August 11, 2008 | David F. Coppedge

Admissions of Ignorance in Evolutionary Theory

For a scientific idea some have proclaimed as a fact no longer in need of proof, and as well-established as gravity, Darwin’s theory of evolution still reveals surprising weaknesses when its defenders speak about the details.  Detecting these weaknesses requires tuning out the media hype, and tuning into scientific papers and pro-evolution journals where evolutionary theory is debated.  Elisabeth Pennisi wrote one such account in Science last week.1  It revealed that the public is getting a very misleading view of evolution – both its operation and the strength of the evidence for it.
    It would seem obvious that evolution needs a genetic basis.  Darwin attempted to explain it in his day, unsuccessfully.  The neo-Darwinian synthesis of the 1930s was supposed to explain it.  Serious questions about how evolution works at the genetic level remain, however, to this day.  This was evident in Pennisi’s use of war metaphors to describe two groups of evolutionists that are “locking horns” over a current issue: whether genes or regulatory elements (in particular, cis regulatory factors) are key to evolutionary change.  The latter, a “fashionable idea,” has been growing in popularity among those in the evo-devo subculture: i.e., evolutionary biologists who focus more on developmental than genetic influences.  When Jerry Coyne and Hopi Hoekstra wrote a pointed critique of the regulatory-element hypothesis in the journal Evolution last year, “Egos were bruised.  Tempers flared.  Journal clubs, coffee breaks at meetings, and blogs are still all abuzz,” she wrote.
    None of the combatants doubt Darwin’s theory in the slightest, of course.  Still, some statements in Pennisi’s account could give a Darwin-doubter cause for gloating.  Consider this paragraph:

[Sean] Carroll [U of Wisconsin] argued that mutations in cis regions were a way to soft-pedal evolutionary change.  Genes involved in establishing body plans and patterns have such a broad reach–affecting a variety of tissues at multiple stages of development–that mutations in their coding regions can be catastrophic.  In contrast, changes in cis elements, several of which typically work in concert to control a particular gene’s activity, are likely to have a much more limited effect.  Each element serves as a docking site for a particular transcription factor, some of which stimulate gene expression and others inhibit it.  This modularity makes possible an infinite number of cis-element combinations that finely tune gene activity in time, space, and degree, and any one sequence change is unlikely to be broadly disruptive.

This sounds like damage control.  Is the standard explanation too risky?  Yet critics of the evo-devo alternative argue that every such “fine-tuning” change must be adaptive to persist through natural selection.  Precious few examples, they say, can be found to illustrate a regulatory change related to a morphological change.  One regulatory change in a mouse, for instance, can make its digits grow slightly longer (see 01/18/2008), but the mutant mouse is hardly ready to take off flying like a bat.
    “Where’s the beef?” challenged Pennisi, giving the floor to Coyne and Hoekstra, who countered that mutations for evolutionary change must occur in genes:

But Hoekstra and Coyne say this enthusiasm doesn’t rest on solid evidence.  In their Evolution article, they picked apart these examples and the rationale behind them.  They pulled quotes from Carroll’s work to criticize his fervor and berated the evo-devo community for charging full speed ahead with the cis-regulatory hypothesis.  “Evo devo’s enthusiasm for cis-regulatory changes is unfounded and premature,” they wrote.  Changes in gene regulation are important, says Hoekstra, but they are not necessarily caused by mutations in cis elements.  “They do not have one case where it’s really nailed down,” she says.

Those be fightin’ words, indeed.  Coyne even used psychological warfare, telling Science, “I’m distressed that Sean Carroll is preaching to the general public that we know how evolution works based on such thin evidence.”
    The opposition did not take this sitting down.  “Almost as soon as their article appeared, lines were drawn and rebuttals planned,” Pennisi reported like a war correspondent.  But did they come back with a knock-down case for evolution?  All Sean Carroll could reply was that his view is the best of a bad lot:

“I am not trying to say that regulatory sequence is the most important thing in evolution,” he told Science.  But when it comes to what’s known about the genetic underpinnings of morphological evolution, “it’s a shutout” in favor of cis elements, he asserts.

