstarter (or similar) program to *actually fund* some or all of the top reviewed proposal. Here is what I propose:</div>
<div>
<br /></div>
<div>
<ol style="text-align: left;">
<li>Any student whose DDIG proposal was rejected without review can send their proposal to me by email on or before <b>December 2</b>. I imagine they can just download a pdf from fastlane and send it along to me. I will treat the proposal as confidential, just as I would if I reviewed it.</li>
<li>I will act as a sort of 'program officer' and solicit 2 or 3 anonymous reviews per proposal. I will ask reviewers to follow precisely NSF reviewer guidelines and make sure they keep the grants confidential, just as if NSF asked them to review. The reviewers will be anonymous to the student.</li>
<li>I will summarize the reviews and send them back to the student. The goal is for them to get feedback about their research ideas from anonymous reviewers.</li>
</ol>
</div>
<div>
<br /></div>
<div>
In addition to providing the students with feedback, and an idea of how their proposal might have reviewed, another goal is to raise awareness of what I see to be unfortunate arbitrariness that is costing our graduate students.</div>
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If you are willing to help, here is what you can do:</div>
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<li>Volunteer to serve as an anonymous reviewer of proposals. Just send me an email: oakley@lifesci.ucsb.edu and tell me you are willing</li>
<li>Spread the word, so that affected students can hear about this and get their proposals reviewed, if they like.</li>
<li>Contact NSF and tell them you support expanding DDIG to all of IOS.</li>
<li>Send any additional ideas or concerns to me by email or as comments on this blog post</li>
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Thank you for listening!</div>
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Todd Oakley, Professor, UCSB</div>
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Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-6821840758756075048.post-2020414471377600022009-12-23T00:08:00.000-08:002009-12-23T00:27:18.621-08:00Ostra-blog 9. Postasterope barnesiIt's unfortunately been too long since I've posted an 'ostra-blog', a post about my main study group, the Ostracoda. If you haven't seen these, I encourage you to read some of them. Most contain little anecdotes, personal vignettes about interesting experiences I've had with ostracods.<br /><br />Try this <a href="http://evolutionarynovelty.blogspot.com/search?q=ostra-blog">link</a>, if you interested.<br /><br />This installment is a quick post inspired by a colleague who is trying to collect bioluminescent <span style="font-style: italic;">Vargula </span>(subject of previous posts). He did some plankton tows out by Catalina Island, and came up with some ostracods, but these are a different family. See our exchange below, and a picture sent by his student:<br /><br /><br />The query:<br />Hi Todd,<br /><br />I apologize for the out of focus, low magnification photo attached -- but is it likely that these ostracods are Vargula tsuji? These are not from a trap, but instead from night surface plankton tows from the dock at Wrigley. These are quite large for ostracods (up to 1.5 mm or so in length, I'd guess), fairly bright orange, and very abundant in the plankton soon after dusk.<br /><br />Thanks for any simple confirmation/rejection of our tentative id. I appreciate it. Sorry again for the low quality image; I'm not at Catalina or I'd take a better one. This was sent to me by a student.<br /><br /><br /><br />The Picture:<br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_x4a19ceueHs/SzHTJ_PLvtI/AAAAAAAAAHk/5ACTUd9kow4/s1600-h/CatalinaCylindro.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 400px; height: 283px;" src="http://2.bp.blogspot.com/_x4a19ceueHs/SzHTJ_PLvtI/AAAAAAAAAHk/5ACTUd9kow4/s400/CatalinaCylindro.jpg" alt="" id="BLOGGER_PHOTO_ID_5418343995250818770" border="0" /></a><br />The reply:<br /><br />No, those are not Vargula, which is in the family cypridindiae. These that you found are in the family cylindroleberididae. I think the common sp out at Catalina is Postasterope barnesi, and this looks like it could be that species. Both are myodocopids, which are larger than the somewhat more common podocopids...