Science and Culture Today | Page 1272 | Discovering Design in Nature

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 ›

[Note: For a more comprehensive defense of Ben Stein’s documentary Expelled: No Intelligence Allowed, please see: NCSE Exposed at NCSEExposed.org] Where was the American Association of University Professors when Richard Dawkins led an unruly internet mob to get Ben Stein’s invitation to speak at the University of Vermont rescinded? They were stone cold silent as Stein was kicked to the curb by UV president Daniel Fogel, at the behest of Dawkins and other intolerant Darwinsts. Now the AAUP has the nerve to issue a statement warning schools not to rescind invitations to outside speakers. General Secretary Gary Rhoades writes: The opportunity to be confronted with diverse opinions is at the core of academic freedom, which is vital to a free Read More ›

Anyone who raises doubts about evolution in public discussions with non-scientists knows the automatic response you always get from the Three Monkeys crowd. Hands wrapped tightly over eyes, ears, and mouth, they chant: See no evil, hear no evil, speak no evil — about Darwin!

That’s not exactly how it comes out. People will say things more like: But science has spoken! Scientists say! Science wins! Which sounds reasonable at first, until you reflect that it’s a little like a Roman Catholic fending off some challenge to his faith by pointing out that 98 percent of Catholic priests agree with Catholic doctrine, and who knows more about Catholicism than Catholic priests? So it must be true. (Or substitute rabbis and Jewish doctrine, pastors and Protestant belief, etc.) As James Le Fanu smartly notes in his new book Why Us? How Science Rediscovered the Mystery of Ourselves (Pantheon), there is a similar circularity to the “Scientists say!” case for Darwinian dogma:

The commitment to Darwin’s materialist explanation of the living world would, in time, become a qualification requirement for all who aspired to pursue a career in biology — where to express doubt (at least publicly) was tantamount to confessing to being of unsound (or at least unscientific) mind.

I’ve been writing this week in praise of Dr. Le Fanu’s extremely lucid, readable, and unapologetic narration of Darwinism’s increasingly obvious failure to account for the evidence of science, with an emphasis on recent advances in our knowledge about the brain and the genome. Then why is the meaning of these advances ignored, greeted with a great, booming silence?

Read Part I here

Jerry A. Coyne is a professor in the Department of Ecology and Evolution at The University of Chicago. In Why Evolution Is True, he summarizes Darwinism–the modern theory of evolution–as follows: “Life on earth evolved gradually beginning with one primitive species–perhaps a self-replicating molecule–that lived more than 3.5 billion years ago; it then branched out over time, throwing off many new and diverse species; and the mechanism for most (but not all) of evolutionary change is natural selection.” ¹

Coyne further explains that evolution “simply means that a species undergoes genetic change over time. That is, over many generations a species can evolve into something quite different, and those differences are based on changes in the DNA, which originate as mutations. The species of animals and plants living today weren’t around in the past, but are descended from those that lived earlier.”²

According to Coyne, however, “if evolution meant only gradual genetic change within a species, we’d have only one species today–a single highly evolved descendant of the first species. Yet we have many… How does this diversity arise from one ancestral form?” It arises because of “splitting, or, more accurately, speciation,” which “simply means the evolution of different groups that can’t interbreed.”³

We have a 2 year old, Saul, who is very attached to his comfort jacket. It’s like a security blanket for him, blue and quilted and thoroughly stained. He doesn’t wear it, since it is too small for him by now anyway. He holds it and sleeps with it, and if you try to take it away from him when he’s in bed — say, to put it in the laundry — watch out. He will be extremely ticked off, crying, fussing.

In an important new book, Why Us? How Science Rediscovered the Mystery of Ourselves (Pantheon), British physician and historian James Le Fanu speculates that Darwinism works that way for many people. It’s a “comfort blanket,” explaining everything about living creatures in tidy materialist terms without having to appeal to mysterious, unknowable forces outside nature. Maybe that’s why scientists and laymen alike get so very upset and even abusive when you try, however gently, to tug it out of their arms.

Darwinism hasn’t been aired out or laundered in about 150 years. It’s a closed loop, effectively unquestionable, despite the fact that major chunks of biological evidence are against it. Le Fanu, about whom I’ve been writing this series, focuses on DNA and the human brain. Darwinism stands for the belief that everything can be explained in natural terms, but these two features of biology unyieldingly defy such comforting explanations.

Consider the Hox “master” genes that determine the spatial configuration of the front and back ends of creatures as diverse as frogs, mice, and humans. The Swiss biologist Walter Gehring showed that “the same ‘master’ genes mastermind the three-dimensional structures of all living things….The same master genes that cause a fly to have the form of a fly cause a mouse to have the form of a mouse.” Stephen Jay Gould admitted the “explicitly unexpected character” of this discovery.