Science and Culture Today | Page 1271 | Discovering Design in Nature

Update: On May 4, 2009, The New York Times, perhaps unsurprisingly, came out with a story casting the swine flu as an example of evolution, titled “10 Genes, Furiously Evolving.” Similarly, the staunchly pro-evolution site LiveScience.com has an article on the swine flu that opens by mocking Darwin-skeptics, stating: “Anyone who thinks evolution is for the birds should not be afraid of swine flu. Because if there’s no such thing as evolution, then there’s no such thing as a new strain of swine flu infecting people.” As is discussed in Luskin’s piece below, such a claim is a cheap-shot that completely mis-states and misrepresents the position of Darwin-skeptics. A few years ago, the media was abuzz over the scare of Read More ›

In a recent blog post titled “Truckling to the Faithful: A Spoonful of Jesus Helps Darwin Go Down,” University of Chicago biologist Jerry Coyne firmly and publicly rejects the attempts by Darwin-lobbying organizations like the National Center for Science Education (NCSE) to convince the American public that Darwinism and Christian faith are compatible. In case these organizations really want to know my opinion, I’m on Jerry’s side. Except that I’m only mostly on his side. You see Jerry is spot on when he writes But his other over-generalizations about Science and Religion being incompatible are, of course, extremely over-simplified. If only Science (capital S) and Religion (capital R) actually existed as such abstractions, Jerry would have the beginnings of an Read More ›

Note: This is Part 4 in a series reviewing Jerry Coyne’s Why Evolution Is True. Read Part 1 here, Part 2 here, and Part 3 here.

So evolutionary theory needs better evidence than the fossil record can provide. Coyne correctly notes: “When he wrote The Origin, Darwin considered embryology his strongest evidence for evolution.” Darwin had written that the evidence seemed to show that “the embryos of the most distinct species belonging to the same class are closely similar, but become, when fully developed, widely dissimilar,” a pattern that “reveals community of descent.” Indeed, Darwin thought that early embryos “show us, more or less completely, the condition of the progenitor of the whole group in its adult state.”¹⁵

But Darwin was not an embryologist. In The Origin of Species he supported his contention by citing a passage by German embryologist Karl Ernst von Baer:

Having one’s position repeatedly mischaracterized by those who refuse to be corrected is an annoyingly common problem for intelligent design. While some people are just sincerely mistaken in thinking that it’s creationism, some — like Ken Miller — know better, but as UK columnist Melanie Phillips points out in “Creating an insult to intelligence,” it’s beneficial to damage people’s reputations by confusing the two:

Intelligent Design not only does not come out of Creationism but stands against it. This is because Creationism comes out of religion while Intelligent Design comes out of science. Creationism, whose proponents are Bible literalists, is a specific doctrine which holds that the earth was literally created in six days. Intelligent Design, whose proponents are mainly scientists, holds that the complexity of science suggests that there must have been a governing intelligence behind the origin of matter, which could not have developed spontaneously from nothing.

We often hear from Darwinians that the biological world is replete with examples of shoddy engineering, or, as they prefer to put it, bad design. One such case of really poor construction is the inverted retina of the vertebrate eye. As we all know, the retina of our eyes is configured all wrong because the cells that gather photons, the rod photoreceptors, are behind two other tissue layers. Light first strikes the ganglion cells and then passes by or through the bipolar cells before reaching the rod photoreceptors. Surely, a child could have arranged the system better — so they tell us.

The problem with this story of supposed unintelligent design is that it is long on anthropomorphisms and short on evidence. Consider nocturnal mammals. Night vision for, say, a mouse is no small feat. Light intensities during night can be a million times less than those of the day, so the rod cells must be optimized — yes, optimized — to capture even the few stray photons that strike them. Given the backwards organization of the mouse’s retina, how is this scavenging of light accomplished? Part of the solution is that the ganglion and bipolar cell layers are thinner in mammals that are nocturnal. But other optimizations must also occur. Enter the cell nucleus and “junk” DNA.

Only around 1.5 percent of mammalian DNA encodes proteins. Since it has become lore to equate protein-coding regions of the genome with “genes” and “information,” the remaining approximately 98.5 percent of DNA has been dismissed as junk. Yet, for what is purported to be mere genetic gibberish, it is strikingly ordered along the length of the chromosome. Like the barcodes on consumer items that we are all familiar with, each chromosome has a particular banding pattern. This pattern reflects how different types of DNA sequences are linearly distributed. The “core” of a mammalian chromosome, the centromere, and the genomic segments that frame it largely consist of long tracks of species-specific repetitive elements — these areas give rise to “C-bands” after a chemical stain has been applied. Then, alternating along the chromosome arms are two other kinds of bands that appear after different staining procedures. One called “R-bands” is rich in protein-coding genes and a particular class of retrotransposon called SINEs (for Short Interspersed Nuclear Elements). SINE sequence families are restricted to certain taxonomic groups. The other is termed “G-bands” and it has a high concentration of another class of retrotransposon called LINEs (for Long Interspersed Nuclear Elements), that can also be used to distinguish between species. Finally, the ends of the chromosome, telomeres, are comprised of a completely different set of repetitive DNA sequences.