<br /><br /> I've found males of this family to be attracted to lights at night. Most myodocopids mate in the water column after sunset, and the males of some sp are attracted to lights. Probably just about all the individuals they found are males, I'd guess. The one pictured looks like a male, based on the tapered carapace (hard for someone to see who hasn't looked at a million ostracods). But an easy way to tell a male in these is that the males have a REALLY long sensory bristle. It's a "hair" (2 actually, one on each side) that emerges from the front of the carapace along with the swimming appendages. But this sensory "hair" is really long, longer than the body in many cases. I actually can't tell from this picture if there are the long sensory bristles because of the focus, but I'll bet they are there... I do see a white line across the carapace in the right spot, but I can't tell if that is part of the swimming appendage, or the sensory bristle....Unknownnoreply@blogger.com2tag:blogger.com,1999:blog-6821840758756075048.post-28180220780745981562009-11-27T16:34:00.000-08:002009-11-27T17:26:03.160-08:00Why is the "black box" so complicated??I received an e-mail question about a <a href="http://www.springerlink.com/content/p52245164l342056/">recent article</a> I wrote with a graduate student. The question shows a common misunderstanding of evolution, and I thought it would be interesting, or at least potentially useful to more that one person, to post my response here.<br /><blockquote><span style="font-size:85%;"><span style="font-family:courier new;">Hi Dr. Oakley,</span><br /><br /><span style="font-family:courier new;"> I am writing a research paper and came across your paper entitled, Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution. I was hoping you could give me your perspective on a question that is part of my research interest.</span><br /><br /><span style="font-family:courier new;"> Since a simpler mechanisms for phototransduction would theoretically work, why would evolution favor a more complicated phototransduction cascade with intermediates such as transducin and PDE? I would greatly appreciate any insight you could provide me. </span></span></blockquote><br />The implication in the e-mail is that evolution is a force that produces sleek perfection. Expensive solutions to problems should not arise by evolution (or at least they should not be maintained), especially if the complexity is unnecessary. This is a <a href="http://www.biology-direct.com/content/2/1/30">modernist view of biology</a>, a view that can be found in 20th Century biological research, and a view that is also common today among students, and the general public outside the field of evolutionary biology. It is a view that results from an often unstated assumption natural selection is a supremely powerful force that leads to perfection.<br /><br />From this Modernist, <a href="http://en.wikipedia.org/wiki/Bauhaus">Bauhaus </a>perspective, it is indeed perplexing to learn that opsin initiates a complex, baroque, <a href="http://en.wikipedia.org/wiki/Rube_Goldberg_machine">Rube Golddberg</a>-like cascade to turn light energy into a nervous impulse. This cascade includes reactions from opsin->transducin->PDE->CNG; each protein signaling in one way or another to another protein down the line - and this description is even VERY simplified compared to the actual complexity!<br /><br />So the question is, why would evolution "favor this complicated phototransduction cascade", when all that seems to matter is that opsin signal directly to the CNG ion channel protein to cause the nervous impulse.<br /><br />The most direct answer is that evolution is not an Intelligent Designer, rather it is a bricoleur, a tinkerer. Evolution acts upon what is available, and things that are useful are kept. In the case of the phototransduction cascade, evolution co-opted existing components: an existing GPCR cascade gained light sensitivity. We know this because the components of phototransduction pre-date opsin (e.g. <a href="http://evolutionarynovelty.blogspot.com/2008/07/evolutionary-origins-of.html">here</a>). Phototransduction was not invented from scratch, in the most efficient way possible. Instead, it was cobbled together using available parts.<br /><br />This can be conceived as an example of a phylogenetic or historical constraint. In other words, history matters. All living things and all components of living things share a common history. Because of this, and because of the interdependence of components of living things, it is usually not easy to completely re-invent something. The number of shared genes in all animals (for example) clearly illustrates that history matters. Components are used and re-used, not invented anew.<br /><br />This answers the proximate question, of why phototransduction is so complex. But doesn't address the question of why all GPCR cascades are so complex. I don't know the answer to this, but perhaps the complexity allows for flexibility. In fact, GPCR cascades are supremely flexible, and underlie signaling from outside to inside cells for many processes in animals, including vision and other senses, hormone signaling, metabolism, development, reproduction, etc, etc.