|
Register | Sign In |
|
QuickSearch
Thread ▼ Details |
Member (Idle past 1435 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Thread Info
|
|
|
Author | Topic: Definition of Species | |||||||||||||||||||||||||||||||||||||||||||||||
Big_Al35 Member (Idle past 829 days) Posts: 389 Joined: |
Science News writes: "For example, a surprisingly high number of genes involved in the inflammatory response - APOL1, APOL4, CARD18, IL1F7, IL1F8 - are completely deleted from chimp genome." I agree that a lot of our differences come to down to interpretation of plain english. The article above however, seems a dubious source of information. The above sentence seems to imply that the gene existed in chimps but has since been deleted. There is no evidence in the article about that fact however. The article goes on to suggest that regulation must be provided by other means in chimps but again no evidence given. Sorry but I can't take this article seriously.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
|
The article has a link at the bottom to the new research article on CNVs it is discussing (Perry et al., 2008) and also the previous initial comparison between chimp /human genomes from Nature (The Chimpanzee Sequencing and Analysis Consortium, 2005).
The data related to the specific genes APOL1, APOL4, CARD18, IL1F7, IL1F8 are from the original Nature paper, in fact there is a table (S.42) in the supplementary data (Word Doc) for that paper which lists about 35 genes which appear to have been completely deleted from the Chimp genome. The way they distinguish a deletion which occurred in the chimp lineage is also by looking at other species. If a gene is only present in humans then it is probably a human innovation, if it is present in humans, gorillas and macaques and absent in chimps then it was probably lost in the chimp lineage. In this case the other species were non-primates like mouse and rat on which we already had a lot of genetic data.
There is no evidence in the article about that fact however. The article goes on to suggest that regulation must be provided by other means in chimps but again no evidence given. The evidence is that chimpanzes have functional inflammatory responses despite not having these specific genes.
Sorry but I can't take this article seriously. You should take this article seriously, it is essentially a slightly modified press release from the Sanger Centre one of the premier institutes of genetic research in the world, if you can't then perhaps it is because you lack the tools to effectively evaluate the quality of the information you are presented with. As an aside to Percy, if you are trying to argue that differences in gene complement are indicative of distinct species then CNVs are so not the way to go, considering that they show there are differences in gene complement within species. TTFN, WK
|
|||||||||||||||||||||||||||||||||||||||||||||||
Big_Al35 Member (Idle past 829 days) Posts: 389 Joined: |
WK writes: if it is present in humans, gorillas and macaques and absent in chimps then it was probably lost in the chimp lineage What an awful assumption to make. I can't imagine what they are thinking to conclude that it was probably lost in the chimp lineage. Anyway from what I have read APOL1 has variants across humans too with africans and europeans having different versions of the gene.
link
|
|||||||||||||||||||||||||||||||||||||||||||||||
Dr Adequate Member (Idle past 314 days) Posts: 16113 Joined:
|
What an awful assumption to make. I can't imagine what they are thinking to conclude that it was probably lost in the chimp lineage. They're thinking: what are the odds that not having these genes was the basal state and that just by coincidence it was added by separate but identical evolutionary events in the lineages which possess it.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9
|
Big_Al35 writes: I agree that a lot of our differences come to down to interpretation of plain english. Right, and I explained how my interpretation of the Wikipedia article on the Chimpanzee genome project concerning gene duplications was correct. Now it's your turn to explain how your interpretation is correct. Give it a try.
The article above however, seems a dubious source of information. The article describes research that appeared in the journal Nature (Initial sequence of the chimpanzee genome and comparison with the human genome) and in the journal Genome (Copy number variation and evolution in humans and chimpanzees), something you would have discovered had you actually read the article. Could you please provide some evidence that you're not just casting aspersions on any ideas you don't like, but that you are instead someone whose opinions are supported by research superior to that that I just cited, and that therefore your characterization of "dubious" has actual merit instead of being the simple name calling that it appears to be?
The above sentence seems to imply that the gene existed in chimps but has since been deleted. There is no evidence in the article about that fact however. I provided the links to the original research, so you should have no trouble finding the evidence if, for some strange reason, you suspect the news article is lying. Why are you so doubtful about deleted genes? It's very strange. Did something you read somewhere tell you that genes can't be deleted?
The article goes on to suggest that regulation must be provided by other means in chimps but again no evidence given. Sorry but I can't take this article seriously. Research often raises unanswered questions. Does this surprise you? --Percy Edited by Percy, : Typo.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9
|
I'm not going in any particular direction. I'm just a tail being wagged by Al. I have no idea where he is going, and I don't think he does either. It appears to me that, not understanding much of what is being said, he's just objecting to random statements. When it's pointed out where his claims are wrong he just picks out more random statements from the latest explanations to object to, and the cycle starts over.
I've been trying to steer him back to the discussion about identifying species differences, but he's ignoring it. --Percy
|
|||||||||||||||||||||||||||||||||||||||||||||||
Big_Al35 Member (Idle past 829 days) Posts: 389 Joined: |
They're thinking: what are the odds that not having these genes was the basal state and that just by coincidence it was added by separate but identical evolutionary events in the lineages which possess it. In other words it's one absurd assumption compounding another crazy assumption. Even if we were to assume that the gene evolved as you indicate, this still doesn't imply two evolutionary events. You make the assumption I guess on the basis that you have assumed a closer relationship between humans and chimps than other primates. Whilst some DNA might suggest a closer relationship, APOL1 suggests a more distant relationship.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9
|
Big_Al35 writes: In other words it's one absurd assumption compounding another crazy assumption. No, Al, try again. Imagine Dr Adequate's post being read in a sarcastic tone, that might help. Here's an analogy to what you're doing. Me and my friend Joe are planning to go to a party. That afternoon Joe calls me and says he can't go because his car broke down and is in the shop and he won't get it back until Monday. So I go to the party anyway, and there's Joe! So I comment to you, "I guess Joe found other means to get here." And you respond, "What kind of absurd assumption is that?" That's how much sense you're making. --Percy Edited by Percy, : Provide analogy.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Dr Adequate Member (Idle past 314 days) Posts: 16113 Joined:
|
In other words it's one absurd assumption compounding another crazy assumption. Those are, to be sure, other words. But it is not the same thing in other words. Try reading it again; and bear in mind that if you don't immediately understand something, it's not always the thing that you don't understand that is stupid. Occasionally it may be you.
