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Author Topic:   Definition of Species
Percy
Member
Posts: 13060
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 301 of 450 (615193)
05-11-2011 8:55 AM
Reply to: Message 300 by Big_Al35
05-11-2011 8:13 AM


Re: Gene Deletion
Big_Al35 writes:

Is this a pseudogene or a real gene?

According to the paper, which you could read yourself so I don't know why you're asking me since you obviously don't trust me any further than you can throw me, it's a real gene.

But again, the important question is why do you care? These are the key questions. Please answer them:

  1. Why did you originally think chimps and humans shared all the same genes?

  2. Once shown that humans have some genes that chimps don't, why did you next assert that chimps have no genes that humans don't?

  3. How does it help your position if chimps don't have genes humans don't? In other words, why do you care? Do you even know? Or are you, as I suspect, just disputing everything without rhyme or reason?

--Percy


This message is a reply to:
 Message 300 by Big_Al35, posted 05-11-2011 8:13 AM Big_Al35 has responded

Replies to this message:
 Message 307 by Big_Al35, posted 05-11-2011 11:42 AM Percy has responded

    
subbie
Member
Posts: 3344
Joined: 02-26-2006
Member Rating: 6.2


(2)
Message 302 of 450 (615195)
05-11-2011 9:29 AM
Reply to: Message 298 by Big_Al35
05-11-2011 5:14 AM


L*tt*r D*l*t**n
By the way, sport, if you're going to use adult words, use the fucking word. We're adults here. Well, some of us are. Randomly substituting asterisks just make you look silly. And believe me, you don't need any help in that direction.


Ridicule is the only weapon which can be used against unintelligible propositions. -- Thomas Jefferson

We see monsters where science shows us windmills. -- Phat

It has always struck me as odd that fundies devote so much time and effort into trying to find a naturalistic explanation for their mythical flood, while looking for magical explanations for things that actually happened. -- Dr. Adequate

...creationists have a great way to detect fraud and it doesn't take 8 or 40 years or even a scientific degree to spot the fraud--'if it disagrees with the bible then it is wrong'.... -- archaeologist


This message is a reply to:
 Message 298 by Big_Al35, posted 05-11-2011 5:14 AM Big_Al35 has responded

Replies to this message:
 Message 305 by Big_Al35, posted 05-11-2011 10:21 AM subbie has acknowledged this reply

  
Wounded King
Member (Idle past 476 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(2)
Message 303 of 450 (615196)
05-11-2011 9:44 AM
Reply to: Message 300 by Big_Al35
05-11-2011 8:13 AM


Re: Gene Deletion/pseudogenisation
The evidence suggest it is a pseudogene in humans but an active gene in chimps. For some further human specific pseudogenes (HSPs) which have become fixed in the human population see Kim et al. (2010). This paper identifies 38 distinct human specific pseudogenes 25 of which are Olfactory Receptor (OR) genes. Some of the non-OR pseudogenes are CMAH, GLRA4, MBL1, MHY16, SIGLEC-13, TDH and KRT41 (for the full list see here. The authors used a more stringent approach than the original human-chimp comparison paper which had identified 120 putative HSPs, the supplementary table I linked to in the last sentence also includes the criteria they used to gategorise many of these as non-authentic HSPs.

Hopefully having established to any reasonable person's satisfaction that chimps have some functional genes humans don't and humans have some functional genes chimps don't why not now relate this back to the topic at hand, the definition of species?

TTFN,

WK


This message is a reply to:
 Message 300 by Big_Al35, posted 05-11-2011 8:13 AM Big_Al35 has not yet responded

Replies to this message:
 Message 304 by Percy, posted 05-11-2011 10:11 AM Wounded King has responded

    
Percy
Member
Posts: 13060
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


Message 304 of 450 (615198)
05-11-2011 10:11 AM
Reply to: Message 303 by Wounded King
05-11-2011 9:44 AM


Re: Gene Deletion/pseudogenisation
Wounded King writes:

The evidence suggest it is a pseudogene in humans but an active gene in chimps.

