My private revenge on the creationists

Who is wise? He who learns from everyone. So said Rabbi Simeon ben Zoma, some 1800 years ago. My private revenge on the creationists is to learn from them what they cannot or will not learn for themselves.

A friend of mine regularly forwards me stuff from a Discovery Institute publication calling itself Evolution News and Views (ENV), although it seems to be devoted to the systematic denigration of each new piece of evidence that enhances our understanding of evolution. Indeed the pretence that the Intelligent Design (ID) movement is anything more than elaborate cover for old-fashioned Separate Creationism is one that grows flimsier with every new issue.

I used to delete these unread, but lately a couple of headlines have caught my eye, and convinced me to start following ben Zoma’s advice. The first of these was back in July, when ENV went, as I wrote, “barking mad” about the fact that Australopithecus sediba seems to have eaten tree bark. This, they claimed, showed that it could not be one of our ancestors, but is an example of a separate Intelligent Design, and should be “relegated to the side of the ledger that’s filled with ape-like non-ancestors.” Leaving aside the question of whether Au. sediba’s high-fibre diet really does help us decide whether we should consider it a grandparent or great-aunt, notice how the very evidence that ENV refers to in support of ID is actually part of one of the most powerful arguments against it. Sediba joins the 20 or so different species intermediate between non-human apes and humans, and its description shows it to have many human-like features. I have no difficulty in acknowledging that ENV is perfectly entitled to consider this creature to be more like a chimp than a human, just as, I expect, they would regard Homo ergaster as more human than chimp, but the implication is the very opposite of what ENV is suggesting. If self-styled Homo sapiens is the product of a separate act of design, then Au. sediba is the product of another. Twenty or so separate designs in the Pliocene, all but one of them now extinct; this doesn’t seem very intelligent.

Now they’ve done it again, taking a paper reporting results that only makes sense in the light of evolution, and, more specifically, of common descent, and managing by a piece of blinkered quote-mining to draw the exact contrary conclusion. The paper in question  (PLoS ONE 7(7): e40861. doi:10.1371/journal.pone.0040861) critically examines the use of what are called microsatellites in the working out of family relationships between species. Microsatellites are very short pieces of DNA, replicated several times over in the DNA of eukaryotes (that means organisms where the cell possesses a separate nucleus, i.e. all organisms more complex than bacteria). They are more vulnerable to change than the rest of the DNA, and as a result are very useful in following recent changes. To quote the first paragraph of the paper,

 As widely used molecular markers, microsatellites have their strength in their high variability [1]. The relative power of the microsatellites over Single Nucleotide Polymorphisms (SNPs) due to the high variability of microsatellites is 4–12 fold for population genetic structure [2], [3], 5–12 fold for association or linkage disequilibrium studies [4] and 10 fold for sibling reconstruction [5].

(SNPs are “single nucleotide polymorphisms”, i.e. the replacement of one of the four “letters”, A, G, C, T, by another.) So we know that microsatellites change faster over time. We also know that it is difficult to sort out family relationships over very long times using conventional DNA techniques, for complex statistical reasons that are well understood.

It therefore makes sense to look very critically at attempts to use microsatellites to sort out relationships between species well separated in time. And here is what they found, quoting from the abstract to the paper:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

(A clade is just any group that includes all the descendants of a particular ancestor. Thus birds are a clade, but dinosaurs are not unless we are willing to call birds dinosaurs. Fish are not a clade, since the split between fish and land vertebrates is more recent than the split between bony fish and sharks, and apes are only a clade if, as I think we should, we include humans among the apes.) Now let’s see what ENV makes of this paper. They quote the abstract, adding their own emphasis, thus:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

And what do they infer?

 There are two ways to interpret this anomaly. One is that microsatellites mutate too fast to maintain the phylogenetic signal. (This is known as a “post hoc rationalization.”) The other is that Darwin was wrong. Data do not show a phylogenetic pattern; they show common design with some variation.

What they infer is the exact opposite of what the paper shows. Firstly, there is no issue of “post-hoc rationalisation”, because the rapid rate of change of microsatellite DNA was already known (I left in the references in my quotation from the paper, just to make this clear). Secondly, and most importantly for our argument, ENV’s own selection from the abstract provides powerful support, if such were needed, for the well established phylogeny. Let’s take their quotation again, and just make a slight change in where we place the emphasis:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

So the data confirm the existence of clades, and match up with the ideas we had formed earlier about how they are related. The “clades more recent than 200 Mya” include flowering plants, birds, mammals, amphibians, bony fishes, and squamata (roughly speaking, lizards and snakes), and microsatellite coverage (the ratio of the number of microsatellites to total amount of DNA) is well correlated within each of these clades, but not between them. Crudely, microsatellite coverage shows that men are more closely related to monkeys than to molluscs, but cannot distinguish the difference between men and molluscs from the difference between men (or molluscs) and mushrooms, because that difference is beyond the range of the technique.

