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Author Topic:   Human-Chimp DNA Difference Trebled
blitz77
Inactive Member


Message 1 of 17 (18223)
09-25-2002 8:02 AM


quote:
We are more unique than previously thought, according to new comparisons of human and chimpanzee DNA.
It has long been held that we share 98.5 per cent of our genetic material with our closest relatives. That now appears to be wrong. In fact, we share less than 95 per cent of our genetic material, a three-fold increase in the variation between us and chimps.
The new value came to light when Roy Britten of the California Institute of Technology became suspicious about the 98.5 per cent figure. Ironically, that number was originally derived from a technique that Britten himself developed decades ago at Caltech with colleague Dave Kohne. By measuring the temperature at which matching DNA of two species comes apart, you can work out how different they are.
But the technique only picks up a particular type of variation, called a single base substitution. These occur whenever a single "letter" differs in corresponding strands of DNA from the two species.
But there are two other major types of variation that the previous analyses ignored. "Insertions" occur whenever a whole section of DNA appears in one species but not in the corresponding strand of the other. Likewise, "deletions" mean that a piece of DNA is missing from one species.
Read the rest of the article here at New Scientist

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 2 of 17 (18241)
09-25-2002 9:55 AM


I was wondering when the creation crowd was going to try to make something of this.
Sadly, it isn't what the titles of the news articles make it out to be:
"But he also found that the DNA of both species was littered with indels. His comparisons revealed that they add around another 4.0 per cent to the genetic differences."
Indels - insertions and deletions - can be many hundreds of base pairs in length.
Such insertions and deleteions are most likely one-time events, so phylogeneticists, for example, consider them as a single unit of change.
Britten just included the base pairs of indels in his count.
It really does not have the impact that the news articles' titles imply.

Replies to this message:
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nos482
Inactive Member


Message 3 of 17 (18243)
09-25-2002 10:08 AM
Reply to: Message 2 by derwood
09-25-2002 9:55 AM


quote:
Originally posted by SLPx:
I was wondering when the creation crowd was going to try to make something of this.
Sadly, it isn't what the titles of the news articles make it out to be:
"But he also found that the DNA of both species was littered with indels. His comparisons revealed that they add around another 4.0 per cent to the genetic differences."
Indels - insertions and deletions - can be many hundreds of base pairs in length.
Such insertions and deleteions are most likely one-time events, so phylogeneticists, for example, consider them as a single unit of change.
Britten just included the base pairs of indels in his count.
It really does not have the impact that the news articles' titles imply.

Even than it is still a high enough number to show a recent common ancestor.

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blitz77
Inactive Member


Message 4 of 17 (18246)
09-25-2002 10:17 AM
Reply to: Message 2 by derwood
09-25-2002 9:55 AM


Hmmm? What was I making it out to be? Anyway, it highlights what previous measurements of the difference were based on-only single based substitutions between the two.
quote:
But the technique only picks up a particular type of variation, called a single base substitution. These occur whenever a single "letter" differs in corresponding strands of DNA from the two species.
As they only compared about 0.3% of the DNA, they only glanced at the differences. Also, there are much greater differences in gene expression and other epigenetic factors.

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Minnemooseus
Member
Posts: 3941
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 10.0


Message 5 of 17 (18250)
09-25-2002 10:48 AM


Wandering to the fringe of the topic:
I've wondered what the genetic differences (in a percent) between living humans. Is it a case that all living humans are 99.9999 (add even more 9's?) percent geneticly identical?
Moose

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 6 of 17 (18258)
09-25-2002 12:01 PM
Reply to: Message 5 by Minnemooseus
09-25-2002 10:48 AM


quote:
Originally posted by minnemooseus:
Wandering to the fringe of the topic:
I've wondered what the genetic differences (in a percent) between living humans. Is it a case that all living humans are 99.9999 (add even more 9's?) percent geneticly identical?
Moose

Well, according to HGP data, individual humans possess an SNP about every 1200 bases (average, of course), not including indels.
That means that any given human differs form any other by some 2.7 million basepairs (again, not counting indels), or 0.08%.
Of course, in order to put the numbers in perspective, one would need to use Britten's technique on all taxa, and I suspect that all such comparisons would yield a similar higher degree of difference.
It is all relative.

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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 7 of 17 (18259)
09-25-2002 12:05 PM
Reply to: Message 4 by blitz77
09-25-2002 10:17 AM


[QUOTE]Originally posted by blitz77:
Hmmm? What was I making it out to be? Anyway, it highlights what previous measurements of the difference were based on-only single based substitutions between the two.
quote:
But the technique only picks up a particular type of variation, called a single base substitution. These occur whenever a single "letter" differs in corresponding strands of DNA from the two species.
Well, even that is not really true. DNA-DNA hybvridization cannot in fact discriminate between single-base pair differences. The only way to do that is by direct DNA sequence comparisons. And when doing so, obviously, indels are taken into account.
quote:
As they only compared about 0.3% of the DNA, they only glanced at the differences. Also, there are much greater differences in gene expression and other epigenetic factors.
Greater than what?
Are not chimp genomes also expressing genes at different rates than us?
It is not that WE are so much more diffeent than chimps than previously thought, it is just a new way of looking at the differences, for one thing, and the type of titles used in these articles are indicative of the anthropocentrism in not only , but
in some scientists, as well. For it is THE difference which may be larger than thought, not that WE are so much different.

