Intelligent design news from the 21st of April to the 27th of April, 2011.
The Discovery Institute has been extremely relaxed with its posting over the last week – partially explaining why this is slightly late, there was no massive compulsion on my part to hastily set the record straight on certain blog posts before other new items swallowed the spotlight – and whether this is an external representation of the internal busyness of the organisation, I’m not sure. Perhaps Casey Luskin was too busy doing proper science-attorney things too blog much this week.
But it doesn’t really matter, there’s enough meat for me to sink my metaphorical blogging teeth into. Also, I remember the last time there was a slump in blogging output from the Discovery Institute: I predicted wonderful things were about to happen, but I was wrong. So, I’ll try not to read anything into it.
This week’s TWiID covers pseudogenes and “Darwinian assumptions”, enzyme evolution and ID, and the traditional religious bias of the Discovery Institute.
Taking his usual stand against evolutionary biology, Casey Luskin wrote this post about pseudogenes as a sort of news-advertising crossover for Jonathan Wells’ new book, The Myth of Junk DNA. Of course, he was also trying to make a point, not just try to sell books, which is what I want to focus on:
Evolutionists have long cited pseudogenes as a type of “junk” DNA that demonstrates an unguided evolutionary origin of the genome. Richard Dawkins typifies this view:
Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.
Sounding much like Dawkins, Francis Collins and Karl Giberson discuss pseudogenes to argue that is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” (Karl W. Giberson and Francis S. Collins, The Language of Science and Faith: Straight Answers to Genuine Questions, p. 43 (InterVarsity Press, 2011).)
But are pseudogenes actually “nonfunctional … faulty duplicates … that do nothing” (Dawkins) or “broken DNA” (Giberson and Collins)? Consider the abstract of a new review article in the decidedly non-pro-ID journal RNA which sounds decidedly different from atheistic evolutionist Dawkins and theistic evolutionists Giberson and Collins:
Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.
(Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, “Pseudogenes: Pseudo-functional or key regulators in health and disease?,” RNA, Vol. 17:792-798 (2011).)
Casey then focuses on this paper as support that the “Darwinian view” of pseudogenes is wrong and is, in fact, hindering research into the potential functions of pseudogenes. But what he’s failing to realise is that Pink et al.’s paper was published without any ID assumptions or reservations about evolutionary theory. While it’s true that an outlook like Dawkins’s (for the sake of rhetoric in his case, probably), if shared by all evolutionary biologists, would lead to a reduction in imaginative research, that’s simply not the case. Scientists have known for a long time that non-coding DNA can have functions independent of transcription (eg. producing protein or polypeptide products via ribosomes), and when you think about it, pseudogenes are an excellent candidate for evolutionary innovation: they already have sequences that are pretty much promoters, allowing them to undergo transcriptional regulation, and their transcription products are many orders of magnitude more likely to contain sequences that can interact in a useful way with cellular systems, due to them being, at one point in time, functional (if only in another sense).
So evolutionary biology, properly interpreted and thought about, doesn’t hinder biological research. Perhaps if Casey wants to really attack the notion of properly non-functional DNA sequences, he should go after the long stretches of repeats found in many genomes. To the best of my knowledge, evolution predicts that these sequences are unlikely to have any major role in biological processes – but, of course, there’s always the potential, however small or unlikely, for something to evolve out of seemingly nothing.
The next post, by the shadowy Evolution News & Views account, is all about Douglas Axe and Ann Gauger’s latest piece of research published in the online, pro-ID journal BIO-Complexity. You might have heard about it: Axe and Gauger took two similar proteins and tried to find out how many amino acid changes would be required to convert one to the function of the other. Their results were simultaneously interesting, not surprising and misinterpreted by the ID community:
New research published in Bio-Complexity calls into question some fundamental assumptions of neo-Darwinian theory and enzyme evolution.
Doug Axe and Ann Gauger from Biologic Institute recently published a paper that addresses this pervasive assumption about the ease of enzyme conversion:
Here, we explore this question by asking how many mutations are needed to achieve a genuine functional conversion in a case where the necessary structural change is known to be small relative to the change commonly attributed to paralogous divergence.
As the authors report, they focused “not on minor functional adjustments, like shifts in substrate profiles, but rather on true innovations — the jumps to new chemistry that must have happened but which seem to defy gradualistic explanation.” Their aim was not to establish ancestry between two particular enzymes, but to identify a functional innovation that should be relatively straightforward within a superfamily and then evaluate how evolutionarily feasible this modest innovation would be.
They began by looking at a large “superfamily” known as the pyridoxal-5′-phosphate (PLP) dependent transferases. This is a well-characterized family of enzymes that share a common fold (shape) but catalyze distinctly different reactions. They identified a pair within that superfamily with very close structural similarity but no functional overlap. Kbl2 is involved in threonine (a type of amino acid) metabolism, and BioF2 is part of the biotin biosynthesis pathway. They then used a three-stage process to identify the sequences mostly likely to confer a functional change.
Gauger and Axe estimate that seven or more mutations would be required to convert Kbl to BioF function.
