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Author Topic:   "Homo troglodytes" Genome Project, DNA 96% {us}
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 1 of 28 (239468)
09-01-2005 10:00 AM


We are related.
From Man, chimps share genes - Comparison of genomes shows thousands are virtually identical (click):
The 67 scientists from five nations leading the chimp genome project are reporting their results today in a series of eight papers published in the journal Nature. Researchers leading the project described their work Wednesday at a Washington press conference.
Lining up 3 billion bits of genetic code, the chimp genome team determined that 96 percent of the protein-coding genes in both chimps and humans were identical, while in some stretches of DNA where genes either regulate other genes or whose function is unknown, as much as 99 percent of the genetic material in both is identical, the scientists concluded.
So we now have complete genome comparisons instead of estimates, and the final count is 96% identical.
This makes us more closely related than many species that are lumped into the same {Genus}, and is more evidence that Chimps should be considered Homo troglodytes as some have suggested.
Among the 35 million tiny bits of DNA in the human genome that differ from chimps, for example, lie clues to the manner in which natural selection -- the basic machinery of evolution -- has given humans the unique ability to walk upright, to use language and to think, reason and develop complex tools, said Dr. Robert Waterston of the University of Washington, the senior author of the principal comparative study. Mutations in the DNA of many of those genes may well have occurred within the past 250,000 years, and because they proved so beneficial, they spread rapidly throughout the human population, he said.
Some classes of genes, however, appear to have changed relatively rapidly in both chimps and humans, the scientists say. They include genes involved in hearing, transmission of nerve signals and production of sperm.
If this can be confirmed, these would be the genetic changes that separated Homo sapiens from Homo heidelbergensis and push back other evidence of the first Homo sapiens occurring a little over 160,000 years ago, from "mitochondrial eve\adam" to the oldest known anatomically modern fossils. This should not be a surprise.
And this would touch on some previous claims of faster genetic change in humans than other apes, while changes in sperm genes would also be evidence of sexual selection.
From Humans March to a Faster Genetic "Drummer" Than Other Primates, UC Riverside Research Says (click):
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.
This last study was touted as "Research Runs Counter to Darwins Theory of Natural Selection"
The process was not random, Dugaiczyk said, and it was not subject to an environmental "natural selection," separating winners and losers as theorized by Darwin.
"We are not contending that natural selection does not exist, but that in this instance it is a chemical process within human chromosomes that explains why humans have an explosive expansion of DNA repeats, and other primates do not," Dugaiczyk said.
However this view ignores the contribution of sexual selection in the development of the human mind and other characteristics.
Run-away sexual selection can easily push the envelope of development faster and further than survival selection, which must wait for opportunistic events to be applied.
Back to the new results on the Chimp Genome:
Again from Man, chimps share genes - Comparison of genomes shows thousands are virtually identical (click):
Scientists have estimated from the fossil record that the evolutionary lineages of humans and the great apes like chimpanzees diverged from a common ancestor between 5 and 8 million years ago, and the chimp genome team believes the split must have occurred roughly 6 million years ago.
Someone here said 4 million and I said I thought it was closer to 7 million; I'll take 6 as a good compromise .
Over all the millennia since that time, relatively few changes have occurred in the chimp genome, Waterston and his colleagues said. That has placed humans at a disadvantage in some areas. Chimps, for example, have been able to resist many infections like HIV and AIDS, and they don't get malaria, diabetes, cancer or Alzheimer's -- while humans can succumb to all these maladies.
Yet, as Collins noted, "we have peeked into evolution's lab," and it's just these differences that could provide a new understanding of those diseases as researchers pursue their quest for prevention and treatment in new directions.
What will creationists (and others who feel the need to regard humans as "special") do when major medical breakthroughs in human health come to us from our cousins?
Enjoy.
ps -- I'm thinking {Human Origins} ...
This message has been edited by RAZD, 09*01*2005 10:01 AM
Edited by RAZD, : replace italic code in title with " seeing as italics don't work in titles anymore?

Join the effort to unravel {AIDS/HIV} {Protenes} and {Cancer} with Team EvC! (click)

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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AdminNosy
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Message 2 of 28 (239487)
09-01-2005 10:54 AM


Thread moved here from the Proposed New Topics forum.

