Any interesting new study shows that evolution may be more predictable than many think:

Associate professor Yousif Shamoo and two students recently conducted experiments on a microbe, G. stearothermophilus, to see how it adapted to different environmental circumstances. In the experiment, the dominant strains of separate generations of the microbe ended up developing the same mutant gene in response to the same environmental hazards"¦"¦ The group then conducted the experiment again, and the same mutations developed. Thus, the experiment suggests that evolutionary development can be predicted, the researchers said.

"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said in a statement. "One of our most surprising findings is that an estimated 20 million point mutations gave rise to just six populations that were capable of vying for dominance. This suggests that very few molecular pathways are available for a specific molecular response."

All of this raises a very interesting question: To what degree can evolution be specified? Could evolution itself be an example of specified complexity?

Of related interest.

Addendum: Another account of the same study.

It's becoming increasingly clear that the eukaryotic nucleus is not a bag of soup whose function is the product of nothing more than randomly diffusing transcription factors, RNA, and DNA. Another study has documented the importance of location within the nucleus.

as red blood cells mature, the beta globin locus progressively moves away from the nuclear periphery, towards the interior. Furthermore, they found that efficient relocalization is dependent upon the locus control region (LCR). Contrary to the existing dogma, this finding demonstrates that gene transcription precedes relocalization "“ establishing the nuclear periphery as the new hot spot.

Here

Changing topics, Robert Shapiro has published another paper on the origin of life. I have not read it, but it looks like he outlines the fundamental flaw in the quest for the elusive self-replicator (Conway Morris, relying on Shapiro, also outlines this reason in his recent book). Shapiro clearly opts for the "metabolism first" school of thinking that has been around for years:

Shapiro outlines how replicator theories, though they have been supported by "prebiotic" syntheses carried out by chemists using modern apparatus and purified reagents, are highly unlikely. The creation of a molecule that can self-replicate requires the combination of diverse chemicals in a long sequence of reactions in a specific order, interspersed by complicated separations, purifications, and changes in locale.

Instead, Shapiro introduces the idea of a "driver" reaction, linked to a free energy source, that helps convert an unorganized mixture into a organized, self-regulated metabolic network.

"If we wish a more plausible origin of life, then we must work with the assumption that life began, somehow, among one of the mixtures of simple organic molecules that are produced by abiotic processes," writes Shapiro. "Nature will be instructing us, rather than we attempting to impose our schemes onto it."

Here

In the comments to this post, ID critic "Hrafn" is arguing mightily that the religious motives of people like Johnson and Dembski means that intelligent design must necessarily be theistic. I was reminded of this when reading this article by Jeffrey Koperski, philosopher at Saginaw Valley State University (HT: Paul Nelson). He has some potent remarks on some of the arguments that are popular with the ID critic crowd, which I'll be quoting beneath the fold.

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A little knowledge can be a dangerous thing. But more often than not, a lack of knowledge is even more dangerous. In Europe, cattle have always been fed with meat and bone meal, made from butchered cows and sheep. In nature, canibalism is rarely practiced, as it increases the risk of becoming infected with the parasites of your dead companions, but farms tried to obviate this risk by boiling the meat at temperaturs known to kill most organisms. What nobody knew at the time was that diseases can also spread through agents that aren't organisms. Meat farmers learned this the hard way, when 157 people died of a variant of Creutzfeldt-Jakob disease from eating beef infected with mad cow disease, caused by a misshapen prion.

Prions are proteins that can adopt different forms, and which can convert other prions into their own forms, like zombies in a horror film infecting the living. The word "prion" is short for "proteinaceous infectious particle" (with the letters scrambled around a bit), as it is predominately seen as an agent of disease. But according to this news article, prions may also play a more positive role, faciliating memory:

Rapid folding of the prion-like protein, CPEB, seems to be what the brain uses to "lock in" memory traces. In other words, we need it to fold.

According to biologist Susan Lindquist at the Whitehead Institute for Biomedical Research outside Boston, under normal circumstances the folding protein forms a long chainlike structure that seems to help nerve cells "” neurons "” solidify connections with each other, maintaining memory. This finding, she said "is an exciting and revolutionary thing."

