Pharyngula

So here I am at the IGERT Symposium on Evolution, Development, and Genomics, having a grand time, even if I did get called out in the very first talk. There were two keynote talks delivered this evening, both of which I was anticipating very much, and which represented the really good side of science: two differing points of view wrestling with each other for consensus and for testable, discriminating differences. They also had dueling t-shirts.

Here’s the argument in brief. The functional part of the genome can be roughly broken down into two components: the coding regions, or the actual bit of DNA that is transcribed and translated into working proteins, and the subset of the non-coding regions that are involved in regulating gene expression. The coding regions are obviously important — they’re what makes the actual meaty, bony, brainy part of the animal, or the leaves and roots and flowers of a plant — but the thing is, we primates share almost all of the same genes with a mouse, which makes one wonder what makes us different from a mouse. Evo-devo proponents have been arguing that the most important changes in evolution have been in the regulatory elements of the genome, in particular the stretches of DNA called cis-regulatory elements (CREs) that flank the coding regions. People and mice share the same keratin genes, and what makes us different is how they are switched on, with variations in regulation that produce furry mice and mostly hairless people. At its most extreme, we could argue that all of us mammals have basically the same coding genes, and all the interesting stuff in evolution has been variations in the CREs, which change how those genes are deployed.

But hang on, the non-evo-devo people rightly cry, while mice and humans might have very similar sets of genes, the coding regions of those genes are not identical, and it is premature to claim that those differences are relatively insignificant … and we also know of variations in coding sequences that make big differences in fitness. We’re grossly overemphasizing the importance of cis elements in evolution, and evo-devo is doing a disservice to the discipline with an excess of hype.

So that’s the context for this evening, with both sides represented in back-to-back keynote talks.

First up was Jerry Coyne, with the provocative title of “Give me just one cis-regulatory mutation and I’ll shut up!” He also showed off his t-shirt, which said “I’m no cis-sy”. Spoiling for a fight, he was…but actually it was a very thoughtful talk in which the first thing he did was reassure everyone that he is not the enemy of evo-devo he has been made out to be, an erroneous impression taken from the Hoekstra and Coyne paper. He cited several comments that put his criticisms in a particularly harsh light, yet at the same time he could quote the paper arguing that evo-devo has great potential, which has not yet been realized. He also mentioned my comment that he was a “rather significant detractor” of evo-devo, saying he was more of a critic. I accept the change. But I do have to say that when I wrote that, it was with both enthusiasm for and anticipation of his arguments.

Right away he made an unassailable case that the importance of CREs in evolution has been oversold. He put up quotes by Hughes, Carroll, Davidson, and Valentine that I have to agree were far too sweeping in their claims for an essentially exclusive pre-eminence of regulatory change (and I made a note to myself that I better be more cautious about my enthusiasms, or Jerry Coyne will catch me).

His approach in the talk was narrow but deep, dealing with specific cases. He marched through a laundry list of examples of cis-regulatory mutations that have been trotted out as examples of the importance of these changes in evolution by the evo-devo crowd, and more or less ripped them apart. Many of the purported effects were by association only — that is, the work hadn’t been done to show the actual mechanism by which the molecular difference was translated into a significant phenotypic change. Others lacked evidence that they actually had any adaptive significance; sure, the mutation changed something in development, but so what? It wasn’t clear that it made any difference to the organism. He also argued that many of the known examples are of morphological loss, which isn’t as impressive as finding morphological additions would be. By the end, he’d found serious weaknesses in all of the cases but one.

(The one, by the way, is Chris Cretekos’s work on mutations that affect limb length and led to the evolution of the bat forelimb. Chris is an old friend from my days in Utah, and he sent me that paper months ago, and it’s sitting on my desktop right now plaintively begging me to write it up. I guess now I better prioritize it!)

Anyway, the bottom line in Coyne’s talk is a demand for greater rigor. You can’t just see a mutation in a developmental gene that has an interesting effect and claim that therefore it is important in evolution. The full range of work in puzzling out the molecular mechanism, in identifying the specific genetic change, in showing the inheritance of the trait, and in demonstrating an adaptive evolutionary role has to be done. And he’s right, of course. Evo-devo has tantalizing bits and pieces ad a lot of promise, but the iron-clad story isn’t there yet.

The second keynote was by Greg Wray, and he took a very different approach. (Oh, and a different t-shirt: “Exons, Schmexons”.) He listed more examples of developmental genes and argued that the evidence of their importance in evolution was stronger than Coyne let on, but he also conceded that he wasn’t going to argue for the pre-eminence of CREs, and that this shouldn’t be an all-or-nothing debate: the evolution of both coding and non-coding regions is important. However, arguing over a list of examples isn’t going to answer the question, since there are going to be biases in ascertainment and inclusion. What he proposed instead is a genome-wide survey for regions that exhibit signs of positive selection. You might suspect that he would say this because he has been carrying out a genome-wide survey for such regions, and you’d be right.

