Skip to comments.New Analyses Bolster Central Tenets of Evolution Theory
Posted on 09/26/2005 3:27:53 AM PDT by Crackingham
When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins. But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests.
If Darwin was right, for example, then scientists should be able to perform a neat trick. Using a mathematical formula that emerges from evolutionary theory, they should be able to predict the number of harmful mutations in chimpanzee DNA by knowing the number of mutations in a different species' DNA and the two animals' population sizes.
"That's a very specific prediction," said Eric Lander, a geneticist at the Broad Institute of MIT and Harvard, and a leader in the chimp project.
Sure enough, when Lander and his colleagues tallied the harmful mutations in the chimp genome, the number fit perfectly into the range that evolutionary theory had predicted.
Evolution's repeated power to predict the unexpected goes a long way toward explaining why so many scientists are practically apoplectic over the recent decision by a Pennsylvania school board to treat evolution as an unproven hypothesis, on par with "alternative" explanations such as Intelligent Design (ID), the proposition that life as we know it could not have arisen without the helping hand of some mysterious intelligent force.
"What makes evolution a scientific explanation is that it makes testable predictions," Lander said. "You only believe theories when they make non-obvious predictions that are confirmed by scientific evidence."
(Excerpt) Read more at washingtonpost.com ...
It's a bit like this. Suppose student A sits next to B, and A determines his answers by coin tosses. When the exams are turned in, B's answers are the same as A's.
Copied, or not?
Are you still keeping your list of threads?
On and off. I'm trying to update my database now; I've got a new data format that outputs text ready for pasting.
Even if this point were accurate, what does it prove? Does it prove that chimps and man have a similar ancestor, that they are different branches off of the same evolutionary trunk, or does it indicate that both chimps and man have the same designer who simply created man as a variation on an existing theme?
What do you make of this?:
Who is warping, twisting, and misrepresenting science in their arguments?
Here's an example:
The hobbits are in a class all of their own, say scientists March 04, 2005
From the article:
HOBBITS, the nickname for the little human relative first discovered last year, were not Homo sapiens but a separate species, analysis of its brain has confirmed.
We now have research that shows these people were "modern":
New 'Hobbit' disease link claimFriday, 23 September 2005
The researchers say their findings strongly support an idea that the 1m- (3ft-) tall female skeleton from Indonesia is a diseased modern human.
And you wonder why the general public is skeptical of the claims evolutionists and scientists make.
"or does it indicate that both chimps and man have the same designer who simply created man as a variation on an existing theme?"
So God looked and said about the chimp "It's no good and I can do better" and zap a little tweak here and a tuck there and we have Patrick Henry?
BTW and FYI, the coding portions of the chimp and human genome are 99% identical.
There are those who think it happened the other way around.
You have been around these threads long enough to have already seen the answer to that question on numerous occasions. This leaves us with a number of possibilities:
We'll leave the selection as an exercise for the lurkers. Just in case the lurkers haven't seen predictions of evolution before, here is a tiny subset of them.
Please point out where the OP said that "creationists can't read".
***I have and I understand it, would you care to elaborate?***
Sorry. It's Nature, not Science. My mistake. Interesting you have it in Science... :)
Nonetheless, I refer you to Cheng et al, Nature: 88 2005.
Here's the full ref and abstract.
Nature. 2005 Sep 1;437(7055):88-93.
A genome-wide comparison of recent chimpanzee and human segmental duplications.
Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong
P, Wilson RK, Paabo S, Rocchi M, Eichler EE.
Howard Hughes Medical Institute, Department of Genome Sciences, University of
Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington
We present a global comparison of differences in content of segmental
duplication between human and chimpanzee, and determine that 33% of human
duplications (> 94% sequence identity) are not duplicated in chimpanzee,
including some human disease-causing duplications. Combining experimental and
computational approaches, we estimate a genomic duplication rate of 4-5
megabases per million years since divergence. These changes have resulted in
gene expression differences between the species. In terms of numbers of base
pairs affected, we determine that de novo duplication has contributed most
significantly to differences between the species, followed by deletion of
ancestral duplications. Post-speciation gene conversion accounts for less than
10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100
copies) of particular segments of DNA have resulted in marked quantitative
differences and alterations in the genome landscape between chimpanzee and
human. Almost all of the most extreme differences relate to changes in
chromosome structure, including the emergence of African great ape subterminal
heterochromatin. Nevertheless, base per base, large segmental duplication events
have had a greater impact (2.7%) in altering the genomic landscape of these two
species than single-base-pair substitution (1.2%).
