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Author Topic:   Definition of Species
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 316 of 450 (615315)
05-12-2011 8:06 AM
Reply to: Message 311 by Big_Al35
05-11-2011 2:39 PM


Re: Gene Deletion
Well we've had a few examples of gene names eg
APOL1, APOL4, CARD18

To be precise those aren't actually gene names, they are gene symbols. The gene names are Apolipoprotein L1, Apolipoprotein L4 and Caspase recruitment domain-containing protein 18.

Human Gene symbols are unique identifiers which are assigned to genes by the HUGO gene nomenclature committee. Gene names are usually a matter of choice of the initial discoverers although it varies depending on the organism, some species have more rigid gene nomenclature than others and many genes end up with various synonyms, for instance CARD18 was previously known as Iceberg.

Unfortunately the designations given to the OR genes in the Gilad paper do not seem to correspond to those on the HORDE database that the sequences came from. To take the OR4C subfamily as an example the HORDE database does have 10 intact genes and 10 pseudogenes, but it has properly assigned gene nomenclature where pseudogenes are designated with a P suffix, i.e. olfactory receptor, family 7, subfamily E, member 18 pseudogene has the symbol OR7E18P.

I'm not sure why the paper uses their own idiosyncratic nomenclature, it is understandable for the chimp sequences they derived de novo through their analysis but not for the human ones, especially since in a subsequent table they use the standard nomenclature. It has the very unfortunate side effect of effectively anonymising all of the actual sequences in the tree.

If I find myself at a loose end I might try Blasting the sequences for the 4c subfamily against the chimpanzee genome and see if I can recover any sort of similar tree.

TTFN,

WK

Edited by Wounded King, : Messed up link fixed


This message is a reply to:
 Message 311 by Big_Al35, posted 05-11-2011 2:39 PM Big_Al35 has not yet responded

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


Message 317 of 450 (617856)
05-31-2011 2:32 PM
Reply to: Message 308 by Percy
05-11-2011 12:54 PM


Re: Gene Deletion
Percy writes:

Again, no one is writing papers on whether chimps have genes that humans do not.

You originally stated that chimps and humans both have genes that the other does not have. Please provide evidence for your claims or alternatively retract your remark.

Percy writes:

But you vastly underestimate the importance of the olfactory genes. While the smell sensors are small and not physically visible they evidently are of critical importance for tetrapods because of the amount of genetic and brain real estate dedicated to them.

You also stated that while humans and chimps share 98% of their genome it was the genes that were different. The article referring to the olfactory genes refers to large numbers of pseudo genes differing between the two species. Infact pseudogenes outnumber real genes by a significant order of magnitude in this article. This suggests that it's not so much the genes but the non functional parts of the DNA that are most different between the two species.

Your reference/evidence therefore contradicts your own argument.


This message is a reply to:
 Message 308 by Percy, posted 05-11-2011 12:54 PM Percy has responded

Replies to this message:
 Message 318 by Wounded King, posted 05-31-2011 4:47 PM Big_Al35 has responded
 Message 319 by Percy, posted 05-31-2011 5:30 PM Big_Al35 has not yet responded

  
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 318 of 450 (617931)
05-31-2011 4:47 PM
Reply to: Message 317 by Big_Al35
05-31-2011 2:32 PM


Re: Gene Deletion
Please provide evidence for your claims or alternatively retract your remark.

You have had a number of examples presented to you from a variety of papers.

You also stated that while humans and chimps share 98% of their genome it was the genes that were different.

Can you give a clear reference for this? Percy certainly did say that the gene complements were different, but I don't remember him suggesting that all or even most of the 2% divergence between chimps and humans was in genes and certainly not in differences in gene complement between the lineages.

The article referring to the olfactory genes refers to large numbers of pseudo genes differing between the two species.

