Register | Sign In


Understanding through Discussion


EvC Forum active members: 64 (9164 total)
3 online now:
Newest Member: ChatGPT
Post Volume: Total: 916,803 Year: 4,060/9,624 Month: 931/974 Week: 258/286 Day: 19/46 Hour: 0/1


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   ID/Creationism - Comparison of Human and Chimp Genomes
Meddle
Member (Idle past 1297 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 1 of 83 (348239)
09-11-2006 9:33 PM


As I said originally my initial post was to understand the other sides point of view, but when you put it like that...
Okay I will go with your suggestion, since I've found this area lacking in Creationist/ID literature. I also find this to be the most compelling evidence in support of evolution.
How would Creationist/ID models be used to interpret artifacts we see in species genomes? For example, looking at the human genome comparing it with chimpanzee's and the other great apes:
(1) In human chromosome 2 there is a telomere sequence and the remnants of a centromere sequence, indicating that this results from the fusion of the chimpanzee chromosomes 2p and 2q.
(2) The presence of endogenous retroviruses at the same position within the genomes of different species.
(3) Both chimp and humans have two 21-hydroxylase genes on their genome - a functional gene and a pseudogene. Both share the same mutation which inactivated the pseudogene.
Finally two questions on how to proceed further in Creationist/ID models:
(4) If humans and chimpanzees are supposed to be entirely separate species, how much value is there in comparing the two genomes?
(5) In terms of ID, at what point would something be declared as 'irreducibly complex'? After such a decision, would study on such an irreducibly complex continue, and if so how? For example Michael Behe's example of the bacterial flagellum.

Replies to this message:
 Message 2 by Adminnemooseus, posted 09-11-2006 9:37 PM Meddle has not replied
 Message 3 by Damouse, posted 10-09-2006 9:03 PM Meddle has not replied
 Message 4 by eggasai, posted 10-19-2006 4:58 PM Meddle has replied
 Message 47 by NewYorkCityBoy, posted 11-04-2006 2:23 AM Meddle has not replied
 Message 82 by Dr Adequate, posted 01-26-2008 6:23 AM Meddle has not replied

  
Meddle
Member (Idle past 1297 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 16 of 83 (358189)
10-22-2006 8:08 PM
Reply to: Message 4 by eggasai
10-19-2006 4:58 PM


Well mick has covered most of what I was going to say.
I've seen the supposed fusion site and the TAG seqeunces, it seems pretty convincing. There is just one problem, there is not one but 9 pericentric inversions that total 20 million base pairs (Mb). One of them is 4 Mb long and the shortest is 2 Mb long. What is more there are inversions riddled throughout the two genomes that are not easily explained as naturally occuring.
So why do you think that nine pericentric inversions to be unlikely, and which genomic rearrangements do you find hard to explain through natural processes?
Having said that, as I said in my original post, I am interested in how creationists explain the genetic evidence. As already mentioned, in the case of the human chromosome 2, we see the remnants of a second centromere region, and an additional telomere sequence. The sequence of this telomere also reverses half way though, in a head-to-head arrangement, and is flanked on either side by the same genes found on the two chimp chromosomes.
Now can this evidence be described based on creationist hypotheses?
Consider this, ERVs (actually LTRs) make up about 8% of the human genome. Do you really expect me to believe that all of this DNA is left over from germline invasions?
http://www.pnas.org/...ontent-nw/full/101/suppl_2/14572/FIG1
I have seen the comparisons and they generally take about half a dozen LTRs and use common alleles as markers. Then they give some convoluted estimate of them arriving independantly in the respective genomes. If we are going to talk about the Transposable Elements the first order of buisness is characterizing them, don't you?
As was described in the article which your linked diagram came from, ERV's are capable of propagating themselves throughout the genome, so germline invasion is not required to account for all present sequences. Also like other transposable elements, this amplification happens randomly, so to reiterate what mick asked, why do humans and chimps share the same transposable elements?

This message is a reply to:
 Message 4 by eggasai, posted 10-19-2006 4:58 PM eggasai has replied

Replies to this message:
 Message 17 by eggasai, posted 10-24-2006 7:07 PM Meddle has not replied

  
Meddle
Member (Idle past 1297 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 31 of 83 (359127)
10-26-2006 7:06 PM
Reply to: Message 10 by eggasai
10-22-2006 5:22 PM


Re: Pause for effect
The problem with the 98.5% similarity between humans and chimp was that it was based on DNA hybridisation, since that was the only method available at the time. Identical sequences will anneal, no matter where they are found, so indels can't be identified with this method. To do that you need an accurate genetic sequence to compare.
Your second article is an abstract from the original 2003 article which used a direct comparison of human and chimp genetic sequences. Of course this value of 95% could change, since the comparison was performed on a 779kb sequence.
As for your first article it's from Time magazine, not exactly a primary science journal.
Edited by Evil Homer, : No reason given.

