science

Remember Ida? The fossil hailed as the “eighth wonder of the world” whose “impact on the world of palaeontology” would be like “an asteroid falling down to Earth”? She was promised to be “the link that connects us directly with the rest of the animal kingdom.” She was touted on a History Channel / BBC documentary, but then there was the bust. Well, Ida’s critics have now gotten around to publishing technical articles critiquing the hyped view promoted to the public last year. A recent news release at the University of Texas, “Recently Analyzed Fossil Was Not Human Ancestor As Claimed, Anthropologists Say,” explains: A fossil that was celebrated last year as a possible “missing link” between humans and early Read More ›

We’ve recently seen a lot of dialogue between proponents of intelligent design and critics of Stephen Meyer’s book Signature in the Cell. For example, Richard Sternberg has a fascinating series that uncovers some hints at function in SINE elements through unexpectedly conserved patterns that contradict the standard phylogeny (see Part 1, Part 2, Part 3, and Part 4). Or, there’s Paul Nelson’s rejoinder to Jeffrey Shallit on whether the weather provides an example of natural processes producing specified and complex information. There’s also Stephen Meyer’s response to Francisco Ayala, as well as responses to Ayala from Jay Richards and David Klinghoffer. I recently decided to jump into this fray, publishing two articles in the latest issue of Salvo Magazine defending Read More ›

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 ›

Ever since Thomas Nagel selected Signature in the Cell as one of 2009’s best books, the Times Literary Supplement has had a vigorous back and forth in its letters section. The last salvo published was by Loughborough University chemistry professor Stephen Fletcher. The response below was submitted by Stephen Meyer to TLS, but they opted not to publish it. To the Editor The Times Literary Supplement Sir–I see that the Professor Stephen Fletcher has written yet another letter (TLS Letters, 3 February, 2010) attempting to refute the thesis of my book Signature in the Cell. This time he cites two recent experiments in an attempt to show the plausibility of the RNA world hypothesis as an explanation for the origin 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}

For over a decade, mathematician Jeffrey Shallit has been an outspoken critic of intelligent design. Recently, in a series of blog posts, he has attacked Stephen Meyer’s book Signature in the Cell (SITC) for what he sees as a variety of shortcomings. Some of Shallit’s criticisms merit careful attention, which we’ll present here in weeks to come.

Other criticisms, however, are fluffy confections, failing to achieve even the slightness of what Hume called “mere cavils and sophisms.” Let’s look at one such bonbon of sophistry, Shallit’s claim that weather forecasting represents a devastating counterexample to SITC’s argument that complex specified information is, universally in human experience, produced by a mind or intelligence.

I’ve followed the back and forth between Francisco Ayala and Steve Meyer with interest. I happened to have just read Meyer’s book Signature in the Cell when I first saw Ayala’s commentary/review on it at the Biologos Foundation website. My initial response was that Ayala obviously hadn’t read the book, and, as a result, made some embarrassing mistakes that any reader of the book would recognize.

Darrell Falk at the Biologos Foundation was apparently responsible for inviting Ayala to comment on Meyer’s book, and has been drawn into the debate.

He published the first part of Meyer’s response to Ayala, but not without first offering his “background comments” about the debate. (I think David Klinghoffer has said what needs to be said about that.) The Biologos Foundation is committed to the “science-and-religion dialogue.” In my opinion, however, they have a peculiar way of fostering dialogue.