And a number of these are cases where the gene has been pseudogenised only in one lineage, therefore representing a situation where the different lineages have distinct complements of intact protein coding sequences. There were also a couple of other articles referenced and there are more still out there, but it is hard to see the point in presenting them when you refuse to accept the evidence already presented to you.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 317 by Big_Al35, posted 05-31-2011 2:32 PM Big_Al35 has responded

Replies to this message:
 Message 320 by Big_Al35, posted 06-01-2011 1:24 PM Wounded King has responded

  
Percy
Member
Posts: 18995
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 319 of 450 (617950)
05-31-2011 5:30 PM
Reply to: Message 317 by Big_Al35
05-31-2011 2:32 PM


Re: Gene Deletion
Hi Al, welcome back!

Big_Al35 writes:

Percy writes:

Again, no one is writing papers on whether chimps have genes that humans do not.


You originally stated that chimps and humans both have genes that the other does not have. Please provide evidence for your claims or alternatively retract your remark.

As WK said, we've already provided that evidence. While probably no one is writing papers where the main topic is whether chimps have genes humans do not, by perusing the literature we were able to find papers that mentioned genes chimps have that humans do not, and that humans have that chimps do not.

It is very likely that there are species more closely related than chimps and humans that share all their genes and only differ in their alleles, and maybe WK can name some, but the general rule is that the more distant the relationship between species the fewer genes they will share.

I'm concerned that you never do anything with the information people provide, you just move on to ask more questions. Unless you can explain why you want this information there's really not much point in continuing to fetch information for you.

You also stated that while humans and chimps share 98% of their genome...

It was actually you who gave the 98% figure back in Message 253:

BigAl35 in Message 253 writes:

Thats very interesting given that we share 98% of our entire genome with chimpanzees and yet only 2-3% of the genome consists of genes!

So if you've found a contradiction it is with yourself.

What is the point you hope to make with the information you keep requesting?

--Percy

Edited by Percy, : Grammar.


This message is a reply to:
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Big_Al35
Member
Posts: 384
Joined: 06-02-2010


Message 320 of 450 (618117)
06-01-2011 1:24 PM
Reply to: Message 318 by Wounded King
05-31-2011 4:47 PM


Re: Gene Deletion
WK writes:

You have had a number of examples presented to you from a variety of papers.

Disagree. You have named only one potential candidate ie C4C1001 which non of us have been able to cross reference with any other source. We still haven't even established if this a real gene or not. Even if you were to tell me that it were, you don't have any cross reference to cement your claim. We can't continue with this debate while Percy continues to make wild claims with no substance behind them.


This message is a reply to:
 Message 318 by Wounded King, posted 05-31-2011 4:47 PM Wounded King has responded

Replies to this message:
 Message 321 by Percy, posted 06-01-2011 2:17 PM Big_Al35 has not yet responded
 Message 322 by Wounded King, posted 06-01-2011 3:52 PM Big_Al35 has responded

  
Percy
Member
Posts: 18995
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 321 of 450 (618124)
06-01-2011 2:17 PM
Reply to: Message 320 by Big_Al35
06-01-2011 1:24 PM


Re: Gene Deletion
Hi Al,

I think if you want me to do more work looking up information for you then you should explain what point you hope to make with this information, because so far you have ignored information previously provided and just moved on to ask another question.

Why is it that you doubt that chimps have genes humans don't anyway? Do you doubt that gorillas have genes humans don't? Monkies? Lemurs? Vietnamiese pot-bellied pigs? Is there any rhyme or reason to your doubts, or do you just like making busy work for people?

So explain to us the implications. If it turns out that humans have genes chimps don't, but chimps have no genes that humans don't, what would that mean for your position? How would it advance your cause?

--Percy


This message is a reply to:
 Message 320 by Big_Al35, posted 06-01-2011 1:24 PM Big_Al35 has not yet responded

  
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 322 of 450 (618148)
06-01-2011 3:52 PM
Reply to: Message 320 by Big_Al35
06-01-2011 1:24 PM


Re: Gene Deletion
You have named only one potential candidate ie C4C1001 which non of us have been able to cross reference with any other source.

