Evolving Thoughts

Darwin was wrong…ish

There’s been a slew of “Darwin was wrong” and “Evolution is more complicated” stories in the media lately. It’s nearing Darwin day so simple minded media hacks can be explained as needing to find the requisite “drama” in their “stories”. But the real picture is a lot more nuanced, and ultimately a lot more interesting, than the dichotomies pedalled by what passes for science journalism these days. I am picking up themes also covered by Larry at Sandwalk, Evolutionary Novelties, and Jason at Evolution Blog.

The targets journalists I wish to attack here are those of New Scientist, Newsweek, The Telegraph, and the media release writers for Texas A&M University. And some of the scientists and philosophers whose comments are reported therein are equally guilty. But not wanting to spoil my own nest I shall leave the readers to work out who I mean…

Okay, let’s begin with the last of my targets. EurekaAlert, which is a service that publishes media releases from universities among other things, recently carried this piece:

Evolutionary process more detailed than previously believed, study shows

New evidence from a study of yeast cells has resulted in the most detailed picture of an organism’s evolutionary process to date, says a Texas A&M University chemical engineering professor whose findings provide the first direct evidence of aspects, which up until now have remained mostly theory.

Sounds fairly innocuous, doesn’t it? But then it says this:

These adaptations, Kao explained, triggered a competition between these segments, known as “clonal interference.”

It’s the first direct experimental evidence of this phenomenon in eukaryotic cells, or cells with nuclei, and it contrasts the widely accepted classical model of evolution, which doesn’t account for simultaneously developing beneficial adaptations, she said. Instead, that model adopts a linear approach, theorizing that a population acquires such adaptations successively, one after another. Rather than a competition occurring, the model posits a complete replacement of one generation by another better-adapted generation.

That wasn’t the case in Kao’s sample.

I read that and blinked a few times… the classical model of beneficial mutations spreading through a population is Muller’s:

i-f79251c2c30b0d6af81a78ce4a1961a9-250px-Evolsex-dia2a.png

From Wikipedia: This diagram illustrates how sex might create novel genotypes more rapidly. Two advantageous alleles A and B occur at random. The two alleles are recombined rapidly in (a), a sexual population, but in (b), an asexual population, the two alleles must independently arise because of clonal interference.

So, it looked like the writer had just got it wrong. Your not-so-humble correspondent sent of a snarky email to the contact, which he assumed was the media release writer. To his shame, it was the author, who very gently disabused me. But there remains a problem with the media release – it doesn’t say anywhere, unless you know the technical jargon (the key term here is “clonal interference”), that this is a rather elegant experiment done with asexual organisms. If you happen to know that yeast are (mostly) asexual, then you’d get it, but the journo who assisted with the release failed to work that out. Leading to philosophers making idiots of themselves and letting the wider media draw the wrong conclusions. Anyway, here is Kao’s and Sherlock’s figure showing that clonal interference is not so simple as had been expected among asexual organisms. The figure represents an actual count, using flow cytometry, of the various mutants in a single colony.

i-ac0718aa442f09c295f8154aec3bb042-Kao.pngThe caption reads in part: “Experimental population (size of approximately 109 cells) from which adaptive clones marked M1?M5 were isolated and subsequently characterized. The times when putative adaptive subpopulations reach their maxima are marked with arrows. Consistent with previous reports13, these adaptive events occur in the glucose-limited population approximately every 50?100 generations.” So, nice result, challenges some simplifying assumptions in the Muller model, but hardly a disproof of the “established evolutionary model”. But it’s not strictly the authors’ fault – models are often taught as being all that we might expect to be the case, when they are actually what we should expect if no other parameters vary. Here, we have a real world case where the parameters of the classical model do indeed vary from the model. The model is not complete.

