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Author Topic:   Definition of Species
Percy
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Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 259 of 450 (614706)
05-06-2011 6:57 AM
Reply to: Message 258 by Big_Al35
05-06-2011 6:46 AM


Hi Al,

You'll have to provide the source for your figures. There were no such figures in my post, nor in the Wikipedia article I referenced, so maybe it came from some posts earlier in the discussion, or from links mentioned in those posts? Let me know.

--Percy


This message is a reply to:
 Message 258 by Big_Al35, posted 05-06-2011 6:46 AM Big_Al35 has not yet responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 261 of 450 (614715)
05-06-2011 8:09 AM
Reply to: Message 260 by Wounded King
05-06-2011 7:16 AM


Wounded King writes:

Hey Percy, now its you that is either using genes in a funny way or getting the biology mixed up. Alternatively you may be using yet another species concept.

We've run into this issue before. My approach of starting simply and gradually adding complexity often draws objections from you. The species divisions getting attention in this thread, such as between chimp and human, include differences in gene sets, even in chromosomes because of the fusion of 2-into-1 possessed by humans.

It is possible to project a better understanding onto replies than is actual there in reality, encouraging one to continue the discussion at what can become for many an inaccessible level, especially when long familiarity with complex details causes some simple but important things to go unsaid.

I do understand that biology is whatever works and that the many simple rules we wish were hard and fast are not, but there are still general principles that are true in a broad or general sense and that are understandable to most. As ring species helpfully make clear for the biological layperson, species is a actually a very fuzzy boundary, but the concept itself of an well-delineated interbreeding population is very clear and very helpful in discussion. Equally helpful is the concept of genetic uniqueness of a species, a point made most simply by assuming that each species has a unique gene set. Once that point is made and understood one can move on and say that even just allele differences can divide species.

I'd like to be more a help than a hindrance in your discussion with Al, I'll do my best.

--Percy


This message is a reply to:
 Message 260 by Wounded King, posted 05-06-2011 7:16 AM Wounded King has responded

Replies to this message:
 Message 263 by Wounded King, posted 05-06-2011 8:49 AM Percy has acknowledged this reply

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 268 of 450 (614880)
05-08-2011 9:20 AM
Reply to: Message 266 by Big_Al35
05-08-2011 7:10 AM


Big_Al35 writes:

Essentially this means that humans and chimps share exactly the same genes making a nonsense of Percy's previous comments.

Chimps have genes that humans do not have, and vice versa. Apparently a great many of the gene differences are due to duplications. See the Wikipedia article on the Chimpanzee genome project that I referenced earlier:

Wikipedia writes:

Gene duplications account for most of the sequence differences between humans and chimps.

I was not able to locate any layperson-level description of the precise gene differences, and I suspect it isn't very well characterized at this point, but the important piece of information is that in general the genetic differences between species range from allele differences only all the way up to sharing very few genes (aside from the fundamental ones like hox genes). Humans and chimps are not a species that differ at only the allele level. Humans and chimps have different gene sets, though they overlap broadly.

You were arguing with WK about whether genetic differences were helpful in identifying species. I'm not sure whether your position is affected by whether chimps and humans "share exactly the same genes," so can you refresh our memory about your position on this?

--Percy


This message is a reply to:
 Message 266 by Big_Al35, posted 05-08-2011 7:10 AM Big_Al35 has responded

Replies to this message:
 Message 269 by Big_Al35, posted 05-08-2011 10:12 AM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 270 of 450 (614885)
05-08-2011 11:56 AM
Reply to: Message 269 by Big_Al35
05-08-2011 10:12 AM


Hi Al,

It appears to me that our difference of opinion comes down to interpretation of plain English about gene duplications. Let me try to put it in explicit terms.

Assume the human/chimp common ancestor had gene X. Some millions of years later the human branch experienced a duplication in gene X, call it X'. The chimp line did not experience this gene duplication. Therefore the human branch now has gene X' that the chimp branch does not.

Of course, as the Wikipedia article on the Chimpanzee genome project states, gene duplications are the source of only *most* of the sequence differences. There are other sources of gene differences. New genes can arise from insertions, for example retroviral insertions, and genes can be deleted.

