Darwin proclaimed wrong AGAIN; we fight back!

The January 24th issue of New Scientist had a garish cover showing the tree of life, with the words “DARWIN WAS WRONG” emblazoned over it.   An editorial bemoaned the phylogenetic errors of the old man, adding a few other buzzwords as well:

A particularly pertinent example is provided in this week’s cover story – the uprooting of the tree of life which Darwin used as an organising principle and which has been a central tenet of biology ever since (see “Axing Darwin’s tree”). Most biologists now accept that the tree is not a fact of nature – it is something we impose on nature in an attempt to make the task of understanding it more tractable. Other important bits of biology – notably development, ageing and sex – are similarly turning out to be much more involved than we ever imagined. As evolutionary biologist Michael Rose at the University of California, Irvine, told us: “The complexity of biology is comparable to quantum mechanics.”

The editors knew in fact that this sensationalistic cover would be appropriated by creationists (as it indeed was), but still said that a “revolution” in biology was in the offing:

As we celebrate the 200th anniversary of Darwin’s birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that “New Scientist has announced Darwin was wrong”. Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.

What is so wrong with the tree of life?  Well,  an article by Graham Lawton asserts that horizontal gene transfer (the movement of bits of DNA between species by “infection”), a phenomenon often seen in bacteria and some protists, and occasionally in complex metazoa, invalidates the whole idea of a tree with bifurcating branches.  This, of course, is nonsense.  Such gene transfer may fuzz out or even obscure genealogies in some prokaryotes, but nobody thinks it’s going to efface the genealogy of most other groups.  Can we expect to find that we’re really more closely related to gibbons than to chimpanzees, a truth that has been obscured by massive horizontal transfer from eating bush meat?  Don’t expect huge changes in the genealogy of life that we’ve already assembled from molecular data.

And chalk up another erroneous and irresponsible journalistic asssertion that Darwinism is dead.  Several of us, including Dan Dennett, P. Z. Myers, and Richard Dawkins, wrote a letter (“Darwin was Right”)  to the editor of New Scientist. You can find it here.  An excerpt:

Of course there’s a tree; it’s just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA. . . .

The accompanying editorial makes it clear that you knew perfectly well that your cover was handing the creationists a golden opportunity to mislead school boards, students and the general public about the status of evolutionary biology. Indeed, within hours of publication members of the Texas State Board of Education were citing the article as evidence that teachers needed to teach creationist-inspired “weaknesses of evolution”, claiming: “Darwin’s tree of life is wrong”.

“Revolutionary” sentiments are rife  in evolutionary biology, but let’s be a little careful before we throw away a paradigm which has, after all, proved to be largely correct for a century and a half.  I didn’t anticipate that Darwin Year would bring the neo-Kuhnians out of the woodwork to clamor for an Extended Evolutionary Synthesis. I still can’t see what’s wrong with the old one!

new-scientist

20 Comments

  1. ennui
    Posted February 19, 2009 at 3:51 pm | Permalink

    Over at PZ’s place, Graham Lawton basically admitted that the offending cover was a marketing ploy. ‘Darwin’ sells better than ‘evolution’, and ‘wrong’ sells better than ‘largely right’. They move more copies by stoking the memes of controversy and paradigm shift, but make more work for the rest of us trying to communicate accurate science.

    Lawton, BTW, is also an editor at NS, and had some input as to the phrasing on the cover.

  2. Stuart Ritchie
    Posted February 19, 2009 at 5:17 pm | Permalink

    Just wanted to say – great blog, and a truly awesome book as well.

    One thing – are you sure you mean ‘Popperians’ as opposed to ‘Kuhnians’? I could be wrong, but I reckon Kuhn was the one with the paradigm shifts, whereas Popper is all about falsifiability.

    Incidentally, there’s a creationist in my home town who runs a shop called ‘Paradigm Shift’. Brilliant!

    • whyevolutionistrue
      Posted February 19, 2009 at 6:13 pm | Permalink

      Of course–Kuhnians. My bad.