Next, we move on to the Newsweek article. This has been critiqued by PZ Murtd, but I wish only to add that this is another case of people claiming that some modern result is “Lamarckian” when all it really is is a refinement of the ever-developing Darwinian tradition. The changes here are standard traits – the ability to respond to environmental changes at the individual level. That trait is inherited in a quite normal manner, and the trait, which is a disposition to grow in a particular way, just like most other developmental traits, is subjected to perfectly ordinary Darwinian selection and drift (note that drift was a post-Darwin theoretical development that has been assimilated into the Darwinian tradition quite solidly; we might say it is evidence that Darwin was wrong).

i-fa03472db867d5479c3c5debe4ef3b7f-haeckel.jpgNow we should look at the Telegraph piece. It basically is following the New Scientist article, but it has a few items in it I would like to comment on. It includes comments that the existence of horizontal transfer undercuts the tree of life: “Evolution is far too complex to be explained by a few roots and branches”. And then there’s this gem: “In Darwin’s The Origin of Species, published in 1859, the British naturalist drew a diagram of an oak to depict how one species can evolve into many.” Ummm, no he didn’t. The sole diagram in the Origin is a stratigraphic schematic of how species might evolve, with lines connecting them. The oak was Haeckel’s innovation and it occurred in 1866 in German (according to Ebach and Williams 38f). Now ever since Gould ragged on Haeckel there has been no excuse for people not knowing this, but the experts quoted all do know this anyway.  

There is a big difference between evolutionary histories of genes and the history of taxa. Swapping genes no more means the “tree of life” is a dead concept than swapping habitats would. There is a mismatch of things being considered. Genes can swap through many processes, both in single celled and multicellular organisms, ranging from simply taking in DNA floating in a medium, through to bacterial “sex”, to introgression of genes through hybridisation, through to the formation of entire species through hyridisation. And none of these, with the possible exception of speciation through hybridisation, affect the tree of life. If we have genes that are inserted into our genome from, say, worms, via a viral infection (as much as 40% of the mammalian genome is viral insertions from other species, including the viruses themselves), that doesn’t affect the fact that we evolved through ordinary speciation processes from a last common ancestor we share with chimps, and so on. And so we get to the New Scientist article. The cover heading is most likely written by a subeditor, or the editor, so we cannot make the journalist responsible for that, any more than the press release above is the fault of the scientists reported by it. But this is truly journalistic drama for the sake of it.

In many ways, we have known Darwin was wrong on various matters, especially heredity, from his own time. Almost nobody accepted his view of heredity, and the previaling view of speciation was due to Moritz Wagner and J. T. Gulick – which we now know as the theory of “allopatric speciation”, although Darwin’s own view, repackaged as “sympatric speciation” has had a revivial of a limited kind. But one thing he was not wrong about was the idea that animal and plant species had common ancestry with other related species. Yes, we know now that plants and occasionally animal species hybridise, but the only effect that has on the topology of the evolutionary tree at that scale, is that occasionally speciation happens to include three or more species rather than the two (ancestor and descendent). This is represented in phylogenetics as an “unresolved cladogram” in which three or more species diverge from the common ancestor of all of them. Now, open your copy of the Origin and look at the diagram Darwin shows there:

i-3f9def8f16eca80b0d8af9fb418fa154-darwin'stree.jpg

Notice that he allows for multiple speciation to occur in a single event? It’s not hybridisation, but the topology is roughly the same. So does this undercut the very idea of a tree of life? I think it does not. In particular the really insanely stupid comment by Eric Bapteste of Pierre and Marie Curie University in Paris that “We have no evidence at all that the tree of life is a reality” is so far from the mark that it makes no sense unless you suppose in his mind the evolution of genes and the evolution of species are supposed to be identical. But the distinction between gene trees and taxonomic trees is as old as genetics, although the terminology is recent. So, all in all, either you have really bad journalism here, of the kind I mistakenly ascribed to the Kao and Sherlock press release, or you have really bad rhetorical devices being used by a number of people who should know better, or both.