  
Dr Jack
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Message 3 of 28 (239506)
09-01-2005 11:10 AM
Reply to: Message 1 by RAZD
09-01-2005 10:00 AM


While there are other genii in which the difference between the species in DNA terms is less than that between Chimps and Humans there most certainly aren't any in which there are such vast morphological differences. Morphology, IMO, remains an entirely valid basis for distinguishing genii. Pan troglodytes is should remain.

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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 28 (239521)
09-01-2005 11:55 AM
Reply to: Message 3 by Dr Jack
09-01-2005 11:10 AM


and yet, in one species:
There is more morphological (surface differences) than between human and chimp.
morphology n. pl. morphologies
1. The branch of biology that deals with the form and structure of organisms without consideration of function.
2. The form and structure of an organism or one of its parts: the morphology of a cell; the morphology of vertebrates.
Thus by your argument we should consider chimps to be Homo sapiens.
Enjoy.
This message has been edited by RAZD, 09*01*2005 11:57 AM

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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John Williams
Member (Idle past 4999 days)
Posts: 157
From: Oregon, US
Joined: 06-29-2004


Message 5 of 28 (239717)
09-01-2005 5:18 PM
Reply to: Message 1 by RAZD
09-01-2005 10:00 AM


All I can say is that it certainly appears scientists have proven that their is an enormously close relationship between Chimps and man. The Chimp Genome project is very exciting and I cannot wait to see what other breakthroughs occur in the way of human origins.

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MangyTiger
Member (Idle past 6354 days)
Posts: 989
From: Leicester, UK
Joined: 07-30-2004


Message 6 of 28 (239796)
09-01-2005 8:42 PM
Reply to: Message 1 by RAZD
09-01-2005 10:00 AM


As far as I can tell this was done for a commom chimpanzee.
I wonder if the bonobo (Pan paniscus) will come out even closer?
I have seen it stated numerous times on Natural History type TV programmes that bonobos are closer genetically to us than common chimps, although I've never come across anything to actually back it up.

I wish I didn't know now what I didn't know then

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


Message 7 of 28 (239798)
09-01-2005 8:58 PM
Reply to: Message 6 by MangyTiger
09-01-2005 8:42 PM


Yes it was done on troglodytes.
I think if you look at the (well done) thread Sylas had on {neander\chimp\human} DNA that this is addressed
http://EvC Forum: Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees
It appears that human\bonobos are more different than human\chimp
Note that {redwolf} is Ted Holden.
Yes, I would like to see the full Bonobos genome, particularly as they appear to be headed for extinction in the wild.
see http://EvC Forum: What is the evolutionary advantage to religion?
This message has been edited by RAZD, 09*01*2005 08:58 PM

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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MangyTiger
Member (Idle past 6354 days)
Posts: 989
From: Leicester, UK
Joined: 07-30-2004


Message 8 of 28 (239800)
09-01-2005 9:05 PM
Reply to: Message 4 by RAZD
09-01-2005 11:55 AM


Human/chimp vs. dog/dog
There is more morphological (surface differences) than between human and chimp.
I'm not sure about this at all.
First off morphological does not just mean surface differences. It can (does) also relate to structural differences, including bones.
The skeltons of chimps and humans can be distinguished by more than just size (by somebody who knows what they are doing - which counts me out ).
I think the most famous/obvious differences relate to the skull. From Bone Clones, purveyors of fine bone reproductions:
When compared to modern humans, the skull of the chimpanzee has massive jaws with large canine teeth, a protrusive face that extends well in front of the eyes, thinly enameled molars and a U-shaped dental arch (an identifying trait of the great apes). The brain is small compared to humans, but is relatively large when compared to other apes and monkeys. Muscle attachments for neck and jaw muscles are very well developed, adding to the chimpanzee’s great strength. The position of the foramen magnum (the hole through which the spinal cord passes) places the skull in front of the spine rather than balanced on top of the spinal column as seen in humans. This fits the typical stance of a chimp, and demonstrates how we can tell about the stance of an animal from its skull.
Can the same be said about the differences in the two dogs in your picture? I'm not expert enough to say for sure, but my money is on "no".