There was a flurry of technical details which I did not get down in my notes — I’ll have to read the paper — but he’s been doing comparative analyses of macaque, chimpanzee, and human genomes to identify regions that show signs of selection, and categorizing those regions by whether they are in regulatory or coding regions of genes. The short answer is that regulatory regions win by a clear majority. The more interesting but complicated answer is that it varies.

Some of the most interesting data he showed was on which genes were showing what kind of changes. Genes of the immune system, for instance, showed little selection for changes in regulation, and lots of selection for changes in the coding regions, which makes sense. These are gene products that interact with a changing environment, so the effective mutations are ones that modify that interaction, and you wouldn’t really expect the developmental regulation between a chimpanzee and a human to differ that much. In developmental genes, on the other hand, two thirds of the variation was in regulation, and one third in coding sequence. Furthermore, the developmental genes that experienced the greatest structural variation were those involved in gametogenesis and maternal effect genes, while it was the zygotic genes that varied most in regulation.

This was all good stuff, but Coyne and Wray were orthogonal to each other and weren’t really hitting each other’s main points. Wray has developed some powerful tools to scan genomes for evolutionarily significant variations, but Coyne is also right that to nail the story down, you need to dig deep into the individual cases — what we’ve got are lots of candidate genes, and Wray has widened the spectrum of possibilities (and has some preliminary evidence that CREs have been very important in evolution), but now someone has to get to work and figure out mechanisms and genetics for each one.

So we had an evening of scientific dissent, with good arguments and good questions from both sides, and every one won, and the meeting is off to a great start. Now, tomorrow I see that the schedule starts at 9am and ends at 10pm, so I might well be worn out by the time it’s over … but for now I am well satisfied.

Comments

  1. #1 Krazy
    April 5, 2008

    Hey, I’m the first to post on this thread!

    ZZZZZZZZZZZZZZZzzz…….

  2. #2 wazza
    April 5, 2008

    Seems to me that it’s probably a bit of both. A lot of scientific controversies seem to be like this:

    “It has to be A!”
    “No, it can’t be A, it has to be B!”

    when actually, it’s probably A and B working together.

    Which is hardly an original observation. But this is: your daughter says you ate all the ramen (we got to talking about cats in rollerskates, which is an excellent way to work up an appetite)

  3. #3 Stuart Ritchie
    April 5, 2008

    Take that, Ben Stein, with your bizarre allegations that ‘Big Science’ stifles dissent and differing opinions!

    Seriously, I hate to relate everything back to the ID controversy, but if those bastards realised that THIS is day-to-day science – encouraging rigour and meticulous checking of the evidence – they’d quickly see how far out their claims about Gods and Designers and Creators are.

  4. #4 wazza
    April 5, 2008

    No they wouldn’t, Stuart

    Because They Have Access To The TRUTH

  5. #5 Jolly Bloger
    April 5, 2008

    Oh ZZzz yourself, this is interesting.

  6. #6 Paul Brown
    April 5, 2008

    wazza:
    “Seems to me that it’s probably a bit of both. A lot of scientific controversies seem to be like this:

    “It has to be A!”
    “No, it can’t be A, it has to be B!”

    when actually, it’s probably A and B working together.”

    …with occasional interference from C and an (as yet undiscovered) ability for D to supress B under certain environmental conditions ;)

    But seriously, yes, the idea that there is one mechanism for deviation between species seems contrary to the marvellous complexity of biochemistry, where the same DNA in the same development environment (identical twins) produces two organisms that are physically distinguishable. Still, I do like the sound of the T-shirts; perhaps they could do me one with one slogan on the front and the other on the back…?

  7. #7 Dana Hunter
    April 5, 2008

    Argh, PZ! You’re so close, yet so far away! When are you going to make it to Seattle so the lot of us can gather, grab drinks, and stand in front of the Discovery Institute cracking IDiot jokes? We could even have some street science if you can snag us some of those duelling t-shirts!

    Now, THAT would be taking science to the people!

  8. #8 wazza
    April 5, 2008

    Paul: if you spin around really fast, you’re a scientific controversy!

    Do you have any relatives in Wellington, NZ? It’s just there’s a campus personality called Rev. Paul Danger Brown.

  9. #9 Jeanette Garcia
    April 5, 2008

    PZ, Welcome to my piece of paradise. Dang. I’m up to my gills with company. Sorry to miss you.

  10. #10 Alan Kellogg
    April 5, 2008

    There are too many simple solutions for too few simple problems
    …John W Campbell Jr.

  11. #11 NP
    April 5, 2008

    You mean nobody got EXPELLED for questioning the status quo?

    Evo devo is a fascinating field, and I wish I could be at the conference even though most of it would probably go over my head.