PS: In another “Film at 11″ press release, it is noted that there are mechanisms of inheritance that are not DNA based. Which we have known for lo! these many years now…

Comments

  1. #1 Greg Laden
    January 23, 2009

    My favorite Darwin Was Wrong piece is Darwin’s Autobiography. Very much fun if you have not read it. The guy was as humble as people of his class and time got.

  2. #2 Graham Lawton
    January 23, 2009

    Dear John,

    Hi, the “really bad” journalist from New Scientist here. Thanks for blogging about my story.

    I really ought to make a sarcastic comment here about “really bad” bloggers, but that would be an oxymoron. (Only kidding – it’s soooo much fun being rude to people on the internet, isn’t it, and so much easier than being rude to them in person!)

    OK, so, I’ve read your criticism of my story and I’m not sure what you’re saying. You have not engaged with my argument at all, you’ve just invented your own, which is called erecting a straw man. I’d be realy happy to discuss the article with you but first you’ll have to explain to me what is “really bad” about it.

    Cheers,
    Graham

  3. #3 John S. Wilkins
    January 24, 2009

    Graham, I get corrected and criticised all the time for my blogging. Why don’t you do what I do – suck it up and try to do better? Also note that I did not call you in particular really bad – in fact I was attacking the Telegraph article. Is reading for meaning difficult in science journalism?

    Oh, and speaking of reading for meaning I will restate the point. Lateral genetic transfer is about gene trees. The tree of life is about taxa. Taxa do not equal genes. And for the groups of what we know now as the eukaryote branches of the tree of life – animals and plants, Darwin’s overall point remains as solid as ever.

  4. #4 Alex
    January 24, 2009

    I’m sick of everything interesting and new in evolutionary theory being used to stir up Darwin controversy.

    We don’t hear that Newton was wrong about fluxions every time that a new discovery is made in analysis.

  5. #5 Ian
    January 24, 2009

    “We don’t hear that Newton was wrong about fluxions every time that a new discovery is made in analysis.”

    Ah! but professor Brown’s Flux Capacitor fixed that problem in 1985, didn’t it?!

  6. #6 Graham Lawton
    January 24, 2009

    OK, but Bapteste et al (recall that I’m a journalist reporting stuff that’s going on, not an academic defending my own ideas) would say that once you’ve got 80 % of genes being tansferred horizontally, the neat concept of taxon melts away.

    BTW, I came in peace, tried to make a joke, so I was a bit miffed to see you have a dig about “reading for meaning”. But I know that blogs are really bad at conveying anything other than sarcasm and sneering (which is one reason I think they suck as a medium) so I’ll let it slide. Keep up the good work.

  7. #7 Graham Lawton
    January 24, 2009

    well, ok, but once you get to a point where 80% of genes have been horizontally transferred your neat and tidy taxon is looking a bit ragged.

  8. #8 RPM
    January 24, 2009

    Mr. Lawton, you represent so many things that are wrong with old media style journalism. I congratulate you for embracing the stereotype.

  9. #9 Dave S.
    January 24, 2009

    But I know that blogs are really bad at conveying anything other than sarcasm and sneering (which is one reason I think they suck as a medium) so I’ll let it slide. Keep up the good work.

    A swat at sarcasm and sneering whilst being sarcastic and sneering.

    Well played sir.

  10. #10 Dave S.
    January 24, 2009

    And I just wanted to point out that I learned my biology from Food Doolittle, one of the scientists whose work was cited. It’s not important, I just thought it an interesting connection.

  11. #11 Moderately Unbalanced Squid
    January 24, 2009

    “OK, but Bapteste et al (recall that I’m a journalist reporting stuff that’s going on, not an academic defending my own ideas) would say that once you’ve got 80 % of genes being tansferred horizontally, the neat concept of taxon melts away.”

    This is where you could have some additional background in organismal- or ecological-level biology.

    The concept of a taxon has not been considered “neat” for a very long time (must be about 40 years now.) Look up “species concepts.” You may want to note that several species concepts are not even genetically based anymore.