This message is a reply to:
 Message 10 by eggasai, posted 10-22-2006 5:22 PM eggasai has not replied

Replies to this message:
 Message 46 by derwood, posted 11-03-2006 10:53 AM Meddle has not replied

  
Meddle
Member (Idle past 1297 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 32 of 83 (359129)
10-26-2006 7:07 PM
Reply to: Message 12 by eggasai
10-22-2006 7:05 PM


Re: number of point mutations is not equal to number of nucleotide differences
For instance, the PtERV1 gene is present in Chimpanzees and OWM but is absent in Asian Great Apes and humans.
For the PtERV1 sequences (not a gene, rather a collection of genes following the basic retroviral structure of ltr-gag-pol-env-ltr) it has been found there is virtually no overlap of insertion locations between species. This suggests it is not the result of vertical transmission from a common ancestor, but instead originated from horizontal transmission (infection after the species had diverged).
http://biology.plosjournals.org/perlserv?request=get-docu...
1) 35 million base pairs (Mb) due to single nucleotide substitutions.
2) 5 million indels, coming to 90 Mb in the respective genomes or 3%-4%.
3) 9 pericentric inversions from 2 Mb to 4 Mb in lenght, totally 20 Mb.
And just to add to those numbers, the human genome is 3 billion base pairs long, and only about 1.5% of this represents protein-coding genes.
With a population of over 6 billion the human genome diverges by 1/10 of 1%, but you know what, we can get back to that one. Let's say that these are permenantly fixed, this would account for the 35 Mb worth of single nucleotide substitutions. What about the indels?
Where did you get this value for the genomic divergence within the human population? Not that I doubt it, it would just be interesting to see what this was based on.

This message is a reply to:
 Message 12 by eggasai, posted 10-22-2006 7:05 PM eggasai has replied

Replies to this message:
 Message 34 by eggasai, posted 10-26-2006 7:53 PM Meddle has replied

  
Meddle
Member (Idle past 1297 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 44 of 83 (359558)
10-28-2006 9:03 PM
Reply to: Message 34 by eggasai
10-26-2006 7:53 PM


Re: number of point mutations is not equal to number of nucleotide differences
Wait a second here, if the homology arguement works in favor of common ancestor then why does the inverse logic not work. You want to focus on anecdotal evidence that favors one small segment of on ERV mutation. It's the progressive nature of the mutation that makes it so appealing a proof of common ancestry but when it is in OWM and not in humans at all you just want to dismiss it.
You might want to reconsider a simple assumption. What rational reason to you have to assume that 8% of the genome is made up of the fossilized remains of viruses. These germline invasions are rare at best, the idea that hundreds of millions of base pairs of DNA are permenantly fixed in genomes by viruses is absured.
The importance of ERV sequences as supporting evidence for common ancestry is that these sequences have been found at the same locations in the genomes of different species. The most likely explanation is that the retroviral DNA integrated itself into the genome of a common ancestor.
By comparison, PtERV sequences are not found in the same locations in the genomes of different species. This is what you would expect of retroviruses randomly inserting themselves into the genomes of separate species.
And as I already said, after integrating into the genome, ERV's are able to copy themselves elsewhere in the host genome. You do not need to rely on germline invasion to account for all the ERV sequences present in our genome. But as I asked in my OP, and as mick reiterated, what is the creationist explanation for ERV sequences?
And just to add to those numbers, the human genome is 3 billion base pairs long, and only about 1.5% of this represents protein-coding genes.
Let me ask you this, the gorilla split with both the human and chimpanzee lineage well before the austropithicene/homo split. Would you expect that 83% of the protein coding genes would show differences at an amino acid seqeunce level? You guys like to make a priori assumptions and use anecdotal evidence but you don't like making predictions. How about the spit between western and eastern gorillas, how much would you expect two seperate species to diverge within the same genus? The gorilla/chimpanzee split goes back further then the austropithecene/homo one, how would you expect the genes to line up?
Firstly I don't see how your questions relate to my quoted remarks. My point was that mutations and rearrangements affect a small proportion of the genome, and protein coding genes only take up a small proportion of the overall genome, so there is room for manoeuvre.
As to your questions, I don't think you can predict an accurate percentage for the divergence of amino acid sequence between species. With the chimp and human genomes we compared the sequences, identifying the mutations and various transposable elements, to get an accurate view of how much they diverge. The same process can be used for gorillas or any other species.
And just what would anecdotal evidence be in this context?
Human Genome Projects website. It's a wonderfull place to go and look at genomics without all of this creation/evolution bluster muddying up the waters.
Do you have a link to where on the HGP website you got that information from?
Edited by Evil Homer, : No reason given.

This message is a reply to:
 Message 34 by eggasai, posted 10-26-2006 7:53 PM eggasai has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024