Some molecular evidence for human evolution

You have the cart in front of the horse. They share traits because they share DNA. If you used completely different DNA then they could have completely different traits. Why would a designer need to share traits between separately created species?

We also have the flip side. You could have drastically different DNA and still have the same traits. For example, you could rewrite the anti-codons on tRNA’s which would allow you to have very different DNA sequences that produce the exact same proteins. Talkorigins has a great section on this concept:

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I have done this with the sequences from the L-GULO pseudogene and turned it into a classroom activity (that I just did with my students yesterday actually!). I picked the gene and the sequences pretty much at random. I used human, chimp, gorilla, orangutan, and macaque. It’s only a ~100bp stretch but it shows the human-chimp sister grouping very clearly, and the fact that macaca is the most divergent. It doesn’t resolve the gorilla and orang phylogeny, but that’s what exercise #2 is for (I switch to protein sequences for that).

The point here is that the evidence for common ancestry is very, very easy to find. I understand the concerns above that it doesn’t clarify things like selection, design, and so forth, but, at least in my mind, DNA sequences alone make common ancestry of all living things on earth about as scientifically certain as humanly possible. (And we have a lot more evidence than just DNA sequences.)

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Did you happen to try a chi-square test?

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I did not, because this is a course for non-SCI majors, so I keep it as math-free as possible, just counting basically. This way, they fully wrap their brains around what is happening and they do the analysis fully themselves, not even a calculator. Their eyes really open wide when they see how easy it is to see evidence for common ancestry. People always think that scientific data is just beyond them, totally inaccessible, and lots of it really isn’t!

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Hey Bill, are you going to explain and provide the supporting evidence for your latest assertion?

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Interesting.

One thing that strikes me is that this sequence of 76 nucleotides is very dense in mutations compared to all the other 694 positions. Why is that the case?
Moreover, this same sequence seems to display an abnormally high number of cases of homoplasy, doesn’t it?
IOW, I am wondering what is going on with this particular sequence?

Because this sequence is made up of all the sites in those genes that have relevant mutations, it’s not an actual 76bp sequence within the 694bp. Read the OP again.

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Thanks.

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Ok, we expect a certain amount of cases of homoplasy but do we expect such a high level of cases, in this case 22 out of 694 positions? This level seems extraordinary high to me, doesn’t it?

I can’t answer for what seems extraordinarily high to you. But no, it isn’t high. Let’s remember that there are only 4 possible states at any position. Given the rarity of transversions, it might be accurate to say that there are only two likely states.

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I think it makes an excellent case for common ancestry, but does it make a strong case for universal common descent, or in your words “common ancestry of all living things on earth”? Many creationists would agree with a significant amount of common ancestry, I think, but disagree that it is truly universal. So do scientists have a sense of how universal it is? In other words, has there been enough tests like what you and @John_Harshman have done across not only multiple sequences in the human genome compared to apes and monkeys, but across the entire “tree of life”?

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Yes, there has, though in fact the deepest comparisons use protein sequences rather than DNA sequences. Still, the difference between what creationists are willing to accept and what’s accessible through DNA sequences is still quite large.

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According @glipsnort’s article at 32, the sum of G-C, A-T, A-G/G-T mutations should be roughly equal to the number of transitions mutations (C-T or A-G). So, in your example, on the 22 cases of homoplasy, we would have expected to see about 50% of transitions, not 100% as it is the case. What is the explanation for this strange observation?

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Several explanations: first, transitions are more likely to be silent than transversions and, if non-silent, more likely to connect similar amino acids; second, the transition bias in mitochondrial DNA is greater than in nuclear DNA; third, you will note that most of the changes are C-T, because there’s a base composition bias making G rare; fourth, transversions are often complicated by subsequent transitions that make them no longer informative for our sample — see, for example, the second to last site.

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Fifth, you need two transversions to get into this list, so the occurrence would only be a quarter as common as transitions, even if transversions were half as common as transitions.

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Very much so. As John noted, when DNA identities approach the statistically undetectable level, protein identities/similarites are still there.

I’ll add that when the protein identities/similarities poop out, there remain structural homologies. Universal common ancestry predicts that we’ll find a lot more of those in the future.

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This is surprising to me, mostly because it seems like a lot of work (both sequencing and the comparison). Do you (or @Mercer or @NLENTS or anybody else) know of any good seminal work reviewing this (establishing universal common ancestry through DNA/Protein sequences) that you could point me towards? I’d like to dig into it a little bit more. As a non-expert, sometimes it’s nice to get a peak inside some of the major results of another field.

For some ribosomal RNA sequences used to infer the deepest phylogenies, they actually do use the DNA sequences(as they would be directly complementary to RNA), because even at these ages ribosomal RNA sequences are decently well conserved. For example, extant bacterial 23s ribosomal RNA sequences have roughly 55-60% sequence identity to extant archaeal ribosomal sequences.

In an attempt to try to show some evidence for universal common descent, and inspired by a blogpost by evograd, almost a year ago I inferred a bacterial, and an archaeal tree using 23s ribosomal RNA sequences. What I wanted to try to show is that, without using outgroup rooting(thus forcing the result), internal nodes in the two trees(inferred independently of each other, using midpoint rooting) still exhibit ancestral convergence. The idea is that if bacteria and archaea really did evolve from a common ancestor, as we go deeper back in time towards the approximate root of each tree, the sequences should become more similar, both with respect to sequence identity, and by alingment scores.

That does indeed appear to be the case. I never finished aligning up all my sequences. I don’t do this professionally so did a lot of copy-pasting into browser windows using online tools to infer trees and get alignment scores, and I still have hundreds of alignments to do, so forgive me if I won’t finish this up anytime soon. But here is a screenshot of a preliminary result:


Alignment scores go from lower=more green, to higher=more red.

Here are the bacterial and archaeal trees with labeled nodes.

The root nodes for the trees are N1 for both. As you can see, alignment scores between nodes in each tree become progressively more red in color as we move closer to the roots of each tree. Interestingly, the particular data set I had collected seems to imply that the true root of my bacterial RNA tree lies closer to node N2(it gets ever so slightly better alignment scores to archaeal sequences), than the midpoint root node N1.

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