Protein sequences, homology and creationism

I came across a creationist (sensu lato) blog that I’d not noticed before: Todd’s Blog (subtitled It is the glory of God to conceal a matter; to search out a matter is the glory of kings. (Prov. 25:2) just so you know where he’s coming from).  In an amusing posting, he’s discussing the signalling protein Notch, following up on a posting by another blogger – Quintessence of Dust – Deep homology and design: why Notch?).  Of course, Notch is widely found across taxa, and I suppose is a classic evidence of evolution (it was originally identified in Drosophila, where the original mutants identified caused notching of wings).  As Todd points out, it’s strictly speaking incorrect to say that different taxa have the same gene: he correctly says that all these taxa in which Notch has been identified actually have homologous genes.

Here’s where he goes a little off track: he describes homology as similar.  In actual fact, the term homology carries with it the sense of similarity as a consequence of shared ancestry.  See for example the Wikipedia entry for homology (biology).

Strange really. He very conveniently includes a diagram which illustrates the ancestry of various Notch homologues (see below).

A phylogeny of Notch homologues

A phylogeny of Notch homologues

What’s interesting here is how Todd wanders around the subject of shared ancestry:

I reject the notion of functional requirement and historic contingency, so that leaves the preference of a designer. The question is why? For what purpose did God arrange Notch proteins in that particular pattern?

(He’s quoting another blogger’s three possible explanations: that it’s the only functional option, it’s contingency, and that it reflects the action of a creator.)  In point of fact, the small section of sequence alignment Todd presents is probably not too helpful: generally such sequence alignments reveal segments of sequence which are more conserved that others.  These conserved segments reflect function: they are conserved because their sequence is constrained by function: change an amino acid residue and you alter the shape or biochemical characteristics of that region of the protein and affect its function.

So, strangely, Todd’s making an argument for evolution here: he’s noting homology between protein sequences of different taxa, shows how these sequences can be assembled diagrammatically to reflect the evolutionary relationships between taxa, but then chucks all that away because it conflicts with his prior beliefs.  Todd goes on to say:

At this point, someone usually raises the idea that God would be deceptive if He created things to look like evolution if they didn’t really evolve. There’s lots of responses to that, but I’m going to stick to the theme and think more carefully about proteins. The truth is that the neat, clean pattern above is something of a rarity in protein homology. More often than not, the pattern of similarities observed in proteins does not make much sense in terms of organismal evolution.

I don’t think he’s correct here: the majority of cases I see in the literature is of protein sequence similarity that does make sense in evolutionary terms.  Indeed, cases where this isn’t the case (for example because of horizontal gene transfer) are flagged up because they are so unusual.  It’s a shame Todd sees the evidence but discards it in favour of superstition.

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  1. barriejohn’s avatar

    Hello, Bob. Nice to have you back!

    I actually knew people who believed that God put the dinosaur bones in the earth to test men's faith! Many also believe that when He created the universe He gave it an "artificial age", and that rock layers were created with the "appearance" of having been laid down over millennia. (This is because the alternative theory, that processes which take thousands of years today could have occurred almost overnight in the past, is so palpably unbelievable – but you've got to admire their cheek!). How on earth could you possibly have any trust in a "God" who stooped so low as to use deception on this scale? The verse which this guy uses on his blog, attributing to God such blatantly human characteristics, is just another indicator that the God of the Old Testament was created in man's image, and not vice versa!!

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    1. GrumpyBob’s avatar

      Yes, good to be back – apart from a 2 week break without internet access, work seems to have taken over my life lately.

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    2. barriejohn’s avatar

      I had a dear friend who was a geologist and soils engineer, and also a keen Anglican (sadly he died of leukaemia aged only 51, in 1997), and he used to mock the fundamentalists whenever a real poser presented itself by saying: "The fairies did it"! However, I came across a more ludicrous explanation than that just recently when looking into the Catholic Church's views on relics at Catholic Answers (a site I would recommend everyone to visit – http://www.catholic.com ). Some poor soul had (supposedly) sent in a question asking how Enoch, Elijah and Mary had been taken up into heaven, and after a long discussion of all the theological implications of this wondrous but mysterious process, the "expert" rounded off his piece by saying: "But God can do what He wants"! Oh well then, let's dispense with common sense altogether, and just make it all up as we go along, since there's no logic or reason to any of it after all!!

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