  12. #12 amph
    April 5, 2008

    Many developmental genes are older than some of the organs or structures in which they have a role. In such cases you can’t deny the role of the cissies. The muscle gene MyoD and the Hox genes, older than us terapods, acquired regulatory elements so that their function was recruited to limb development. This is well documented and I am sure there are many more examples. Also, I am convinced that subtle changes in the timing of activation of certain genes have a major impact on development. It is of course difficult to produce really convincing evidence that this has happened, but it seems we’re talking about testable hypotheses here. We know that delayed expression of a Hox gene (in the same species) causes an abnormal phenotype. We know that a Drosophila deformed gene can replace the function of one of its mouse orthologs. Expression is obviously more important in that case than are the biochemical properties of the gene product. I suspect more such experiments have been done.
    An obvious problem with the CREs is of course that they are so difficult to accurately identify, and then, to recognize them in a different species, whereas every idiot can recognize corresponding coding sequences between species.

  13. #13 Dylan
    April 5, 2008

    I was at a lecture yesterday given by Sean Carroll where he argued that mutations in CREs are the best way to generate morphological changes during development and contrasted this with physiological changes where mutations in coding sequences are more likely to be relevant. So it may well be the case that the likelihood type of mutation (coding or regulatory) varies according to the type of change (form or function put crudely) happening.

  14. #14 TheMonkeyMan
    April 5, 2008

    It is a real shame that these huge conferences that have wider significance to Biology can’t be recorded and/or streamed for those who can’t make it, as those two talks sound fantastic albeit completely unrelated to my own research.

  15. #15 djlactin
    April 5, 2008

    This pas de deux is an excellent example of the difference between science and religion: In science, when people have different ideas, they argue rigorously, then pursue evidence that can test the ideas and ultimately cause one or both to be rejected. Then they get together for a beer and discuss what to do next.

    In religion, if people have different ideas they argue rigorously then split into sects. Because there is no evidence.

  16. #16 blf
    April 5, 2008

    In religion, if people have different ideas they argue rigorously then split into sects. Because there is no evidence.

    Shouldn’t that be?: In religion, if people have different ideas they offer ridiculous arguments, split into sects, and start real shooting wars. Because there is no evidence.

  17. #17 Peter Ashby
    April 5, 2008

    Furthermore, the developmental genes that experienced the greatest structural variation were those involved in gametogenesis and maternal effect genes, while it was the zygotic genes that varied most in regulation.

    That bit I thought was fascinating. One thing that is going to bedevil this is that many of the changes are going to be subtle. For eg I was involved in mapping the regulatory regions of the mouse Myf5 muscle regulatory gene where chordate evolution is written on the genome in clumps of regulatory sequences. The evolutionarily newest region, that driving expression in the limbs is even the furthest away. But to prove a significant evolutionary novelty using this you need to got to a fish, and possibly a cartilaginous fish at that (teleost pectoral fin muscles are probably proto limb muscles). So while it is blinding obvious, proving it is very far from trivial.

    Also if you have a gene that is expressed in human brains during development but not mouse brains you may not be able to prove which sequence is responsible since the factors that turn it on in human brains may not be present in the mouse so the transgenes will not be expressed. So how do you prove that it is a brain element except in tissue culture, hoping that it will be expressed in neurons/glia and not fibroblasts or liver cells, something that is easy to dismiss as not good enough.

    So Coynes’ criticisms might be right, but I think some reality as per what is possible needs to enter the fray too.

    Peter

  18. #18 ostratodd
    April 5, 2008

    Thanks very much for this summary. I wish I could be at the meeting, but the timing didn’t work out for me.

    For anyone who is interested in this topic of structural vs. regulatory change; I wrote a little highlights piece in the journal Evolution & Development, where I take the same position as wazza (both A and B are true). Of course neither Coyne nor Wray would disagree that both types of mutations are important. Quoting Gould and Lewontin’s classic Spandrals paper:

    “In natural history, all possible things happen sometimes; you generally do not support your favored phenomenon by declaring rivals impossible in theory. Rather, you acknowledge the rival but circumscribe its domain of action so narrowly that it cannot have any importance in the affairs of nature. Then, you often congratulate yourself for being such an undogmatic and ecumenical chap. ”

    In my EvoDevo article, I cite both Coyne and Wray, but mostly I talk about a really nice piece of science by Sweeney and colleagues describing the evolution of cephalopod lenses. Here is the pdf:

    http://www.lifesci.ucsb.edu/eemb/labs/oakley/pubs/EDtodaysMCexam.pdf

    and here is another take on the same data:

    http://evolutionarynovelty.blogspot.com/2007/10/from-cutting-room-floor.html

  19. #19 Tim Tesar
    April 5, 2008

    Now this is the type of controversy that SHOULD be taught in biology class (though perhaps this particular one is too advanced for high-schoolers).

  20. #20 Liam
    April 5, 2008

    I don’t understand.. If the non coding bits regulate gene expression then aren’t they code too?

  21. #21 wazza
    April 5, 2008

    Coding DNA is made up out of three-base groups which, when transcribed into RNA, code for specific amino acids, making up the long chains which fold into proteins.

    Regulatory bits, however, code pieces of RNA which act directly, for example fragments of microRNA which stick to the RNA sequence of a specific gene and prevent it from being read by ribosomes.