How should Figure A be interpreted to reach this conclusion? It looks like it's pairing each human genes with the corresponding chimp gene, so just above C4C1001 we see that C4C975 is paired with H4C720, but C4C1001 is not paired, and given the hierarchy it looks like a duplicated gene that branched off.

Also, how does one distinguish genes from pseudogenes in the figure?

Thanks for the help!

--Percy


This message is a reply to:
 Message 303 by Wounded King, posted 05-11-2011 9:44 AM Wounded King has responded

Replies to this message:
 Message 306 by Wounded King, posted 05-11-2011 11:03 AM Percy has acknowledged this reply

    
Big_Al35
Member
Posts: 290
Joined: 06-02-2010


(2)
Message 305 of 450 (615199)
05-11-2011 10:21 AM
Reply to: Message 302 by subbie
05-11-2011 9:29 AM


Re: L*tt*r D*l*t**n
subbie writes:

By the way, sport, if you're going to use adult words, use the fucking word. We're adults here. Well, some of us are. Randomly substituting asterisks just make you look silly. And believe me, you don't need any help in that direction.

Who the fuck are you? I wasn't talking to you anyway.

--------------------------------------------------------------------------------


This message is a reply to:
 Message 302 by subbie, posted 05-11-2011 9:29 AM subbie has acknowledged this reply

    
Wounded King
Member (Idle past 476 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 306 of 450 (615201)
05-11-2011 11:03 AM
Reply to: Message 304 by Percy
05-11-2011 10:11 AM


My bad
You are right it may be a chimp specific expansion rather than a human pseudogenisation event. I was trying to find the actual sequences in the Human Olfactory Data Explorer (HORDE) but unfortunately none of the terms there correspond to the nomenclature in the paper, I took human OR4C10P, which is a pseudogene, to be the orthologue of the chimp sequence, but now I'm doubtful if that is correct.

From the figure itself there is no way to tell the functional genes (intact) from the pseudogenes, quite why they didn't bother to do this is beyond me since they go on to say how many there are of each. Given this omission there is not actually enough information to tell which orthologous pairs are both intact or in which one or both members are pseudogenised. I suppose since the point of the figure was simply the expansions this is understandable, but it would have been nice information to have.

TTFN,

WK


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 Message 304 by Percy, posted 05-11-2011 10:11 AM Percy has acknowledged this reply

    
Big_Al35
Member
Posts: 290
Joined: 06-02-2010


Message 307 of 450 (615206)
05-11-2011 11:42 AM
Reply to: Message 301 by Percy
05-11-2011 8:55 AM


Re: Gene Deletion
Percy writes:

How does it help your position if chimps don't have genes humans don't? In other words, why do you care? Do you even know? Or are you, as I suspect, just disputing everything without rhyme or reason?

Having read the article a couple of times now I still can't confirm whether this is a real or a pseudo gene. I can't find a single other source which verifies the C4C1001 gene either. The name of the gene consisting purely of numbers and letters is intriguing too.

Given that humans and chimps have vast physical differences, I can't understand why you would choose as your only example, a "sense of smell" gene. I am not trying to be disputatious but aren't there any more worthy examples that are more suitable for study?


This message is a reply to:
 Message 301 by Percy, posted 05-11-2011 8:55 AM Percy has responded

Replies to this message:
 Message 308 by Percy, posted 05-11-2011 12:54 PM Big_Al35 has responded
 Message 309 by Coragyps, posted 05-11-2011 1:43 PM Big_Al35 has responded

    
Percy
Member
Posts: 13060
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(1)
Message 308 of 450 (615212)
05-11-2011 12:54 PM
Reply to: Message 307 by Big_Al35
05-11-2011 11:42 AM


Re: Gene Deletion
Big_Al35 writes:

Having read the article a couple of times now I still can't confirm whether this is a real or a pseudo gene.

