Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 77 (8905 total)
Current session began: 
Page Loaded: 04-26-2019 7:58 AM
26 online now:
Percy (Admin), Phat (AdminPhat), vimesey (3 members, 23 visitors)
Chatting now:  Chat room empty
Newest Member: WookieeB
Post Volume:
Total: 850,247 Year: 5,284/19,786 Month: 1,406/873 Week: 302/460 Day: 2/52 Hour: 1/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
RewPrev1
...
1718
19
2021
...
30NextFF
Author Topic:   Definition of Species
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 271 of 450 (614886)
05-08-2011 12:29 PM
Reply to: Message 270 by Percy
05-08-2011 11:56 AM


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.


This message is a reply to:
 Message 270 by Percy, posted 05-08-2011 11:56 AM Percy has responded

Replies to this message:
 Message 272 by Wounded King, posted 05-08-2011 1:50 PM Big_Al35 has responded
 Message 275 by Percy, posted 05-08-2011 3:54 PM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 272 of 450 (614888)
05-08-2011 1:50 PM
Reply to: Message 271 by Big_Al35
05-08-2011 12:29 PM


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


This message is a reply to:
 Message 271 by Big_Al35, posted 05-08-2011 12:29 PM Big_Al35 has responded

Replies to this message:
 Message 273 by Big_Al35, posted 05-08-2011 3:08 PM Wounded King has not yet responded
 Message 276 by Percy, posted 05-08-2011 4:03 PM Wounded King has not yet responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 273 of 450 (614892)
05-08-2011 3:08 PM
Reply to: Message 272 by Wounded King
05-08-2011 1:50 PM


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


This message is a reply to:
 Message 272 by Wounded King, posted 05-08-2011 1:50 PM Wounded King has not yet responded

Replies to this message:
 Message 274 by Dr Adequate, posted 05-08-2011 3:54 PM Big_Al35 has responded

    
Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


(1)
Message 274 of 450 (614894)
05-08-2011 3:54 PM
Reply to: Message 273 by Big_Al35
05-08-2011 3:08 PM


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.


This message is a reply to:
 Message 273 by Big_Al35, posted 05-08-2011 3:08 PM Big_Al35 has responded

Replies to this message:
 Message 277 by Big_Al35, posted 05-08-2011 6:57 PM Dr Adequate has responded

  
Percy
Member
Posts: 18378
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


(1)
Message 275 of 450 (614895)
05-08-2011 3:54 PM
Reply to: Message 271 by Big_Al35
05-08-2011 12:29 PM


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.


This message is a reply to:
 Message 271 by Big_Al35, posted 05-08-2011 12:29 PM Big_Al35 has not yet responded

    
Percy
Member
Posts: 18378
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


(1)
Message 276 of 450 (614896)
05-08-2011 4:03 PM
Reply to: Message 272 by Wounded King
05-08-2011 1:50 PM


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


This message is a reply to:
 Message 272 by Wounded King, posted 05-08-2011 1:50 PM Wounded King has not yet responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 277 of 450 (614908)
05-08-2011 6:57 PM
Reply to: Message 274 by Dr Adequate
05-08-2011 3:54 PM


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.


This message is a reply to:
 Message 274 by Dr Adequate, posted 05-08-2011 3:54 PM Dr Adequate has responded

Replies to this message:
 Message 278 by Percy, posted 05-08-2011 8:34 PM Big_Al35 has not yet responded
 Message 279 by Dr Adequate, posted 05-08-2011 9:12 PM Big_Al35 has not yet responded
 Message 280 by Wounded King, posted 05-09-2011 6:29 AM Big_Al35 has responded

    
Percy
Member
Posts: 18378
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


(1)
Message 278 of 450 (614909)
05-08-2011 8:34 PM
Reply to: Message 277 by Big_Al35
05-08-2011 6:57 PM


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.


This message is a reply to:
 Message 277 by Big_Al35, posted 05-08-2011 6:57 PM Big_Al35 has not yet responded

    
Dr Adequate
Member
Posts: 16094
Joined: 07-20-2006
Member Rating: 9.0


(1)
Message 279 of 450 (614910)
05-08-2011 9:12 PM
Reply to: Message 277 by Big_Al35
05-08-2011 6:57 PM


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.


This message is a reply to:
 Message 277 by Big_Al35, posted 05-08-2011 6:57 PM Big_Al35 has not yet responded

  
Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 280 of 450 (614927)
05-09-2011 6:29 AM
Reply to: Message 277 by Big_Al35
05-08-2011 6:57 PM


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


This message is a reply to:
 Message 277 by Big_Al35, posted 05-08-2011 6:57 PM Big_Al35 has responded

Replies to this message:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Wounded King has responded

    
Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 281 of 450 (614942)
05-09-2011 11:00 AM
Reply to: Message 280 by Wounded King
05-09-2011 6:29 AM


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.


This message is a reply to:
 Message 280 by Wounded King, posted 05-09-2011 6:29 AM Wounded King has responded

Replies to this message:
 Message 282 by Dr Jack, posted 05-09-2011 11:13 AM Big_Al35 has not yet responded
 Message 283 by Percy, posted 05-09-2011 11:22 AM Big_Al35 has responded
 Message 284 by Wounded King, posted 05-09-2011 11:50 AM Big_Al35 has not yet responded
 Message 289 by Dr Adequate, posted 05-09-2011 7:02 PM Big_Al35 has not yet responded

    
Dr Jack
Member (Idle past 216 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 282 of 450 (614946)
05-09-2011 11:13 AM
Reply to: Message 281 by Big_Al35
05-09-2011 11:00 AM


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.


This message is a reply to:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Big_Al35 has not yet responded

  
Percy
Member
Posts: 18378
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.8


(1)
Message 283 of 450 (614947)
05-09-2011 11:22 AM
Reply to: Message 281 by Big_Al35
05-09-2011 11:00 AM


Gene Deletion
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


This message is a reply to:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Big_Al35 has responded

Replies to this message:
 Message 285 by Wounded King, posted 05-09-2011 12:04 PM Percy has acknowledged this reply
 Message 286 by Big_Al35, posted 05-09-2011 5:23 PM Percy has responded
 Message 290 by Big_Al35, posted 05-10-2011 6:26 AM Percy has responded

    
Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 284 of 450 (614955)
05-09-2011 11:50 AM
Reply to: Message 281 by Big_Al35
05-09-2011 11:00 AM


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


This message is a reply to:
 Message 281 by Big_Al35, posted 05-09-2011 11:00 AM Big_Al35 has not yet responded

    
Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 285 of 450 (614958)
05-09-2011 12:04 PM
Reply to: Message 283 by Percy
05-09-2011 11:22 AM


Re: Gene Deletion
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


This message is a reply to:
 Message 283 by Percy, posted 05-09-2011 11:22 AM Percy has acknowledged this reply

    
RewPrev1
...
1718
19
2021
...
30NextFF
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2019