    So yeah, coding is different from regulatory

  22. #22 Steve Ulven
    April 5, 2008

    Coming back from Dan Dennett yesterday I heard on NPR that Frans deWaal is going to be at the Minnesota Zoo on Tuesday in the IMAX theater at 7pm. What planetary alignment or other credulous horseshit is going on to make Minnesota a popular attraction for smart people to come and talk? Just a couple weeks ago was the American Atheists conference. The past two days was Dan Dennett, now Tuesday is Frans deWaal.

    The Oregon thing is probably a bit over my head, but I absolutely love watching smart people talk. Since the American Atheists conference (my first experience seeing smart people talk, besides a few college classes, and I mean a few), I have become an addict. What am I going to do after Tuesday? How will I get my fix? To my knowledge, nobody else that is not an idiot (keep in mind, the republican convention will be here soon) will be doing any talks here after that.

  23. #23 amph
    April 5, 2008

    Liam, I agree that the system of regulatory elements can also be considered sort of part of a code. However, the genetic code usually refers to the codon usage in protein encoding genes and RNA.

    Wazza, go do your mol biol 101 homework. Most regulatory elements are thought to bind transcription factors either directly or indirectly.
    ÁRNAs are yet a different story. If DNA encodes one of them, that DNA is by definition ‘coding DNA’ even though the RNA encoded is not translated into protein.

    Enough semantics.

  24. #24 wazza
    April 5, 2008

    Dude, I’m a BTEC dropout polsci undergrad, working on mostly high school and first year knowledge. I’m always willing to be corrected. But I don’t see the difference. More detail, maybe?

    thanks anyway. :)

  25. #25 wazza
    April 5, 2008

    I should note that I dropped out of BTEC because I hated commercial law, not because my biology knowledge was poor, and I’ve read a lot of the literature for my own amusement. But I’ve never been formally educated beyond the first year of university in any science. The fact that even I can disprove the bs of the IDiots says something, ne?

  26. #26 Andy
    April 5, 2008

    Very interesting summary – thanks! As a paleontologist, one of the chief things I’d like to see added to evo-devo is a lot more of the “evo”. I’ve been to countless talks at SICB and other meetings that promise to address the evolution of this or that character – and then completely ignore what the fossil record has to say about it. Granted, there are some wonderful exceptions (for instance, looking at developmental patterns in the tetrapod limb, and bird fingers), but these are few and far between.

  27. #27 Odonata
    April 5, 2008

    PZ – Thanks a lot for the summary of the evening talks. I wish I were there. I hope you continue to keep us posted on what is happening when you have a chance.

  28. #28 redbeardjim
    April 5, 2008

    More detail, maybe?

    Well, you write that “Regulatory bits code pieces of RNA which act directly”. Most regulatory bits don’t even do that — they’re sequences of DNA that proteins recognize and bind to, thereby influencing whether or not a nearby coding region gets transcribed at all, or under what circumstances.

  29. #29 Peter Ashby
    April 5, 2008

    There are two separate processes, translation and transcription. In transcription DNA is written to RNA, the alphabet is different hence the term. Like transcribing Russian words in Cyrillic into the Latin alphabet. In translation the RNA is read and translated into protein where the language is different, not just the letters. This is like taking a Cyrillic word and not only using the Latin alphabet but changing the word for it’s English (or French etc) meaning.

    So the DNA that codes for micro rnas is still coding DNA, even if no protein is made. Regulatory regions can be in the introns, the tail of the gene, upstream or downstream and may be a long way away 200kilobases or more away. The limb enhancer of mouse Myf5 is in that class. They are often pallindromic and consist of a core region that is invariant and flanking sequences that may vary. The binding site of the E proteins for eg is CANNTG (it is pallidromic because it reads the same in reverse on the other strand, C-G; T-A).

    Individual binding sites are often clustered into groups with others and these units are termed Enhancers as they enhance the expression of the gene.

    You can demonstrate that proteins bind to these sites by doing an Electrophoretic Mobility Shift Assay or Band Shift. You radiolabel small lengths of DNA with your site in the middle and mix it with proteins, ideally nuclear proteins and run them on a gel. Pieces of DNA bound by protein are slowed down since the complex is bigger and may be less negatively charged so is shifted up the gel. You can demonstrate that a specific protein binds by either only putting that protein in or by adding antibodies specific to the protein, which by adding yet more mass will cause even more retardation, or a supershift. You demonstrate that the site is specific by mutating the sequence in an ordered manner and abolishing binding.

    You show that the sites have biological activity by connecting them to reporter genes (enzymes that can be detected by their activity) and showing greater or more specific expression in cells or animals/embryos.

    For the record I have down all the above though the fact that I had finally done some bandshifts and successfully was cause for some mirth in the lab ;-)

  30. #30 rjb
    April 5, 2008

    Wazza,

    Regulatory DNA is not transcribed. The regulatory DNA is the region of DNA that binds to various factors and either allows the coding sequence to be transcribed, or prevents it from being transcribed. So the regulatory regions are not read by RNA polymerase in 3-base codons. The regulatory regions act like light switches that turn on a light somewhere. The different factors present in different cells determine whether the light gets turned on. So the argument here is about what is more significant in evolutionary change… changing the nature of the light itself (the coding sequence), or changing the switches that control when and where you turn the light on (the regulatory sequences).

