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Author Topic:   Human - Chimp split 4 million years ago?
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 1 of 33 (386872)
02-24-2007 11:17 AM


Study moves chimp-human split to 4 million years ago
quote:
Chimpanzees and humans split from a common ancestor just 4 million years ago -- a much shorter time than current estimates of 5 million to 7 million years ago, according to a study published on Friday.
The researchers compared the DNA of chimpanzees, humans and our next-closest ancestor, the gorilla, as well as orangutans.
They used a well-known type of calculation that had not been previously applied to genetics to come up with their own "molecular clock" estimate of when humans became uniquely human.
"Assuming orangutan divergence 18 million years ago, speciation time of human and chimpanzee is consistently around 4 million years ago," they wrote in their study, published in the Public Library of Science journal PLoS Genetics, available online at
http://genetics.plosjournals.org/ ... /journal.pgen.0030007 (note - I've shortened the link)
Just last May, David Reich of the Broad Institute at the Massachusetts Institute of Technology and Harvard Medical School's Department of Genetics found evidence that the split probably took 4 million years to occur, although his team put the final divergence at just 5.4 million years ago.
"I don't think it really contradicts our paper," Reich said in an e-mail exchange.
"We were focusing on a maximum time for the common ancestor of humans and chimpanzees, while they were focusing on a best estimate," added Reich, who reviewed Hobolth's paper before it was published.
From PLoS link:
quote:
To estimate speciation times and ancestral population sizes we have developed a new methodology that explicitly utilizes the spatial information in contiguous genome alignments. Furthermore, we have applied this methodology to four long autosomal human-chimp-gorilla-orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years) and ancestral population sizes much larger than the present-day human effective population size. We also analyzed X-chromosome sequence data and found that the X chromosome has experienced a different history from that of autosomes, possibly because of selection.
After using a statistical correction for substitution rate heterogeneity, Patterson et al. [2] found that the variance in coalescence times is too large to be accounted for by instant speciation and a large ancestral effective population size, and that the speciation process therefore must have been complex. Particularly, the X chromosome shows a deviant pattern, which also led them to conclude that HC gene flow ceased and final speciation occurred as recently as 4 Myr ago. This date is generally believed to be the most recent time compatible with the fossil record, if the Millennium man and Sahelanthropus are not on the human lineage.
That would put australopithicus very close to the split.
This is still a mathematical model of split time based on some kind of uniform rates of mutation ... or at best an average rate.
I'm not sure that such models are valid for periods of speciation, when there can be more impetus for divergence to reduce direct competition.
Enjoy
ps - Human Origins forum ...

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AdminNosy
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Posts: 4754
From: Vancouver, BC, Canada
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Message 2 of 33 (386878)
02-24-2007 11:46 AM


Thread moved here from the Proposed New Topics forum.

  
ramoss
Member (Idle past 612 days)
Posts: 3228
Joined: 08-11-2004


Message 3 of 33 (386929)
02-24-2007 7:59 PM
Reply to: Message 1 by RAZD
02-24-2007 11:17 AM


Just how well established is the model for a 'genetic clock' for mutations to begin with? I know it is an assumption, but what kind of evidence do we have that backs up that mutations happen at a measurable rate. Does this take into account changes in life expectancy?? How does this 'mutation clock' actually work?

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 4 of 33 (386996)
02-25-2007 9:15 AM
Reply to: Message 3 by ramoss
02-24-2007 7:59 PM