If you want something completely unequivocal, this article titled DNA Chunks, Chimps And Humans: Marks Of Differences Between Human And Chimp Genomes from Science News makes an explicit statement about deletions where it quotes Dr. George Perry from Arizona State University:

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."

Hopefully this puts this issue to rest, so getting back to the original issue, can you refresh our memory on your discussion with WK about whether genetic differences are helpful in species identification.

--Percy

Edited by Percy, : Grammar.


This message is a reply to:
 Message 269 by Big_Al35, posted 05-08-2011 10:12 AM Big_Al35 has responded

Replies to this message:
 Message 271 by Big_Al35, posted 05-08-2011 12:29 PM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(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

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 287 of 450 (615020)
05-09-2011 5:47 PM
Reply to: Message 286 by Big_Al35
05-09-2011 5:23 PM


Re: Gene Deletion
Hi Al,

You're continuing to bounce around with objections to this and that without rhyme or reason, as if you have no substance behind your objections, you just like objecting.

First you claim, without any reason, that chimps and humans have all the same genes, so we show you genes humans have that chimps don't.

So now you say, "Okay, so humans and chimps don't share all the same genes, but I bet you can't come up with any genes chimps have that humans don't."

Why, Al? Why do you think this? It can't be your voluminous and encyclopedic mastery of all things biological, because you have none. It can't be your record of many correct arguments in this thread, because you have very few. So you have little knowledge in this area, and your record in this thread is one of error after error, so what is it that makes you believe you're right this time, Al? Why do you doubt that chimps have genes humans don't?

And what on Earth has it to do with the topic?

--Percy


This message is a reply to:
 Message 286 by Big_Al35, posted 05-09-2011 5:23 PM Big_Al35 has not yet responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 291 of 450 (615086)
05-10-2011 8:31 AM
Reply to: Message 290 by Big_Al35
05-10-2011 6:26 AM


Re: Gene Deletion
Big_Al35 writes:

And if you can't see where I am going with this discussion maybe you shouldn't be discussing this topic.

Having constructed your house of straw with no effort or thought, with stairways that empty into closets and windows installed in floors, you nonetheless demand that others somehow make polite and treat it as if there were sense in it. If you have anything substantive and true to say instead of merely carrying on the labor of the ignorant by casting aspersions at things you don't understand then I suggest you say it instead of issuing senseless one sentence retorts that contribute nothing.

--Percy

Edited by Percy, : Grammar.


This message is a reply to:
 Message 290 by Big_Al35, posted 05-10-2011 6:26 AM Big_Al35 has responded

Replies to this message:
 Message 292 by Big_Al35, posted 05-10-2011 12:18 PM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 293 of 450 (615119)
05-10-2011 1:34 PM
Reply to: Message 292 by Big_Al35
05-10-2011 12:18 PM


Re: Gene Deletion
Hi Al,

I bet you're a hell of nice guy in real life and probably very knowledgeable and successful in whatever you do. Heck, I bet you can even drive and text at the same time! But when it comes to biology you're a complete idiot.

Even worse, you seem to have no criteria against which to judge your competence regarding topics biological, and so you carry blithely on as if completely unaware of the carnage of error, mistakes and ignorance that lies in your wake.

I'm sure this can only be because you have a great deal of competence in something, and you somehow believe that this competence should be transferable into whatever other field you care to direct it at. Sadly that's not the case, not for you, not for anyone. Even great masters in one branch of science become, without study, mere laypeople in others. Knowledge of a topic comes from hard study of that topic, not some other topic.

Just as only great billionaires down on their luck can end up owing billions instead of the mere hundreds of thousands of us normal people, your confidence in your competence has led you to foolish gambles (e.g., "Chimps and humans share all the same genes") and intellectual bankruptcy on a grand scale, and it seems impossible that you could ever make up such a deficit.

--Percy


This message is a reply to:
 Message 292 by Big_Al35, posted 05-10-2011 12:18 PM Big_Al35 has responded

Replies to this message:
 Message 294 by Big_Al35, posted 05-10-2011 1:43 PM Percy has responded
 Message 296 by Big_Al35, posted 05-10-2011 2:03 PM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 295 of 450 (615124)
05-10-2011 1:55 PM
Reply to: Message 294 by Big_Al35
05-10-2011 1:43 PM


Re: Gene Deletion
Al, we're all waiting for you to actually respond to the replies to you. The criticism you're drawing is due to your lack of meaningful responses. Please stop with the one-liners and say something rational and on-topic that actually contributes to the discussion.

