tag:blogger.com,1999:blog-6821840758756075048.comments2023-09-25T09:44:38.184-07:00Evolutionary NoveltiesUnknownnoreply@blogger.comBlogger277125tag:blogger.com,1999:blog-6821840758756075048.post-79115879366848888402017-10-08T00:06:19.751-07:002017-10-08T00:06:19.751-07:00You write about bacterial photosynthesis and give ...You write about bacterial photosynthesis and give bacteriorhodopsin as an example, which is wrong, since bacteriorhodopsin is in fact an arcaeal rhodopsin. An example for bacterial rhodopsins is proteorhodopsin.Anonymoushttps://www.blogger.com/profile/05716162241174844946noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-59934558090962758892017-07-29T10:36:53.505-07:002017-07-29T10:36:53.505-07:00Although as I think a little more about it, some s...Although as I think a little more about it, some senior postdocs do get quite a few review requests, in my experience - so not a perfectly discrete line at Assistant Prof.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-92064141082497073112017-07-29T10:33:47.027-07:002017-07-29T10:33:47.027-07:00Thanks Carl - yes, I agree that is a valid point I...Thanks Carl - yes, I agree that is a valid point I had not considered.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-5141459063828520182017-07-29T09:43:48.138-07:002017-07-29T09:43:48.138-07:00Good thoughts. I largely agree but I think you can...Good thoughts. I largely agree but I think you can only divide by the number of co-authors who are at the assistant professor level or higher. My graduate students (and usually postdocs) don't receive enough requests to be able to review one paper per submission. So when I submit as a PI, I need to be ready to do the reviewing to cover the reviewing obligations of the others in the lab.Carl Bergstromhttps://www.blogger.com/profile/10360537964073475816noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-69830123243905488762016-03-03T07:13:43.626-08:002016-03-03T07:13:43.626-08:00Yes, I believe that his disagreement is mainly sem...Yes, I believe that his disagreement is mainly semantic, and population geneticists tend to see distinctions between character identities and character states as nothing more than semantic quibbling and not something that reflects the way in which development is structured. That's why he lumps evolution of halteres and origin of wings from forelimbs in the same category. If Dan was comparative morphologist he would see that there are certain patterns in morphological evolution, and perhaps the most important one is individuation of serially repeated body parts. But I'd bet you that he wouldn't be so dismissive if he had read Ken Weiss's paper on duplication with variation from 1990; I know that he really has a lot of respect for him.Anonymoushttps://www.blogger.com/profile/15668432866034699214noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-1455548447146277572016-02-25T11:43:55.003-08:002016-02-25T11:43:55.003-08:00That would be a permissive (but still potentially ...That would be a permissive (but still potentially valid) definition, Des, and would definitely occur in microevolution. The new protein of two domains has to start as a polymorphism in a population. Your host-switch case could also be novel. A single amino acid change in an olfactory receptor may change the perception of an odor but might not change a behavior. A different change might have the same properties, but together they might have a threshold affect and shift host preference to a new fruit. This is literally more than a sum: it is epistasis.<br /><br />Among the most novel things I know of in microevolution are “novel” genes. As listed in the abstract of this paper (http://www.pnas.org/content/103/26/9935.short), they might arise from “exon shuffling, gene fission/fusion, retrotransposition, duplication-divergence, and lateral gene transfer” — all clearly recycled but maybe “novel” depending on your definition. The most novel case of all, and the focus of that paper, are “de novo” genes. Even these aren't actually de novo, though. They are made up of DNA that was previously not protein-coding, but that DNA is itself made up of a bunch of dead bits of old genes. If you wanted to assemble a new gene from random AGCTs you would never get there, but the base composition of junk DNA is non-random due to its previous functions.Thomas Turnerhttps://www.blogger.com/profile/10115504815393463372noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-56290070146416531572016-02-25T11:18:23.969-08:002016-02-25T11:18:23.969-08:00Fun and thought provoking read Todd! Tom, towards ...Fun and thought provoking read Todd! Tom, towards your first point, would it be helpful to define a true novelty as something that emerges from the combination of two (or more) pre-existing components that is greater than the sum of those components? Alternatively, novelty is not an extension of a current function.