Intelligent design news from the 28th of April to the 18th of May, 2011.
Finally! It’s back again, your fix of ID news and discussion. To make up for my three-week-long absence, this post will cover five of the top ID blog posts from the past three weeks. Lucky for me then that it hasn’t been an especially busy time for the ID community during my break – otherwise I’d have a much bigger job on my hands.
Anyway, enough grovelling, let’s get into it.
Today’s posts are about Osama bin Laden and junk DNA, Oxford University and evolutionary mathematics, dissent in the evolutionary ranks, enzyme evolution, and, of course, junk DNA.
First up this week, David Klinghoffer plunged headfirst into newsploitation mode, trying to somehow link Osama bin Laden’s recent death with intelligent design. It’s masterful, it really is. Trust me:
President Obama is said to have known the whereabouts of Osama bin Laden since September but chose to wait until May to authorize action against him. Why the delay? Could it perhaps have been to provide a super-timely news hook for the rollout of Jonathan Wells’ new book, The Myth of Junk DNA? If so, an additional note of congratulation is owed to Mr. Obama.
How do you think OBL’s body was identified? By a comparison with his sister’s DNA, evidently those non-coding regions singled out by Darwin defenders, among the pantheon of other mythological evolutionary icons, as functionless “junk.” Indeed, the myth has featured in news coverage of Osama’s death. Reports the website of business magazine Fast Company:
Because your parents give you some of their DNA, they also give your siblings some of the same genetic code — which is why sibling DNA tests work. They sometimes concentrate on areas of the genome called “junk DNA” which serves no biological function but still gets passed along to offspring. By testing for repeat strands of DNA code in these areas, it’s possible to work out if two individuals are related as siblings.
The Toronto Star strikes a similar note:
When testing against a relative’s DNA, scientists often look to parts of the genome described as junk DNA which are passed on to all offspring.
Readers of this space and of Dr. Wells’ book, published this month, will know how thoroughly the myth has already been debunked in peer-reviewed scientific literature. Unfortunately, the news hasn’t yet reached the general interest media, and it continues as what Richard Dawkins might call a powerful “meme” in the public’s thinking about evolution. In fact, in Daniel Dennett’s book Darwin’s Dangerous Idea, junk DNA is given as one of the scientific predictions made for Darwinian evolution by Dawkins himself.
If Darwin is right, there ought to be huge swaths of ancestral garbage cluttering the genome, serving no purpose other than to identify otherwise unidentified forensic remains. So if those huge swaths turn out after all to be vitally important to the functioning organism, what does that say about Darwin’s theory? Ah, that’s exactly the question addressed in Jonathan Wells’ book.
Let’s see how many Darwin lobbyists have the guts and honesty to acknowledge that another icon has fallen. They have not, on the whole, left themselves a lot of room for deniability on this.
So really, the post is just an excuse to mention Jonathan Wells’s new book again? Great. You had us going there for a while, David.
Some anti-ID bloggers have attacked the first paragraph of the post with vigor as being ridiculous: I mean, Obama really tried to do that? Really? Of course, well, it is a joke. It’s a bad joke, to be sure, but a joke nonetheless. David’s not being serious.
A lot of people in the anti-ID community see ID proponents as being unintelligent pot-stirrers, but this is rarely the case, at least for the upper levels of the Discovery Institute. No, they know what they’re doing, they’re not stupid. They might be misguided, biased and uninformed, but they don’t lack a savvy sense of self-awareness. If anything, public relations is the Discovery Institute’s strongest suit, even given their religious/scientific image problems.
No, David’s post was just a publicity stunt to draw attention to both themselves and Wells’s new book, which they have been heavily promoting recently. Such behaviour should come as no surprise to any ID critic who knows what he/she is up against.
The next post was written, again, by David Klinghoffer about Oxford University’s decision to advertise for a new research position in the field of evolutionary mathematics. According to David, this obviously means that the theory of evolution is shaky, because why would you want to employ researchers if your ideas were perfect?
File this one under: Mission Impossible. An Oxford college, St. John’s, is advertising to hire a pair of researchers to undertake a tough assignment: shore up the admittedly unsteady mathematical foundation of Darwinian theory, specifically in the ever distressing area of population genetics.
In a downloadable document of particulars for the two-year assignment, the college frankly concedes that ranged against them the new hires will face, well, basically the entire rest of the scholarly field that studies the subject. Biologists may accept that “natural selection leads to organisms that maximize their fitness,” the document observes.
However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is.
For half a century, mathematicians have been telling Darwinists to get stuffed. If only that would change! Maybe if we enter the figures again and push the “equals” button on our hand calculator just one more time, it will give a different answer. I’ve sometimes wished the same in seeing what the balance in our family checking account will be once those outstanding checks are cashed.