Exactly - hence creationism is incorrect.
I know the article. I have read it and I have read the abstract (I noted your "Science" as irrelevant - I personally know one of the authors). My question to you was concerning your post #44. What is your point?
You've got the time machine in reverse this morning. The prediction was made before the facts were even known to exist in this case. At least we know you don't do science.
But it is evidence that they both descended from 'common ground', so to speak.
Mr.Grumpy is a troll.
The talk origin tract indicattes that repeat elements should always be seen in organisms with a common ancestor. In this case there are duplication events in common ancestors, but not human, The talk origin tract would make one think this contradicts common descent.
It doesn't take in to account there can be deletions such as observed whereby Gorilla, Chimp and Orangutan have elements in common, but not human.
As more genomes are sequences and analyzed there will be a lot of these sort of ostensible descrepancies.
Articles meant as evangelical polemic, such as cited here, and mindlessly parrotted here by some, present a false picture of molecular evolution's complexity.
But they're not. They're measuring mutations in humans and chimps, which occur according to evolutionary predictions, which conclusively indicate not only common descent, but when, within a relatively short time frame, humans and chimps shared our last common ancestor.
Evolution "scientists" must be part kangaroo!
We're not "part" anything. We did, however, share a common ancestor with kangaroos, probably around 110 million years ago when our placental ancestors branched off.
I think they're succumbing to the temptation to arrange the facts to fit their theory
What's your explanation for why mutation rates in both nuclear and mtDNA exactly fit evolutionary predictions? Do you have an explanation?
Then add in having the same misspellings, grammar errors, and ink smudges and spills in the same places......
"repeat elements should always be seen in organisms with a common ancestor"
Supply a referenced quote for this, please.
I know. Perhaps some nice chocolaty flavored Exlax.
It proves common descent -- not that we and chimps had a similar ancestor, but that we share a common ancestor. How do we know this? Well, for one of many reasons, because DNA mutates at a remarkably constant rate. Now some parts of DNA code for things that we select for on a daily basis -- someone born with no arms is less likely to live than someone with two arms, so a mutation that codes for no arms quickly dies out. But most mutations have no effect on an individuals ability to survive, and those survive, and are measurable. By comparing the mutations present in both human and chimp DNA, we can tell just how long it was we branched off (imagine a genetic stop watch) -- and amazingly, the date we get is exactly what we find in the fossil record.
Read the t.o referenced article. Itchyman has parrotted it in the past and linked to it and today Patrick Henry linked to it.
Indeed, many argue that chimps and bonobos evolved after humans did.
On it's face, your comment is not only silly, but nonsensical. Maybe that's what you meant and my receiving it was limited by the medium.
They just haven't demonstrated the ability. When you are on a debate team, you have to be able to argue both sides of a question equally well. If you participate in a discussion, you need to be able to state your opponent's position accurately.
These are elementary qualifications that creationists fail to meet when arguing against evolution.
Not really. You made the claim that "nothing can come from nothing". Isn't that exactly what creationism tries to claim occurred? Current cosmological, geological, and biological theories make no such claim.
Man and Chimp were created with enough difference to belong to two different 'kinds' just like God created them.
Who is warping, twisting, and misrepresenting science in their arguments?
Actually, if you read the article, you will see that it pertains to the statistical analysis of epidemiological and medical studies, not science research in general. I made my points when that thread was current on FR. But then again, anti-science sentiments run deep in the creationist camp so anything else that can be warped to their agenda will be warped.
The proof is in the pudding. So far, it seems the more that gets posted about evolution, the less the creationists seem to understand. It seems clear to me that they either don't read, or skim over a lot becaue they don't want to understand the material.
So if any two species with a 4% difference in their genome are different kinds? What is the barrier? 1%, 2%, 3%?
btw, I didnt' make a claim, I stated a fact. If you have evidence that anything comes from nothing, then THAT would be worthy of more conversation!
Interesting how you run away to ad hominum circle the wagon mentality.
Is there any of you who actually know or care about science as opposed to religious proselyltizing?
The Nature article, co-authored by someone you know, as you say, shows clearly there are shared elements in chimp, gorilla and in one case orangutan as well that are not in human.
Does this mean therefore gorilla, chimp and orangutan have a common ancestor different than human?
The t.o. tract makes the case that this sort of observation would indicate that.
