Four comments on DNA and evolution, with references

As usual on Twitter, it’s possible to gallop through many claims which take a wretchedly long while to unpick, if they are not referenced.

Here’s an unpicking of some Tweets from @JamesPlaskett to @ergrieve :

@JamesPlaskett 11 August

a) similarity greets the eye reflected in blueprint. Why should that tell u anything new?

b) Some simple organisms have more DNA …than humans, e.g snails + goldfish. That confounds the argument for common descent

c) Some animals look + behave very similarly whilst showing enormously differing DNA, e.g. frogs. There are some 3,000 types, all v. froggy but DNA differs more than that between bats + blue whales.

d) If the genomic similarity did show common ancestry it would of itself say nothing of how they split.

Seatbelts on, everyone:

a) similarity greets the eye reflected in blueprint. Why should that tell u anything new?

DNA & other genetic evidence shows similar DNA in similar creatures, and the greater the bodily (phenotypic) similarity, the greater the genetic similarity. This is certainly what you would expect from evolutionary standpoint, but it’s not clear what you would expect from other standpoints.

Yet, sequencing studies also show a branching tree in non-functional elements, the parts of the genome that are not part of the blueprint, and shows the same tree in those bits of DNA which contribute to the less vital parts of proteins, all of which can wander apart by genetic drift. The new DNA story of the evolution of the cytochrome c protein matches entirely the old amino-acid-sequence story:
http://www.ncbi.nlm.nih.gov/pubmed/181584

If rRNA is at all relevant, we have had the most detailed tree yet produced using base sequences:
http://www.zo.utexas.edu/faculty/antisense/downloadfilestol.html

I think that is just stunning.  This evidence of molecular drift is very highly supportive of the branching tree of evolution, and is impossible to account for by any process involving design/creation (which can’t explain why there are non-functional parts of DNA at all, let alone why tiny differences are found in them in similar species).

Summary: http://phylointelligence.com/genetics.html

b) Some simple organisms have more DNA …than humans, e.g snails + goldfish. That confounds the argument for common descent

“More DNA”: does that mean the number of chromosomes? We don’t understand everything about why different organisms have different numbers of chromosomes (the karyotype), but what we do understand I think is completely consistent with common descent.

Carp typically have 50 chromosomes. Goldfish have 100. This seems a straightforward instance of polyploidy (genome duplication), of no great significance. [Polypoidy seems important in speciation events, and may confer selective advantages, like greater body size.] There is certainly no significance in comparing the goldfish number of 100 to the human number of 46.

‘Snails’ are a big group, and not all of them have more chromosomes than 46. Numbers I have found range from 14 to 56; one garden snail, Helix aspersa, has 56, while another, Cepaea nemoralis, has 44. Molluscs in general seem to have started with 13, and polyploidy and other rearrangements have produced the range we now see. Again, I’m not sure what significance is being read into these findings.

Karyotypes, far from contradicting common descent, are often helpful in confirming relatedness inferred from other evidence (e.g. most great apes have the same chromosome number, 48; most carp have 50). The exceptions also support common descent: the goldfish karyotype is clearly derived from the basic carp karyotype; they don’t have 50 new and original chromosomes.

The best example of karyotype analysis supporting common descent is, why do humans have 46 chromosomes, while chimps have 48, if we are supposed to be so closely related? Yet human chromosome 2 bears all the hallmarks of being made out of two other ape chromosomes, including having an ‘endpiece’ (telomere) in the middle. The simplest explanation is that our set of 46 comes from a common ancestor with apes which had 48. There’s a detailed discussion here:

http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/

Analysis has been done, reconstructing family trees based on chromosome arrangement, similar to those done with cytochrome c and rRNA sequences. Here’s one for molluscs:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194838/

So, chromosome numbers very much support the evolutionary story about common descent.

c) Some animals look + behave very similarly whilst showing enormously differing DNA, e.g. frogs. There are some 3,000 types, all v. froggy but DNA differs more than that between bats + blue whales.

This point I find puzzling: I haven’t been able to find it made and explained elsewhere (is it original to HJP?), despite spending some time searching online, so I’m going to have to do some reconstruction.

This point is based on some sort of quantificition of the range of ‘differing DNA’, but I’m not sure if that’s a claim about karyotypes or genomes.

If it’s a claim about the genome, I can’t find any statistics about the ranges among frogs and mammals. Frankly, not that many species have had their whole genome sequenced. The genome sequence commented on here:

http://newscenter.berkeley.edu/2010/04/29/xenopus_genome/

shows that frogs fit in family tree of evolution, and have many commonalities with other classes of organism, in support of the idea of common descent.

If it’s a claim about karyotypes: the range of diploid chromosome counts among bats is between 16 and 50; the number for whales is generally 44 with a few 42s. The range for frogs is something like 14-54, as far as I can tell. The claim that frog karyotypes are importantly more diverse than are those of mammals is not supported.

http://bentley.tosm.ttu.edu/personnel/RJBaker/Publications/112-Karyotypic%20evolution%20in%20bats-Baker%20and%20Bickham-1980.pdf

http://www.tandfonline.com/doi/abs/10.1080/03749444.1981.10736629#.UhHo1W07yP8

But let’s assume that it’s true, that karyotypes are more different among frogs than among mammals. Evolution of chromosome arrangements takes time; we might expect this process to have produced a greater range in frogs for that reason alone (last common ancestor of all frogs was maybe 200 million years ago, LCA of bat/whale=?60mya).

Also, from what we can see, “evolutionary changes in chromosome numbers have taken place about twenty times faster in mammals than in frogs”, so we’re catching up! That also fits your intuitions based on the overall differences in body form of mammals and frogs.

http://en.wikipedia.org/wiki/Frog#Evolution http://www.pnas.org/content/71/8/3028.full.pdf

Just counting chromosomes tells you nothing about how different the actual genes are, of course. Polyploidy does not necessarily result in any differences in form or behaviour. Frogs which differ in their chromosome number can be very difficult to tell apart.

http://munews.missouri.edu/news-releases/2011/1227-frogs-use-calls-to-find-mates-with-matching-chromosomes-university-of-missouri-researchers-find/

So, if I’ve understood the point being made, I suggest this isn’t a line of argument helpful to the anti-Darwinian camp. If I’ve misunderstood, explanations and/or references to any and all of the original data are invited.

[By the way, the original claim said “800 types of frog”, now we’re up to 3,000, but the best estimate for the number of species of tail-less amphibian (‘frogs and toads’) I still think is 5,000.]

d) If the genomic similarity did show common ancestry it would of itself say nothing of how they split.

In case of chromosomal arrangements, it tells us a lot about how they might have split. Species with different chromosome arrangements will likely not be interfertile. Agreed, it’s hard to demonstrate natural selection using DNA, but observed mutation rates in DNA fit entirely what we need to provide the raw material of natural selection (e.g. Nilssen and Pelger 1994 see earlier post: https://minorityattack.wordpress.com/2013/08/03/jamesplaskett-dialogue-of-the-deaf-pt-2-points-of-difference/).

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