--Percy


This message is a reply to:
 Message 294 by Big_Al35, posted 05-10-2011 1:43 PM Big_Al35 has not yet responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(2)
Message 297 of 450 (615145)
05-10-2011 4:18 PM
Reply to: Message 296 by Big_Al35
05-10-2011 2:03 PM


Re: Gene Deletion
Hi Al,

I'm just a participant in this thread. Moderators are discouraged from moderating threads in which they are participating.

I appreciate WK corrections when they are actually corrections, but I think you lack the necessary background to understand WK's feedback to me, since it primarily stems from a difference of opinion about the appropriate level of detail for discussing with someone like yourself.

In case it helps, I don't think you're at any risk at all of moderator action. I sympathize with the difficult task you face of one person against several, but much of the difficulty you're experiencing is of your own making. You can't expect the real world to correspond to things you just happen, for who knows what reason, to think are true. If you're going to post messages insisting on things that you haven't first checked out then you have to accept the consequence that you're very likely to often be wrong. But it's easy to stop this pattern: research first, digest and understand second, post third.

I think you should read the material you haven't responded to yet, research and think through your answer, then present it.

--Percy


This message is a reply to:
 Message 296 by Big_Al35, posted 05-10-2011 2:03 PM Big_Al35 has responded

Replies to this message:
 Message 298 by Big_Al35, posted 05-11-2011 5:14 AM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


(1)
Message 299 of 450 (615179)
05-11-2011 7:31 AM
Reply to: Message 298 by Big_Al35
05-11-2011 5:14 AM


Re: Gene Deletion
Big_Al35 writes:

So let me get this right, you have chosen to talk sh*t because you think I am talking s*it? It is a strange world that you inhabit.

I think you're a blowhard who uses bluster to accomplish what his intellect cannot.

I will not be responding to you until you answer the question that I asked.

People, especially WK, have been answering your questions since you joined this thread, and you haven't responded meaningfully yet. Why would that change now?

You were the one who suggested that that humans and chimps both have genes that the other does not possess. Please give me an example of a gene, by name, which a chimpanzee has but a human does not.

Didn't you see WK's Message 288? He cited Gilad et al., 2005. Here's a relevant excerpt:

Genome Research writes:

...there is a human ortholog for almost every chimpanzee OR gene. However, there are also some species-specific expansions. A chimpanzee expansion within OR subfamily 4C (Fig. 2A), and three human expansions in subfamilies 2A, 4F (also noted by Linardopoulou et al. 2001), and 6C (Fig. 2B,C,D).

And if you go to the article and follow the links to the figures you'll see all the details for olefactory genes chimps have that humans do not. Gene designations that begin with the letter H are human, those beginning with C are chimp. An example of a gene that chimps have that humans do not is C4C1001 in Figure A.

But the important question is why you want this information, Al? What are you going to do with it? You haven't done anything with any of the other information provided to you, and so I expect you're not going to do anything with this information either. You're just going to move on to ask more disputatious questions just for the sake of being disputatious.

But I would be delighted to be proven wrong, so go ahead and carefully examine and analyze the information, then provide a rational and intelligent response to it, hopefully explaining why you doubted that chimps could have genes humans don't and making clear that it wasn't just some idea out of the blue that flitted into your mind.

Your problem, Al, is that you don't seem to realize that there are some things that we know. Sure, there are lots of things we do not know and even will never know, but still, there are some things we do know. Your modus operandi seems to be assume that no matter what we say that there is no way we could possibly know it, and you therefore challenge it while, for some perverse reason known only to yourself, asserting that it couldn't possibly be true, with the unsurprising result that you're found wrong time and time again.

No one's trying to hornswoggle you, Al. We're only telling you what we know. I know a bit and try to keep things simple. WK knows a lot and prefers a detailed and meticulously accurate approach. But nobody here, except you, is making things up.

--Percy


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 300 by Big_Al35, posted 05-11-2011 8:13 AM Percy has responded

  
Percy
Member
Posts: 19627
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


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

  
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