This message is a reply to:
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Andya Primanda
Inactive Member


Message 8 of 17 (21078)
10-30-2002 3:40 AM
Reply to: Message 7 by derwood
09-25-2002 12:05 PM


bump. Dr. Page, can you put your argument in a nutshell? The Harun Yahya committee attacked me over it and I am unable to give a definite answer to them...
http://www.harunyahya.com/70reply_andya_primanda.php

This message is a reply to:
 Message 7 by derwood, posted 09-25-2002 12:05 PM derwood has replied

Replies to this message:
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derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 9 of 17 (21124)
10-30-2002 3:43 PM
Reply to: Message 8 by Andya Primanda
10-30-2002 3:40 AM


quote:
Originally posted by Andya Primanda:
bump. Dr. Page, can you put your argument in a nutshell? The Harun Yahya committee attacked me over it and I am unable to give a definite answer to them...
http://www.harunyahya.com/70reply_andya_primanda.php

Sure:
Common techniques of assessing genetic distance consider indels (insertions and deletions) to be one-time events, regardless of the size. So an insertion of a retroelement of 100 base pairs is considered a single 'difference' because the entire chunk was put in at once.
Britten's technique would consider such an insertion as 100 'differences' because of the number of bps involved.
I have no problem with that per se, providing we apply the technique universally, that is, apply it to all genetic distances.
Doing this makes everything more geneicallt distant form everything else, so in a real sense, it makes no difference.

This message is a reply to:
 Message 8 by Andya Primanda, posted 10-30-2002 3:40 AM Andya Primanda has replied

Replies to this message:
 Message 11 by Andya Primanda, posted 10-31-2002 12:36 AM derwood has replied

  
Tranquility Base
Inactive Member


Message 10 of 17 (21134)
10-30-2002 6:16 PM
Reply to: Message 5 by Minnemooseus
09-25-2002 10:48 AM


Moose
We are about 99.9% similar to each other in terms of DNA base-pairs. One in every 1000 bp will be differnt between you and your neighbour.
So that's about 30 million variations across 3.1 billion bps. Only a small fraction of the genome is coding DNA (about 3%) suggesting about 1 million differneces in these regions (probably less due to preferential conservation in coding regions).
The differences between individuals are 'allelic' meaning that the set of genes (at least for healthy individuals) is identical. The changes simply adjust strengths of interactions and catalyases.
If your body is working then all of your tens of thousands of nanomachine types will be happily going about exactly the same jobs that they are performing in your neighbour.
[This message has been edited by Tranquility Base, 10-31-2002]

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Andya Primanda
Inactive Member


Message 11 of 17 (21153)
10-31-2002 12:36 AM
Reply to: Message 9 by derwood
10-30-2002 3:43 PM


I see. So, has anyone done that? If by this technique the human-chimp 99% dif is pushed back to 95% then every other distance would also be enlarged. Any papers on this?

This message is a reply to:
 Message 9 by derwood, posted 10-30-2002 3:43 PM derwood has replied

Replies to this message:
 Message 12 by derwood, posted 11-04-2002 10:50 AM Andya Primanda has replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 12 of 17 (21526)
11-04-2002 10:50 AM
Reply to: Message 11 by Andya Primanda
10-31-2002 12:36 AM


quote:
Originally posted by Andya Primanda:
I see. So, has anyone done that? If by this technique the human-chimp 99% dif is pushed back to 95% then every other distance would also be enlarged. Any papers on this?
I doubt it - the 'new' technique was only recently proposed.
But, one can easily do such an analysis themselves - go to GENBANK and get some sequences, align them, and count away.
Or go here:
http://www2.norwich.edu/spage/alignmentgam.htm
And do the same.

This message is a reply to:
 Message 11 by Andya Primanda, posted 10-31-2002 12:36 AM Andya Primanda has replied

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Andya Primanda
Inactive Member


Message 13 of 17 (22322)
11-12-2002 2:32 AM
Reply to: Message 12 by derwood
11-04-2002 10:50 AM


Dr Page, I have read the original article. (Britten 2002, PNAS). Now, I had seen that indels cannot be treated the same way as base replacements. Each base replacement equals 1 evolutionary step while each insertion/deletion event can make great differences. How do I translate the indels into evolutionary steps? By counting their average length & number?

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Replies to this message:
 Message 14 by derwood, posted 11-12-2002 5:52 PM Andya Primanda has replied

  
derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 14 of 17 (22387)
11-12-2002 5:52 PM
Reply to: Message 13 by Andya Primanda
11-12-2002 2:32 AM


quote:
Originally posted by Andya Primanda:
Dr Page, I have read the original article. (Britten 2002, PNAS). Now, I had seen that indels cannot be treated the same way as base replacements. Each base replacement equals 1 evolutionary step while each insertion/deletion event can make great differences. How do I translate the indels into evolutionary steps? By counting their average length & number?
That I do not know. I have not read Britten's paper yet, so I do not know exactly what his method it.
I'm not sure what you mean by 'evolutionary steps' - is that the term Britten uses?

This message is a reply to:
 Message 13 by Andya Primanda, posted 11-12-2002 2:32 AM Andya Primanda has replied

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 Message 16 by Andya Primanda, posted 11-12-2002 10:28 PM derwood has replied

  
Andya Primanda
Inactive Member


Message 15 of 17 (22404)
11-12-2002 10:21 PM
Reply to: Message 14 by derwood
11-12-2002 5:52 PM


Here is the link to the PNAS article. It's free in Indonesia, anyway.
Just a moment...
The NCBI entry
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels.
Britten RJ.
California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625.
Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by repeatmasker (http://ftp.genome.washington.edu/RM/RepeatMasker.html).
PMID: 12368483 [PubMed - in process]

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