  3. John Cozijn
    Posted February 19, 2009 at 7:27 pm | Permalink

    This sort of thing was always going to happen in this anniversary year and, were it not for the creationist mischief-makers, a bit of sensationalist pot-stirring can often be useful in exciting broader public interest.

    The trick is to use this to our advantage. The current ID strategy is “teach the controvery”. Okay, here you have it: controversy. But nowhere is there the slightest suggestion of supernatural designers let alone creation. The fact of evolution is not in dispute.

    So biology does have controversies that might be of interest to students, and there would be no harm in discussing the NS pieces in class, even in Texas, including the editorial.

    Winning the war against creationism does not mean biology has to present a monolithic front of universal agreement, hiding its lively debates in the shadows of the academy, as if they were some kind of embarrassment. The actual practice of science is fundamentally energised by the dream of every researcher to overturn a ruling paradigm. That dream is very rarely realised, of course, since the ultimate test is evidence applied by the brutal processes of peer-review and replication.

    So let’s turn strength into weakness and teach the controversies, the real controversies, as a way of inducing a real interest in science.

  4. Hempenstein
    Posted February 19, 2009 at 10:37 pm | Permalink

    It would seem that the Beavis and Butthead generation has weaseled its way into editorial ranks.

  5. downunder fan
    Posted February 20, 2009 at 1:56 am | Permalink

    Thanks for responding to New Scientist and being involved in writing a great letter!

    Agreed with everything you said.

  6. Lazy
    Posted February 20, 2009 at 6:37 am | Permalink

    It would be very nice if someone would post the whole letter here (or somewhere else)

  7. Posted February 20, 2009 at 2:06 pm | Permalink

    Such gene transfer may fuzz out or even obscure genealogies in some prokaryotes, but nobody thinks it’s going to efface the genealogy of most other groups.

    The organisms where HGT is an issue make up the majority of the tree of life. So, I think it is a major problem.

  8. Posted February 20, 2009 at 7:20 pm | Permalink

    Peer-reviewed paper strongly supports ID.

    Laib JA, Marin JA, Bloodgood RA, Guilford WH.

    The reciprocal coordination and mechanics of molecular motors in living cells.

    Proc Natl Acad Sci U S A. 2009 Feb 12. [Epub ahead of print]

    PMID: 19221028 [PubMed - as supplied by publisher]

    ABSTRACT:
    Molecular motors in living cells are involved in whole-cell locomotion, contractility, developmental shape changes, and organelle movement and positioning. Whether motors of different directionality are functionally coordinated in cells or operate in a semirandom “tug of war” is unclear. We show here that anterograde and retrograde microtubule-based motors in the flagella of Chlamydomonas are regulated such that only motors of a common directionality are engaged at any single time. A laser trap was used to position microspheres on the plasma membrane of immobilized paralyzed Chlamydomonas flagella. The anterograde and retrograde movements of the microsphere were measured with nanometer resolution as microtubule-based motors engaged the transmembrane protein FMG-1. An average of 10 motors acted to move the microsphere in either direction. Reversal of direction during a transport event was uncommon, and quiescent periods separated every transport event, suggesting the coordinated and exclusive action of only a single motor type. After a jump to 32 degrees C, temperature-sensitive mutants of kinesin-2 (fla10) showed exclusively retrograde transport events, driven by 7 motors on average. These data suggest that molecular motors in living cells can be reciprocally coordinated to engage simultaneously in large numbers and for exclusive transport in a single direction, even when a mixed population of motors is present. This offers a unique model for studying the mechanics, regulation, and directional coordination of molecular motors in a living intracellular environment.

  9. nick nick bobick
    Posted February 20, 2009 at 8:28 pm | Permalink

    Oh Charlie, Charlie, Charlie

    Just what exactly in the paper you cite above gives any support for ID?