Wow. Er, there’s no easy way to back up from that…
I feel like the St. John’s document is rather overstating a non-problem, which is probably why David jumped on it in the first place. Perhaps they were referring to the inefficiency of natural selection in small populations, where neutral drift reigns supreme over fluctuating allele frequencies? Or perhaps, just perhaps, David was isolating a quote in order to make the contention of the document seem more dramatic. Here’s the quote in a larger amount of context:
The concept of fitness optimization is routinely used by field biologists, and first-year biology undergraduates are frequently taught that natural selection leads to organisms that maximize their fitness. Dawkins’ The Selfish Gene (1976) promoted a conceptual integration of modern evolutionary theory in which genes are viewed as optimising agents, which is extremely influential and widespread today and encompasses inclusive fitness theory and evolutionarily stable strategies as well as general optimality ideas. However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. One underlying cause is that the link between natural selection and fitness optimization is much more sophisticated than the usual optimization principles associated with dynamical systems, namely Lyapunov functions and gradient functions.
Note that there is a difference between the maximisation of fitness and general increases in fitness. No mathematician would deny that natural selection cannot increase fitness, that would be absurd. (Which leads to a strange implication: does David Klinghoffer think that natural selection cannot increase fitness?) What is clearly in question is how effective is selection at increasing fitness: what are the theoretical and practical restrictions on fitness increase in various situations?
Think about this another way – if this problem was as major as David is making it out to be, why would the project be for only two researchers? Why is it not attracting major attention in the scientific community? It makes little sense to blow this up into a huge issue. Evolution is safe from mathematical falsification, and it’s only small details that need to be worked out – hence this project.
Next up – Anika Smith wrote about an exchange between Karl Giberson and William Dembski. I mention it for a revisitation to the old idea of there being significant challenges to evolutionary theory from within the scientific community, something that ID proponents have both fantasised about and perpetrated as much as they can in popular culture:
When he finally does get around to addressing Dembski himself, Giberson objects to Dembski’s use of marketing metaphors as an ad hominem attack, which is strange considering that Dembski wrote that this is something that scientists and people with ideas generally ought do to communicate and advance them, with nothing cynical or slimy about it. Either Giberson is hypersensitive and looking for an excuse to display his lofty umbrage, or he is working to avoid the actual questions raised by Dembski’s review. Most likely it’s both.
He does, however, give us a nice quote for giggles:
The scientific literature is not filled with growing concerns about the viability of the theory; scientific meetings do not have sessions devoted to alternative explanations for origins; and leading scientists are not on record objecting to the continuous and blinkered embrace of evolution by their colleagues.
Apparently, these scientists (who are emphatically not ID proponents) and these meetings and these papers are somehow overlooked by Giberson. This may be because he’s not engaged with the science himself, trusting in others to tell him whether or not it works out, which is what he recommends we all do:
My response, which I provided at greater length a while ago on the BioLogos site, is “Of course we cannot confront the data ‘on our own’.”
It’s strange that Giberson would emphasize the need for logic and reasoning, then go right back to his appeal to authority — as long as it’s the proper, respected authority in the right community. (You know, not those evangelicals who are so intellectually impoverished.)
It’s not that evolution does not have dissenters in the ranks, so to speak – that’s the hallmark of healthy science, every theory should have its opponents so as to prevent scientific knowledge from inadvertently becoming stale – it’s just that when these dissenters’ arguments are weighed up and examined, they aren’t of much substance. Jerry Fodor seems to take issue with the very idea of natural selection itself, Lynn Margulis has some funny, mostly unsubstantiated ideas about symbiosis being the major evolutionary force, and the Altenberg 16, from what I can tell, was a conference that discussed ideas of evolution past the Modern Synthesis, something that has been coming for a while, but as more of an add-on to existing ideas, not the paradigm shift or wholesale rejection of evolution that ID proponents have been craving.
Evolutionary theory has criticism, yes, but it is neither significant criticism, in terms of numbers, nor legitimate criticism, in terms of ideas and arguments. Dissenters are at the basal level we would expect for a theory as major and as old as evolution – and ID proponents are trying to make a mountain out of that molehill.
In a pseudonymous post, Evolution News & Views interviewed Ann Gauger about her and Douglas Axe’s latest paper in BIO-Complexity on enzyme evolution. I touched on this paper in the last TWiID and hopefully explained why the results don’t have much impact on evolution, but this interview has an extremely interesting section near the end – it appears that they’re at least aware of the specific problem with their paper, but they don’t seem to be acknowledging it as a major one:
AG: [...] Alternatively, what if what we see now is the fortuitous product of one-way evolution? Ancestral proteins diverged into modern enzymes in a contingent fashion, following the paths natural selection and random mutation laid down, but epistatic interactions acquired over time now prevent any simple adaptive path between modern forms. That might be why it is so difficult to convert modern enzymes from one function to the other.
This pretty much cuts their paper in half, in terms of its implications for evolution, so why aren’t they saying so?
To refresh your memory from three weeks ago, Gauger and Axe took a modern protein, Kbl, and attempted to evolve a protein with equivalent function to BioF, another modern protein in the same enzyme superfamily as Kbl, but with a different enzymatic function. They found that it took seven mutations to switch between functions, something they claim is beyond the reach of stepwise evolution, as the intermediate stages were not functional (or were very weakly functional). My (and a lot of other ID critics’) criticism of the paper is that they weren’t testing an evolutionary hypothesis – they were transitioning from one modern protein to another, not from an ancestral protein to one of either Kbl or BioF1, which is not what would have happened in the evolutionary history of this particular enzyme family.
