Posted by PvM on July 31, 2004 | Comments (3) | TrackBack (0)

Not surprisingly the Discovery Institute is getting a good mileage out of Gonzalez’s thesis. Next I will explore the link between Privileged Planet, Rare Earth and the Intelligent Design movement.
The book “Privileged Planet” presents a very poorly supported design argument in which the authors make claims about measurability and habitability which cannot be supported. In fact, when the authors try to link their ideas with Dembski’s ideas, they only accept chance as an alternative to ‘design’ implicitly accepting that regularities (laws of nature) can in fact be ‘designers’. Rather than strengthening the design inference, the authors have managed to undermine the design inference. The observed coincidences (can we say cherry picking) leading to a claim of correlation are not scientifically supported but do make for some interesting apologetic tools.

Recently the book was reviewed in Nature: “Bright Blue Dot” by Douglas A. Vakoch in Naturel Vol 24 p 808-809

Continue reading  “The Privileged Wedge”

Posted by PvM on July 30, 2004 | Comments (0) | TrackBack (0)

Evolution reveals biochemical networks and functional modules Christian von Mering, Evgeny M. Zdobnov, Sophia Tsoka , Francesca D. Ciccarelli , Jose B. Pereira-Leal , Christos A. Ouzounis §and Peer Bork, PNAS December 23, 2003  vol. 100 no. 26  15428-15433

The combined history of genomes provides a glimpse at past evolutionary events, revealing selective forces that acted at all levels of cellular and organismal function. Although the individual gene and its immediate regulatory elements form the primary unit of selection, evolution does not stop there (1). Instead, selection can also act on entire groups of genes, leading to joint transfers of genes between genomes (2, 3), concerted gene loss (4), gene fusion events (5), coregulation of genes through common regulatory elements (6), and the creation and maintenance of operons containing nonhomologous but cotranscribed genes (7, 8).

Posted by PvM on July 29, 2004 | Comments (33) | TrackBack (0)

RNA networks, protein networks all seem to exhibit a scale-free structure. I intend to show that this scale free structure and other aspects of these networks not only can be expected from simple evolutionary principles but also how this scale free structure helps explain such issues as modularity, robustness, and evolvability.

Characteristics of scale-free networks

As is well known DNA sequences map to RNA or protein structures.

• There are far more sequences than structures

• Contains few highly-connected motifs and many less connected nodes

• Motifs have a neutral network which extends throughout sequence space

For these frequent structures, their networks expand through sequence space, this means that gor any given fold, one can traverse through sequence space (that is change every nucleotide position) without changing the structure of the fold. In addition these structures are close in the sense that any such structure is within a small distance from any random sequence.

These findings have significant implications for our understanding of evolution.

Continue reading  “Scale Free Networks”

Posted by Jason Rosenhouse on July 29, 2004 | Comments (35) | TrackBack (0)

The good folks over at the Access Research Network have this post up about some recent work published in the PNAS. The paper in question is entitled “Nitrate Assimilation in Plant Shoots Depends on Photorespiration” and is available here. A readable summary of the paper's findings can be found here.

The primary finding of the paper is that the photorespiration system in plants, which decreases the efficiency of photosynthesis, also serves an important function in allowing plants to convert nitrate into organic forms of nitrogen. Prior to this work it was commonly thought that the photorespiration was just an evolutionary vestige from a time when the atmosphere contained more carbon dioxide than it does today.

The ID's are presenting this as an indictment of evolutionary theory. The ARN summary concludes with this observation: “Evolutionary presuppositions stood in the way of scientific progress. A design model would have simply tried to determine the reason for the phenomenon. ”

To put it kindly, this is hardly the only interpretation of the facts. I have posted a complete reply to this piece of ID silliness over at EvolutionBlog. While crafting my reply, I contacted Dr. Arnold Bloom of UC Davis, the lead author of the paper. I showed him the summary of his work at ARN. He was not amused, and he gave me permission to use his reply in my posting. Check it out!

Posted by PZ Myers on July 29, 2004 | Comments (0) | TrackBack (0)

It hasn't been a good week for biology. I've just learned that Francis Crick has died, and while I was at SDB I heard news that grieved me even more: Ed Lewis has died.

