Tag Archives: Biochemistry

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

William Dembski reviews a new book by two theistic evolutionists

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From Patheos, an opening statement by William Dembski. This is the first part of a four-part debate with two scientists of the Biologos group, which advocates for theistic evolution. (And not to be confused with the Biologic Institute, which is supportive of intelligent design).

Excerpt:

Throughout their book, Giberson and Collins overconfidently proclaim that Darwinian evolution is a slam-dunk. Thus one reads, “There has been no scientific discovery since Darwin–not one–which has suggested that evolution is not the best explanation for the origin of species” (21-22). No theory is that good. Every theory admits anomalies. Every theory faces disconfirming evidence. Repeatedly readers are informed that mountains of overwhelming evidence support Darwin’s theory and that the authors are “unfamiliar with any premier scientists who reject evolution.” And just so there’s no doubt, in that same paragraph, they reiterate, “There are certainly a few scientists who reject evolution . . . But these are never premier scientists.”

Oh, you reject Darwinian evolution; you can’t be a premier scientist. What counterexample would convince Giberson and Collins to retract such a claim? How about Henry Schaefer’s signature on a “Dissent from Darwin” list? Schaefer heads the computational quantum chemistry lab at the University of Georgia, has published over a thousand peer-reviewed journal articles, and is one of the most widely cited chemists in the world. Then again, Giberson and Collins look askance at this list (according to them, it has too many emeriti professors and not enough biologists). But why engage in such posturing about scientific pecking order in the first place? The issue is not who’s doubting Darwinism, but what are the arguments for and against it and whether they have merit. Giberson and Collins’ constant drumming of mainstream and consensus science is beside the point–science progresses by diverging from the mainstream and by breaking with consensus.

Because Giberson and Collins assert that natural selection is such a powerful mechanism for driving evolution–and one that admits no reasoned dissent–it’s worth recounting here briefly why the intelligent design community is so skeptical of it. It’s not, as theistic evolutionists often suggest, that we have a desperate need to shore up faith and morality and are using ID as our instrument of choice to accomplish that end. Rather, it’s that natural selection is, in essence, a trial and error tinkering mechanism for which all evidence suggests that its power is quite limited. Trial and error works fine when you have something that’s functional and are trying to enhance it or adapt it to a new situation.

But for natural selection, as a trial and error mechanism, to traverse vast swatches of biological function space, we need to see an extended series of small gradual structural changes (under neo-Darwinism, these are genetic mutations leaving effects at the phenotypic level) that continually improve, or at least maintain, function, with evolving functions and evolving structures covarying and reinforcing each other. But we know of no detailed testable (macro-)evolutionary pathways like this in any field, whether in the evolution of living forms or in the evolution of language or in the evolution of technologies. In fact, when we can trace such evolutionary pathways, we find that significant change happens in creative leaps, not via trial and error tinkering.

Everyone who has read Dembski’s opening remarks in this four-part series is raving about the quality of what he’s written. I was hoping to wait for the response before publishing his opening salvo, so we could balance it, but no reply has appeared yet. For me, there is only one issue in the debate about the origin of life: if natural causes can create life from non-life with the time and resources available on the early Earth, then show me the mechanism. That’s all I want to see – the evidence that natural causes can do the creating that the naturalists say that it can do. I don’t want to hear about feelings, possibilities, what God could or couldn’t do, philosophy, what church you attend, your favorite hymn, the way you were raised, your religious experiences, etc. I just want to see you prove that nature can do all the creating that you say it can do.