baselines and fixation rates
Just how well established is the model for a 'genetic clock' for mutations to begin with?
The problem is: how do you baseline it?
You can measure current rates of mutation and then assume that the rate stays constant (we wouldn't have a baseline long enough to do otherwise), but then you need some kind of measure of how many get fixed in the population - that's going to be another estimate (one I have some trouble with as we know that selection pressure can change this), and it is also going to be some rather uniform or average rate (due to lack of model for rate change or data to base one on that is more than a few years long).
What they apparently did on this study was to use an 'accepted' age of the orangutan split as a baseline:
quote:
The researchers compared the DNA of chimpanzees, humans and our next-closest ancestor, the gorilla, as well as orangutans.
"Assuming orangutan divergence 18 million years ago, speciation time of human and chimpanzee is consistently around 4 million years ago,"
So this is based on an average rate of mutation fixing in the orangutan line applied to the gorilla-chimp-human lineage.
The problem I have is that we also have some evidence that the human lineage has more fixed genes than the chimp lineage:
http://www.newsroom.ucr.edu/cgi-bin/display.cgi?id=875
quote:
The team, which also included Rosaleen Gibbons, Lars J. Dugaiczyk, Thomas Girke, Brian Duistermars and Rita Zielinski, identified over 2,200 new human specific Alu DNA repeats that are absent from the chimpanzee and most likely other primates.
" The explosive expansion of the DNA repeats and the resulting restructuring of our genetic code may be the clue to what makes us human," Dugaiczyk said. “During the same amount of time, humans accumulated more genetic novelties than chimpanzees, making the human/chimpanzee genetic distance larger than that between the chimpanzee and gorilla.”
Metaphorically speaking, Dugaiczyk said, “Humans and other primates march to the rhythm of a drum that looks identical; the same size, shape and sound. But, the human drum beats faster.”
And having a different number of fixed genes also means a different rate of fixing genes - if we assume mutations average out to a relatively constant rate.
A different rate of fixing genes makes sense because there are several different selection processes going on, processes that necessarily run at different rates: genetic drift, survival selection and sexual selection. The relative importance of each process can shift depending on circumstances and behavior patterns.
(Note - Personally I think the reason for the higher human rate is sexual selection - if not runaway sexual selection - with the evidence being the apparent skin bareness, extremely long head hair, and a creative brain that increased in size until it endangers the life of the mother and child at birth - it's maxed out.)
So if we know that two branches have evolved at a different rate of fixing genes how can we assume a same or average rate anywhere else without it being suspect?
It seems to me that these genetic clock studies are looking at the data from the wrong viewpoint.
Rather than looking at the data and trying to develop an age from common ancestor based on assumed rates of mutation they should be looking at the data with all the current best fossil dating evidence for age from each common ancestor and be looking at what that means for the rate of fixing mutations in those populations.
That would be information worth knowing.
Enjoy.
Edited by RAZD, : subtitle

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jbuchanan
Junior Member (Idle past 6232 days)
Posts: 1
Joined: 03-06-2007


Message 5 of 33 (388445)
03-06-2007 2:17 AM


Hi, I am someone who is both inquisitive and skeptical of Darwinian descent with modification. One of the main reasons I have always been a skeptic of Darwinism is not necessarily because of the evidence,but rather the mechanism, which is often overlooked and dismissed as a given when discussing the evolution of life.
Darwinists contend that humans and all life share a common ancestor, yet shy away from explaining exactly HOW we evolved from this elusive ancestor. They then go on and say they know its true because DNA analysis and morphological comparisons demonstrate it. Well that's all fine and dandy but tell us HOW it happened. This where Darwinists fail to understand the scope of some of their grandiose claims.
I believe it is for that reason that many ardent atheists, such as Fred Hoyle, did not embrace Darwinism; because under scrutiny the proposed mechanism (natural selection acting on random variations caused by genetic mutations) was not enough to account for all the intricate complexities intrinsic to life.
As far as human evolution is concerned, I have yet to be shown a sufficient mechanism whereby an apelike creature can turn into something like a human. Did ape-like creatures gradually mutate into humans over millions of years, or were there other forces at work? As far as I've seen, mutations do not supply the kind of raw material necessary to transform an ape-like creature into a human. Can someone explain?
Edited by AdminPhat, : fixed paragraph

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New Cat's Eye
Inactive Member


Message 6 of 33 (388519)
03-06-2007 10:49 AM
Reply to: Message 5 by jbuchanan
03-06-2007 2:17 AM


As far as I've seen, mutations do not supply the kind of raw material necessary to transform an ape-like creature into a human.
What "kind of raw material" that is necessary are you referring too?

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cavediver
Member (Idle past 3643 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 7 of 33 (388576)
03-06-2007 2:35 PM
Reply to: Message 5 by jbuchanan
03-06-2007 2:17 AM


As far as human evolution is concerned, I have yet to be shown a sufficient mechanism whereby an apelike creature can turn into something like a human
I think you'll find that the mechanism is shaving...