<br /><br /><br />Interestingly, this question showed me yet another new perspective on the flawed argument for Intelligent Design. ID proponents suggest that when we see something outlandishly complex, then it must have been designed by an intelligent agent. However, as this question points out, extravagant complexity is not a sign of intelligence. Why use 50 components when 2 will suffice? Elegant simplicity is far more intelligent than excessive complexity. Again, evolutionary biology provides a logical and plausible explanation for the biological processes that we are coming to understand.Unknownnoreply@blogger.com7tag:blogger.com,1999:blog-6821840758756075048.post-67597395517267350992009-11-21T13:54:00.000-08:002009-11-21T15:25:32.247-08:00Dispatch from the front lines of Ray Comfort's Krazee crusadeThe "special" 150th anniversary edition of Origin of Species - the one with 59 pages of anti-scientific banana mush as an introduction - was handed out at UC-Santa Barbara on Thursday. Word on the street was that a number of campuses were hit on Wednesday, and by ~10:30am on Thursday, we at UCSB were starting to feel somehow let down, like we wouldn't get our chance to see the circus, and maybe just a little like a wallflower at the junior high dance.<br /><br />Then the news hit. Graduate student Sabrina poked her head into my office around 11 and asked if I was ready. I was. Mostly I wanted my souvenir. Graduate student Chris Evelyn was already on the scene. Chris is an evolutionist with a strong competitive streak, and he was not about to let Ray Comfort's propaganda be distributed freely. Chris had found two people handing out the books near our library, and he contacted Sabrina, who let me know. I rattled off an e-mail to our Biology email list, and headed off to battle. <br /><br />Aside from people paying to throw pies in the face of frat boys (fund raiser), demonstrations to save ESS (UCSB's exercise department is getting cut), flyers from "Jews for Jesus" (sounded interesting, but I didn't get one), and some other activity and demonstrations around the library (Free Palestine!), I saw no copies of the Origin, and no sign of Chris or Sabrina.<br /><br />"We're over at the UCEN", Sabrina sent me a text. I walked 5 minutes over to the University Center. It was another fine Santa Barbara day, crystal clear blue skies, 70 degrees, and crisp shadows from the intense sunlight. The Comfort-ites, two of them, had run out of books. They had each carried a backpack-full to near the library, where Chris had found them. Now they were making plans to get more books. They had to park in Isla Vista, a 15-20 minute walk from the library. Chris followed them to their van - he didn't want a single book to be handed out without an NCSE flyer. Sabrina and I went back by the library to wait for the return.<br /><br />By that time, my email had hit the biology department. About 10-15 other biologist found us and together we waited for the return of the banana editions. Independent of us, an Undergraduate Skeptics group called SURE was on the scene. They were prepared with flyers from <a href="http://www.dontdissdarwin.com/links.php">Don't Diss Darwin</a> and had written a <a href="http://ucsbskeptics.blogspot.com/">counter argument</a> to Comfort's banana-mush preface. Chris, still following the distributors, kept us updated by text messages. "They have hundreds of books in a van!"<br /><br />Finally, they arrived, and I got my copy. I talked a bit to one of the distributors. "Jason" had a full red beard and wore a baseball cap. I learned he lives in Ojai, and he's 35 and unemployed. He had a calm demeanor, and he didn't know what he was getting into. He had recently joined a bible study group, and his friend "Mike" asked him to help pass out some books. He did not expect any sort of confrontation at all, and went out of his way to make clear that he didn't really know about what was in the book. He'd hand out a book and say things like "make sure you get a flyer and see the other side of the argument".<br /><br />The other distributor, "Mike" was a older than Jason, maybe 60. He was a bit more evasive, and for a while seemed to want to get away from the skeptics and the biologists. I didn't get a chance to talk to Mike myself, but I learned that he was a veteran of military service. After a while, he too was telling people to get our flyers, to be fair. Poor Mike - most everyone I saw was a biologist just trying to get one of these laughable souvenirs. Poor Jason - he was just helping out a new friend, handing out some books.<br /><br />We invited Jason and Mike to come to our screening of "Judgment Day: Intelligent Design on Trial". They declined. Their goal was to hand out all the books. Chris made sure flyers were present, and the Skeptics were troopers, too, sticking with the distributors through the evening; although several came to the screening.<br /><br />After the screening, I got another text from Sabrina "Debating going on near the library". I already had plans to take my kids to the UCSB soccer game, first round of the NCAA tourney (we won, 1-0). Chris and Sabrina, and probably Nathan, were fighting the good fight though, and I think almost no books were handed out without a flyer or NCSE banana-bookmark, or both, as accompaniments.