I wish I didn't know now what I didn't know then

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


Message 9 of 28 (239810)
09-01-2005 9:48 PM
Reply to: Message 8 by MangyTiger
09-01-2005 9:05 PM


Re: Human/chimp vs. dog/dog
Can the same be said about the differences in the two dogs in your picture? I'm not expert enough to say for sure, but my money is on "no".
Of all of those differences the only one that I would agree doesn't fit the different dogs is
The position of the foramen magnum (the hole through which the spinal cord passes) places the skull in front of the spine rather than balanced on top of the spinal column as seen in humans.
The others are much smaller at younger ages due to the extensive neoteny in humans:

from http://dsc.discovery.com/news/afp/20031006/laughter.html
hmmmm, same reaction to tickling?
Great Dane Skull (note size of snout and teeth):
From http://www.evolutionnyc.com/..../product-id/29151.html
I can't find just skull of a small dog (to show the teeth), but this might give something of the idea:
From http://www.gobaeng.de/product_info-products_id/3729
(pugs may have been selected for neoteny characteristics too)
Is one difference enough to justify a different Genus?
Thanks.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 10 of 28 (239863)
09-02-2005 4:31 AM
Reply to: Message 4 by RAZD
09-01-2005 11:55 AM


Your argument fails on three counts.
Morphology does not mean surface features; it means the physical structure of the animal. Scientists were perfectly able to distinguish superficially very similar animals (such as Echinacea and Hedgehogs) using morphology long before genetic analysis became available, indeed before evolution was even identified.
Humans and chimps have far more morphological differences than even the most diverse of dog breeds - whose differences amount to variations in size and shape without any significant changes to the underlying body structure or muscle groups. Humans have significantly different jaws, hips, legs, feet, muscle structure, head shape, spine organisation and brain structure.
Dogs are considered the same species because they can interbreed; chimps and humans cannot. And are also an example of artificial selection which, frankly, bends things somewhat.
This message has been edited by Mr Jack, 09-02-2005 04:34 AM

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 11 of 28 (239959)
09-02-2005 1:14 PM
Reply to: Message 7 by RAZD
09-01-2005 8:58 PM


quote:
Yes it was done on troglodytes.
I think if you look at the (well done) thread Sylas had on {neander\chimp\human} DNA that this is addressed
http://EvC Forum: Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees -->EvC Forum: Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees
It appears that human\bonobos are more different than human\chimp
I don't see your conclusion in that thread. I'd be quite surprised if there were a substantial difference between human/bonobo and human/chimp genetic distances, since chimps and bonobos have been evolving for the same length of time since their split. There could be small effects due to different mutation rates, different generation times and even different levels of selective constraint, but they would probably be very hard to detect.

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randman 
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Posts: 6367
Joined: 05-26-2005


Message 12 of 28 (240168)
09-03-2005 1:28 AM


may be of interest here
As well as providing new insight into the evolution of chimps, the landmark discovery shatters the widespread belief that humans and chimps did not coexist since they diverged from a common ancestor five to eight million years ago.
The researchers found startling evidence of the cohabitation as they unearthed fossils attributed to Homo erectus or Homo rhodesiensis in the same geologic layer less than a mile away.
Since modern chimp populations are now confined to wooded west and central Africa, whereas most hominid fossils have been found in the semi-arid East African Rift Valley, it has been long speculated that ancient chimps and humans diverged from their common ancestor when hominids left the jungles and moved east to the less wooded grasslands.
"People used to believe that the origin of humans had to do with their leaving the forest and beginning to walk on two legs. Our discovery shows that the forest-savanna dichotomy used to explain the split between the chimpanzee and human lines does not add up," McBrearty, who discovered the fossils, told Discovery News.
McBrearty and Jablonski also found fossilized remains of fish, hippopotami, crocodiles, turtles, gastropods and other moisture-loving animals.
The remains would suggest that 500,000 years ago that chimps and ancient Homo inhabited a wet, wooded area surrounding a lake.
http://dsc.discovery.com/...briefs/20050829/chimpfossil.html
Personally, this is interesting because it confirms a hunch, that all those scenarios declaring man began to walk upright when the land dried up to grassy Savannahs was essentially a myth based on very little actual evidence.
But not knowing all the details of molecular dating of the theorized divergence with human/chimp ancestors, I wonder if this new discovery affects that in anyway? Anyone know here?

