Tag Archives: Peer-Review

Commentary

Protein binding: by chance or intelligent design?

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Dr. Fazale Rana has this interesting post up on protein binding at Reasons to Believe.

Excerpt:

Nobody likes getting the flu. In fact, the influenza virus represents a serious health challenge. For most people it causes a few days of misery, but tragically for others, it takes their lives.

Biomedical researchers are looking for ways to develop therapies against the strains of the influenza virus that avoid destruction by the immune system or fail to respond to antiviral drugs. Recently scientists from the University of Washington and The Scripps Institute made progress toward this end. They designed novel proteins from scratch that bind to the stem region of hemagglutinin, a viral protein that plays a central role in the infection process.1 The hope is that the new proteins will have therapeutic use and also help with diagnosis.

This advance has obvious biomedical importance. It also contributes toward understanding the fundamental nature of protein-protein interactions (PPIs), and with this insight comes powerful new evidence that life stems from a Creator.

Often, in order to carry out their function, proteins must interact and bind in a highly specific manner with other proteins. These PPIs are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

A large and varied population of proteins crowds the cell’s interior. Even the simplest bacterium harbors several thousand different types of proteins, along with numerous copies of the other biomolecules inside it. The jam-packed environment complicates things. Proteins are more likely to encounter the “wrong” partners than the ones they are designed to interact with.

Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions. As it turns out, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions. Recent work by Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also designed carefully.

In other words, protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life.

The rest of the article talks about all the intricate and cutting-edge engineering and computation done by the scientists to create a situation where the proteins could bind, and then ends with this:

When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:

…cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2

If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?

If you have to involve human intelligence to this degree, then I think that the best explanation is intelligent design.

Commentary

Prominent atheist philosopher gives mixed review of intelligent design

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Consider this report on a peer-reviewed assessment of intelligent design by the prominent atheist philosopher Thomas Nagel.

Excerpt:

Prof. Thomas Nagel, a self-declared atheist who earned his PhD. in philosophy at Harvard 45 years ago, who has been a professor at U.C. Berkeley, Princeton, and the last 28 years at New York University, and who has published ten books and more than 60 articles, has published an important essay, “Public Education and Intelligent Design,” in the Wiley InterScience Journal Philosophy & Public Affairs, Vol. 36, issue 2…

[…]Prof. Nagel’s paper is a significant and substantial opening, at America’s highest intellectual level, that encourages all intelligent, educated, informed individuals — particularly those whose interest in this issue derives from intellectual curiosity, not the emotional advocacy excitement for any side — that it is legitimate as a matter of data, science, and logic, divorced from all religious texts and doctrines, to consider that intelligent design may be a valid scientific approach to understanding how DNA and the complex chemical systems of life came to attain their present form. Prof. Nagel’s article is well worth the price to put it in the library of any inquiring mind.

The actual paper is here.

Now for the summary of the paper, with supporting quotes:

Professor Nagel has read ID-supportive works such as Dr. Behe’s Edge of Evolution (p. 192). He reports that based on his examination of their work, ID “does not seem to depend on massive distortions of the evidence and hopeless incoherencies in its interpretation” (pp. 196-197). He reports that ID does not depend on any assumption that ID is “immune to empirical evidence” in the way that believers in biblical literalism believe the bible is immune to disproof by evidence (p. 197). Thus, he says “ID is very different from creation science” (p. 196).

Prof. Nagel tells us that he “has for a long time been skeptical of the claims of traditional evolutionary theory to be the whole story about the history of life” (p. 202). He reports that it is “difficult to find in the accessible literature the grounds” for these claims.

Moreover, he goes farther. He reports that the “presently available evidence” comes “nothing close” to establishing “the sufficiency of standard evolutionary mechanisms to account for the entire evolution of life” (p. 199).

He notes that his judgment is supported by two prominent scientists (Marc Kirschner and John Gerhart, writing in the Oct. 2005 book Plausibility of Life), who also recognized that (prior to offering their own theory, at least) the “available evidence” did not “decisively settle[]” whether mutations in DNA “are entirely due to chance” (p. 191). And he cites one Stuart Kauffman, a “complexity theorist who defends a naturalistic theory of emergence,” that random mutation “is not sufficient” to explain DNA (p. 192).

Prof. Nagel acknowledges that “evolutionary biologists” regularly say that they are “confiden[t]” that “random mutations in DNA” are sufficient to account for “the complex chemical systems we observe” in living things (p. 199) — but he disagrees. “Rhetoric” is the word Professor Nagel uses to rejects these statements of credentialed evolutionary biologists. He judges that the evidence is NOT sufficient to rule out ID (p. 199).

He does not, however, say that the evidence compels acceptance of ID; instead, some may consider as an alternative to ID that an “as-yet undiscovered, purely naturalistic theory” will supply the deficiency, rather than some form of intelligence (p. 203).