<br /><br /><br /><br />A little activism was fun, and I was proud that evolutionism and rationalism had a much stronger presence than anti-science banana-mush. Although this sort of thing can be energizing, in the end, I mostly feel bad for Mike and Jason. This feeling was echoed by an email I got just now from Chris.<br /><br />Chris thinks that, in the end, all this was just a cheap scam perpetrated by Ray Comfort. We found out that Mike put up money to buy these books. Comfort wrote a bunch of crap, tagged it to the beginning of Darwin's classic, published cheap copies, and then used his propaganda machine to get gullible buyers to spend their money.<br /><br />I shouldn't be surprised. This to me is the lowest point of religion: the fact that (somehow) charismatic, yet underhanded people seem always to be able to lighten people's wallets in the name of religion. It's happened for centuries. Still, seeing it in action, and meeting the victims, makes me feel completely empty. I'm reminded of a time when I visited New York City and street con artists pulled cash right out of the hand of my friend. The rest of the trip was not the same. It seems to me that Ray Comfort is no better than one of these street con-artists. Perhaps it would've been more fun to be at UCLA, <a href="http://www.spencerfern.com/">where Ray himself was,</a> instead of witnessing his victims gradually realize they were caught in a scam.Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-6821840758756075048.post-68227149174659041472009-11-04T10:49:00.000-08:002009-11-04T10:54:46.340-08:0010 Great advances in evolution-Nova Betapbs.org has a new format for their web-based information on Evolution. There is a lot of great information there. <a href="http://www.pbs.org/wgbh/nova/beta/evolution/ten-great-advances-evolution.html">Here </a>is an article by Carl Zimmer entitled "Ten Great Advances in Evolution", which draws upon similar material to his new textbook.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-54700220715781808922009-10-01T09:08:00.000-07:002009-10-01T09:09:23.527-07:00Conference and Blog contestDear Colleagues,<br /><br />Apologies if you have already received notice of this opportunity.<br /><br />It is my great pleasure to announce that the National Evolutionary Synthesis Center (NESCENT) in Durham will be funding 2 travel awards for Science Online 2010 in Research Triangle Park, NC. This annual (un)conference (<a href="http://www.scienceonline2010.com/index.php/wiki/">http://www.scienceonline2010.com/index.php/wiki/</a>) to "explore science on the web" takes place January 15-17 and is free to attend. Two awards for $750 each are meant to offset the costs of participating in the conference and are open to anyone from any country. To qualify, you need to write a blog post about evolutionary research that was published in 2009!<br /><i><br />"To apply for an award, writers should submit a blog post that highlights current or emerging evolutionary research. In order to be valid, posts must deal with scientific results appearing in 2009. Posts should be 750‐1500 words, and must mention the NESCent contest."</i><br /><br />For more details: <a href="http://deepseanews.com/2009/09/travel-awards-for-scienceonline-2010/">http://deepseanews.com/2009/09/travel-awards-for-scienceonline-2010/</a><br /><br />Please spread the word on your own blogs, tweets, webpages, news blurbs ,etc. It is great for such a prestigious organization to support online science communication in this way!Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-6821840758756075048.post-79051631085071020942009-09-21T08:54:00.000-07:002009-09-21T10:10:10.554-07:00Refuting Comfort's Eye evolution claimsAs I mentioned in my last <a href="http://evolutionarynovelty.blogspot.com/2009/09/cameron-comfort-co-opt-darwins-origin.html">post</a>, Comfort and Cameron will be distributing co-opted copies of Darwin's ...<span style="font-style: italic;">Origin</span>... I've looked at the introduction Comfort wrote. Of course it contains the same old tired anti-evolutionist arguments that have not changed in hundreds of years, despite the fact the field of evolutionary biology has matured into a rich, detailed, predictive science that forms the core of modern understanding of all biology.<br /><br />[If you don't read the entire rather long post, please read the last 2 paragraphs]<br /><br />A prime reason evolutionists don't often debate these simplistic claims is that it's been done before, for hundreds of years, and anti-evolutionists keep re-using the same tired arguments, ignoring advances in science. Scientists really like to argue, but not about things that have been resolved for hundreds of years, over and over again, in increasing detail.