Saturday, July 29, 2017

How many manuscripts to review?

Question from a colleague about how many manuscripts to review:

I saw your note about being awash with review requests on Twitter. 

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?

I still learning the rules here on when is OK to say no to things.

My fairly off-the-cuff response (although it is something I've thought about over the years): 

Well, I don’t think there is any rule at all against saying ’no’; especially to review a paper. 
Before agreeing to review, I must:

1. Be very interested to read the manuscript
2. Confident I am qualified to critique at least 1 major aspect of the paper
3. Not be reviewing more than 2 other manuscripts already at the time (unless REALLY interested in it)
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). 

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.

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).

If declining, I try to do so quickly, and recommend someone else.  

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.

Tuesday, February 14, 2017

Exaptation vs Neo-functionalization vs Co-option

I just reviewed a paper that equated Neo-functionaliztion, exaptation, and co-option - using the terms interchangeably. 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.

In my understanding of the terms, “Neo-functionalization” implies that a *duplicated* structure (usually a gene, but not always) gains a new function. As Vinny puts it:

"b/c neofunc is a process in which a homologous character maintains ancestral function"

Exaptation” 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.

Co-option is a bit similar to both neo-functionalization and exaptation; but I think there are subtle differences. Co-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 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.

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.

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.

Ganfornina M.D., Sánchez D. 1999. Generation of evolutionary novelty by functional shift. Bioessays. 21:432–439.

Oakley T.H. 2007. A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evol. Dev. 9:514–516.

Thursday, December 22, 2016

tsujii abounds

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.

I've collected V. tsujii 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.

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 tsujii 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 here. 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.

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 tsujii. I've seen hilgendorfii in this abundance and Photeros annecohenae, but never tsujii.

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 link. 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.

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.

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:

Adult    males: 49
Adult females: 228
Brooding females: 3
Juveniles: 348

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!

We also sorted a sample of the juveniles to get an idea of the demographics, with these results:

A-1: 121
A-2: 153
A-3: 75
A-4: 12
A-5: 1

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.

Wednesday, November 16, 2016

Drafting Sisters or Public Goods - how tree-like is evolution?

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.

I want to set the stage for that discussion in the context of similar questions for gene trees and species trees.

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.....

Sisters or Public Goods? How tree-like is the evolution of genes, modules, cell types, organs, or species?

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” (Cavalli-Sforza and Piazza 1975)), 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 (Oakley et al. 2007), 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 (McInerney et al. 2011), 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?

Thinking about evolutionary history at multiple levels
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.
All of life shares common descent and biologists use tree thinking (Plachetzki and Oakley 2007) 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” (Oakley et al. 2007). 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 (Friedrich 2006; Oakley et al. 2007; Buschbeck and Friedrich 2008; Oakley and Rivera 2008) and cell types furcate to become sister cells, perhaps often by subdividing functions of the ancestral cell (Arendt 2008; Arendt et al. 2009). 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 (Plachetzki and Oakley 2007), morphological features, tissues, and organs (Geeta 2003; Oakley et al. 2007; Buschbeck and Friedrich 2008), and cell types (Arendt 2008).
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 (Haggerty et al. 2013) 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 (Hahn and Nakhleh 2016; Pease et al. 2016) 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.

Economic classification of goods
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).

Table 1. The classification of goods

Excludable (high)
Excludable (low)
Rivalrous (high)
Private Goods
Car, apple, parking spot
Common Pool Goods
Fish stock, public park bench
Rivalrous (low)
Club Goods
Private golf course, satellite TV
Public Goods
Air, public radio signal,

Public Goods in Macroevolution
Recent papers applied the concept of public goods to macroevolutionary topics like the tree of life and novelties. McInerney et al (2011) 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 (2011) 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 (2011) 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.
Erwin (2015) 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.
The macroevolutionary applications above differ from public goods applications to microevolution, especially by ignoring costs. Frank (2010) defined a public good as “An individually costly 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 (Hamilton 1975), parasite virulence (Frank 1996), ‘tragedy of the commons’ scenarios, and cases where microbes produce public goods like nitrogen (West et al. 2002) or iron-scavenging molecules (Kümmerli et al. 2009). 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 (Smith and Szathmary 1997).  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.

Measuring Excludability with Treeness

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.

Saturday, October 15, 2016

What grad students need to know about submitting a grant proposal

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.

I hope I will remember to show this post to my future students, and I hope others can find it useful too.

1. The Institution (e.g. The University) officially submits many grants, NOT the individual student. 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) - most are submitted by the institution. 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.

The fact that the institution submits grants has several important downstream effects.

2. Your practical deadline will be earlier than the final proposal deadline.  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.