  12. #12 jj
    January 24, 2009

    This “Darwin was wrong, let’s reconsider Lemark” crap is really starting to annoy me. Yes, we all know there are flaws in Darwin’s theory, that’s why it’s a scientific theory – it can be modified to fit the data (not the other way, as creationists like to do). Science is self correcting people! Darwin had no mechanism for heredity, making much of what we know about evolution impossible for anyone 150 years ago to grasp. And the “tree of life” being debunked? It’s a freakin’ metaphor, of course it isn’t going to describe the flow of species from a common ancestor perfectly. Once again, without the knowledge of genes, how could Darwin understand things like hybridization, or the fact that Virus’s can transfer genes? Dumb Dumb Dumb, mind numbingly so.

    well, ok, but once you get to a point where 80% of genes have been horizontally transferred your neat and tidy taxon is looking a bit ragged.

    Please explain. Remember the “tree” is a link to the most common ancestor, if genes some how get inserted into an individual (population), they still have that common ancestor with a population that does not.

  13. #13 Wes
    January 24, 2009

    I really ought to make a sarcastic comment here about “really bad” bloggers, but that would be an oxymoron. (Only kidding – it’s soooo much fun being rude to people on the internet, isn’t it, and so much easier than being rude to them in person!)

    But I know that blogs are really bad at conveying anything other than sarcasm and sneering (which is one reason I think they suck as a medium) so I’ll let it slide. Keep up the good work.

    Lawton’s comments here and on Rosenhouse’s blog are a paragon of psychological projection. Also, in addition to his confusion regarding the distinction between gene trees and species trees, I think he may be a bit confused as to the meaning of the word “oxymoron”.

    I’m gonna go read Carl Zimmer’s blog to remind myself that “competent science journalist” is NOT an oxymoron.

  14. #14 Johnny
    January 24, 2009

    Graham’s on a rampage through the blogosphere!

    Since he was kind enough to mention me in his comments posted to Sandwalk, I posted some comments at my site and linked back to here: http://ecographica.blogspot.com/2009/01/whys-graham-so-glum-lawton-critiqued.html

  15. #15 Dave Wisker
    January 24, 2009

    OK, but Bapteste et al (recall that I’m a journalist reporting stuff that’s going on, not an academic defending my own ideas) would say that once you’ve got 80 % of genes being tansferred horizontally, the neat concept of taxon melts away.”

    Mr Lawton might ask himself just where on the tree of life one finds 80% of genes being transferred horizontally, then he might realize the overall metaphor is actually pretty solid.

  16. #16 RBH
    January 24, 2009

    Johnny wrote

    Since he was kind enough to mention me in his comments posted to Sandwalk, I posted some comments at my site and linked back to here:

    I urge Lawson to consider Johnny’s suggested cover art for the next issue of New Scientist. It’ll sell like hotcakes, and since that’s the criterion for successful science journalism, it’s win-win.

  17. #17 slpage
    January 24, 2009

    Eagerly awaiting the arrival of a copy of New Scientist with a cover bearing the teaser “Newton Was Wrong” next time some theoretical physicists come up with some wacky far out new hypothesis, that way I can run around the internets posting that Darwinism is true because Newton was a YEC…

  18. #18 John S. Wilkins
    January 24, 2009

    Nobody mention MOND. Damn! I just did, but I think I got away with it!

  19. #19 Chris Nedin
    January 24, 2009

    #17

    (goody, I get to repeat a comment)

    Na, the next cover is obvious:

    GALILEO WAS WRONG

    Galileo claimed that Jupiter had 4 moons when it actually has over 63!

    This would be on an intellectual par with the “Darwin was wrong” cover.

  20. #20 Thony C.
    January 25, 2009

    Alex wrote:

    We don’t hear that Newton was wrong about fluxions every time that a new discovery is made in analysis.