<br /><br />Comfort's simplistic, tired arguments are no exception. I'll focus on his section on eye evolution. The arguments boil down to:<br /><br /><ol><li>It looks soooo complex. It had to be designed.</li><li>Comfort can't imagine how "random" processes could drive evolution.</li><li>There are a bunch of parts working together, and each couldn't originate without the other.</li></ol>Of course there is nothing new here. For #1, <a href="http://en.wikipedia.org/wiki/David_Hume">Hume </a>famously critiqued the design argument in the 1700's. It part, this is a false analogy: Watch is to human designer as Complex biological feature is to God.<br /><br />#2 Natural selection is not a random process, e.g. <a href="http://www.amazon.com/Blind-Watchmaker-Evidence-Evolution-Universe/dp/0393315703">Blind Watchmaker</a>.<br />#3 There is no evidence that "separate" parts of the visual system cannot work separately, and in fact it is known that parts DO function separately. As one of many possible examples, the cnidarian polyp <span style="font-style: italic;">Hydra magnipappillata</span> uses photosensitivity without eyes or brain (<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001054">ref</a>).<br /><br />Below, I will paste Comfort's text, and a few comments on his text.<br /><span style="font-size:85%;"></span><blockquote><span style="font-size:85%;">Or, consider the human eye. Man has never developed a<br />camera lens anywhere near the inconceivable intricacy of the<br />human eye. The human eye is an amazing interrelated system of<br />about forty individual subsystems, including the retina, pupil,<br />iris, cornea, lens, and optic nerve. It has more to it than just<br />the 137 million light-sensitive special cells that send messages<br />to the unbelievably complex brain. About 130 million of these<br />cells look like tiny rods, and they handle the black and white<br />vision. The other seven million are cone shaped and allow us<br />to see in color. The retina cells receive light impressions, which<br />are then translated into electric pulses and sent directly to the<br />brain through the optic nerve.<br /><br />A special section of the brain called the visual cortex<br />interprets the pulses as color, contrast, depth, etc., which then<br />allows us to see “pictures” of our world. Incredibly, the eye,<br />optic nerve, and visual cortex are totally separate and distinct<br />subsystems. Yet together they capture, deliver, and interpret<br />up to 1.5 million pulse messages per millisecond! Think<br />about that for a moment. It would take dozens of computers<br />programmed perfectly and operating together flawlessly to<br />even get close to performing this task.</span></blockquote>Yes, eyes are pretty complicated - that is one reason they are fun to study and understand from a scientific perspective.<br /><span style="font-size:85%;"><br /><blockquote>The eye is an example of what is referred to as “irreducible<br />complexity.” </blockquote><br /></span>There is no evidence that eyes or any other biological structure are 'irreducibly complex'. <a href="http://www.springerlink.com/content/p52245164l342056/">Here </a>is a paper describing processes that have led to the evolutionary origins of "phototransduction", the cascade of protein signaling events that results in animals' ability to detect light.<br /><span style="font-size:85%;"><blockquote><br />It would be absolutely impossible for random<br />processes,</blockquote><br /></span>It would indeed be difficult for purely random processes to evolve complex systems, but natural selection is not a random process.<br /><span style="font-size:85%;"><br /><blockquote>...operating through gradual mechanisms of genetic<br /><www.apologeticspress.org articles="" 2835="">mutation and natural selection, to be able to create forty<br />separate subsystems when they provide no advantage to the<br />whole until the very last state of development.</www.apologeticspress.org></blockquote><www.apologeticspress.org articles="" 2835=""></www.apologeticspress.org></span>This is factually wrong. For example, one of these eye "subsystems" provides an advantage to <span style="font-style: italic;">Hydra</span> even though the animal does not possess other of the "subsystems". As mentioned above, <span style="font-style: italic;">Hydra </span>utilizes phototransduction without lens, retina, brain, or even pigment cells. One response to light is for the animal to scrunch into a ball, hypothesized to purge its one-way gut at first morning light. [If there is a designer, at least She had a sense of humor when She made one-way guts - what a great design that is!]. So as evidenced by mouse trap tie clips in the Dover trial; claims of irreducible complexity usually represent a lack of imagination about what sub-systems can do.