<br /><br />In your example, if two domains fuse to create a new kind of protein whose function could only come from the fusion of those domains, then that would be a novelty. The domains are not novel, but the new protein itself is.<br /><br />Re the number zero-- zero as a digit to represent the count of nothing is probably not novel. But maybe we could see it's role in mathematics as novel, since in mathematics zero is not just a placeholder for a null quantity and has unique mathematical properties.<br /><br />Dan's examples of venoms-- venoms are composed of genes who's relatives had other functions. But venoms are not *just* digestive enzymes. The sum of their activity comes from the unique combinations of digestive enzymes+other stuff that makes them lethal in very specific ways. The function of venoms is greater than the sum of the individual digestive enzymes that go into it. You could throw together a suite of digestive enzymes and inject it into an animal and have nothing happen. And sure, venoms have evolved multiple times independently, maybe multiple times independently from digestive enzymes even, but they are still novelties. <br /><br />Final example: eyes. Let's define a extremely simple eye as two light sensitive cells next to each other associated with pigment. The phototransduction cascade it uses is pre-existing. The pigment synthesis pathway is pre-existing. Maybe even the cell type these are expressed in is pre-existing. What makes this eye a novelty? It is the combination of expression of the phototransduction cascade in adjacent cells AND the association of those cells with pigment synthesis that allows a new function that was previously unattainable by any of the pieces alone-- directional light sensing. <br /><br />So then what isn't a novelty? Can novelties even exist at a popgen scale? Based on what I outlined above, new beak morphologies in Darwins finches aren't novelties. The evolution of host preference from hawthorns to apples is probably not a novelty. Still cool, interesting and important, but not evolutionary novelties. We can do popgen analyses on venoms, watch evolutionary arms races between predators and prey. On the other hand, watching the arm race now is watching modifications of current function, not seeing the emergence of an entirely new function from parts that had previous functions. Can we find populations in a non-venomous species with non-venomous ancestors that have become venomous? Could we consider that watching the emergence of an evolutionary novelty at a popgen scale?<br /><br />I have now officially spent too much time writing up this comment instead of my current manuscript but I'm really interested in this conversation. Never sorry.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-19303488090930714022016-02-25T11:10:57.240-08:002016-02-25T11:10:57.240-08:00It does seem somewhat of a macroevolutionary patte...It does seem somewhat of a macroevolutionary pattern, because the sampling period matters. If you look back all the way to the origin of life, it seems right to say something novel has evolved between then and now (life). Intermediate sampling periods seem more ambiguous but still reasonably 'novel" (e.g. eyes). Even 4 billion years ago, however, there were many small steps that were just using what was already available, and the novelty emerges in hindsight as a macroevolutionary pattern. Macroevolutionary process I'm not sure about, but macroevolutionary pattern seems right.Thomas Turnerhttps://www.blogger.com/profile/10115504815393463372noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-22906009086578904052016-02-25T10:40:34.002-08:002016-02-25T10:40:34.002-08:00Thanks Tom. Yes, it is mainly a semantic/definitio...Thanks Tom. Yes, it is mainly a semantic/definition issue about novelty. It is actually a bit of a paradox. I understand the idea that evolution recycles and uses existing parts all the time. But the simple fact that we have biodiversity indicates that there was novelty somewhere along the line. Otherwise, we logically would need to posit a homunculus that had ALL of biodiversity at the origin of life that just got recycled differently in different lineages.