The main body of the paper does not mention the gene. That's because the paper is not about that gene, nor about whether chimps have genes humans do not. Probably no one has written a paper about whether chimps have genes humans do not because, incredible as it must seem to you who doubt the possibility, no one else doubts this. What would be incredible would be that after 7 million years of separate evolution that no new genes could have emerged on the chimpanzee side. So with regard to finding the evidence you requested the best we can do here in this thread is find papers on other topics that in passing touch on specific gene differences.

WK and I seem to agree that it is more likely than not that this is a gene rather than a pseudogene given the way it is presented in Figure A, but the paper doesn't say specifically. I suppose we could search for a paper that is more specific, but before we put any additional effort into this I think you should explain why you think this is important to your case. Please include in your explanation why pseudogenes are not just as significant as genes, since the paper describes many that are functional in one species (genes) and not in the other (pseudogenes). There's not much difference in effect between a non-functional gene and an absent gene. A former gene that is now a non-functional pseudogene is going to have pretty much the same effect as if it had been deleted and is now absent.

As amazingly accurate as cell division is, there is still much potential for error in the processes of division for asexual cells and of both gamete production and fusion in sexual species. Copying errors ranging from simple base substitutions, additions and deltions up to complete duplications and deletions of genes and even entire chromosomes are possible. In some flowering plants there is evidence of duplication of the entire set of chromosomes. New genes can also arise through gene insertions, for example, retroviral insertions.

So given all the possible things that can go wrong at the genetic level during reproduction and even subsequent life, why is it that you doubt that any and all of these happen in the history of species, including chimps and humans?

Given that humans and chimps have vast physical differences, I can't understand why you would choose as your only example, a "sense of smell" gene. I am not trying to be disputatious but aren't there any more worthy examples that are more suitable for study?

Again, no one is writing papers on whether chimps have genes that humans do not. We found evidence where it happened to pop up in Google searches. 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.

--Percy

Edited by Percy, : Grammar.


This message is a reply to:
 Message 307 by Big_Al35, posted 05-11-2011 11:42 AM Big_Al35 has responded

Replies to this message:
 Message 317 by Big_Al35, posted 05-31-2011 2:32 PM Percy has responded

    
Coragyps
Member
Posts: 5118
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 2.2


(1)
Message 309 of 450 (615217)
05-11-2011 1:43 PM
Reply to: Message 307 by Big_Al35
05-11-2011 11:42 AM


Re: Gene Deletion
The name of the gene consisting purely of numbers and letters is intriguing too.

This statement is hereby nominated for the Web-Wide WTF??? Award for May, 2011.

How are genes typically named, Big_Al?


This message is a reply to:
 Message 307 by Big_Al35, posted 05-11-2011 11:42 AM Big_Al35 has responded

Replies to this message:
 Message 310 by subbie, posted 05-11-2011 1:57 PM Coragyps has not yet responded
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subbie
Member
Posts: 3344
Joined: 02-26-2006
Member Rating: 6.2


(2)
Message 310 of 450 (615219)
05-11-2011 1:57 PM
Reply to: Message 309 by Coragyps
05-11-2011 1:43 PM


Gene naming
How are genes typically named, Big_Al?

Well, I've got several pair of Wranglers, my wife likes Lee and I've also got a very old pair of Levi's that I've cut off because the knees wore through but I can still get them around my waist after 20 years. Now, I do think that the Levi's are called 505, so maybe that might intrigue Big Al, but at least they're Levi's and not just 505.

Edited by subbie, : Subtitle


Ridicule is the only weapon which can be used against unintelligible propositions. -- Thomas Jefferson

We see monsters where science shows us windmills. -- Phat

It has always struck me as odd that fundies devote so much time and effort into trying to find a naturalistic explanation for their mythical flood, while looking for magical explanations for things that actually happened. -- Dr. Adequate

...creationists have a great way to detect fraud and it doesn't take 8 or 40 years or even a scientific degree to spot the fraud--'if it disagrees with the bible then it is wrong'.... -- archaeologist


This message is a reply to:
 Message 309 by Coragyps, posted 05-11-2011 1:43 PM Coragyps has not yet responded

  
Big_Al35
Member
Posts: 290
Joined: 06-02-2010


Message 311 of 450 (615222)
05-11-2011 2:39 PM
Reply to: Message 309 by Coragyps
05-11-2011 1:43 PM


Re: Gene Deletion
How are genes typically named, Big_Al?