This is original research, what other sources would you cross reference it to? On top of which your claim simply isn't true, I gave you references for several other genes, Message 303, which had been inactivated in the human lineage but not in chimps including CMP-Neu5Ac hydrolase (CMAH) and Myosin Heavy Chain 16 (MYH16).

Still lets give you yet another example to see how you fudge and slide your way around it; Several studies detail a variety of immune system genes that are distinct betwen humans and chimps, those absent in the human lineage include KIR2DL6, KIR2DL7, KIR2DL9, KIR3DL4 and KIR3DL5 (Moesta et al., 2009 ;Abi-Rached et al., 2010).

TTFN,

WK


This message is a reply to:
 Message 320 by Big_Al35, posted 06-01-2011 1:24 PM Big_Al35 has responded

Replies to this message:
 Message 324 by Big_Al35, posted 06-02-2011 6:22 AM Wounded King has responded

  
Taq
Member
Posts: 8172
Joined: 03-06-2009
Member Rating: 4.2


Message 323 of 450 (618158)
06-01-2011 5:02 PM


Just a few more examples:

quote:
Science. 2005 Sep 9;309(5741):1693.
A human-specific gene in microglia.
Hayakawa T, Angata T, Lewis AL, Mikkelsen TS, Varki NM, Varki A.
SourceGlycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093, USA.

Abstract
Recent studies have shown multiple differences between humans and apes in sialic acid (Sia) biology, including Siglecs (Sia-recognizing-Ig-superfamily lectins). Comparisons with the chimpanzee genome indicate that human SIGLEC11 emerged through human-specific gene conversion by an adjacent pseudogene. Conversion involved 5 cent untranslated sequences and the Sia-recognition domain. This human protein shows reduced binding relative to the ancestral form but recognizes oligosialic acids, which are enriched in the brain. SIGLEC11 is expressed in human but not in chimpanzee brain microglia. Further studies will determine if this event was related to the evolution of Homo.


quote:
Identification of human specific gene duplications relative to other primates by array CGH and quantitative PCR.
Armengol G, Knuutila S, Lozano JJ, Madrigal I, Caballín MR.
SourceDepartment of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
Abstract
In order to identify human lineage specific (HLS) copy number differences (CNDs) compared to other primates, we performed pair wise comparisons (human vs. chimpanzee, gorilla and orangutan) by using cDNA array comparative genomic hybridization (CGH). A set of 23 genes with HLS duplications were identified, as well as other lineage differences in gene copy number specific of chimpanzee, gorilla and orangutan. Each species has gained more copies of specific genes rather than losing gene copies. Eleven of the 23 genes have only been observed to have undergone HLS duplication in Fortna et al. (2004) and in the present study. Then, seven of these 11 genes were analyzed by quantitative PCR in chimpanzee, gorilla and orangutan, as well as in other six primate species (Hylobates lar, Cercopithecus aethiops, Papio hamadryas, Macaca mulatta, Lagothrix lagothricha, and Saimiri sciureus). Six genes confirmed array CGH data, and four of them appeared to have bona fide HLS duplications (ABCB10, E2F6, CDH12, and TDG genes). We propose that these gene duplications have a potential to contribute to specific human phenotypes.

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


Message 324 of 450 (618210)
06-02-2011 6:22 AM
Reply to: Message 322 by Wounded King
06-01-2011 3:52 PM


Re: Gene Deletion
WK writes:

Still lets give you yet another example to see how you fudge and slide your way around it

There is no obligation upon me to explain what I intend to use this information for as Percy would have you believe.

Ahh finally we have something to work with ie MYH16. It's not a case of trying to wriggle out of anything. If you make a claim like the one Percy made you should be able to back it up with evidence. I note that the evidence had to come from you and not Percy?

Why can't Percy back up his own claims?