3. There are other forms and signatures needed, besides those required by the grant.  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.

4. You need to contact your grant administrator early. 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.

Based on the above considerations, I recommend the following timeline:

About 1-2 months in advance:
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

About 1 month in advance of deadline:
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:

  1. The Title of the Grant Proposal
  2. The projected start date of the proposed work
  3. The duration of the proposed work
  4. A sketch of the budget
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)

C. For NSF, get your fastlane ID, or for other agencies, make sure you have any accounts that you need.

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. 

I won't go into writing strategies here, this is about the administrative hurdles.

About 2 weeks before the deadline

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.

F. Finalize the proposal, incorporating comments from colleagues.

About 1 week before the deadline.

G. Have your grant administrator contact the Office of Research to review your full proposal.

Just before the deadline

H. Make any final changes to your proposal. Some may be indicated by OR.
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.

And remember, "A grant is never done, the deadline just arrives."

After the deadline
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.

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!

Monday, March 7, 2016

Why is English - and biology - so Complicated?

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.
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.
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 Back to the Future 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.
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.
“Hi, Joanne Remmings”, she said.
“MacGyver”, Angus replied, shaking her hand.
“Oh I’ve heard about you”, her eyes widening, “you’re the guy that does the ‘whatchamacallits’, you know, ‘macgyverisms’.”

“Macgyverisms?”, Mac asked, with a touch of smugness.

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 MacGyver 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.

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 Malia, 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.
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.
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 “managed to macgyver 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.

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.

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?

All of these entities are so complicated because they are evolved. Because they have history. 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.

Wednesday, February 24, 2016

Response to Judge Starling on Novelty

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.

Here is my version of what happened:

1. I saw Dan Graur's post on "All of Evolutionary Biology in 12 Paragraphs" linked here, a provocative claim to distill all of evolutionary biology into 237 words. Very interesting! Do I agree?

Well, #10 stood out to me as false, especially the claim that "there is no true novelty in evolution"

Update: The full statement is here "10. Evolution cannot create something out of nothing; there is no true novelty in evolution."

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.

My first response to the 12 paragraphs was this tweet:
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.

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.

Next, someone else had the same critique I did about #10 of the 12 paragraphs. Here is what bluebear tweeted:

Dan responded, and I replied to that response as follows:

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".

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:
Dan then tweeted:

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:

Professor Graur then asked to what I was referring, and I answered as follows:

This led to his reading the book in an impressively fast amount of time. He just as quickly dismissed the book, writing:

A bit later, he wrote a longer critique of the book on tumblr, linked here.

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.

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.

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). 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.

**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.

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.
Todd Oakley recommended the book. I became intrigued. Now, that I finished reading it, I’m not impressed. It is a very pompous philosophical treatise
Pompousness is a rather subjective critique that is unrelated to the content of the arguments in the book.
that attempts to explain everything from the evolution of organisms to the fate of unattended picket fences by using a single law.

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.

It’s a law whose purpose is to find an answer to Life, the Universe, and Everything,
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.

but as opposed to number 42 in The Hitchhiker’s Guide to the Galaxy by Douglas Adams, McShea & Brandon’s First Law is neither amusing nor original.  

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.”
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.
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.)
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).

 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".
However, it took me a while to understand that the two authors are either talking about entropy without mentioning the term entropy,
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.

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.

or about variance in a random genetic drift process without saying so.

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.
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.
As noted by Mohan Matthen from the University of Toronto, the two parts of the law are equally problematic.
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.
Ummm, so if this can be easily shown to be false, has it been shown false?

The additional clause “in the absence of constraint,” in which “constraint” is undefined, is untestable and hence unscientific.

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.

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.
Other reviews, such as by Noël Bonneuil from the Institut National d'Etudes Demographiques and Kele Cable from the University of Minnesota were also quite lethal in their verdicts on the merits of the book. 
“Biology’s First Law” is clearly neither a first nor a law.
Okay, why?
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. 
If you don’t believe me that none of the ideas in McShea & Brandon’s book are original, kindly read Brooks & Wiley’s 1986 Evolution as Entropy to judge for yourself. As noted previously, before making extravagant claims, kindly read the literature. 
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:

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).

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 we gratefully acknowledge the intellectual debt. "

There are other citations too.

So, who needs to kindly read the literature before making extravagant claims?

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?

I’ll finish by quoting an anonymous critic on Amazon, “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.”
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.
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.
Thank you for the back handed compliment.

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.

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.

Anyway, the latter Todd Oakley owes me $14.04 and half a pound of candy as compensation for his book recommendation. 
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.

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.

Evolution cannot create something out of nothing; there is no
true novelty in