The 98 percent figure is still valid. It refers to the coding, or functional portion of DNA. The 96 percent figure refers to the other 95 percent of DNA, which does not code for proteins and which has few known functions. Generally, it's referred to as junk, but some of it is known to have limited function.
Nor do they try to make claim to that, nor does science claim to have all the answers. The best science can do is explain the appearance of physical evidence and make predictions as to what physical evidence will be found next if we look for it. That's all the theory of evolution does (and the other theories that are mistakenly grouped with it (i.e. radiometric decay theory, continental drift theory, Big Bang theory, etc.)).
Carl Sagan's solution was to pretend that there was no first cause.
That's Carl Sagan's view. I think it's God. Scientists have varying theological views. This has nothing to do with the science, though. Apples and oranges.
A willing mind may glean that if 2 percent was an existing gap, then 4 percent is more of an existing gap, certainly not bad news for anyone who thinks God created all things to reproduce after their kind.
What I can never figure out is why there doesn't seem to be any Islamic IDers quoting the Koran (or Hindus, Buddhists, etc quoting their repective authorities) on these crevo threads. If there were, perhaps X-ians would realize how ridiculous it looks quoting the Bible.
What makes a book written during King James' reign and transcribed over time from writings made by itinerant wanderers (similar in look/demeanor to homeless people one sees walking the roadsides today) such an authority? I guess that why it's called 'faith'.
I dated a pretty chimpanzee in High School - she loved hanging in trees and beating up the football guys.
I dated a pretty chimpanzee in High School - she loved hanging in trees and beating up the football guys.
Actually there are. darwinism-watch.com has been used as an authority on these threads.
Actually, not really.
And another funny thing is earlier on this thread someone said the coding regions show 99%.
And I've always wondered why so many Christians focus on the first paragraph of Genesis when there is so much more to the Bible!
What's not really. If I made a factual error, cough up a reference. It wouldn't be the first time.
Go to post 62 and read the last sentence of the Eichler group abstract.
Well then, I suggest that it is incumbent upon evos to match scripture for scripture (Bible<->Koran). Perhaps the X-ians would begin to realize how meaningless it is to quote words written by goat herders 1,5000-2,000 years ago.
I think you are misrepresenting differences in alleles as differences in gene sequences, but I will have to wait for someone more knowledgeable to respond.
I find it rather unlikely that numbers in a reviewed article are far off. I find it rather likely that interpreters of originals will confuse terms.
I generally have the inclination to not state directly but to guide people to answers so that they will learn. It's kind of like the "give a man a fish and he eats today; teach him to fish and he eats for life."
The 98-99% is based upon the entire sequence, not just coding.
From the consortium article (Nature 437, 69-87 (1 September 2005) | doi: 10.1038/nature04072):
Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover approx 2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.
Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies12, 33, 34. The differences between one copy of the human genome and one copy of the chimpanzee genome include both the sites of fixed divergence between the species and some polymorphic sites within each species. By correcting for the estimated coalescence times in the human and chimpanzee populations (see Supplementary Information 'Genome evolution'), we estimate that polymorphism accounts for 14−22% of the observed divergence rate and thus that the fixed divergence is approx1.06% or less.
You can see this number is based upon sequence of 2.4 trillion bases -- not just the coding regions.
As far as where the other numbers come from, I will present an entire news report (a good one as far as reports in the popular press go) that quotes Eichler, the senior author of the duplication analysis from the same issue (abstract and reference cited in my 62). Read the article below. It touches on this topic very directly and indicates the outdated nature of the t.o. tract Patrick Henry linked to earlier. From Eurkea Alert http://www.eurekalert.org/pub_releases/2005-08/hhmi-anv083105.php
A new view of human-chimpanzee genome differences Comparisons of the human genome and the newly completed draft of the chimpanzee genome have unearthed major differences between the patterns of large duplicated segments of DNA in the two species. These segmental duplications -- which straddle large stretches of DNA -- appear to have had a significant impact in altering the genomic landscape of apes and humans.
The popular understanding of the genetic differences between chimpanzees and humans should be recast in light of the findings of major differences in segmental duplications, said the senior author of the study, Evan Eichler of the Howard Hughes Medical Institute at the University of Washington School of Medicine.
The traditional comparison cited in textbooks is that the difference is 1.2 percent, based on variations in single base-pairs in gene sequences. "But our data on these duplications shows a 2.7 percent difference, base per base, between chimps and humans," said Eichler. "So when we talk about how similar chimps and humans are, we really need to be careful that we are referring to variation in the whole genome as opposed to just those single-base-pair changes."