Even if we were to assume that the gene evolved as you indicate, this still doesn't imply two evolutionary events. I have no idea what you're talking about.
You make the assumption I guess on the basis that you have assumed a closer relationship between humans and chimps than other primates. No: on the basis that chimps do not lie outside a clade which includes humans and gorillas and macaques. --- Let me try to explain the reasoning by analogy. Suppose you have seen 100 of the same make of car. 99 of them have a winged horse as a hood ornament. One of them does not. If you had to chose between the following two explanations, which would you find most likely? (1) The hood ornament is standard, but one car has lost its hood ornament.(2) Having no hood ornament is standard, but 99% of drivers have by complete coincidence chosen to accessorize their cars in exactly the same way. Both accounts of the history of the cars is possible; but one of them is overwhelmingly more probable, is it not? Edited by Dr Adequate, : No reason given.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
|
You make the assumption I guess on the basis that you have assumed a closer relationship between humans and chimps than other primates. Whilst some DNA might suggest a closer relationship, APOL1 suggests a more distant relationship. It isn't 'some' DNA which suggests a closer relationship, it is the overwhelming majority of the DNA, based on cross species comparisons between multiple different species. If you can present a more parsimonious explanation of all the genetic data than humans and chimps being each other's closest extant relative then go ahead, but you can't simply cherry pick a single gene and argue chimps and humans are more distantly related from that single data point. TTFN, WK
|
|||||||||||||||||||||||||||||||||||||||||||||||
Big_Al35 Member (Idle past 829 days) Posts: 389 Joined: |
DrA writes: (2) Having no hood ornament is standard, but 99% of drivers have by complete coincidence chosen to accessorize their cars in exactly the same way. What utter bu*lsh*t. I don't think this even warrants a reply.
WK writes: It isn't 'some' DNA which suggests a closer relationship, it is the overwhelming majority of the DNA Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation. Hardly overwhelming.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.3
|
Big_Al35 writes: Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation. Hardly overwhelming. Phylogenies are not constructed by looking at crude % differences! They're constructed by tracking specific genetic changes.
|
|||||||||||||||||||||||||||||||||||||||||||||||
Percy Member Posts: 22505 From: New Hampshire Joined: Member Rating: 4.9
|
Big_Al35 writes: What utter bu*lsh*t. I don't think this even warrants a reply. You replied.
Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation. Hardly overwhelming. But that wasn't the argument you were responding to. Several genes present in humans and missing from chimps were listed. WK described the way that they determine that they were deleted in chimps rather than rising anew in humans, and that was by comparing with other species like mice and rats. Since mice and rats had these genes, presumably the common ancestor of humans and chimps also had these genes, and then the branch leading to chimps lost these genes while the branch leading to humans did not. Other scenarios are possible but ridiculously unlikely. For example, humans could have developed precisely the same genes as mice and rats while chimps did not. Or there could have been a horizontal gene transfer from mice and rats over to humans. If you can't tell how ridiculously unlikely these scenarios are then you shouldn't be discussing this topic. --Percy
|
|||||||||||||||||||||||||||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
|
Hardly, when chimps and gorillas have a 97% correlation and humans and gorillas have a 97% correlation while chimps and humans have a 98% correlation Well again, this is one of the times when some source or context for your numbers would be helpful. Have we not just finished discussing a whole lot of different things that such % values can represent, from nucleotide level substitutions, through indels and up to entire gene deletions? Even so, I'm not sure what point you think you are making. I made a specific claim, that in the overwhelming majority of genetic sequences chimp and human are each other's closest relative. You aren't countering that claim by pointing out that they are both less closely related to gorillas, you are just agreeing with me in a highly idiosyncratic manner. I didn't say that the degree by which chimps and humans were more related was overwhelming. I said that the extent of the genome over which this was the case was overwhelming, i..e the vast majority of the genome coding and non-coding, as opposed to the one gene comparison you were trying to use to argue against it. I'm quite happy to stipulate that there are probably many more genes where humans and gorillas or chimps and gorillas will tree out more closely, but that isn't the case for the vast majority of sequences. You seem to be moving farther and farther away from trying to have a genuine discussion. By dismissing Dr. A's point so cavalierly you are essentially dismissing maximum parsimony, one of the key methods used in phylogenetics, with nothing more than a wave of your hand. All you seem to be bringing to this discussion is contrariness. TTFN, WK
|
|||||||||||||||||||||||||||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Hi Percy,
Just to be clear, while they did perform alignments of mouse and rat with the human and chimp genomes, that doesn't mean that all of the chimp deleted sequences were present in mouse and rat. For example the APOL gene cluster, including APOL1, seems to be primate specific. Sorry if what I wrote was misleading. TTFN, WK
|
|
|
Do Nothing Button
Copyright 2001-2023 by EvC Forum, All Rights Reserved
Version 4.2
Innovative software from Qwixotic © 2024