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Author Topic:   Human Evolution (re: If evolved from apes, why still apes?)
Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 71 of 128 (455558)
02-12-2008 9:20 PM
Reply to: Message 67 by Wounded King
02-12-2008 8:27 AM


Re: Keeping up with the literature
Indels don't change the overall sequence, though: they shift everything up or down the line, but conserve the sequence except at the location of insertion/deletion. So, whether the similarity is listed as 99% or 95% is largely a matter of viewpoint.
The sequences that were shifted are, in fact, still homologous (shared between chimps and humans).
In terms of gauging evolutionary relatedness, frameshifts are largely misleading, because, even though there is a difference in location, the sequence is still the same. Homology reaches farther than the 95% you give it by incorporating frameshifts. So, skepticfaith's assertion--that we've now found that we're not so close to chimpanzees because the difference is 5%--is flawed.

Signed,
Nobody Important (just Bluejay)

This message is a reply to:
 Message 67 by Wounded King, posted 02-12-2008 8:27 AM Wounded King has replied

Replies to this message:
 Message 72 by Wounded King, posted 02-13-2008 5:09 AM Blue Jay has replied

  
Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 74 of 128 (455724)
02-13-2008 2:42 PM
Reply to: Message 72 by Wounded King
02-13-2008 5:09 AM


Re: Keeping up with the literature
Wounded King writes:
In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.
I guess I have to agree with this: the two ideas kind of delineate the outer boundaries of the argument, don't they?
Wounded King writes:
Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance?
It's not: the two are equal gauges, because they both represent a single change in the genome. A view based on sequence-divergence puts the deletion as more influential, when in fact it represents no more evolutionary distance than the point-mutation.
This is a quote from the article you cited by Britten (PNAS, 2002), which is the only one I have been able to read yet:
It appears appropriate to me to consider the full length of the gaps in estimating the interspecies divergence. These stretches of DNA are actually absent from one and present in the other genome. In the past, indels have often simply been counted regardless of length and added to the base substitution count, because that is convenient for phylogenetics. (emphasis added)
It is convenient for phylogenetics, and it makes more sense when dealing with evolutionary distances. Sequence divergence only shows how different the two species are, not how long they've been separated from one another. Using deletion lengths (as Britten did) to represent how close humans are to chimpanzees would inflate their importance relative to point mutations, making it look like we diverged X+Y mya when, in fact, we diverged only X mya (X and Y >0).
In fact, Britten acknowledges this later in the paper:
More nucleotides are included in insertion/deletion events (3.4%) than base substitutions (1.4%) by much more than a factor of two. However, the number of events is small in comparison. About 1,000 indels listed in Tables 2 and 3 compared with about 10,000 base substitution events in this comparison of 779,142 nt between chimp and human. (emphasis added)
So, a big deletion is still just one deletion, and still happened at one time, even if it removed hundreds of nucleotides of base-pair homology. Deleting 54,773 base pairs in one swoop (or several swoops) is very different from changing 54,773 base pairs slowly over 54,773 separate mutation events. They would have the same end result, and so may represent the same amount of "sequence divergence," as per Britten's standards. But the first could have happened between me and my son (i.e. in 1 generation), while the second probably won't have happened in my evolutionary descendants 51 million years down the road (assuming my lineage lasts that long).
If you then compared these two genes (my son vs evolutionarily-distant descendant) using Britten's sequence-divergence strategy, you would then come to the conclusion that I am more closely related to my 51-million-years-down-the-road descendant than I am to my own son (at least at that locus). Multiple such deletions across the genome would make it even harder.
So, if you're talking just about genetic similarity (as I assume you are), then skepticfaith's estimate is probably closer. But, if you're talking about evolutionary relatedness (which is closer to the topic of this thread), skepticfaith's estimate is an inflation of the distinction between us and chimps.