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Chiroptera
Inactive Member


Message 8 of 33 (388581)
03-06-2007 3:04 PM
Reply to: Message 5 by jbuchanan
03-06-2007 2:17 AM


Hello, jbuchanan, and welcome to EvC.
quote:
They then go on and say they know its true because DNA analysis and morphological comparisons demonstrate it.
Actually, "they" know that common descent is true because of all the evidence that supports it. Evidence, by the way, that must exist if evolution were true and, if the evidence were different, would show that evolution was false. And evidence that cannot be explained without evolution.
One example of evidence, as you point out, comes from morphological comparisons. By carefully comparing the different species, we know that they can be categorized within a nested hierarchical scheme. It is obvious that if the theory of common descent were true, we should be able to see such a nested hierarchical scheme; in fact, if we didn't see such a pattern, that would be a serious blow against the theory of evolution. On the other hand, there is no reason to presuppose that a creator would simply created species according to such a pattern.
Now the reason that we think that humans and chimpanzees share a common ancestor is that they sit near each other on the "tree of life". If the tree of life indicates phylogenic relationship (and why else would there be a "tree of life"?) then this indicates that humans and chimpanzees share a recent common ancestor.
-
quote:
As far as human evolution is concerned, I have yet to be shown a sufficient mechanism whereby an apelike creature can turn into something like a human.
That's fine. But the evidence suggests very strongly that humans did, in fact, evolve from a common ancestor. That much is certain. We may even call it a fact. What could the mechanism be? Well, the only current theory is that it occurred through natural selection acting on randomly occurring variations. This is because we have actually observed natural selection act in some cases, and so it is a known mechanism. Furthermore, we do not know of anything that would prevent natural selection to produce humans from an apelike creature. And all other mechanisms that have been proposed have been shown to be false.
So where does the inheritable variation on which natural selection acts come from? That, too, is a good question. So far, from what we know about heredity, is that the nuclear chromosomes in our cells are the material through which physical traits occur. Furthermore, we know that the duplication of genetic material that occurs to produce offspring is not perfect; differences occur, differences which cause variations in physical features. So it is logical to deduce that these genetic mutations are the cause of variations in inheritable features.
-
So it is possible that the evolution of humans from earlier ape ancestors (which undoubtably did occur, according to the evidence) proceeded through a different mechanism. We currently have someone on another thread trying to resurrect the old idea of orthogenesis, for example. However, the currently accepted model of natural selection on variations in features produced by chromosomes seems to work, and we don't have any other potentially workable models.
Edited by Chiroptera, : Added clause to penultimate sentence in second paragraph.

Actually, if their god makes better pancakes, I'm totally switching sides. -- Charley the Australopithecine

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zcoder
Member (Idle past 6208 days)
Posts: 66
Joined: 03-19-2007


Message 9 of 33 (390433)
03-20-2007 11:25 AM
Reply to: Message 8 by Chiroptera
03-06-2007 3:04 PM


quote:
That's fine. But the evidence suggests very strongly that humans did, in fact, evolve from a common ancestor. That much is certain. We may even call it a fact. What could the mechanism be? Well, the only current theory is that it occurred through natural selection acting on randomly occurring variations. This is because we have actually observed natural selection act in some cases, and so it is a known mechanism. Furthermore, we do not know of anything that would prevent natural selection to produce humans from an apelike creature. And all other mechanisms that have been proposed have been shown to be false.
That answer still danced around with theory to glue it together.
quote:
But the evidence suggests very strongly that humans did, in fact, evolve from a common ancestor
I make bold the word suggests which is used to suggests but still
not a fact.
quote:
What could the mechanism be? Well, the only current theory is that it occurred through natural selection acting on randomly occurring variations
Here theory was use I think a recap of the meaning of theory is in odyer.
In common usage, people often use the word theory to signify a conjecture, an opinion, or a speculation. In this usage, a theory is not necessarily based on facts; in other words, it is not required to be consistent with true descriptions of reality.
quote:
we do not know of anything that would prevent natural selection to produce humans from an apelike creature.
But also never see it in real life eather, nore the opposite?
The author of this was treading on ice, glued with theory and uncertain(suggests) areas.
Zcoder....