The second implication from this failure to convert functionality is the question of whether a neo-Darwinian process of step-by-step conversion from one enzyme to another is actually feasible. The two enzymes in this study were very similar enzymes, yet even with generous estimates for mutation rate, gene duplication rate, and no fitness cost for carrying the extra gene, there does not seem to be enough time for mutations of this sort to occur:
To summarise: they found that more than seven mutations would be required to functionally convert Kbl to BioF, and this is evidence against evolutionary mechanisms because the intermediates would not be functional for either Kbl or BioF function, forcing the hypothetical gene duplicate to evolve neutrally, and seven mutations is far outside the number (they say) that can be achieved by neutral drift alone.
Okay. There are some problems here.
Firstly, while BioF and Kbl are within the same superfamily, meaning that they share sequence and structural similarity, there is no evidence to infer an ancestral relationship between an earlier form of Kbl and modern BioF, which is essentially what this experiment was testing. If the data suggested that, then this paper would be making a very valid point, but since nobody thinks that BioF evolved from a Kbl precursor, it’s making a useless statement.
Secondly, even if BioF and Kbl had the proper phylogenetic relationship, testing for functional evolution from modern Kbl to modern BioF is inappropriate: as I mentioned, BioF would have evolved, most likely, from an ancestral form of Kbl, which could have had substantial differences in sequence from modern Kbl. Going from one modern enzyme to another does not model the evolutionary process at all accurately.
Thirdly, and finally for now, their method of experimental evolution did not model what would have actually happened in nature. While proteins can be, in computer simulations, converted from one function to another through numerous simultaneous amino acid changes, this obviously happens somewhat infrequently in nature, and a substantial amount of protein evolution occurs gradually via point mutations. However, mutations that affect function are not the only ones possible – thermodynamic stability and protein folding are also very important in the evolution of proteins, so mutations that affect these aspects are also selected for. In the absence of stability compensation mutations to conserve functionality, yes, multiple simultaneous mutations may be hypothetically required to jump from one enzymatic function to another. And the fact that this paper didn’t go into these important mutations is telling about how they wanted the evolutionary process to look as implausible as possible.
So, there are three substantial criticisms of Axe and Gauger’s paper. I’m sure there are plenty more out there, but quite frankly, they’re unnecessary for labeling it bad research. BIO-Complexity had yet to impress the scientific community that it has anything substantial to offer the world of evolutionary biology.
The final post for this week is by Gailon Totheroh, all about Michael Dowd and “evolutionary Christianity”. I’m mentioning this post not because it has anything particularly interesting to say about Dowd’s views, but because it reveals the religious cards that the Discovery Institute holds, sitting so carelessly with their backs toward a mirror. Of course, everyone knows that the ID movement is religious in root and general nature, but you’d think that the DI would be more discrete about their bias towards “traditional religion” – ie. Catholicism, orthodox Judaism and evangelical Protestantism:
Who is Michael Dowd? He calls himself an evangelist. Not surprisingly, he can be found in churches preaching. But Dowd’s gospel is not one where sin is rebellion against God, but rejection of Darwin.
Likewise, salvation doesn’t come from Jesus on a Roman crucifix, but merely embracing the emergent Universe. Thus, we should Thank God for Evolution, the title of his 2008 magnus opus. Subtitled “The Marriage of Science and Religion,” the popular book-endorsed by no less than six Nobel Laureates-unfolds a central theme that standard Darwinism is scientifically accurate andreligiously inspiring.
With faith-evolution controversies running unabated, Dowd’s Darwin-for-all-occasions may seem a hard sell. Yet Dowd’s effusive friendliness and seeming openness are swaying many his direction. His sales technique even wins over atheists and Christian evangelicals.
Still, Dowd is a mover-and- shaker who doesn’t move everybody to awe. The unwilling might include those who question Neo-Darwinism in whole or part, those who are uncomfortable with religion, and conservative adherents of traditional religions.
Oh no, you wouldn’t want to upset those conservative adherents of traditional religion, those people that make up such an overwhelming majority of DI fellows and associates. Bad idea.
Despite his co-option of theological language, there is little left of traditional monotheism, let alone traditional Christianity, in Dowd’s worldview. Indeed, the “supernatural” itself doesn’t exist according Dowd; it’s merely an invention of the Western mind. “Evidence suggests that the only place that the so-called supernatural realm has ever existed has been in the minds and hearts (and speech) of human beings–and only quite recently.” Accordingy, the God of the Bible is no more real than the Greek gods Poseidon or Helios, and the Bible itself is a jumble of “old mythic stories” that provides no real guidance for the challenges we face today: “Ours is a time of space telescopes, electron microscopes, supercomputers, and the worldwide web. It is also a time of smart bombs, collapsing economies, and exploding oil platforms. This is not a time for parsing the lessons given to a few goatherds, tentmakers, and camel drivers.” (emphasis added [by Gailon])
Ouch. It seems like the ID movement gets very defensive about people attacking the concept of the supernatural, yet when pressed, they often claim that ID is not necessarily supernatural (and I agree). It just goes to show you what biases they’re working from.
Rapid fire ID news!
- An implicit response to yours truly. Why… so… implicit?
- ID in Hungary? Proof that pseudoscience doesn’t need a passport to cross borders.
- If I wanted to be mean and nasty, I would say that being brain-dead and being an ID proponent aren’t mutually exclusive…
- Again, another mention of yours truly, but did they understand what I meant?