<br /><br /><span style="font-size:85%;"><www.apologeticspress.org articles="" 2835=""><br /></www.apologeticspress.org></span><blockquote><span style="font-size:85%;"> Ask yourself<br />how the lens, the retina, the optic nerve, and all the other parts<br />in vertebrates that play a role in seeing not only appeared<br />from nothing, but evolved into interrelated and working parts.</span></blockquote><span style="font-size:85%;"><br /><br /></span><span style="font-size:100%;">This sounds like an argument against divine design, which claims that eye parts came from dust. In fact evolutionary biology teaches us that <a href="http://www.amazon.com/Gene-Sharing-Evolution-Diversity-Functions/dp/0674023412/ref=sr_1_1?ie=UTF8&s=books&qid=1253550624&sr=1-1">proteins of the lens came from other proteins</a>.</span><br /><span style="font-size:85%;"><www.apologeticspress.org articles="" 2835=""><br /></www.apologeticspress.org></span><blockquote><span style="font-size:85%;">Evolutionist Robert Jastrow acknowledges that highly trained<br />scientists could not have improved upon “blind chance”:</span></blockquote><span style="font-size:85%;"><span style="font-size:100%;"><br />To paraphrase Orgel - evolution is cleverer than you are; that doesn't mean that goddidit. </span></span><span style="font-size:100%;">Again, natural selection is not "blind chance".</span><br /><span style="font-size:85%;"><www.apologeticspress.org articles="" 2835=""><br /></www.apologeticspress.org></span><blockquote><span style="font-size:85%;"><br />The eye appears to have been designed; no designer<br />of telescopes could have done better. How could<br />this marvelous instrument have evolved by chance,<br />through a succession of random events? Many people<br />in Darwin’s day agreed with theologian William<br />Pauley, who commented, “There cannot be a design<br />without a designer.”</span></blockquote><span style="font-size:85%;"><br /><br /><span style="font-size:100%;">William Paley, not Pauley. Yes it is truely amazing that evolution produced eyes, and other complex things like livers or brains. Nevertheless, it is a well established scientific fact that evolution did produce these traits.</span><br /><br /><blockquote>And this marvelous design occurs not just in humans, but<br />in all the different creatures: horses, ants, dogs, whales, lions,<br />flies, ducks, fish, etc. Think about what the theory of evolution<br />claims: the eyes, in working pairs, of all these creatures slowly<br />developed over millions of years. Each of them was blind until<br />all the parts miraculously came together and interrelated with<br />the others, because all parts are needed for the eye to function.<br />Then each creature had its two eyes work in harmony with<br />the brain to interpret those images. Fortunately, each of these<br />creatures simultaneously evolved whatever matching parts<br />each would need: sockets, skin, eyelids, eyelashes, tear ducts,<br />muscles to blink, etc.</blockquote><br /><span style="font-size:100%;">Again, Comfort is arguing more against his own claims that against evolution. Eyes appearing separately in every tetrapod is VERY unlikely, but this is what the creationist fable of eye origins would entail. In fact, evolutionary biology teaches us that all living things share a common ancestry, and that shared features usually evolved once, prior to the common ancestor of creatures sharing a trait. This is backed up by mounds of genetic evidence showing shared use of many genes in most animal eyes, including opsin, Pax-6, and many more.</span><br /><br /><blockquote>You’ve probably been led to believe that the first simple<br />creatures had rudimentary eyes, and that as creatures slowly<br />evolved their eyes evolved along with them. However, that’s<br />not what scientists have found. Not only is there no evidence<br /><br /><br />Robert Jastrow, “Evolution: Selection for perfection,” Science<br />Digest, December 1981, p. 86.</blockquote><span style="font-size:100%;">It is simply false that scientists have found the first simple creatures to have had complex eyes. "The first simple creatures" Comfort seems to be referring to are trilobites. There are highly complex arthropods, far far far removed from the first simple creatures. Trilobites are not even the first animals, not even the first arthropods.<br /></span><br /><br /><blockquote>of this occurring, but some of the most complex eyes have<br />been discovered in the “simplest” creatures.<br />Riccardo Levi-Setti, professor emeritus of Physics at the<br />University of Chicago, writes of the trilobite’s eye:<br /><br />"This optical doublet is a device so typically<br />associated with human invention that its discovery in<br />trilobites comes as something of a shock. The realization<br />that trilobites developed and used such devices half a<br />billion years ago makes the shock even greater. And a<br />final discovery—that the refracting interface between<br />the two lens elements in a trilobite’s eye was designed<br />in accordance with optical constructions worked out<br />by Descartes and Huygens in the mid-seventeenth<br />century—borders on sheer science fiction...The design<br />of the trilobite’s eye lens could well qualify for a patent<br />disclosure. "<br /><br />--<span><span style="font-size:85%;">Riccardo Levi-Setti, Trilobites (Chicago: University of Chicago<br />Press, 1993), pp. 57–58.