  10. downunder fan
    Posted February 21, 2009 at 12:44 am | Permalink

    Peer-reviewed paper demolished ID’s flagellum argument

    Renyi Liu and Howard Ochman

    Stepwise formation of the bacterial flagellar system

    Proc Natl Acad Sci U S A. April 24, 2007 vol. 104 no. 17 7116-7121

    ABSTRACT:
    Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

    http://www.pnas.org/content/104/17/7116.abstract

  11. Posted February 21, 2009 at 10:23 am | Permalink

    From the referenced paper:

    “Comparisons of the complete genome sequences of flagellated bacteria revealed that the flagellum is based on an ancestral set of 24 core genes for which homologs are present in genomes of all bacterial phyla. The most striking finding from our analysis is that these core genes originated from one another through a series of duplications, an inference based on the fact that they still retain significant sequence homology. The individual core genes show phylogenetic histories congruent with one another, and this core flagellar phylogeny is largely consistent in its deepest branches with the phylogenetic relationships as currently resolved for Bacteria. Taken together, these results indicate that the core set of flagellar genes arose and was assembled from a single or few ancestral sequences, and that the individual genes diversified, before the shared ancestor of Bacteria.

    The conclusions drawn in this paper may be based on a false assumption: the phylogenetic significance of sequence homology.

    All living things are related and sequence homologies are demonstrable across numerous forms.
    Sequence homologies are strong evidence for relatedness and most likely support the notion of a common origin but may not be an indicator of a phylogenetic relationship.

    Another problem with this analysis is the mechanism of assembly of the parts. No explanation is given as to cause of this assembly.
    I have nails, springs, pieces of wood and pieces of wire in my garage that are homologous to components of a mousetrap, but I would be hard-pressed to explain how these components assembled themselves into a mousetrap without invoking an intelligent input

  12. Posted February 21, 2009 at 2:32 pm | Permalink

    “Just what exactly in the paper you cite above gives any support for ID?”

    The evidence resides in the interpretation of the data. These processes and systems that are described in this paper are composed of multiple structures and multiple processes that adapt means to ends. The structures support other structures, the processes support other processes and the structures and processes together support the system. All of these factors are subsequently integrated into a functional system whose goal is to carry out a single function. You can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

    “Look round the world: contemplate the whole and every part of it: you will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions, to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy, which ravishes into admiration all men, who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human design, thought, wisdom and intelligence. Since therefore the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of men; though possessed of much larger faculties, proportioned to the grandeur of the work, which he has executed…” – Cleanthes to Demea in David Hume (Dialogues Concerning Natural Religion)

    (BTW, although Hume is alleged to have defeated this argument, in fact he was wrong. It’s still a powerful defense of design in nature)

  13. downunder fan
    Posted February 21, 2009 at 4:15 pm | Permalink

    Dear Marshall

    First of all, ID proponents have tried to argue for years that the evolution of the flagellum is too complex for evolutionary theory to account for. Your initial response should be that the ID argument no longer has any substance. Evolutionary theory and genetics can now provide a reasonable explanation for the evolution of the flagellum. Note that this was never a concern for biologist, because there are many things in nature that have yet to be studied. However now you’re trying to move the ID argument to: (1) attack an “assumption” of homology; and, of course, (2) sounding the old gong of ‘it’s too complex to have evolved’.

    At the very least you should have the intellectual honesty to admit that the original ID criticism is no longer reasonable.

    Sounding the old gong: Creationists should realize by now that the design argument is old and useless. Let’s not revisit that one here. The organizing principle of natural selection and genomic mutational processes (transposition, gene duplication, etc) give us an interesting and extremely useful research program, which has real world benefits and explanatory power. The design argument is not only weak but it doesn’t give science a research program or any real world benefits and it has little explanatory power. Let’s just say that drawing on what goes through your mind when you look at the crap in your garage would never get anything meaningful published in science. Thank “god” that creationism isn’t science or we’d be slipping back into the dark ages and religion would again be eroding the explanatory power of modern science.

