Do-While Jones and the Pattern of Differences in Cytochrome-C

The Pixie

Well-known member
Not quite Indiana Jones and the Temple of Doom..

A guy who insists he is an IDist and not a creationism (like there is a difference) is citing a paper by Do-While Jones to refute evolution, and more specifically the evidence from cytochrome amino acids sequences, when comparing differences between species.

LOL already exposed you on this one...
Dr. Denton’s Figure 12.1, “The Cytochromes Percent Sequence Difference Matrix” 3, is an abridged version of the 1972 Dayhoff Atlas of Protein Structure and Function Matrix of nearly 1089 entries showing the percent difference between 33 species. Denton’s abridged matrix shows that molecular biologists can easily recognize which cytochrome C sample came from a fish and which came from a mammal.
“However, the most striking feature of the matrix is that every identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of another group. Transitional or intermediate classes are completely absent from the matrix. 4”
Sorry, did I say this is a paper? My bad. This is just a personal web page.

But Do-While is a biologist, right? He does know what he is talking about? No. He is an electrical engineer.

Okay, but he does cite up-to-date science, right? No. His web page list four references, and all are one book, Michael Denton's Evolution: A Theory in Crisis, published 1985. So a book from well over 30 years ago, that presumably references even older science.

But Denton stands by that right? No. Since the book was published, a lot of biologists pointed out it was flawed, and to his credit, Denton changed his position. His later book, Nature's Destiny, in 1998, embraces common descent - though it advocates directed evolution.

So what is wrong with Do-While's argument? It comes down to a fundamental misunderstanding of evolution.

If the existence of cytochrome C in “higher forms” of animals is the result of evolution from a common ancestor, then one would expect to see a logical progression. That is, the cytochrome C of an invertebrate (like a worm) would be slightly different from a bacteria. A “primitive” vertebrate (like a fish) would have those same differences, plus a few more. As you progress along the presumed evolutionary path to amphibians, reptiles, mammals, primates, ending with humans, you should see the changes in cytochrome C accumulate.

He sees it as a progression, which it is. But what he fails to grasp is that modern bacteria and worms are as much the result of four billion years of evolution as we are. To him, bacteria were around first, so modern bacteria must be the same as ancient bacteria, with the same cytochrome-c. Worms were a bit later, so modern worms must have cytochrome-c that is just a bit different from bacteria cytochrome-c. Fish are a bit later still, so all modern fish have cytochrome-c that is a bit more different - but the same for all fish, because they are all fish, right?

No, Do-While. It is not like that.

In reality, bacteria split off from animals a long time ago, and both bacteria and animals have been evolving ever since, and so accumulating differences in the cytochrome-c. It has been a very long time since bacteria and worms diverged, and therefore we expect a relatively large number of differences in their cytochrome-c.

When you understand evolution, the pattern of differences is easy to explain - and is indeed in general terms what evolution predicts. The differences are very well correlated with how long ago the two species diverged.

A simple list of the number of differences compared to human cytochrome-c:
  • Chimpanzee 0
  • Rhesus monkey 1
  • Rabbit 9
  • Pig 10
  • Dog 10
  • Horse 12
  • Penguin 11
  • Moth 24
  • Yeast 38

But to fully appreciate the data, you need to also look at the differences between other species. This can be seen here.

This is the same data Denton had (Dayhoff 1972), and Do-While is therefore citing. Whether Do-While actually looked at the data, I would not like to say...


Active member
Do-While also has an essay on how cladistics is wrong because he can arrange metal brackets in a hierarchy. Or something like that.