</span></span><br /><br />How could the amazing, seeing eye have come about<br />purely by blind chance? Based on the evidence, wouldn’t a<br />reasonable person conclude that the eye is astonishingly<br />complex and could not have evolved gradually, and that each<br />creature’s eyes are uniquely designed?<br /><span style="font-size:85%;"><br /></span>Even Charles Darwin admitted the incredible complexity<br />of the eye in The Origin of Species:<br /><br />To suppose that the eye, with all its inimitable<br />contrivances for adjusting the focus to different<br />distances, for admitting different amounts of light,<br />and for the correction of spherical and chromatic</blockquote><br /><br /><blockquote>aberration, could have formed by natural selection,<br />seems, I freely confess, absurd in the highest degree."<br /><br />Even more incredible, though, is that Darwin went on<br />to say that he believed the eye could nonetheless have been<br />formed by natural selection. He was right on one point. If a<br />Designer is left out of the equation, such a thought is absurd<br />in the highest degree.</blockquote><br /></span><span style="font-size:100%;">Yes, it is still amazing - and still true - that eyes evolved. No natural selection still cannot be equated with blind chance.<br /><br /></span><span style="font-size:100%;">At least he included the end of this famous quote, where Darwin writes that anyone with any bit of logical reasoning ability can see that evolution can produce even complicated things.<br /><br /><br />I didn't spend a lot of time on this because these arguments of Comfort are not worth a lot of my time. They are tired, recycled, un-creative jabs at evolution that have been known to be false for hundreds of years.<br /><br />In the end, I'll use Comfort's own words to describe what he is doing to evolution. He was writing about Buddhism, but his words apply nicely to his ignorance of evolutionary biology:<br /><br /><br /><blockquote>Amazingly, the religion of Buddhism [substitute 'Ray Comfort' for 'Buddhism'] denies that God [substitute 'Evolution' for 'God'] even exists. It teaches that life and death are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help you deal with your fears, but it doesn’t square with reality.</blockquote>A few word changes lead to:<br /><br /></span><span><span style="font-size:100%;">Amazingly, the religion of <span style="font-weight: bold;">Cameron and Comfort </span>denies that <span style="font-weight: bold;">evolution </span>even exists. It teaches that <span style="font-weight: bold;">two hundred years of hard work by countless scientists across the globe to elucidate the details of evolution</span> are sort of an illusion. That’s like standing at the door of the plane and saying, “I’m not really here, and there’s no such thing as the law of gravity, and no ground that I’m going to hit.” That may temporarily help <span style="font-weight: bold;">Comfort and Cameron</span> deal with <span style="font-weight: bold;">their </span>fears, but it doesn’t square with reality.</span></span><br /><span style="font-size:100%;"><br /></span>Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-6821840758756075048.post-23510819519343426132009-09-19T10:25:00.001-07:002009-09-19T10:38:23.532-07:00Cameron Comfort Co-Opt Darwin's OriginI've had my head in the sand writing revisions of papers before the quarter starts, so I'm sure there is information all over the net about this that I am not integrating here, sorry. But apparently, Kirk Cameron and Ray Comfort have co-opted Darwin's ..<span style="font-style: italic;">Origin of Species</span>... and inserted creationist propaganda into in introduction that is mixed with some facts (i.e. biographical facts on Darwin). It also includes propaganda linking Nazi-ism and evolution, etc.<br /><br />They plan to had out published copies at the 'Top 50' research institutions in the US. Cameron in a video mentions he will come to a local university personally (here at UCSB? UCLA? I'm not sure what "local" is to Mr. Cameron).<br /><br />Apparently, Richard Dawkins has been involved in getting the word out to evolutionists to expect this, kudos to him and his crew for doing that.<br /><br />I personally disagree with the plan of action I'm told Dawkins' camp is promoting (I haven't confirmed that he is actually promoting this). That plan entails obtaining as many copies of the book as possible and removing the Comfort introductory propaganda. <br /><br />In my opinion, this is not a good strategy. It seems that this could look desperate, as if scientists actually have something to worry about (when it comes to the facts of evolution, we do not have to worry), and it looks like book burning or censoring.