This week Inside Catholic republished an absolutely brilliant essay by Discovery Institute Senior Fellow Benjamin Wiker on the problem of evil. This essay is one of the most thoughtful replies to the problem of evil — that the existence of evil evidences against God’s existence — I’ve seen packed into a short essay. It is a must read. Wiker describes how, in a feat of fuzzy thinking, evolution typically plays into dialogue on the problem of evil. Evolutionary answers to the problem, he argues, are more likely to do away with evil than explain it. And among the many important questions Wiker poses is whether we really want all evil purged from the earth. Take a look to see his Read More ›

In the Darwinist repertoire, a standard response to evidence of design in the genome is to point to the existence of “junk DNA.” What is it doing there, if purposeful design really is detectable in the history of life’s development? Of course this assumes that the “junk” really is junk. That assumption has been cast increasingly into doubt. New research just out in the journal Nature Genetics finds evidence that genetic elements previously thought of as rubbish are anything but that. The research describes tiny strands of RNA, previously thought to be junk, that now turn out to play a role in gene expression. Another finding by Dr. Geoff Faulkner shows that “retrotransposons,” a further variety of “junk” as the dogma previously taught, play a similar role.

Nearly half of the mammalian genome (less than 45 percent) is comprised of DNA sequences thought for decades to be but evolutionary flotsam and jetsam or junk: retrotransposons. Found along every one of our chromosomes, retrotransposons mobilize within our cells via RNA copies, copies that are then converted into DNA and afterward pasted into different DNA sites. To be sure, the vast majority of these “jumping gene” duplicates, well over a million elements, appear to be little more than pseudogenes, defective images of master templates that merely drift by mutations into a phylogenetic oblivion.

Retrotransposons appear to fit the neo-Darwinian story perfectly. First, the master templates of these elements seem to serve no other purpose than to promote their own replication at the expense of the cell, and so, by the criteria of Richard Dawkins’s 1976 book The Selfish Gene, retrotransposons are selfish genes par excellence. Second, the DNA progeny of such “endogenous viruses” are without a doubt marred in various ways, as just mentioned. Relative to the original, in other words, they are junk. Third, a retrotransposon inserted into a chromosome can disrupt normal gene functions, and mutations due to these sequences have long been detected. Fourth, only a comparative few retrotransposons are conserved across different groups of mammals, with most of the DNA families being restricted to certain families, genera, or even species. Humans and mice as well as mice and rats can readily be separated solely on the basis of their retrotransposon profiles. So the bulk of these sequences do not merit being retained by natural selection.

Note: This is Part 3 in a series reviewing Jerry Coyne’s Why Evolution Is True. Read Part 1 here and Part 2 here.

Coyne goes on to discuss several “transitional” forms. “One of our best examples of an evolutionary transition,” he writes, is the fossil record of whales, “since we have a chronologically ordered series of fossils, perhaps a lineage of ancestors and descendants, showing their movement from land to water.”⁹

“The sequence begins,” Coyne writes, “with the recently discovered fossil of a close relative of whales, a raccoon-sized animal called Indohyus. Living 48 million years ago, Indohyus was… probably very close to what the whale ancestor looked like.” In the next paragraph, Coyne writes, “Indohyus was not the ancestor of whales, but was almost certainly its cousin. But if we go back 4 million more years, to 52 million years ago, we see what might well be that ancestor. It is a fossil skull from a wolf-sized creature called Pakicetus, which is bit more whalelike than Indohyus.” On the page separating these two paragraphs is a figure captioned “Transitional forms in the evolution of modern whales,” which shows Indohyus as the first in the series and Pakicetus as the second.¹⁰

Gary Rhoades at AAUP responded to my original post. My own response is below the fold.

Dear Mr. Crowther,

Apparently patience is not one of your stronger virtues, at least not in this case. If you were really interested in my response, or in the position of the AAUP, you might have had the courtesy to give me a reasonable amount of time to respond to your letter below (which came to me at 3:33p.m. EST today, whereas your posting below was 1:24 p.m today, though the time zone is not posted).

Upon returning to my emails late this afternoon, after addressing some other pressing matters earlier in the afternoon, I come to find that you have already posted the following on your organization’s website:

He pastes in this blog post.

Friday in Washington, D.C. The American Enterprise Institute (AEI) hosted an event titled “Genes, Neuroscience, and Free Will.” The panel, which discussed whether new findings in neuroscience and genetics have destroyed our notion of free will, consisted of James Q. Wilson (Pepperdine), David Brooks (New York Times), Charles Murray (AEI), Sally Satel (AEI), and moderator Christina Hoff Sommers (AEI). I won’t bother to record the differing views of the panelists, for their differences were very few and very far between. Essentially, they all argued that we have an innate sense of free will and that findings in genetics and neuroscience have not undermined it because: (1) sure, genes determine behavior, but not 100%; often the environment contributes to our behavior Read More ›