Of course, this is what Gauger is talking about in the above quote – history constrains the evolutionary process to only what paths are available to the enzyme at the time. Downstream, two rivers might have to jump their banks to join, but upstream their ancestral river split into two without any problems. The same is true of proteins: two modern enzymatic functions are hard to transition between, but earlier in time (“upstream” of the phylogenetic tree) the progression would have been easier. Note that it’s not necessarily a “transition” at all when it happens in nature – as with the rivers, each potential modern protein could have been contained in one common ancestral protein, which then had its gene sequence duplicated, allowing for multiple paralogs to evolve separate functionalities from the same starting point.
Unfortunately, instead of seeing this major flaw in their paper, Ann Gauger (presumably sharing the same thoughts as Douglas Axe) wrote it off as another confirmation of intelligent design:
But if protein evolution is so highly constrained, either ancestral proteins would have had to be remarkably designed indeed, or we must have been extremely lucky that just the right variants appeared whenever needed to provide new functions. More studies that examine the constraints on adaptive evolution of proteins are needed.
Any work on enzyme evolution (or any evolution, for that matter), to the ID proponent, can be boiled down to that statement in order to defend ID. “How lucky it is that mutation just happened to create protein variants that were functional!”, implying that any pathway to a new protein, however well-demonstrated, is still implausible because it involved chance event, which may not have actually happened historically. And with that you can see the ID movement’s logic at its most raw: anything less than 100% certainty of specific evolutionary pathways for all of life’s diversity is not good enough, lending plausibility to intelligent design as the best explanation for that diversity by default.
Isn’t it strange that most scientists don’t take them seriously?
The last post this week is by, for the third time, David Klinghoffer, who seems to be overtaking Casey Luskin in the highly recent posting frequency stakes (a highly important competition over at Evolution News & Views). David wrote about junk DNA, as, of course, it was once again time to plug Jonathan Wells’ new book, The Myth of Junk DNA:
Over the weekend, Jonathan Wells’s The Myth of Junk DNA broke into the top five on Amazon’s list of books dealing with genetics — a list normally dominated at its pinnacle by various editions of Richard Dawkins’ The Selfish Gene. Not bad, Jonathan.
The juxtaposition with Dawkins’ Selfish Gene is appropriate, notwithstanding the demurrals of biochemist Larry Moran et al. Dawkins and other Darwinists, such as Jerry Coyne, have indeed posited that neo-Darwinian theory predicts that swaths of the genome will turn out to be functionless junk. The Junk DNA argument has been a pillar of the Darwin Lobby’s efforts to seduce public opinion and influence public policy. Professor Moran wants to imagine that Dawkins never held that neo-Darwinism predicts junk DNA. But that’s not how other Darwinists see it. (Compare, for example, Dennett’s Darwin’s Dangerous Idea, page 316.)
First off, nice job, Jonathan. The Amazon Genetics Top Five is a lofty goal, and now that you’ve achieved it, don’t let it get to your head. Okay, I don’t mean to be snarky, but Stephen C. Meyer’s Signature in the Cell got onto the Amazon Top 10 Science books for 2010 list, so you’ve got a bit to live up to, especially when the Discovery Institute’s famous PR team is involved.
Secondly, Larry Moran, over at Sandwalk, responded to this post by David, and raised some extremely good, if unlikely-to-persuade-an-ID-proponent-of-their-truth, arguments:
The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a “pillar” of support for evolution. That’s hard to do when their understanding of evolution is so flawed that they don’t see the difference between “Darwinism” and evolution by random genetic drift.
Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. They been told this but they keep repeating their error. There’s a word for that kind of behavior.
It’s easy to see how they got confused. It’s because they’re IDiots. It’s partly because they don’t understand that an argument for inheritance of a few pseudogenes is not the same as an argument that more than 50% of our genome is junk. There are plenty of scientists who will use the pseudogene argument to challenge Intelligent Design Creationism but who don’t believe that MOST of our genome is junk.
Well put2. Larry then goes on to explain the difference between Dawkins’ concept of “selfish DNA” and “junk DNA”, and discusses some further points. Make sure you read it, especially if you don’t know much about what junk DNA actually is.
Rapid fire ID news!
- It’s a pity non-theistic philosopher Bradley Monton doesn’t quite grasp the logic of scientific inquiry well enough…
- A large thread on theistic evolutionists’ perceptions of ID. Wade through if you dare.
- A much smaller thread on agnostics and atheists who accept ID. Rather telling, really.
- This is just a pure, traditional creationist argument right here. What self-respecting, modern ID proponent would get behind it?
- But I thought ID was compatible with common descent!
- An ancestral protein could be reconstructed using paleoenzymological techniques, involving phylogenetic analysis and statistical modelling. ↩
- Even though I would never use the term “IDiot” myself, but that’s just my preference for keeping these sorts of discussions at a certain personally-respectful tone. ↩