  31. #31 amph
    April 5, 2008

    Sorry Wazza, no offense. OK here goes. DNA can be transcribed in RNA. Some RNAs are translated in protein, some have different functions: ribosomal RNA, tRNA, ÁRNA… The latter have a regulatory role, just as some proteins have regulatory functions.
    I think “DNA not transcribed in RNA” defines noncoding DNA. Sometimes such DNA is bound by a transcription factor (yes, a regulatory protein) and somehow this turns a nearby (or not so nearby) gene on or off. See the difference? It is the difference between RNA-RNA interactions you were talking about and protein-DNA interactions, where the DNA would be a CRE.
    BTW I agree with your #2 comment, but I am sure those guys in Oregon with them T-shirts are fully aware of it. They are obviously playing the devil’s and god’s advocate and having lots of fun. Wish I was there, it’s raining here anyway.

  32. #32 defectiverobot
    April 5, 2008

    I understood barely a word of what you wrote, but I read the whole thing. I read the whole thing because you the enthusiasm was so apparent it was nice to see you happy for a change.

    I also read it because as I got about three sentences into it, it struck me, as some other posters have already said, it completely illustrates the difference between science and religion. Science has debate, religion has propaganda.

    Even without knowing that facts about those sad few who are portrayed in Expelled, we can reasonably argue that they were expelled precisely because they were unable to engage in vigorous debate, primarily because they had nothing to debate! ID has proven to be nothing more that fiction propped up by propaganda; yours is real science.

  33. #33 wazza
    April 5, 2008

    OK, guys you can stop now…lol

    I have been educated. Thoroughly.

    Defectiverobot: YES! That’s why we fight. Because we love the debate, and ID kills it. Mostly by making the scientists speechless at its stupidity.

  34. #34 David Marjanovi?, OM
    April 5, 2008

    Regulatory bits, however, code pieces of RNA

    Most don’t. Most are just places where either some part of the transcription machinery binds (promoters, enhancers) or where proteins bind that prevent the transcription machinery from binding or from moving (operators, silencers). They don’t get transcribed themselves and are thus not coding. Genes for miRNA, siRNA and all that jazz are coding DNA.

  35. #35 David Marjanovi?, OM
    April 5, 2008

    Regulatory bits, however, code pieces of RNA

    Most don’t. Most are just places where either some part of the transcription machinery binds (promoters, enhancers) or where proteins bind that prevent the transcription machinery from binding or from moving (operators, silencers). They don’t get transcribed themselves and are thus not coding. Genes for miRNA, siRNA and all that jazz are coding DNA.

  36. #36 amph
    April 5, 2008

    OK, guys you can stop now…lol

    Heh heh. Seems some of us (incl me) were waiting for a chance to show off there (elementary) knowledge.

  37. #37 David Marjanovi?, OM
    April 5, 2008

    ARRRGH! Next time when someone asks a basic mol. bio. question, I’LL JUST SHUT UP! I promise!

  38. #38 David Marjanovi?, OM
    April 5, 2008

    ARRRGH! Next time when someone asks a basic mol. bio. question, I’LL JUST SHUT UP! I promise!

  39. #39 Sharon
    April 5, 2008

    Evo-devo always manages to blow my mind a little bit. Well, not always, but certainly my first introduction to hox genes did.

    I wonder why Wray chose 3 very closely related species instead of maybe 3 more diverse mammals. There’s probably a lot of good reasons, but at first blush it seems that changes in the genome (for both regulatory sequences and exons) would be easier to detect between more diverse species.

  40. #40 Dutch Delight
    April 5, 2008

    So, did anyone complain that their feelings were hurt because people were so strident with their opinions?

  41. #41 SvenDiMilo
    April 5, 2008

    Sharon, it’s not my field, but I think that Wray is not trying to detect ust any changes in the genome–that’s trivially easy, and, as you say, easier for more distant relatives. He’s looking for specific kinds of differences that show evidence of selection as the mechanism for change, and therefore needs to start with a similar background. I think.

  42. #42 BaldApe
    April 5, 2008

    Take that, Ben Stein, with your bizarre allegations that ‘Big Science’ stifles dissent and differing opinions!

    But couldn’t they have saved themselves a lot of time and trouble by skipping all those messy experiments and just had a debate?

    Also:

    I read the whole thing because you the enthusiasm was so apparent it was nice to see you happy for a change.

    Here Here! It’s great to read some really interesting biology and not another expose of teh stoopid.