This message is a reply to:
 Message 322 by Wounded King, posted 06-01-2011 3:52 PM Wounded King has responded

Replies to this message:
 Message 325 by Panda, posted 06-02-2011 6:31 AM Big_Al35 has not yet responded
 Message 326 by Percy, posted 06-02-2011 6:55 AM Big_Al35 has responded
 Message 327 by Wounded King, posted 06-02-2011 1:46 PM Big_Al35 has not yet responded

  
Panda
Member (Idle past 2034 days)
Posts: 2688
From: UK
Joined: 10-04-2010


Message 325 of 450 (618211)
06-02-2011 6:31 AM
Reply to: Message 324 by Big_Al35
06-02-2011 6:22 AM


Re: Gene Deletion
You have the examples you asked for.
So....what next?

This message is a reply to:
 Message 324 by Big_Al35, posted 06-02-2011 6:22 AM Big_Al35 has not yet responded

  
Percy
Member
Posts: 18995
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 326 of 450 (618213)
06-02-2011 6:55 AM
Reply to: Message 324 by Big_Al35
06-02-2011 6:22 AM


Re: Gene Deletion
Big_Al35 writes:

Ahh finally we have something to work with ie MYH16.

And also KIR2DL6, KIR2DL7, KIR2DL9, KIR3DL4 and KIR3DL5 that WK enumerated in the next paragraph. This is in addition to the other gene that chimps have that humans don't that we provided before your brief absence .

It has now been shown that humans have genes chimps don't, and that chimps have genes humans don't, and we're curious what you're planning to do with this information.

--Percy


This message is a reply to:
 Message 324 by Big_Al35, posted 06-02-2011 6:22 AM Big_Al35 has responded

Replies to this message:
 Message 328 by Big_Al35, posted 06-03-2011 4:03 AM Percy has responded

  
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 327 of 450 (618254)
06-02-2011 1:46 PM
Reply to: Message 324 by Big_Al35
06-02-2011 6:22 AM


Re: Gene Deletion
Ahh finally we have something to work with ie MYH16.

Finally, as in 2 months ago when I first posted that information?

TTFN,

WK


This message is a reply to:
 Message 324 by Big_Al35, posted 06-02-2011 6:22 AM Big_Al35 has not yet responded

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


Message 328 of 450 (618385)
06-03-2011 4:03 AM
Reply to: Message 326 by Percy
06-02-2011 6:55 AM


Re: Gene Deletion
Percy writes:

we're curious what you're planning to do with this information

Well I could add this information to an an article that I am currently writing or I could write it on a piece of toilet tissue and wipe my ass with it. Why do you care?


This message is a reply to:
 Message 326 by Percy, posted 06-02-2011 6:55 AM Percy has responded

Replies to this message:
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 Message 330 by Percy, posted 06-03-2011 6:21 AM Big_Al35 has not yet responded
 Message 331 by tesla, posted 06-10-2011 12:51 PM Big_Al35 has responded

  
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 329 of 450 (618386)
06-03-2011 5:01 AM
Reply to: Message 328 by Big_Al35
06-03-2011 4:03 AM


Re: Gene Deletion
Why do you care?

He cares because this is supposed to be a thread for discussing ways of defining species. If you aren't interested in that topic then you should make another thread to discuss the specific genetic differences between chimps and humans.

TTFN,

WK


This message is a reply to:
 Message 328 by Big_Al35, posted 06-03-2011 4:03 AM Big_Al35 has not yet responded

  
Percy
Member
Posts: 18995
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 330 of 450 (618387)
06-03-2011 6:21 AM
Reply to: Message 328 by Big_Al35
06-03-2011 4:03 AM


Re: Gene Deletion
Hi Al,

Is everything okay? Before your brief absence you seemed pretty intent on making a case that we can't really determine the relatedness of species, but now something else seems to be occupying your mind that you're not telling us. What's up?

--Percy


This message is a reply to:
 Message 328 by Big_Al35, posted 06-03-2011 4:03 AM Big_Al35 has not yet responded

  
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