New Jerry Smith

User Socratism at Theology Web, when he is not speculating about genetic tinkering on the part of pre-Flood Atlanteans, sometimes hits upon a good question.

In this thread, he points out (as best as I can tell, correctly) that mouse and rat cytochrome C are identical to the hypothetical mammalian common ancestor, while primate cytochrome C is the most removed from the mammal common ancestor. It has already been pointed out that cytochrome c is highly conserved, and that it isn't too great a suprise that any mammal is identical on that molecule to the common ancestor. Nevertheless, he makes an excellent point:

Since modern mice, rats, and primates are equidistant from the common ancestor, and since mice and rats have a much shorter generation time than primates, we should see the opposite of what we see. Primates should be closer to the common ancestor, and mice and rats should be further removed.

Is there a good explanation for this? What comes to my mind is the possibility that someone did a poor job hypothesizing the common ancestor's cytochrome. Perhaps they were biased by ideas of a mouse-like ancestor?

Any thoughts?

Coragyps

A couple of non-expert musings until the experts get here:
1) I would think that reconstructing the last common ancestor's cytochrome C would be fairly tricky, and would bet a case of beer that mouse and rat CyC is not identical to whatever it was
2) Primates today have much longer generations than mice, but primates 20 million years ago were small animals with presumably shorter life cycles - and rodents and primates diverged maybe 60 million years ago? Or more?
3) Mutation rates in the DNA for CyC weren't necessarily the same in the mouse-kind and the primates after their split.

And, as you say, a mouse-like ancestor is just what we humans have, if you use the vernacular definition of mouse: a four-legged little scurrying guy. That definition, though, is scientifically useless.

New Jerry Smith

I would tend to agree, but if this chart is correct, then Socratism is correct. I don't know how this chart was compiled, or from where they found the cytochrome-c sequence of the mammalian ancestor. But, if it is correct, then you and I would be wrong in thinking mouse and rat CyC is not identical.

EDIT: It just occurred to me to look on the website where the chart was hosted for clues. Apparently the parent page, http://members.aol.com/BobSBend/ , belongs to a creationist, and there is no specific mention of how the chart was compiled.... it may be that the answer is easier than I thought.

Tom Ames

Short answer: reconstruction of an ancestral sequence is highly dependent on:

• method used (parsimony vs. likelihood)
• model assumed (accelerated vs. delayed transition in parsimony analyses, substitution model in likelihood analyses)
• taxon sampling.

Unless the tree and the assumptions are published with the reconstructed sequences, there's no way of knowing how reasonable they are.

Coragyps

NJS: It may be that the chart is correct, but it's damn sure an odd chart: 21 amino acids selected somehow from the 104 that are in human or chimp CyC, and no explanation of what any of it means that I could find. But it is awfully decent of the author to tell us that wheat and prawns aren't mammals.

Edit to add: Voet & Voet's Biochemistry has the full sequences for about 40 organisms - the first column in your link's table may be residue 4 of mammalian cytochrome C.

theyeti

Looking at the sequences posted there, the differences are too few to yeild a robust phylogeny among the mammals. That's why Cytochrome C data is usually used to derive relationships between larger groupings -- typically class level and beyond. If you'll notice, most mammals differ by only one or a few amino acids. Nevertheless, the changes group exactly how you'd expect them to group if evolution is true. But given that the primates represented there have a whopping 5 changes and rat and mouse have 1 since the hypothetical common ancestor, you're not talking about much of a difference in relative terms.

And the hypothetical common ancestor sequence is just that: hypothetical. It's based on working backwards from an evolutionary scenario given the actual sequences available. Why it's set to be very close to rat and mouse I don't know off hand (it is not identical; there is one mutation, P44A). I assume it comes naturally through phylogenetic assumptions and would make perfect sense if I were to work my way through the tree builidng. But it's senseless to take this as being somehow data that contradicts evolution, because the hypothetical common ancestor is not data in any sense.

Finally, it's well established that there are mutational hot-spots and cold-spots. They are of great relevance when it comes to molecular clocks, but of limited relevance when it comes to phylogenetics. Phylogenies tend to work out fine even if some sequences in some lineages tend to accumulate mutations faster than others. But pointing out faster-than-expected change for such a tiny section of DNA, assuming that's the case here, doesn't prove anything about evolution.

theyeti

Gringo

If all those mammals listed in that chart of the website, including the marsupials and placentals, have descended from a common ancestor within the past 60-70 million years, then it would seem to add support for common descent, wouldn't it? After all, the chimp, human and rhesus monkey are the same. Maybe a whale, a dog, a bovine and a rodent do share a more recent common ancestor than they do with us. What we need in this chart is a platypus

RufusAtticus

I'm in the process of grabbing CYC sequences and building a phylogeny. For now here is a link to CYC at OMIM.

notto

The given chart from BobBend was done by someone who was a frequent poster to theologyonline.com. When asked to reveal his methods at how he determined the hypothetical for the common ancestor, he either refused, or simply said it was done by "eyeballing" the data. When pressed on why he made the particular choices, he refused to answer. The choices were all subjective.

It is only one possibility and was constructed with the end game in mind through fairly invalid methods.

Take it with a grain of salt. You could construct you own through this same "eyeballing" process and come up with whatever you wish the common ancestor to be like.

New Jerry Smith

I did let it get past me that the linked chart was not the complete CyC, but cherry picked parts of it. On the other hand, I checked the list that Bald Ape posted, and they hyp common ancestor was still closest to mouse, rat, and guineau pig. I'd like to know where Bald Ape got his hyp common ancestor.