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-10767626100692322952016-02-25T09:46:07.007-08:002016-02-25T09:46:07.007-08:00Thanks for posting this. I think the specific disa...Thanks for posting this. I think the specific disagreement about novelty is mainly semantic. If you fuse two domains to create a new type of protein, is that new or recycled? Here is what would help me understand Dan's definition of novelty: in what OTHER processes is there true novelty? In human thought & culture, for example, you might also posit that there are novel ideas, perhaps like the number zero. Alternatively, you might think that all ideas are built on/from other ideas. The number zero was only thought up after the idea of numbers was thought up and people certainly already understood not having any of something, so these ideas were just combined. Thomas Turnerhttps://www.blogger.com/profile/10115504815393463372noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-12622451849255730662015-03-20T13:52:01.272-07:002015-03-20T13:52:01.272-07:00OtterJill -- I whole heartedly agree. The Giants f...OtterJill -- I whole heartedly agree. The Giants fought valiantly, and they fought hard. A delayed steal to tie the game!! Incredible! They were striving to win the whole time! They fought back from down 5-0, at least. This was a beautiful baseball game, except for the time limit.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-34565629242089605282015-03-20T13:45:36.709-07:002015-03-20T13:45:36.709-07:00Great essay Todd! The only part of the story that ...Great essay Todd! The only part of the story that could be added to get the full flavor of the evening was that the Giants had also just staged a valiant and impressive comeback in the 5th inning, so emotions were all over the place.OtterJillhttps://www.blogger.com/profile/00400578571877288521noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-1987345677431830372015-03-20T12:39:03.330-07:002015-03-20T12:39:03.330-07:00Brendan -- the full Pledge is here:
Pledge
I tr...Brendan -- the full Pledge is here:<br /><br />Pledge <br /><br />I trust in God <br />I love my country <br />And will respect its laws <br />I will play fair <br />And strive to win <br />But win or lose <br />I will always do my best<br /><br /><br />The interpretation of "I will always do my best" could be at odds with "Strive to Win" in the time limit case. Unless "do my best" implies "do my best to win" (while "I will play fair").Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-70857270642852369032015-03-20T12:34:02.429-07:002015-03-20T12:34:02.429-07:00One more important argument for ethical speed up:
...One more important argument for ethical speed up:<br /><br />Speeding up the game does NOT rob an opportunity from the other team (like stalling could). In fact, it explicitly ALLOWS the other team the opportunity to come back and score at the bottom of the last inning for a legitimate, complete win. That would be a better win than time simply running out.<br /><br />I maintain speeding up the game IS competing at your best - at your mental/strategic best - (even if not physical best). We do risk giving up outs while not having a big enough lead, but that is part of the decision, part of the strategy.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-42640994164903926262015-03-20T10:19:10.091-07:002015-03-20T10:19:10.091-07:00This is all real. The game is under protest, but n...This is all real. The game is under protest, but not for speeding up the game. There is a question about exactly when the light came on. Brewers quickly got 3 up 3 down in the last inning, but it is not clear when exactly the official light came on relative to the last out.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-6770222986003288002015-03-20T10:09:44.498-07:002015-03-20T10:09:44.498-07:00So is this all reality? Or just discussion? Did ...So is this all reality? Or just discussion? Did the Brewers "win"? I'm a bit surprised the little league motto was "play to win", since I always thought it was about inclusion (and many of the rules dictate that). Winning is exclusive.<br /><br />Nice write up Todd - excellent thought food.