    Just as a matter of interest would you care to elucidate what exactly has been proved wrong in Newton’s system of fluxions by any subsequent developments in analysis?

  21. #21 Luna_the_cat
    January 25, 2009

    Chris Nedin #19, I think you nailed it. If you don’t mind, I may quote you.

  22. #22 Adam Ierymenko
    January 25, 2009

    There is a certain amount of truth here. I always say that calling evolutionary theory “Darwinism” is like calling physics “Newtonism.” I see the evolutionary theory as a body of scientific work that is always under construction, just like physics, mathematics, biology (of which it is a sub-discipline), etc.

  23. #23 Dr M.Wainwright
    January 25, 2009

    GET USED TO THE IDEA-IT’S NOT DARWIN’S THEORY!

    Why is it that in all the hype and falsehoods written already about Darwin in this his bicentennial beanfeast year one extremely important fact is omitted,namely that neither Darwin,nor Wallace originated the theory of natural selection. We know this is a FACT because both Darwin and Wallace admitted that they were beaten to the theory by Patrick Matthew and Charles Wells. Now, if these two great naturalists can except that they were not the first to originate natural selection why do journalists,and others, keep writng that natural selection is Darwin’s theory(or that Wallace beat him to it).When creationists do similar things they are called liars or worse! Why do Darwinophiles get away with it?(search Google for “wainwrightscience” for more details).
    Dr Milton Wainwright,Dept Molecular Biology and Biotechnology,University of Sheffield,UK.

  24. #24 Chris Nedin
    January 25, 2009

    Luna (#21)

    Help Yourself

  25. #25 Michael Fugate
    January 26, 2009

    Mr Lawton might do well to take heed of a quote I saw in “The Wit and Wisdom of Abraham Lincoln”. “It is better to be thought a fool than to open your mouth and remove all doubt.”

  26. #26 Jake
    January 26, 2009

    I’ll leave the science to the Phds. However, I think a bigger social issue is at play here.

    Mr. Lawton, I don’t think you came in peace. You went from gently unctuous and condescending to enraged teenage girl pretty quickly. It actually reminds me of the kind of thing my younger sister would find on her myspace comments after rubbing some queen bee the wrong way in middle school. Come on, drop the bigger man act. Dudes a Ph.D. He knows he’s logical fallacies. A logical fallacy is a component of an argument which, being demonstrably flawed in its logic or form, renders the whole argument invalid by the way. There that doesn’t feel very good does it? Play nice next time and maybe you won’t get such an irate response.

    Your attacks on the blogs are a little unfounded. Yes, because of the democratization media has found it self undergoing since the internet has come of age any Angry Joe with a wifi connection and spell check can let his repressed animus run rampant across a myriad of unmoderated threads and comment boards, but that doesn’t mean everyone who has a blog is out for blood.

    That being said, I don’t think the intentional sensationalism constitutes a breach of any kind of journalistic ethics or that this a “bad article”. I feel that Lawton didn’t have much of a choice. Those sort of marketing tactics are a necessity in today journalistic paradigm. Since culture consciousness has sold its ancestral home in the printed word moved into the new cyber condos, the paper press has fallen on hard times. Most bloggers are not full time journalists and their paycheck doesn’t hinge on whether or not their tirade about old people on the bus gets X number of hits. Journalist on the other hand only eat what they can kill.

    Since bloggers have no finical (or only a marginal) stake in the amount of readers they attract they are able to provide a less lurid and melodramatic account of what ever their subject matter is. Which, granted, would be pretty dull except that they have the freedom to drop the tired journalistic formalities and say things like “and in conclusion Pat Robertson is a total D***wad” and infuse their articles with that “sarcasm and sneering” edge.

    The converse to lacking a finical motive is that it also means lack of finical means. Bloggers rarely have the time or money to act as primary sources (granted their are notable exceptions) and typically draw from mainstream media outlets (at least where science is concerned). So instead of replacing sources like Newsweek and New Scientist the common mans blogs act as a sort of loyal opposition.