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Chiroptera
Inactive Member


Message 10 of 33 (390448)
03-20-2007 1:13 PM
Reply to: Message 9 by zcoder
03-20-2007 11:25 AM


I'm sorry that you didn't like the wording of my post, Z. Let me rephrase it.
The available evidence makes it quite clear, with no doubts, that the known species have evolved from a common ancestor, and, in particular, that humans and chimps share a recent ancestor.
Genetic mutations are known to create new genes, some of which are useful to the organism, and natural selection is known to favor individuals with certain sets of alleles over others.
It is quite reasonable, therefore, to assume that natural selection acting on genetically caused variations is the driving force behind common descent. It is possible, though, that the macroevolution that is observed to have occurred over the last three and half billion years is caused by a different mechanism. However, seeing how no other mechanism has withstood scientific scrutiny, and seeing how no one has cogently explained why natural selection is insufficient to have caused macroevolution, it is reasonable to assume that natural selection is the cause.
Now, common descent is a fact; natural selection is a reasonable candidate for the mechanism, although admittedly there may be other factors at work. But someone has to either identify those other factors and/or explain why natural selection is not sufficient in itself.
-
quote:
The author of this was treading on ice....
Actually, the ground beneath my feet is quite solid and steady. Maybe when you sober up you'll find out how steady the footing really is.

Actually, if their god makes better pancakes, I'm totally switching sides. -- Charley the Australopithecine

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 11 of 33 (390750)
03-21-2007 7:24 PM
Reply to: Message 5 by jbuchanan
03-06-2007 2:17 AM


topic please
Hi, I am someone who is both inquisitive and skeptical of Darwinian descent with modification.
This topic is specifically about the genetic information about a common ancestor to both humans and chimpanzees. To discuss this topic you need to read the referenced article and comment on what it says, not bring in other topics.
Your whole post is a much more general question that is beyond the scope of this thread - you should start a new topic for it or find an existing one that discusses general evolution questions.
I'll look forward to discussing your issues when you do that.
Thanks.

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we are limited in our ability to understand
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 12 of 33 (390754)
03-21-2007 7:29 PM
Reply to: Message 9 by zcoder
03-20-2007 11:25 AM


genetics & common ancestors ... and the topic
Replying to the part that is at least vaguely on topic:
quote:
But the evidence suggests very strongly that humans did, in fact, evolve from a common ancestor
I make bold the word suggests which is used to suggests but still not a fact.
The genetic information is discussed in the article linked and referenced on Message 1. If you care to discuss that then point out the problems with the article.
Thanks.

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we are limited in our ability to understand
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RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 13 of 33 (390758)
03-21-2007 7:37 PM
Reply to: Message 10 by Chiroptera
03-20-2007 1:13 PM


original article
anyone interested in the PLOS article referred to in the OP it is at
Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
This discusses the genetic evidence for common ancestors with humans, chimps, gorillas and macaques.
Enjoy.

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we are limited in our ability to understand
by our ability to understand
RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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DorfMan
Member (Idle past 6081 days)
Posts: 282
From: New York
Joined: 09-08-2005


Message 14 of 33 (390900)
03-22-2007 2:22 PM
Reply to: Message 13 by RAZD
03-21-2007 7:37 PM


Re: original article
quote:
This discusses the genetic evidence for common ancestors with humans, chimps, gorillas and macaques.
This explains my need to scratch in unusual places at inopportune times. I'm upset with evolution. So much progress and so little progress....where it would be seemly.
The look of the future!

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whaler777
Junior Member (Idle past 4343 days)
Posts: 12
Joined: 05-07-2007


Message 15 of 33 (402356)
05-25-2007 11:02 PM


Obviously words like possibly,perhaps and if seem to be used as concrete evidence. I have had in numerous times teachers of Public schools and Highschools stating to their students that evolution has no evidence to support what they say and that it is only a theory. Why is this being done in the school systems if evolution exists to be true? Also why don't other theory exists. This evolution sounds like the book "War Of The World" (one big hoax). I also would like to see more people that are taking their time and energy to explore other theories so we can stay away from indoctrination. And as far as the Chimp theory goes, what force was in place to decide so many chimps would become human and are there angry chimps out there because they weren't selected? If this force was evident then why doesn't it do it again?
Edited by whaler777, : No reason given.
Edited by whaler777, : No reason given.

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