Eichler led the research team which published the comparative genome analysis in the September 1, 2005, issue of the journal Nature. Their research article was one of several analyses that accompanied a report on the draft sequence of the chimpanzee genome. Eichler also participated in the chimpanzee genome project.
Eichler and his colleagues in Seattle collaborated with researchers from the University of Bari in Italy, the Max Planck Institute for Evolutionary Anthropology, the Washington University School of Medicine in St. Louis, Children's Hospital of Oakland Research Institute and the National Library of Medicine.
Duplications of extensive segments of DNA occur during the production of sperm or eggs because of a predisposition of certain sites along the chromosomes to undergo breakage and rearrangements, Eichler explained. The resulting segmental duplications are evolutionarily important because they give rise to extra copies of genes that allow evolution to more freely "experiment" with mutations that could give rise to new traits, said Eichler. However, they can also lead to some two dozen genetic diseases.
Comparative analysis of segmental duplications in humans and chimpanzees could give important insights into why such specific abnormalities tend to occur and when these events arose. "The chimp can provide us historical information about ancestral states of disease," said Eichler. "We know that there are some disease 'architectures' that are shared between chimp and human, so we know that is the ancestral state. But other predisposing structures have arisen only in the human lineage, so such comparisons can provide important information on the genetic histories of disorders and disease susceptibilities of the human species."
In their analysis, the researchers mapped the draft chimpanzee sequence data onto the human genome sequence as a reference. With their comparative map, they used sophisticated computational analysis to distinguish three categories of segmental duplications -- those found in humans but not in chimpanzees; those found in chimpanzees but not in humans; and those shared between humans and chimpanzees. The researchers looked for duplications greater than about 20,000 base pairs in length.
Their analysis revealed that about a third of the duplications were found in humans but not in chimpanzees. "This was surprising, because it tells us that there is a high frequency of de novo duplications that arose over the time of human and great ape evolution," said Eichler. "In contrast there are a lot of theories out there that duplications emerge and are maintained through selection or other processes such as gene conversion."
In analyzing the chimpanzee-only duplications, the researchers found that chimpanzees showed fewer sites of duplication than humans, but they did have a great number of copies of the duplicated segments. Of particular interest to the scientists, was that a few of the shared duplications were often "hyperexpanded" in the chimpanzee.
In one of the more extreme cases, while the human genome showed four copies of one segment, the chimpanzee genome showed some 400 copies. "Such hyperexpansions are interesting because they occur on the ends of chromosomes," said Eichler. "In the case of the segment that showed such massive duplication, it occurred near a region that in the great apes is broken into two chromosomes, but in humans is the fused chromosome two." Such a difference hints at some chromosomal instability in both species that resolved itself differently in humans than in chimpanzees, he said.
Eichler was also intrigued by the data indicating that chimpanzee-only or human-only duplications tended to occur near regions of shared human-chimpanzee duplications -- a phenomenon the researchers dubbed "duplication shadowing." Discovery of this phenomenon, he said, could lead to greater understanding of the properties of chromosomal regions that tend to experience instabilities. "Such regions are pretty important from an evolutionary perspective, because a lot of people operate under the assumption that these types of mutational processes are randomly distributed," said Eichler. "But in essence, they are not. There is probably something about these regions that has made them particularly hot in terms of change over the course of evolutionary time."
The next major project the researchers will tackle is trying to understand what the differences in segmental duplication mean for the species in terms of the evolution of genes embedded in those segments. "At the top of our list is to work out which of the genes in the duplications show signatures of natural selection," said Eichler. "This is a big question, because our hypothesis is that the big differences in structure between humans and chimps arose or might be tolerated because of important adaptations in the genes themselves." There are a few examples of such rapidly evolving duplicated genes, but these genes have not been systematically analyzed due to the difficulties in characterizing genes in these regions of the genome.
When the genome of another great ape, the orangutan, is completely sequenced, the data should provide researchers with the opportunity to gain even more insight into evolutionarily important genetic differences between humans and other primates, he said.
As far as this:
***I will have to wait for someone more knowledgeable to respond.***
Yes, I understand you need to speak with a priest of your sect to know how to continue.
I'm not going to do your work.
Feigning disinterest is a nice out.
Somewhat strange that you would jump in but then immediately opt out citing ignorance.
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