    Homology: I think I get what you’re saying here, but you’re not very clear nor do you give much detail about your criticism. Labeling it “false” way over steps your ability to construct a sound argument. Presumably you’re suggesting that there is a flaw in assuming that similar sequences are homologous (i.e. similar because of descent from a common ancestor)? You’d need to clarify this. However, there are very well defined mechanisms that explain similarity of DNA sequences because of descent and an enormous volume of literature on this topic. One simple and elegant demonstration of sequence evolution and descent is that transition type DNA changes (A to G or C to T, in either direction) accumulation more quickly that transversion type changes (A to C or T, G to C or T, in either direction). This because the chemistry of transition changes is simpler than transversions. The literature is extensive on mechanisms and models of DNA sequence change and homology.

  14. 386sx
    Posted February 22, 2009 at 8:13 am | Permalink

    You can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

    Wow, you found some stuff that’s really really way complex and stuff like that. Awesome dood!

  15. Posted February 22, 2009 at 11:51 am | Permalink

    “First of all, ID proponents have tried to argue for years that the evolution of the flagellum is too complex for evolutionary theory to account for.”

    I never made that argument. Complexity is not the issue. The problem is obtaining organization by random events.

    “Creationists should realize by now that the design argument is old and useless.”

    I’m not a creationist, I’m an agnostic and a scientist. And the design argument is stronger than ever!

    David Hume wrote:
    1. “For the design argument to be feasible, it must be true that order and purpose are observed only when they result from design. But order is observed regularly, resulting from presumably mindless processes like snowflake or crystal generation. Design accounts for only a tiny part of our experience with order and “purpose”.

    2. “Furthermore, the design argument is based on an incomplete analogy: because of our experience with objects, we can recognise human-designed ones, comparing for example a pile of stones and a brick wall. But to point to a designed Universe, we would need to have an experience of a range of different universes. As we only experience one, the analogy cannot be applied. We must ask therefore if it is right to compare the world to a machine – as in Paley’s watchmaker argument – when perhaps it would be better described as a giant inert animal.”

    My reply to his first claim is that organization is not the same as order.

    My reply to his second claim is that the analogy is valid because we are not comparing our universe to other universes, we are comparing structures, processes and systems that are found on Earth to each other.

    “Presumably you’re suggesting that there is a flaw in assuming that similar sequences are homologous (i.e. similar because of descent from a common ancestor)?

    I’m saying that serial homologies support the notion of a common origin.
    But they do not support the notion of an evolutionary phylogeny.

    More here:
    http://www.charliewagner.com/casefor.htm

  16. downunder fan
    Posted February 22, 2009 at 4:18 pm | Permalink

    Dear Marshall

    The ‘god’s design’ argument is weak because it is just asserting an interpretation. Anyone can assert an interpretation of the world and therefore anyone can claim they know best. We achieve very little real progress in human understanding and it is scientifically unhelpful. Typically the person asserting the “intelligent” design interpretation has a religious agenda. I find it almost impossible to accept that a proponent of ID is uncontaminated by religion.

    Assertions can’t be formally rejected. They don’t build up a theory, comprise models or mechanisms, or have predictive power. For example, when someone points out that a characteristic does not look like god’s design then a counter assertion is made to account for the characteristic. It goes nowhere and it is an explanatory vacuum. Question: list a set of characteristics that would enable someone to reject the assertion of god’s design in nature.

    The biggest point is this. If you’re confident that the design of god argument is so strong and you’re a scientist convinced of it, why are you wasting time on a blog? You should be writing this up for a peer-reviewed journal and pushing for the biggest revolution in science in 150 years. If you’re correct then you’ll be a very famous person and make a significant contribution. It is your duty to do this for the good of humanity. However, when you step out of the blog-sphere and into the science literature, asserting a simple interpretation of nature isn’t any good for maintaining a sustained argument with sound reasoning. Moreover, most assertions are useless for articulating the framework of a viable research program. (PS. Please don’t parrot the creationist claim that there is a global conspiracy in science to keep ID proponents out of the science literature, it is untruthful)

    Before you venture into the real world of science you’ll need to brush up on the theory and studies of natural selection – there is nothing random about natural selection. You seem to display the same lack of understanding as the creationist when you say that “The problem is obtaining organization by random events.”