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PaulK
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Member Rating: 2.2


Message 13 of 28 (240182)
09-03-2005 3:09 AM
Reply to: Message 12 by randman
09-03-2005 1:28 AM


Re: may be of interest here
quote:
Personally, this is interesting because it confirms a hunch, that all those scenarios declaring man began to walk upright when the land dried up to grassy Savannahs was essentially a myth based on very little actual evidence.
But not knowing all the details of molecular dating of the theorized divergence with human/chimp ancestors, I wonder if this new discovery affects that in anyway? Anyone know here?
Sciecntists make speculative reconstructions based on the available evidence. To call such reconstructions "myths" is to fail to understand what is going on. (And even ignores the article which explicitly describes the idea as speculation). Of course speculative ideas can be wrong, but this evidence (and by that I mean the hominid fossils) isn't conclusive either.
And no, it doesn't affect the molecular dating in any way. How could it ?. It does confirm that the human and chimps lineages had diverged by the time of the fossil specimens but that's no surprise at all. THe article tells us that the fossils were 500,000 years old and that the divergence was 5-8 million years ago. How could the fossils affect the molecular dates ?
This message has been edited by PaulK, 09-03-2005 03:10 AM

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Lithodid-Man
Member (Idle past 2931 days)
Posts: 504
From: Juneau, Alaska, USA
Joined: 03-22-2004


Message 14 of 28 (240196)
09-03-2005 3:59 AM
Reply to: Message 3 by Dr Jack
09-01-2005 11:10 AM


Shoutings from the invert camp
Mr. Jack,
I am forced to respectably disagree with you on what morphological characteristics quantify differences between species and/or genera (not genii, plural of genius not genus). As an invertebrate zoologist with a great interest in human evolution I have always been skeptical of the differences perceived between fossil and extant members of the Hominidae, Homininae in particular.
I think it is very difficult to objectively look at differences in things that resemble ourselves. I think the study of human evolution has been clouded by this difficulty. In the pop-sci realm it has not better been illustrated than in the book Lucy The beginnings of humankind by Johanson and Edey. In their chapter 13 they discuss the analysis of what the fossils may be. The possibilities they explore are genus Homo, genus Australopithecus, or ‘something else’.The analysis concludes that the fossils (Lucy and the others representing Austrlopithecus afarensis) are australopithecines. Where I take exception is that the genus Pan was never considered (while they repeatedly made comparisons to this genus) as an alternate possibility.
I wish I had better photos but I want to illustrate the difference between accepted congenerics in crustacean biology:
and
The first is less than 50 mm across the carapace the second is commonly 150 mm and above. Both are in the same genus and this is supported by abundant morphological data including larval development. I would argue that the difference between a dungeness crab and a dwarf cancer crab are orders of magnitude more than between a human and a chimpanzee. The numbers of invert congenerics that differ more than that would stagger the imagination.
This message has been edited by Lithodid-Man, 09-03-2005 04:09 AM
This message has been edited by Lithodid-Man, 09-03-2005 04:25 AM

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


Message 15 of 28 (240223)
09-03-2005 8:45 AM
Reply to: Message 12 by randman
09-03-2005 1:28 AM


Re: may be of interest here
randman writes:
Personally, this is interesting because it confirms a hunch, that all those scenarios declaring man began to walk upright when the land dried up to grassy Savannahs was essentially a myth based on very little actual evidence.
To add to what PaulK has already said, this particular hypothesis has been invalidated by the fossils of upright walking hominids that pre-date the arrival of the savannah environment.
It would also appear that we had already evolved our penchant for {less hairy appearance} by then, but that is a separate issue (see the sexual selection thread where these points are discussed).
You seem to have some problems with the concept of falsifyable theories, as this is not the first time you have refered to such as myths. All theories, even the best possible derived scientific theories based on multiple divergent piles of evidence that have passed many falsification tests, can always be invalidated by the nest piece of information found.
This does not make them "myths" it makes them mistakes based on insufficient information. Certainly when the "Savannah Theory" of pedestrian development was proposed it was based on the evidence available at the time.
The active falsification of theories is how science moves forward, because the next theory takes into account the new information and then makes predictions for what we should find.
Enjoy.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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