In light of these considerations, Prof. Nagel says that “some part of the high school curriculum” “should” include “a frank discussion of the relation of evolutionary theory to religion” but that this need not occur in biology classes if the biology teachers would find this too much of a “burden” (p. 204). Significantly, Prof. Nagel — who is a professor of law as well as a professor of philosophy — concludes that, so long as the proposal is not introduced by religiously-motivated persons “as a fallback from something stronger,” but by persons “more neutral” or “without noticeable religious beliefs,” it would be constitutional to “mention” ID in public school science classes, because doing so genuinely furthers “the secular purpose of providing a better understanding of evolutionary theory and of the evidence for and against it” (p. 203). He makes clear that the “mention” must be a “noncommittal discussion of some of the issues” (p. 205).

So Nagel does NOT think that ID is a slam dunk, just that it is worth considering in science classrooms. Teach the controversy, that’s always the right approach. Be open-minded. Look at the evidence before you decide.

News

Peer-reviewed journal apologizes for censoring pro-ID article

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From Evolution News. (Excerpt below, with links removed)

Excerpt:

In one of their favorite soundbytes, members of the Darwin lobby like to assert that intelligent design scientists do not publish peer-reviewed research. That claim is manifestly false. But the fact that intelligent design scholars do publish peer-reviewed articles is no thanks to Darwinists, many of whom do their best to ensure that peer-reviewed articles by intelligent design scientists never see the light of day.

Witness the brazen censorship earlier this year of an article by University of Texas, El Paso mathematics professor Granville Sewell, author of the book In the Beginning and Other Essays on Intelligent Design. Sewell’s article critical of Neo-Darwinism (“A Second Look at the Second Law”) was both peer-reviewed and accepted for publication by the journal Applied Mathematics Letters. That is, the article was accepted for publication until a Darwinist blogger who describes himself as an “opinionated computer science geek” wrote the journal editor to denounce the article, and the editor decided to pull Sewell’s article in violation of his journal’s own professional standards.

The publisher of Applied Mathematics Letters (Elsevier, the international science publisher) has now agreed to issue a public statement apologizing to Dr. Sewell as well as to pay $10,000 in attorney’s fees.

“It’s hard to imagine a more blatant assault on intellectual freedom and the free exchange of ideas,” says attorney Pete Lepiscopo with the California firm of Lepiscopo and Morrow, which represented Sewell.

Lepiscopo points out that in retracting Sewell’s article, Applied Mathematics Letters “effectively accepted the unsubstantiated word and unsupported opinion of an inconsequential blogger, with little or unknown academic background beyond a self-professed public acknowledgment that he was a ‘computer science grad’ and whose only known writings are self-posted blogs about movies, comics, and fantasy computer games.” This blogger’s unsupported opinion “trumped the views of an author who is a well respected mathematician with a Ph.D. in Mathematics from Purdue University; a fully-tenured Professor of Mathematics at the University of Texas–El Paso; an author of three books on numerical analysis and 40 articles published in respected journals; and a highly sought-after and frequent lecturer world-wide on mathematics and science.”

After Dr. Sewell’s article was pulled, Darwinian zealots crowed about their achievement and maliciously speculated that the article was withdrawn because it wasn’t really peer-reviewed or because it was somehow substandard. The journal, meanwhile, left Dr. Sewell to twist in the wind, seemingly endorsing the Darwinists’ smears. The journal editor Dr. Rodin wrote a groveling letter to the Darwinist blogger who complained to him in which he agreed that publishing Sewell’s article would involve “impropriety.” Rodin further apologized “for our erroneous judgement in even considering this paper for publication.”

Dr. Rodin and his journal now have to issue a public statement providing “their sincere and heartfelt apologies to Dr. Sewell… and welcom[ing] Dr. Sewell’s submission of future articles for possible publication.” More important than the apology, the journal has to set the record straight by reiterating that “Dr. Sewell’s article was peer-reviewed and accepted for publication” and by making clear that his article was not withdrawn because of “any errors or technical problems found by the reviewers or editors.”

Wow. I actually clicked on some of the links in the post at Evolution News and was carried off to the lands of naturalistic blogging. It’s amazing how confident they are in their little echo chambers, but I cannot fathom why this should be since they are unwilling to debate their views in public. To me, you can only know something if you are willing to hear the criticisms against it. If you censor all your opponents and hang around in little online chat rooms gloating to your choir about how smart you are and how right you are, why think that you really know anything about what you are talking about?

The only way to be sure about any issue is to listen to both sides in a debate, and let your opponents have a hearing. I would not feel confident in asserting anything if I only heard the arguments on one side of the question. Not only do the Darwinbots seem to be confident in asserting their views without hearing their opponents, they are actually arrogant and insulting about it. But before you can be trumpet your victory in a disagreement, doesn’t there have to be an actual debate first? Canceling the debate by censorship doesn’t mean that you won the debate.  It means you’re scared of debate.

Here’s what you do. Slap a defamation lawsuit on the blogger who complained for a million dollars and let them have their day in court to explain why they said what they said. Then we’ll find out which side has the blind faith and which side has the knowledge.