Lewis was one of the giants of Drosophila genetics. He was a student of Thomas Hunt Morgan, and one of the rare practitioners of pure genetics at the time molecular biology was swallowing up the field. He's mentioned several times in Jonathan Weiner's book, Time, Love, Memory (you've all read it, right? If not, get it—it's a wonderful view of neurobiology and genetics and molecular biology, from the perspective of Seymour Benzer). I'll quote a few passages from that book that give a taste of what Lewis was like.

Continue reading "Edward B. Lewis, 1918-2004" (on Pharyngula)

Posted by John M. Lynch on July 29, 2004 | Comments (5) | TrackBack (3)

Reuters via CNN is reporting the death of Francis Crick, the co-discoverer of the structure of DNA. After the double-helix discovery and subsequent Nobel Prize, Crick continued his research at Cambridge University’s Medical Research Council, focusing on the genetics of viruses, protein synthesis and embryology. Subsequently, he moved to La Jolla, where he served as president of the Salk Institute for Biological Studies. There, he turned his attention to the study of the brain and the nature of consciousness.

Posted by PZ Myers on July 28, 2004 | Comments (3) | TrackBack (0)

Tangled Bank #8 is online right now. Follow the links and read about biology!

I am also semi-online—I just got back home after screaming across the Montana mountains and the Dakota prairies with Calgary cowboys, Canadian mounties, and a few frustrated creationists in hot pursuit. I've got a pile of great stuff from the SDB conference (including some stuff from a fun evo-devo session) to dump out of a scribbled-upon notebook onto the web, but first...sleep. Lots of sleep.

Posted by PvM on July 27, 2004 | Comments (5) | TrackBack (0)

In this posting I will start exploring the importance of neutrality on evolution. In fact as the evidence will show, neutrality is not only a requirement for evolvability but it also can be selected for itself. In other words, evolutionary principles can lead to neutrality and evolution will tend towards areas with many neutral neighbours

Neutrality is a fascinating concept which has been shown of importance in understanding RNA and protein evolution.  Additionally the vaste neutral networks may help understand ‘convergent evolution’. Perhaps the lack of sequence similarity, but strong phenotype similarity can be understood by neutral evolution and drift. In other words, due to the vasteness of neutral networks, the sequence may have drifted while the phenotype remained basically the same. Thus what may appear to be convergent evolution may very well have been divergent evolution after all. And homologies, which fail to be detected at the sequence level may still exist at the phenotype level.

Continue reading  “Icons of ID: Neutrality”

Posted by PvM on July 27, 2004 | Comments (2) | TrackBack (0)

Thanks to Nobody on ARN I was made aware of the following story on Growing Tiny Totally Tubular Formations

Would this be another example of false positive for an ID hypothesis?

Tubular structures found on a Martian meteorite had been suggested as evidence of life, he said.

Goldstein pointed out that finding a chemical means to grow such self-organizing systems highlights the fact that living organisms are not needed to create such structures.

Posted by Ed Brayton on July 26, 2004 | Comments (14) | TrackBack (0)

It was requested that I provide a pointer here on PT to a discussion I've been having on my blog, Dispatches from the Culture Wars. The subject of that discussion was a critique I wrote of an article by Robert Meyer entitled Were We Fooled by Stephen J. Gould?, on a site called intellectualconservative.com. My original critique can be found here, and the continuing discussion from emails can be found here. Mr. Meyer's article was one of the worst examples of either ignorance or rank dishonesty from creationists that I have ever encountered. He claims, for example, that Gould was "honest enough to admit" that evolution was in "grave crisis", that he denied the existence of transitional forms, and that Punctuated Equilibrium was the same thing as Goldschmidt's hopeful monster idea. All three of those statements are so blatantly false that either Meyer is utterly ignorant of the subject upon which he is pontificating, or he is flat out lying. Anyway, check out the discussion and jump in if you feel like it.

Posted by PZ Myers on July 25, 2004 | Comments (0) | TrackBack (0)

Another Tangled Bank is coming up this week. Send your links to good science and medicine writing to Reagan Kelly, who will be hosting it at reagank.com. (The usual e-mail address for submissions is still messed up, so send it direct to the host, or to me).