<br /><br />-BrendanAnonymoushttps://www.blogger.com/profile/00013756078842956563noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-85014476210512943422014-04-28T10:39:51.923-07:002014-04-28T10:39:51.923-07:00Totally agree with you. Now, I´m checking myodocop...Totally agree with you. Now, I´m checking myodocopids from SE and SW sectors from the Gulf of Mexico and it´s very difficult to find out which species we have because their descriptions are old, incomplete or they can be new. But, we go back to the same point, since there are a few specialist in myodocopid ostracodes in this area with whom I can corroborate species. Lorena OM.LOMhttps://www.blogger.com/profile/15647211083836159335noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-24686063962487616782014-04-28T10:38:35.949-07:002014-04-28T10:38:35.949-07:00Totally agree with you. Now, I´m checking myodocop...Totally agree with you. Now, I´m checking myodocopids from SE and SW sectors from the Gulf of Mexico and it´s very difficult to find out which species we have because their descriptions are old, incomplete or they can be new. But, we go back to the same point, since there are a few specialist in myodocopid ostracodes in this area with whom I can corroborate species. Lorena OM.LOMhttps://www.blogger.com/profile/15647211083836159335noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-46957600805510441542013-12-28T13:24:39.871-08:002013-12-28T13:24:39.871-08:00How nice to see this pop up in my feed. Welcome ba...How nice to see this pop up in my feed. Welcome back!RBHhttps://www.blogger.com/profile/13562135000111792590noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-48559228776161643922013-12-27T19:48:10.587-08:002013-12-27T19:48:10.587-08:00Chinese uses reduplication extensively and at seve...Chinese uses reduplication extensively and at several "levels". In a written character, an element may be repeated to make a new character emphasizing that aspect. The common example is 木=wood/tree, 林=woods, 森=forest. In spoken language, two syllable words seem to be preferred, so a single syllable is often repeated (e.g. the family: baba, mama, gege, jiejie, didi, meimei) or two synonymous characters are joined to make a word: 朋友 friend/friend, 看见 see/see. And then words can be reduplicated for a softening or intensifying effect. A simple example: xiexie (thank you), xiexie xiexie (thank you very much).<br />There is more info here: http://mandarin.about.com/od/grammar/a/Reduplication.htmDustynoreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-73582704203509544882013-11-26T13:02:57.632-08:002013-11-26T13:02:57.632-08:00I changed the deadline to December 2 because that ...I changed the deadline to December 2 because that is a Monday.Todd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-20369494815282850842013-11-21T13:30:35.924-08:002013-11-21T13:30:35.924-08:00Love the idea of maybe crowd funding some of the s...Love the idea of maybe crowd funding some of the students' projects. There's already a platform for this: https://www.microryza.com/<br /><br />Good luck!<br /><br />Elizabeth Ballou, PhD<br />Research Fellow<br />Aberdeen Fungal Group<br />University of Aberdeen, UK<br />www.erballou.comeorbluehttps://www.blogger.com/profile/04816659003550248054noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-3126941332148228462013-11-21T11:38:41.404-08:002013-11-21T11:38:41.404-08:00On twitter, I started the hashtag #ArbitraryDDIGOn twitter, I started the hashtag #ArbitraryDDIGTodd Oakleyhttps://www.blogger.com/profile/14309149952900395185noreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-35338555034438793452013-09-25T11:07:05.534-07:002013-09-25T11:07:05.534-07:00In light of today's dismissal of global warmin...In light of today's dismissal of global warming silliness, Lea's closing statement, "...as global warming reduces available tundra territory...", is a good reminder to stick to the facts when posting in a blog that will follow you forever. Otherwise colleagues will be made aware of how frightened you were by noises in the closet and how you, too, drank the boogey-man Kool-Aid. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6821840758756075048.post-19650101549716983702011-07-08T12:16:37.795-07:002011-07-08T12:16:37.795-07:00I know it has been years since the original post w...I know it has been years since the original post was posted, but I wanted to thank you for expressing your evolutionary thoughts. I agree, lineal evolution makes no sense, and is obviously flawed. Nature, in my opinion, is not driving life towards the most complex, but rather favoring those that are most adapt to survive - which in the case of bacteria means simplicity. The mere fact that complexity survives along side simplicity suggests that there is no predilection for one or the other. I would be extremely interested in finding other sources of information or at least more information. Thank you.Eamonnhttps://www.blogger.com/profile/17415124161191244227noreply@blogger.com