    This whole thing about the “the design argument is stronger than ever!” is just creationist propaganda and hype in blogs and books. Demonstrate this claim to us by us by citing a the peer-reviewed paper in biology that explicitly states that the intelligent design assertion is strong, or even being seriously discussed for that matter. I suggest that you probably spend far to much time home alone on the internet.

    If your confidence matches your ability, then I will be looking forward to seeing “Marshall Nelson” in the published literature and will be the first to write with congratulation. Unfortunately, at this stage I can’t see beyond a “scientist” making an assertion (which is a worry in itself).

    Blogs are easy, making a contribution to science will require a lot more. Can I make a prediction? Ok thanks. I think you’ll just keep blogging and asserting the same old stuff to whoever listens.

  17. Posted February 22, 2009 at 7:57 pm | Permalink

    “Typically the person asserting the “intelligent” design interpretation has a religious agenda. I find it almost impossible to accept that a proponent of ID is uncontaminated by religion.”

    I am uncontaminated by religion. I gave it up when I was 16. I may be the world’s only agnostic ID’er.

    “why are you wasting time on a blog? You should be writing this up for a peer-reviewed journal and pushing for the biggest revolution in science in 150 years.”

    To keep my mind active, avoid boredom and for amusement. My life is basically over. I’m 65 and retired. I’m also a paraplegic with prostate cancer. My time to do research is past.

    “Before you venture into the real world of science you’ll need to brush up on the theory and studies of natural selection – there is nothing random about natural selection. You seem to display the same lack of understanding as the creationist when you say that “The problem is obtaining organization by random events.”

    ROFLMAO!

    You clearly don’t know me very well.
    Google my name (Charlie Wagner) on talk.origins and visit my website.

    “Demonstrate this claim to us by us by citing a the peer-reviewed paper in biology that explicitly states that the intelligent design assertion is strong, or even being seriously discussed for that matter.”

    The mention of intelligent design in a peer-reviewed paper would be the “kiss of death” for any scientist who wants to get papers published, have grants approved or obtain a position in a large university. Hell hath no fury like a darwinian evolutionary biologist who is scorned! The vultures will gouge his eyes out.

    “I suggest that you probably spend far to much time home alone on the internet.”

    Indeed.

    “I think you’ll just keep blogging and asserting the same old stuff to whoever listens.”

    We live in hope and die in despair.
    Maybe I’ll get to finish my book:
    “How Really Smart People Can Believe Really Stupid Things” (Jerry, I’m giving you the first copy!)

  18. downunder fan
    Posted February 22, 2009 at 8:45 pm | Permalink

    Now that was a surprising revelation!

    I’ve never heard of you before, but you have a somewhat colorful wiki.

    http://rationalwiki.com/wiki/Charlie_Wagner

    The opening statement of your entry (which is classified in the “Category: Pseudoscience”) is: “Charlie Wagner is an inept proponent of Intelligent Design. He specifies that he does not attribute a religious agenda to his support of Intelligent Design, and the notion has been hijacked by those who do.[1] Yet all of his arguments for intelligent input are rife with problems. He posts comments to online forums about evolution versus intelligent design to get attention.[2]”

    The rest of your wiki entry is very much consistent with the line of argument you’ve shown here. I’m sure you’ll be off to trawl more forums and post similar provocations.

  19. Posted February 23, 2009 at 6:31 pm | Permalink

    “The rest of your wiki entry is very much consistent with the line of argument you’ve shown here. I’m sure you’ll be off to trawl more forums and post similar provocations.”

    I’d like to know who took the time and effort to write that!

    Except for the quotes, most of it is simply not true.


2 Trackbacks/Pingbacks

  1. [...] on any idea that combines the words “Darwin” and “wrong.”  (Remember their “Darwin was wrong” cover a year ago?)  Well, they’ve befouled themselves again, this time by publishing, without any [...]

  2. [...] was Darwin wrong? As I noted at the time, New Scientist claimed that HGT is so pervasive among species that “the tree of life is not a [...]

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