This phenomenon, if shown to be widespread, would add an interesting layer to the adaptability of eukaryotes. Many responses to the environment (such as the "fight or flight" response) involve the activation of genes to make the appropriate proteins, but a prion-mediated signal can spread quickly, without any new molecules having to be produced. Furthermore, prions can be inherited in their active shape through the cytoplasm, raising the spectre of Lamarck. But what's even more interesting is that "CPEB acts much the same and can transmit inherited information in yeast, without needing genetic material, meaning DNA or RNA." If an organism as distantly related to us as yeast uses prions, it raises the possibility that we are dealing with a system of considerable age.

Thanks to reader Bilbo for directing my attention to this story.

I tend to think that when scientists find an idea useful they … well, they will use it. I also think that after the idea has been around for long enough to be well-tested, make predictions, etc. that scientists start treating the idea not just as something useful, but also as something true or real. And if some philosopher of science tells these scientists that this useful idea is against the "rules" of science, scientists tend to ignore them. See this paper by 2004 Nobel Prize winner Frank Wilczek, for example. Wilczek basically says "I'm working on a theory that is already falsified and there's really nothing you can do about it, Popper."

Methodological naturalism is a recent term for the rule that science must be restricted to natural processes or the rule that science cannot refer to the supernatural or the rule that scientists, while doing science, must act as if the supernatural does not exist. Keep in mind that this is very often claimed to be part of the very definition of science. It is a rule that has to be followed in order for something to be science.

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Critics of Neo-Darwinism are often admonished to remember the research it has inspired and the fulfilled predictions it has made. However, such advise wouldn't be entirely fair unless we were also asked to remember the cases where Neo-Darwinism has bet on the losing horse. So, without further ado, here is Ernst Mayr, one of the major architects of the Neo-Darwinian synthesis, on the hopeless prospects of finding "deep homology":

Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. The saying "Many roads lead to Rome" is as true in evolution as in daily affairs.
Ernst Mayr, Animal Species and Evolution (Harvard University Press, 1963), p. 609

Mayr's theoretical argument is hard to gainsay, but unfortunately, reality refused to butt. One of the great suprises of evo-devo was the discovery that hox genes, which are used to construct structures such as limbs and eyes, are shared between mice and flies, the common ancestor of which lived 600 million years ago. Interested readers are invited to check out my old post on this subject, titled "Carroll and the ancient genetic tool kit".

David Penny continues to make the case that bacteria are derived from a more complex, eukaryotic-like state:

Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand…..If the first eukaryotes were a fusion of ancient bacteria and archaea, as some scientists suspect, there should be clues in the eukaryote genome and proteome that point back toward these putative ancestors. Penny and colleagues say those clues simply aren't there. Instead, the say the fusion theory is "surprisingly uninformative" when it comes explaining the special genetic and cellular features of eukaryotes. Most of the proteins that eukaryotes and bacteria share, for instance, are only distantly related and probably came from the common ancestor of both bacteria and eukaryotes.

From Here

Related analyses are found here and here.

We're being hit with the same wave of spam as Uncommon Descent, forcing me to spend only the briefest amount of time running through the list of comments held in moderation before deleting them en masse. Regular commenters don't have to worry about this, as the software recognizes them and sends their comments straight through. But if you're a new commenter, your comments will be held in moderation queue, with the possibility that they've been deleted along with the spam. So if you've written something that haven't turned up, send me an e-mail (the adress is in my profile) and I'll make sure that your next comment gets through.

My co-telician Guts has announced that he'll be retiring from the blog, due to time pressures. You're probably scratching your head right now, thinking, "Guts who?" Guts was our faithful programmer, working in the murky depths of the machinery, ensuring that the blog ran smoothly. So if you've never noticed Guts, it's because he's been so good at what he does. However, if you've been around since the first cruddy, bug-packed version of the blog launched, you'll see how far he's gotten us.

He's promised to write in the comments from time to time, which is good thing, since I hate goodbyes. So I'll just tip my hat and thank Guts for the great work he's done for us all.

Last month, this article had intelligent design critics up in arms about how a Candadia research council was oppressing the academic freedom of a researcher because of its doubts about the theory of evolution. The researcher, Brian Alters, had applied to the Social Sciences and Humanities Research Council for grants to study the effects of the popularization of intelligent design, which was denied by a comittee for the council. The story about evolution-doubting censors was based on excerpts from the rejection letter, which Alters read aloud during a public lecture, that indicated that the committee felt there was inadequate "justification for the assumption in the proposal that the theory of evolution, and not intelligent-design theory, was correct."

In this week's Nature, Yves Gingras, a former board member of the council, replies. I've put the full text of his letter below the fold.

Update: Thanks to commenter "Incognito" for catching the typo in this post's title.

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