Evolution

The Smithsonian has a new human origins exhibit, “What does it mean to be human?” specially targeted at swaying student visitors who might doubt Darwinian evolution. The most amusing part of the exhibit proudly explains that evolution predicted we’d lack evidence for evolution; that’s how we know it’s true! That’s right, this is how the nation’s most prestigious natural history museum presents evolution: evolution predicts that evolution is supported both when we do and when we don’t find confirming fossil evidence. Consider the following from the educator’s guide: Misconception: Gaps in the fossil record disprove evolution. Response: Science actually predicts gaps in the fossil record. Many species leave no fossils at all, and the environmental conditions for forming good fossils Read More ›

David Berlinski’s collection of essays, The Deniable Darwin, garnered a favorable review over at Hot Air, where CK Macleod had this to say: The Deniable Darwin collects essays written from 1996 to 2009 mostly on the same general theme: That the insufferable pretensions and aggressive self-certainty of science ideologues prevent us from justly appreciating how much we actually have learned about the natural world, and how wonderfully little that is. He applies his dauntingly well-informed, remorselessly cogent skepticism to several fields of study — theoretical physics, mathematics, linguistics, molecular biology — but it’s his dismantlement of Darwinism that he takes to center stage for a virtuoso recital. Macleod understands that critics of Berlinski are wrong to accuse him “of the Read More ›

Recently I was e-mailed by an individual who had read the book Coming to Peace with Science, by Darrel Falk, president of the BioLogos Foundation. This person was interested in a response to the arguments for human/ape common ancestry in Dr. Falk’s book. Not having read Dr. Falk’s book before, I wrote back that I hadn’t yet read the book but had a strong suspicion that it would argue that shared non-functional (aka “junk”) DNA between humans, apes, and other species is evidence of their common ancestry. This is an extremely common argument from theistic evolutionists–Francis Collins made it in The Language of God (and Collins wrote the foreword to Dr. Falk’s book). Of course in 2010, we’re seeing more Read More ›

Remember the analogy of the two moons I used yesterday to discuss the distribution of SINEs in the mouse and rat genomes? Well, I am going to use it again today, but only for a moment.

Moon Mysteries and the Lunarlogos Foundation

Suppose you are keenly interested in the topography of one of the moons, named Y6-9. Suppose also that the books you first select to read on the topic are popular works, written by “experts” who are “living legends.” As you read through the works, you find paragraphs here and there about how utterly decrepit Y6-9 is, and how this space body exemplifies eons of random events. The authors argue that we already knew all there was to know about that moon back in 1859, and that the evidence demonstrates either that God doesn’t exist or that the deity left the cosmos to itself after the Big Bang.
You find, however, that these books almost totally ignore the findings of the billion-dollar missions sent to the surface of Y6-9 since the 1960s. Indeed, there is next to nothing in them about Y6-9’s actual geology.

So you contact the Lunarlogos Foundation, a Christian group that promotes such books. You tell them that you have a few specific questions about the Y6-9 mission findings. The response you get is that because you are a layman, you would not be able to comprehend the details. Besides, the Lunarlogos folks say, the mainstream experts have spoken authoritatively about the subject and that should be enough for you. As a consolation, though, they send you a CD that has songs that are sung by one of their founding members.

Yesterday I promised that I would show you a mysterious genomic signal, and today I shall fulfill that promise. The previous blog was devoted to describing the linear distribution of LINEs and SINEs along mammalian chromosomal DNA. We saw that L1 retrotransposons tend to be densest in the regions where Alus and Alu-like elements are the least common and vice versa. I included the following figure from an article co-authored by Francis Collins¹ that showed this compartmentalization of LINEs and SINEs along over a hundred million genetic letters of rat chromosome 10:

The blue line indicates the distribution of SINEs along a 110-million base pair interval of rat chromosome 10. (From Fig. 9d of Ref. 1.)

Taxon-Specific Elements: The SINEs Aren’t The Same

Intriguing as this non-random distribution of repetitive elements may be, it gets even more interesting when one realizes that SINEs are specific to taxonomic groups. Each primate genome has distinct subfamilies of the Alu sequence. The mouse genome, on the other hand, has no Alus but it does have three unique SINE families called B1, B2, and B4. While mouse B1 shares some sequence similarity with Alu, it has no relationship to the B2 or B4 elements; the latter two are also unrelated to each other. What then about the rat SINEs along chromosome 10, which were depicted as a blue line? Well, the genome of the rat has one main SINE family called ID, for the “Identifier” sequence. The ID elements have nothing in common at the DNA sequence level with the mouse B1s, B2s, or B4s, and they are wholly dissimilar to Alus.

I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.

Here is an example. While reading the “critique” of Steve Meyer’s book, Signature in the Cell, by Francisco Ayala, a number struck me that I know to be incorrect. The integer that I am referring to is “25,000” and it is claimed to be the known tally of genes in our chromosomes:

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences…

Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.¹ Some of the latter range in length from being quite short–only 20 or so genetic letters–to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.^{2, 3, 4} (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.^{2, 3, 4}

The evolution of antibiotic resistance is typically the result of small changes allowing for survival in a microbe or other organism under special circumstances where the organism faces extremely strong selection pressure due to the presence of some antibiotic drug. In other cases, it is the result of the transfer of pre-existing antibiotic resistance genes from one microbe to another, and the selection of such microbes in an environment containing antibiotics. Even in the first example, evolution does not produce a truly new function. In fact the change produced often makes the microbe less fit when the antibiotic is removed–it reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost Read More ›

The recent front page New York Times article on academic freedom legislation offers a stark reminder that the intelligentsia is very worried about the prospect of teachers gaining academic freedom, as a bill presently in the Kentucky legislature would allow, “to help students understand, analyze, critique, and review scientific theories in an objective manner, including but not limited to the study of evolution, the origins of life, global warming, and human cloning.” From 2008-2009, 12 academic freedom bills were submitted into state legislatures, including Florida, Alabama (2), South Carolina (2), Missouri (2), Michigan, Louisiana, Oklahoma, Iowa, and New Mexico. Now in 2010, there are 3 bills already, including bills in Kentucky, Missouri, and Mississippi. The Kentucky bill contains an excellent Read More ›

In the Texas Republican Party primary this week, voters in one part of the state narrowly rejected pro-teach-the-controversy State Board of Education member Don McLeroy. At the same time, voters in another part of the state (Dallas) dumped anti-teach-the-controversy Board member Geraldine Miller in favor of a candidate who has expressed support for teaching the strengths and weaknesses of evolution.

The most interesting thing about incumbent Geraldine Miller’s remarkable defeat by newcomer George Clayton is the unintentional role the pro-Darwin Dallas Morning News may have played in her downfall.