That one statement could come as a shock to students who have been taught all their lives that evolution by natural selection acting on genetic mutations is well understood.  The article degenerated from here into the battle of the T-shirts and other fluff.  Coyne, for instance, sported a T-shirt that said “I’m no CISsy,” and entitled his talk at a recent conference, “Give me just one cis-regulatory mutation and I’ll shut up.
    Pennisi reported statistics from pro-evo-devo people purporting to show the extent of regulatory elements involved in mutated genes.  “Yet even these data are inconclusive,” another was quoted admitting.  At the end of the article, there was no winner.  Pennisi’s closing theme, with variations, was how little is known.  Everyone was making excuses.  Evo-devo devotees complained that associations between regulatory elements and morphological effects are hard to measure.  “I really want to emphasize,” Carroll bluffed, “that evo-devo [researchers] haven’t come to this way of thinking simply through storytelling” but through data.  Was this a response to ridicule he has heard?  Or was it a backhanded charge that his opponents are the storytellers?  Either way, it’s hard to feel his conclusions are compelling when the relevance of certain regulatory elements, and their interactions, are confusing, and “the numbers may be misleading.”  How much more so when genetic mutations can affect the regulatory elements themselves?  What role do RNA elements play?  What about gene duplications?  Patricia Wittkop (U of Michigan) suggested there may be more noise than signal when she said, “The important question is about finding out whether there are principles that will allow us to predict the most likely paths of change for a specific trait or situation.”  It would seem any scientific claim needs such principles to be deemed scientific.
    If the evolutionists cannot resolve their conflict, they can at least improve their battlefield protocols.  Pennisi ended with this:

With so much unknown, “we don’t want to spend our time bickering,” says [Gregory] Wray [Duke U].  He and others worry that Hoekstra, Coyne, and Carroll have taken too hard a line and backed themselves into opposite corners.  Coyne doesn’t seem to mind the fuss, but Hoekstra is more circumspect about their Evolution paper.  “I stand by the science absolutely,” she says.  “But if I did it over again, I would probably tone down the language.


1.  Elisabeth Pennisi, “Evolutionary Biology: Deciphering the Genetics of Evolution,” Science, 8 August 2008: Vol. 321. no. 5890, pp. 760-763, DOI: 10.1126/science.321.5890.760.

The vast majority of the public, including high school students, never sees the bickering between Darwiniacs over the most fundamental aspects of their theory.  That’s why you need to see it exposed here.
    The lesson in this story is that almost nothing is understood in their tale at a scientific level.  Evolutionists want us to believe that humans have bacteria ancestors.  All the amazing structures in all of life had to emerge from a simple, primordial cell by some undirected biological process at the genetic level.  When it comes to positive evidence for such a fantastic, astonishing claim, the paltry best these true believers could exhibit were inconclusive effects of mutations or regulatory elements on existing complex species: reversible changes to the amount of armor on stickleback fish, bristles or the lack of them on fruit flies (with no idea whether they provide any adaptive advantage), slightly longer digits on mice, and other trivia.  When it comes to negative evidence, look at how both sides falsified each other.  The charges and counter-charges were hilarious.  They go like this:
“You have no evidence.”
“Oh yeah?  Well, we have a lot more than you!”
This is like the Dumb and Dumber T-shirts you see friends wearing at amusement parks.  We’ve taken off the Darwiniacs’ white lab coats and shown you their T-shirts: not just Dumb and Dumber, but Fussy and Fussier, and Deceived and Deceiver.  Should such people be “preaching to the general public” that “they know how evolution works, based on such thin evidence”?  Look under the T-shirt and you see just a skeleton with no scientific fitness.  “Where’s the beef?” indeed.  These Popeyes (05/31/2005) will find no salvation in spinach (01/24/2005).  Their ID nemesis, already fit to the hilt, has already eaten it all.  Skinny lightweights only win in the cartoons.

(Visited 76 times, 1 visits today)
Categories: Genetics, Media

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.