<br /><br />Instead, I think a concise pamphlet refuting the bogus claims of the introdution would be outstanding. It could have references and web links, and could also expose what I see as the breathtaking inanity of Comfort and Cameron's crusade against critical, rational thinking.<br /><br />It would be great if someone like the NCSE were involved. Time is short and an organized response would nice.<br /><br /><br />Below, I attach an email that was sent around here at UCSB, which includes web links to some of this stuff:<br /><br /><br /> Colleagues,<br /><br /> We all loved Kirk Cameron on Growing Pains:<br /> <a class="moz-txt-link-freetext" href="http://www.youtube.com/watch?v=6Vo2i3NFq78&feature=related">http://www.youtube.com/watch?v=6Vo2i3NFq78&feature=related</a><br /> <a class="moz-txt-link-rfc2396E" href="http://www.youtube.com/watch?v=6Vo2i3NFq78&feature=related"><http://www.youtube.com/watch?v=6vo2i3nfq78&feature=related></a><br /><br /> Years later we were amused and perhaps a bit alarmed at his<br /> 'Origin of the Banana' video:<br /> <a class="moz-txt-link-freetext" href="http://www.youtube.com/watch?v=2z-OLG0KyR4">http://www.youtube.com/watch?v=2z-OLG0KyR4</a><br /> (That's Ray Comfort there with him)<br /><br /> But in November of 2009 he and Ray Comfort are taking it to the<br /> next level: <a class="moz-txt-link-freetext" href="http://www.youtube.com/watch?v=GN9zpf5cT0M">http://www.youtube.com/watch?v=GN9zpf5cT0M</a><br /><br /> The Important thing for us: *THIS GIVE AWAY WILL HAPPEN AT<br /> UCSB! On November 19th!<br /> *<br /> Richard Dawkins has proposed a strategy: Collect as many of these<br /> books as possible, remove the 50 page intro and donate the copies<br /> to schools, libraries, or the whoever<br /> (<a class="moz-txt-link-freetext" href="http://www.facebook.com/group.php?gid=155609217391">http://www.facebook.com/group.php?gid=155609217391</a>)<br /><br /> We can stick with this strategy or come up with something else but<br /> we should do <b class="moz-txt-star"><span class="moz-txt-tag">*</span>SOMETHING<span class="moz-txt-tag">*</span></b><br /><br /> Basically we need to get organized if they are coming here. Ready<br /> with information &/or to get these books. Ready with pamphlets<br /> answering his questions or just trying to keep them off campus?<br /><br /> *Who would be into meeting within the next couple of weeks to<br /> start to get ourselves organized?*<br /><br /> If you are not ready for action now here are some highlights from<br /> Comfort's 50 page Intro:<br /><br /> 1) So, even though we share 96 percent of our genetic make-up with<br /> chimps, that does not mean we are 96 percent chimp. Be careful you<br /> don’t fall for the illogic of this “evolutionary proof,”<br /> 2) here are some interesting questions for the thinking<br /> evolutionist: Can you explain which came first—the blood or the heart—and why?<br /> 3) You’ve probably been led to believe that the first simple<br /> creatures had rudimentary eyes, and that as creatures slowly<br /> evolved their eyes evolved along with them. however, that’s not<br /> what scientists have found.Unknownnoreply@blogger.com3tag:blogger.com,1999:blog-6821840758756075048.post-81376678916878751952009-09-09T14:48:00.001-07:002009-09-09T14:58:34.092-07:00Phylogenetics Conference - SeattleActually, the meeting is more general than "phylogenetics", but I'd like more phylogeneticsts to attend (and this was my "campaign" platform when running for secretary of the division of systematic biology. "Campaign" is quoted since I'm less than 100% positive I wanted to win). The title of this blog post is an attempt to get people from <a href="http://treethinkers.blogspot.com/">dechronization </a>interested in the conference- this blog is on their roll, so the title appears.<br /><br />The meeting is the <span style="font-style: italic;">Society of Integrative and Comparative Biology</span> (formerly American Zoologist), <a href="http://sicb.org/meetings/2010/">which will run from Jan 3-7, 2010 in Seattle</a>.<br /><br /><span style="font-weight: bold;">Note the abstract deadline of Sept 11 2009</span>. This is often a hard deadline without extensions!! So we'd better get crackin'!<br /><br /><br />Strengths of the meeting are student funding and in general its being student friendly. Topical strengths include physiology (comparative), evo-devo, and invertebrate biology. Given my interest in eye evolution in inverts, it's become my main meeting. There is often a strong showing of phylogeneticists, usually those using phylogenetic tools to address comparative biological questions, with fewer people presenting on phylogenetic methods for methods' sake, the strength of the summer evolution meetings.Unknownnoreply@blogger.com1