  43. #43 Scott Hatfield, OM
    April 5, 2008

    This was a great post, part gossip and part discussion of ideas. One actually gets the impression that the social activity of scientists is an important part of doing science, and that the scientific community is actually involved in self-examination, self-criticism, etc. What a pity that this message is far less likely to reach the public. Typically, our foes will spin discussions like this in one of two ways:

    1) These disagreements are meaningless, because no one challenges the basic premise of blind, purposeless change!

    2) Darwinists disagree! This is a theory in crisis!

    Anyway, echoing another poster, nice to see some enthusiastic, vigorous treatment of science to go with the carping about pseudoscience!

  44. #44 Copernic
    April 5, 2008

    Ohhhh, so this is the controversy they’ve been talking about.

    Then I’m all for it. Teach the controversy. Kids may actually learn something then.

    J

  45. #45 DanioPhD
    April 5, 2008

    Sharon (#37): That’s an awesome question, and Sven (#39) is right on the money with his answer. In fact, the new, sparkly *BIG IDEA* that became clear to me in listening to these two wonderful talks was exactly that: What selective advantages, or constraints, dictate whether a mutation in a coding vs. non-coding region will amount to something, in an evolutionary sense? Greg Wray’s presentation of comparing the genomes of humans and chimps was particlarly illustrative–we’ve known for years that the differences between human and chimp DNA sequence are pretty miniscule, but we’re obviously quite different in form and function, most notably in the cognitive arena. Focusing the genome wide analysis on genes with known neural developmental and/or functional roles revealed that most positive selection mutations in these genes occur in the non-coding (cis-regulatory) regions. Hence a clear evolutionary mechanism seems to have been revealed for this particular case: Starting with a standard-issue ape brain, mutations in regulatory regions of neuronal factors resulted in increased growth and connectivity in regions of cognition, language, creativity, etc. Parallel changes in regulation of sugar metabolism kept pace with the increased energy demands of a giant, uber-functional brain. Cool!

    Wray went on to show a very comprehensive data set of distribution of positive selection by protein function across the human genome–a really nice graphical representation of what proportion of adaptive mutations have occurred in structural versus regulatory regions, and the ‘choices’ make a lot of sense when considering the respective functions of those genes, the lifestyles of the different tissue types they occupy at various developmental stages, etc.

    It’s a most powerful means of analysis, and I’m sure I wasn’t the only zebrafish researcher in the room gleefully rubbing my hands together.

    And yeah, this is the kind of controversy that would be a blast to teach. It’s definitely going into my bag of tricks. :)

  46. #46 Glaisne
    April 5, 2008

    Nice! Well written and interesting synthesis, and I’m an ecologist! I usually don’t find molecular biology stuff all that interesting but I liked this a lot. I see the beginning of an article for Scientific American here!

    So, I was thinking along the lines of what wazza said. I think both processes would occur. The question is to what degree would one or the other occurs and under what conditions. Generally, we find in nature that when we hypothesize about potential competing processes that are possible in nature we find that both happen to one degree or another depending upon certain conditions.

    This is a great example for students to learn about the process of science!

  47. #47 Dave Carlson
    April 5, 2008

    Great post. I can’t wait to hear more about the convention!

  48. #48 G
    April 5, 2008

    Thanks for the summary, I wish I’d been there. It would be interesting to here more about Wray’s approach. I guess I’m slightly skeptical about comparisons of positive selection rates between coding and non-coding DNA using phylogenetic approaches, as coding and non-coding DNA will have very different regimes of constraint making such comparisons difficult. I’ve posted briefly about that here.

  49. #49 SC
    April 5, 2008

    Thank you for this! Fascinating.

    I’m also particularly pleased that neither of the speakers tried to orzel his way out of the debate, presuming that his opponent was unreasonable and would reject his evidence out of hand and thus not offering any. That would have made for a much less interesting and enlightening encounter.

  50. #50 Ron Sullivan
    April 5, 2008

    David Marjanovi?, OM in # 36: ARRRGH! Next time when someone asks a basic mol. bio. question, I’LL JUST SHUT UP! I promise!

    Please don’t. Things like this are the chocolate chips in the big ol’ Pharyngula cookie, and seeing even slightly different wording from several people does help to clarify concepts for confused civilians like me.

    So: thanks!

  51. #51 Ferrous Patella
    April 5, 2008

    “This was all good stuff, but Coyne and Wray were orthogonal to each other and weren’t really hitting each other’s main points.”

    So basically, they spent their time framing the issue.
    [ducks]

  52. #52 DLC
    April 5, 2008

    Nothing like a good bit of scientific discourse.
    and arguing things back and forth.
    I recall when there was a bit of consternation caused when Steven Hawking made an unscheduled request to speak at a physics convention. People were expecting a big argument, and got an entirely different argument than they were expecting.
    Hawking provided mathematical proof that black holes do indeed lose energy, now known as Hawking Radiation.

  53. #53 Nix
    April 5, 2008

    One actually gets the impression that the social activity of scientists is an important part of doing science

    Well, duh. How could anyone doubt this for an instant? Scientists are human beings: name any intellectual field where the social activity of the participants isn’t an important aspect of how the field really functions, and I’ll show you one populated entirely by AIs.