    Anyway, I think maybe instead of trying to ignore the realities of your chosen profession you should justify them. The story is geared to shock and awe. It has to be in order to sell papers and therefor in order to continue informing the general public about science (a noble enough pursuit). “Darwin Was Wrong!” is a much zipper title then “Darwin’s fundamental principles may be improved upon pending further study!”. However, I don’t think a little lip gloss makes the story any less interesting or any less factually valid.

    Anyway dude, never read what people write about you. You’ll end up doing the needless self doubt shuffle or rationalize your self away into self deception. Or, worse yet, end up portraying your self to have the emotional range of 12 year old on some stranger’s science blog.

  27. #27 Chris L
    January 27, 2009

    Now I remember why I stopped reading New Scientist. Cosmos is better anyway.

    But PZ Muhaha hasn’t read his West-Eberhard, has he? :-) And while Darwin didn’t have the right idea about inheritance (although I wonder about that: he obviously spend a lot of time talking to animal and plant breeders, he must have had an inkling that the standard model of his time wasn’t what happened), from my reading of Origin he wouldn’t have turned up his nose at the idea of developmentally mediated evolution.

  28. #28 RBH
    January 28, 2009

    John Pieret points out that the New Scientist article has already apparently been cited by a creationist Board member in support of weakening the Texas science standards (see here for the original story):

    Barbara Cargill, a Republican who supported the weaknesses requirement, said there have been “significant challenges” to the theory of evolution and she cited a recent news article in which a European scientist disputed Darwin’s “tree of life” showing common ancestors for all living things.

    What’s even more entrancing, New Scientist reports the same thing, but neglects to mention Cargill’s implicit citation of Lawton’s “Darwin Was Wrong” story as support for her proposal.

    Where is Graham Lawton these days? Busily showing that Galileo was wrong when he thought there were just four moons of Jupiter?

  29. #29 Marion Delgado
    January 29, 2009

    It’s more accurate to say Graham Lawton was wrong than Darwin was wrong, but both are correct, and neither is germane, and neither is exactly news.

  30. #30 Anne
    January 31, 2009

    Hi John – BBC is coming out with a special on Sunday related to this issue. It’s bound to be just as controversial, I think: host David Attenborough calls the effects of Genesis “devastating” for the natural world. I have referenced this post of yours in a new entry about it on my own (new) blog, “100 Days of Science.” I’d be honored if you’d check it out: http://anneminard.com/2009/01/30/day-7b-genesis-has-produced-devastation/

  31. #31 MikeB
    February 2, 2009

    Anne – I’ve just watched the Darwin programme (alas not in HD), and its gives probably one of the most concise and clear explanations of what Darwin thought I have ever seen – simply wonderful. I suspect that David Attenborough will get even more hate mail, but the vast majority of people watching it will be as blown away as I was.

    If you can get it on IPlayer, then watch it as soon as possible, although you will have to wait to order the ‘tree of life’ poster, I’ve just tried and the server is seemingly having difficulty keeping up with demand!

    Well done to Attenborough and the BBC. As for the creationists – bring it on!

  32. #32 John S. Wilkins
    February 2, 2009

    Anne, you had deleted it before I got a chance to read it. Alas.

  33. #33 Dr M.Wainwright
    February 2, 2009

    WHAT NO MENTION OF MATTHEW!
    I thought David Attenborough’s documentary could have been produced in 1960 when I was a school biology student.Of course he made no mention of Patrick Matthew, or the fact that both Darwin and Wallace admitted that Matthew and Charles Wells beat them to the theory of natural selection;but then like creationists, Darwin enthusiasts need their reassuring fairy tales about how Darwin came to “borrow” his ideas!(search google for “wainwrightscience” for “It’s Not Darwin’s or Wallace’s Theory”)

    Dr Milton Wainwright,Dept Molecular Biology and Biotechnology,University of Sheffield,UK.