Signed,
Nobody Important (just Bluejay)

This message is a reply to:
 Message 72 by Wounded King, posted 02-13-2008 5:09 AM Wounded King has replied

Replies to this message:
 Message 75 by Wounded King, posted 02-13-2008 7:36 PM Blue Jay has replied

  
Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 76 of 128 (455834)
02-14-2008 12:17 AM
Reply to: Message 75 by Wounded King
02-13-2008 7:36 PM


Re: Keeping up with the literature
Wounded King writes:
In terms of the topic in the immediate past molbiogirl was specifically talking about genetic similarity.
After another review, I have to concede this point to you. I guess I got a little muddled by reading too fast.
I would agree that for constructing a phylogenetic tree you would probably be better of going with traditional approaches, I'm not sure if anyone has really tried using indels and other forms of copy number variation as a basis for such analyses.Building a phylogeny is not the be all and end all of evolutionary relatedness I would suggest.
I'm not sure I understand what else you think there could be to evolutionary relatedness than phylogeny. After all, phylogenies, when done correctly, are taken to directly represent evolutionary relatedness. Furthermore, the basic definition of "phylogenetics" is the study of evolutionary relationships between organisms.
I guess ecological and behavioral differences are important, too, but these can't really be considered evolutionary distinctions, because dolphins and penguins aren't fish, even though they live in the water and swim like fish.
Anyway, this is all off-topic. Maybe we could start a new thread to discuss genetic factors in evolutionary relatedness. I'm not a geneticist (though I did do undergrad research in proteomics and bioinformatics), but I'm sure there's plenty I could learn from you about genetics and evolution.
Thanks.

Signed,
Nobody Important (just Bluejay)

This message is a reply to:
 Message 75 by Wounded King, posted 02-13-2008 7:36 PM Wounded King has replied

Replies to this message:
 Message 77 by Wounded King, posted 02-14-2008 4:28 AM Blue Jay has replied

  
Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 78 of 128 (456265)
02-16-2008 6:04 PM
Reply to: Message 77 by Wounded King
02-14-2008 4:28 AM


Re: Keeping up with the literature
All I mean is that while classical phylogenetics can tell you plenty about who is most closely related to you and reconstruct an evolutionary history of cladogenesis, it tells you very little about what the actual functional basis is for the differences between one species from another in terms of phenotype.
See, I understand this perfectly. And, this fits right back in with kakip's original topic, and with skepticfaith's continuation thereof.
The differences between us and chimpanzees in behavior and phenotype are the reason we can coexist with the chimpanzees, as opposed to requiring their destruction or assimilation into us as a condition of our rise to the "civilized condition." We didn't have to remove or replace them, because their use of a different habitat and a different way of life (both more suited to their phenotypes) didn't place them as competitors for our niche. To the contrary, we competed with ourselves more than with them.
I think the misconception happening here is that the chimpanzee and the gorilla are relict populations of the lower life-forms from which evolutionists purport our species to have evolved, and that they are therefore mindless brutes who failed to make the transition to human. They are a failure, and we are the success story.
The problem is that the theory of evolution is not anthropocentric in nature. The chimpanzee has evolved from our common ancestor as much as we have, and is therefore equally "advanced," if the term must be used (evolutionists prefer 'derived').
It has been stated by skepticfaith (and refuted by molbiogirl) that chimpanzees are more like our common ancestor than we are. The problem is that the fossil record for chimpanzees isn't as complete as the record for humans, so we can't confidently identify the common ancestor, per se. Australopithecus seems most logical of the fossils we know for sure, because it has facial and cranial features that more closely resemble a chimpanzee's (boxed dental arcade, long canine roots, no nose bridge, larger brow ridge, etc.), but hips, legs and foramen magnum more like us than them.
For the time being, Australopithecus serves as a grand transitional fossil (and will continue to serve as such for some time), because of its mix of human-like and chimpanzee-like traits. However, we may, in the future, find an earlier fossil which shows better the transition from chimpanzee-like ape to Lucy (such fossils have been reported, but their remains are too few to be of diagnostic quality).

This message is a reply to:
 Message 77 by Wounded King, posted 02-14-2008 4:28 AM Wounded King has not replied

  
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