  54. #54 Sharon
    April 5, 2008

    Sven and Danio: Well, that makes a certain amount of sense. Thanks!

  55. #55 Ms NC
    April 5, 2008

    I tend to agree with your conclusion of the argument, and believe that the weakness of evolutionist has always been the “hammering” part. Evolutionary processes are seen only when examining a wide spectrum of cases (organisms) and acordingly evolutionists are dealing with those wide spectrum ideas, mechanisms, molecules etc.
    It started with Darwin that was able to see the biggest picture of life, but it was up to a gardener to find the genetic mechanism to back it up.
    To be honest, as a beginner (just graduated my BS) I too find the wider mechanisms much more fascinating than some specific fish or frog or chick molecule. But then again I encountered researchers that could tell wonderfull things about developmental processes found in their labs, but when asked about the specific molecular pathways and mainly about the downstream processes and molecules, started to mumble things about “not interesting enough” and “not my working area”. Maybe I’m wrong, but I think that throwing that responsibility to the air and ignoring the boring parts hoping that someone else will deal with those is one major thing that holds back the Evo Devo research.

  56. #56 Steve Matheson
    April 5, 2008

    Wow, thanks for a thorough and riveting account of the debate. I hope we’ll get more like it. I think this has to be one of the most exhilarating eras in the history of evolutionary biology, but maybe that’s just because I’m a developmental biologist who’s irrationally enraptured by evo-devo. Like you, PZ. :-)

    I’ve been promising a review of the bat forelimb paper on my blog for many weeks. I’ll race you, and it’ll be interesting to compare notes when you’re done.

    I’ll be interested to hear whether yeast or plants come up; I think John Doebley’s work on teosinte has implicated both types of genetic change in the radical morphological transformation from teosinte to corn. And I assume Carroll’s most recent work in Cell has been discussed.

  57. #57 Lisa J
    April 5, 2008

    Thanks for this great summary, PZ. It sounds like a really great conference that you’re at. I agree that, of course, both coding regions and CREs are important, but I am inclined to think that CREs are much more important than we know, and have likely driven evolutionary change moreso than mutations to coding regions. I am starting to keep them more in mind in my own research, it’s a very exciting area.

  58. #58 Hank Roberts
    April 5, 2008

    Is there any pair of similar organisms small enough, and mapped, so we can imagine taking the CREs and exchanging them?

    (Do bacteria have these?)

  59. #59 Steve Matheson
    April 5, 2008

    Hank–
    “Is there any pair of similar organisms small enough, and mapped, so we can imagine taking the CREs and exchanging them?”
    Yep. Reviewed in same issue.

  60. #60 Ralph Haygood
    April 7, 2008

    I’m Ralph Haygood, a postdoc working with Greg Wray. I’m responsible for the meta-analytic findings Greg presented in Oregon, and with my colleague Olivier Fedrigo, I also led the survey Greg mentioned for evidence of positive selection on promoter regions of human genes.

    You say, “What [Wray] proposed instead is a genome-wide survey for regions that exhibit signs of positive selection. You might suspect that he would say this because he has been carrying out a genome-wide survey for such regions, and you’d be right.” It’s true we’ve carried out a genome-wide survey for positive selection on promoter regions (Nat. Genet. 39:1140–1144; the article is available at http://ralphhaygood.org/publications/PromoterRegionsMany.html). However, the meta-analytic findings (“which genes were showing what kind of changes”) are based on not only our survey but also five other surveys published since 2003 (Clark et al., 2003; Nielsen et al., 2005; Bustamante et al., 2005; Pollard et al., 2006; Prabhakar et al., 2006; we cited all these in the Nat. Genet. article, so look there for bibliographic data). The meta-analytic findings gain strength from the diversity of data and methods used in these studies.

    In my judgment, the apparent tendencies of some kinds of trait to undergo adaptation predominantly through changes in coding rather than regulatory sequences or vice versa is far more interesting than whether coding or regulatory changes are more abundant. It will be most interesting to see whether the trends we observe in human evolution prevail in other taxa.

  61. #61 VWXYNot?
    April 7, 2008

    As someone who previously examined the evolution of cAMP Response Elements within larger cis-regulatory elements, the CRE acronym is quite confusing! Great post though, thanks for giving us an insight into the shenanigans that go on at conferences!

  62. #62 Ralph Haygood
    April 7, 2008

    I see the commenting system mangled the URL for the Nat. Genet. article; it’s

    http://ralphhaygood.org/publications/PromoterRegionsMany.html

    I should also have said, thanks for the thoughtful post.

  63. #63 DanioPhD
    April 7, 2008

    In my judgment, the apparent tendencies of some kinds of trait to undergo adaptation predominantly through changes in coding rather than regulatory sequences or vice versa is far more interesting than whether coding or regulatory changes are more abundant.

    I couldn’t agree more, Ralph. This part of Greg’s talk, with the distribution of positive selection by protein function, just rocked my world.