ENV, of course, has its own suggested explanation for this fact:

Design researchers, by contrast, might be surprised at the variations, but not worried. They had no need to predict a phylogenetic pattern. ID advocates could accept quite a bit of variation by epigenetic coding algorithms that respond to environmental cues.

We can now set up a direct competition between the evolutionary and the Intelligent Design explanations, using data in the body of the paper (which I rather suspect that the ENV team haven’t actually read). We do this by comparing a recent clade that provides and inhabits highly variable environments, with an ancient clade that shows much less variation. For example, mammals and gastropods (slugs and snails). If microsatellite cover reflects recent ancestry, mammals should be similar to each other while gastropods (which have been around far longer) should not. If microsatellite cover reflects “environmental cues”, whether the reference is to the internal or external environment of the organism, then mammals should be diverse while gastropods are similar. And the answer is clear. Using the microsatellite cover test, mammals show up as similar, while gastropods don’t.

So yet again, we have an important and interesting paper that strongly confirms, and adds further detail to, the established scientific account, being presented by the self-styled “Intelligent Design community” as evidence against the very things that it establishes.

This post is also available on the BCSE website.

Save Siccar Point: an open letter to Scottish Borders Council

 

Subject: 12/00929/FUL Objection Comment. Addressees prs@scotborders.gov.uk  and ped@scotborders.gov.uk. Cc. Scottish Natural Heritage: anne.brown@snh.gov.uk; Scottish Environmental Protection Agency: Stephanie.Balman@sepa.org.uk; Crown Estates: enquiries@thecrownestate.co.uk; Dunglass Estate: info@dunglassestate.com

Esteemed Councillors,

I write to protest in the strongest possible terms about plans to build a waste pipeline cutting through land immediately adjacent to Siccar Point, which is an integral part of its geological and aesthetic setting.

I had the privilege of visiting Siccar Point this summer. The appearance of the Point itself was familiar to me from illustrations, but the setting, with Old Red Sandstone cliffs exposed to the north, and to the south a beach along which ran the older strata, tilted up on end, was a revelation. Yet it is precisely across this shoreline that there are now plans to build a concrete-encased waste pipe for the disposal of vegetable washings of high organic content.

Siccar Point is the most important single site in the entire history of geology. It is here that James Hutton, prominent member of the Scottish Enlightenment, found the first convincing evidence of deep time, of ongoing cycles of uplift and erosion, the insight central to the newly born science of geology. It features in textbooks the world over. It is a place of pilgrimage not only for professional scientists, but for all who cherish the workings of our planet. It is a unique educational resource, attracting students, scholars, and members of the general public from far and wide, and I must say that for me the experience of visiting it surpassed all expectation.

The entire significance of the location is, that it is the meeting point of the Old Red Sandstone with the much older underlying greywacke, with the latter folded and tilted so dramatically that the originally horizontal strata now lie vertical. These older strata are actually seen to better advantage on the shoreline directly south of the Point, where they present a spectacle of unrivalled majesty and beauty. It is precisely across this shoreline that it is now proposed to build a waste pipeline. I find it incredible that anyone could wish to do such a thing.

There are other, secondary, considerations which in themselves should give pause for thought. How wise is it to run a pipeline of this kind down a steep and unstable cliff? What will the consequences be of erosion and possible exposure, or even fracture, of the pipe? Is it sensible to be discarding such a volume of rotting vegetable matter along this historic coast line, also home to busy holiday resorts, and a playground for young children? Have not serious doubts been expressed about how close the end of the proposed pipeline is to the low water mark? What will the impact be on the marine environment and local fishing of all this added organic matter? Should we, indeed, be disposing of this material as waste, or converting it into a resource by composting? But all of these are, as I said, secondary to the primary concern for the site itself.

My own credentials: I am a former chemistry professor, now honorary senior research associate at Glasgow University. I have been involved in research topics related to geology for over 30 years. My work in this area has been funded by NASA, I have been an associate of NASA’s Astrobiology Institute, and I have served on the editorial board of the journal Origins of Life and the Evolution of Biospheres. Hutton’s work features in my most recent book, From Stars to Stalagmites, as it must in any book that describes the relevant period in the history of science, the fundamentals of geology, or (coming closer to home) the achievements of the Scottish Enlightenment.

Respectfully,

Paul S. Braterman, MA, DPhil., DSc.