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

This new one C4C1001 does not follow that convention ie four letters and a number but then I have no idea how they choose the names and thats why I said I was intrigued. Do you have any ideas about how they name genes?

Edited by Big_Al35, : No reason given.


This message is a reply to:
 Message 309 by Coragyps, posted 05-11-2011 1:43 PM Coragyps has not yet responded

Replies to this message:
 Message 312 by Theodoric, posted 05-11-2011 2:45 PM Big_Al35 has responded
 Message 316 by Wounded King, posted 05-12-2011 8:06 AM Big_Al35 has not yet responded

    
Theodoric
Member
Posts: 4518
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.1


(1)
Message 312 of 450 (615225)
05-11-2011 2:45 PM
Reply to: Message 311 by Big_Al35
05-11-2011 2:39 PM


Re: Gene Deletion
Do you have any ideas about how they name genes?

Ever hear of google?
This message is a reply to:
 Message 311 by Big_Al35, posted 05-11-2011 2:39 PM Big_Al35 has responded

Replies to this message:
 Message 313 by Big_Al35, posted 05-11-2011 2:50 PM Theodoric has responded

    
Big_Al35
Member
Posts: 290
Joined: 06-02-2010


Message 313 of 450 (615226)
05-11-2011 2:50 PM
Reply to: Message 312 by Theodoric
05-11-2011 2:45 PM


Re: Gene Deletion
Ever hear of google?

Hey, thanks for that. I will have to give that a try sometime. Not now though...I have to clip my toe nails first. You have to prioritise you know.


This message is a reply to:
 Message 312 by Theodoric, posted 05-11-2011 2:45 PM Theodoric has responded

Replies to this message:
 Message 314 by subbie, posted 05-11-2011 3:03 PM Big_Al35 has not yet responded
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subbie
Member
Posts: 3344
Joined: 02-26-2006
Member Rating: 6.2


Message 314 of 450 (615228)
05-11-2011 3:03 PM
Reply to: Message 313 by Big_Al35
05-11-2011 2:50 PM


Re: Gene Deletion
Big_Al35 writes:

Ever hear of google?

Hey, thanks for that. I will have to give that a try sometime. Not now though...I have to clip my toe nails first. You have to prioritise you know.

Way to reach for the stars, Sport!


Ridicule is the only weapon which can be used against unintelligible propositions. -- Thomas Jefferson

We see monsters where science shows us windmills. -- Phat

It has always struck me as odd that fundies devote so much time and effort into trying to find a naturalistic explanation for their mythical flood, while looking for magical explanations for things that actually happened. -- Dr. Adequate

...creationists have a great way to detect fraud and it doesn't take 8 or 40 years or even a scientific degree to spot the fraud--'if it disagrees with the bible then it is wrong'.... -- archaeologist


This message is a reply to:
 Message 313 by Big_Al35, posted 05-11-2011 2:50 PM Big_Al35 has not yet responded

  
Theodoric
Member
Posts: 4518
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.1


(1)
Message 315 of 450 (615229)
05-11-2011 3:23 PM
Reply to: Message 313 by Big_Al35
05-11-2011 2:50 PM


Re: Gene Deletion
Well I have little patience for people that want to be spoon fed. Take some responsibility to alleviate your ignorance and do some basic research. God forbid, you might actually learn something.


Facts don't lie or have an agenda. Facts are just facts
This message is a reply to:
 Message 313 by Big_Al35, posted 05-11-2011 2:50 PM Big_Al35 has not yet responded

    
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