  64. #64 Mark Ptashne
    April 11, 2008

    In this blog on the evo devo controversy the problem is set out as follows:

    “Here’s the argument in brief. The functional part of the genome can be roughly broken down into two components: the coding regions, or the actual bit of DNA that is transcribed and translated into working proteins, and the subset of the non-coding regions that are involved in regulating gene expression. …..Evo-devo proponents (eg Wray) have been arguing that the most important changes in evolution have been in the regulatory elements of the genome, in particular the stretches of DNA called cis-regulatory elements (CREs) that flank the coding regions… Others, eg Coyne, have said the case is not proved and changes in proteins themselves could be the driving factor in evolution…

    This accurately reflects how many cast the problem, but I think the formulation is incomplete and misleading. Here’s why, a long story in a nutshell:

    Put the problem this way: how does Nature employ essentially identical enzymes – and a rather limited set at that – to produce organisms as distinct say as flies and humans? (As shown in bacteria, Nature can evolve new kinds of enzymes, but hasn’t for the cases we are considering).

    Answer: there are two classes of enzymes:

    1. Those that direct intermediary metabolism – each of these (in effect) recognizes a single small-molecule substrate, and each has remained essentially unchanged throughout evolution.

    2. Enzymes that recognize macromolecules – eg RNA and DNA polymerases, kinases, phosphatases, ubiquitlylating enzymes, proteases, etc etc – these typically have MULTIPLE possible substrates. For example, RNA polymerase can transcribe any of thousands of genes; the ubiquitylating enzymes can modify any protein, and so on. Specificity – i.e. substrate choice – is imposed on these enzymes by ‘recruitment’ – for example, a transcriptional activator is merely an ‘adapter’ that, with one surface contacts a specific site on DNA and with another contacts polymerase (or some other component of the transcriptional machinery) and, by these simple binding interactions, recruits the polymerase to a specific gene where transcription commences. ‘E3 ligases’, to take another example, perform exactly the same function for ubiquitylating enzymes: each recruits a different protein, by virtue of simple binding interactions, to the enzyme.

    This way of looking at ‘regulation’ was set forth in the book Genes and Signals by myself and Alex Gann and I think is now accepted where it is understood.

    The point in the current context is that ‘cis-regulatory’ changes in DNA is ONE way to influence whether or not a specific protein (enzyme or other protein) is present in a specific cell at a specific time. Thus, by introducing a site that binds ‘activator’ X in front of a gene, that activator will now recruit the polymerase to that gene, thereby giving polymerase a new or changed ‘specificity’.

    But obviously this is just one of MANY ways to evolve difference in what genes are expressed at what time during development, which proteins are present or destroyed, and so on. Those other ways all involve changes in protein sequence: changing the DNA specificity of a transcriptional activator, for example, or changing the specificity of an E3 ligase. These changes can involve just a few amino acids. And/or, as is often the case, small specificity-determining domains are added to or removed from enzymes and recruiters to change specificity in the sense we are now talking about.

    It seems evident – does it not ? – that the course of evolution, recent evolution, at least, has involved these kinds of changes – changes not just (and perhaps not primarily) in cis-regulatory sites in DNA, but also in protein sequences that impart different specificities to enzymes (and to other proteins as well, I might add). (We have a different set of E3 ligases when compared with flies, and so on. ) Thus the driving force in this recent evolution would indeed be regulatory changes, but many, perhaps most, would not fit the criteria for such as set forth in the typical statement of the problem. .

  65. #65 Batboy
    April 11, 2008

    Dear Prof. Ptashne,

    Your point above is one that I will definitely keep in the front of my mind in future. Thanks for the insight.

    Reading the first edition of your wonderful “A genetic switch” in an undergraduate molecular biology class inspired me to get my butt in a lab & do some research and led to my first science love (phage genetics). After 20 years you’re still teaching and inspiring me!

    Cheers,

    Chris Cretekos

    < <<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>
    For the non-aficionado that may be reading this: Dr. Ptashne points out that the argument as it is usually set up in Evo-Devo circles is whether evolutionary changes in the way genes are regulated are more or less important than changes in the way the products of genes function in programming morphological and behavioral diversity between species. What we actually look at, however, is whether an important change (mutation) is in coding sequence or not in coding sequence. We assume that any important non-coding change affects regulation and that any coding sequence change alters the biochemical function of the gene’s product. He very correctly points out that the latter is not a fair assumption: Changes within the coding sequence can also be regulatory in nature.

  66. #66 PZ Myers
    April 12, 2008

    Yes — it’s always more complicated than you think, and the argument has been simplified too much. I think that actually the disagreement here was slightly different: both sides would agree that all kinds of genetic changes were important in evolution, and that it takes a lot of hard work to demonstrate them; Coyne was saying that the advocates of regulatory change have not done as good a job of supporting their ideas as they should, and Wray was saying that they have, and showed some of his evidence.

  67. #67 PZ Myers
    April 12, 2008

    Oh…and I’m a big fan of Genes and Signals myself.

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