The chimp Y chromosome has now been fully sequenced, and the results are astounding. A study in Nature reveals that the chimp Y chromosome is radically different than the human Y chromosome.[1] The chimp’s Y chromosome has only two-thirds the number of distinct genes/gene families, and 47% of the protein coding regions compared to its human counterpart. Furthermore, more than 30% of the entire chimp Y chromosome has no counterpart in humans. Even those segments that do have counterparts in the human Y chromosome are often located in different regions of the chromosome.
One the lead researchers, David Page, told Nature News that “it looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”[2] Of course, this reinvention has to be explained in terms of common descent, so they speculate that the chimp Y chromosome experienced a loss of DNA, while humans experienced a gain. The surprise of the scientists involved, however, demonstrates that this find is counter-intuitive to Darwinian expectations.
HT: Evolution News & Views
[1]Jennifer F. Hughes, David Page, et al, “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content”; Nature 463, 536-539 (28 January 2010) | doi:10.1038/nature08700; Received 3 August 2009; Accepted 24 November 2009; Published online 13 January 2010; available from http://www.nature.com/nature/journal/v463/n7280/full/nature08700.html; Internet; accessed 30 April 2010.
[2]Lizzie Buchen, “The Fickle Y Chromosome”; available from http://www.nature.com/news/2010/100113/full/463149a.html; Internet; accessed 30 April 2010/
Thinking to Believe 
April 30, 2010 at 5:51 pm
Why is this finding “counter-intuitive to Darwinian expectations”?
Why did the Intelligent Designer create a human Y chromosome such that dozens of genes found in the X chromosome are missing from the Y chromosome, a reality that means that almost all cases of hemophilia are in males?
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May 1, 2010 at 3:56 pm
Philip,
You would have to ask the scientists who mapped the genome why they were so stunned by this finding. Given what I have read, however, they were shocked that the Y chromomose was so different given how similar the rest of the genomes are. If humans and apes diverged 6-7 million years ago, the sex chromosome shouldn’t be so different.
Jason
Jason
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May 1, 2010 at 7:38 pm
“Stunned”? “Shocked”? Bit of an exaggeration, yes?
“If humans and apes diverged 6-7 million years ago, the sex chromosome shouldn’t be so different.”
Did you read your own link (The Fickle Y Chromosome)? I think your link answers your question.
Now, about that Designer of your? Any idea why the Designer forgot to put all those genes on the Y chromosome?
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May 1, 2010 at 9:32 pm
Phillip asks:
Any idea why a computer isn’t working properly? I guess it wasn’t designed.
The question you ask, and others like it (dysteleology), is off-topic. This is the second time you’ve posted material not relevant to the thread. That said, questions like yours have been answered time and again by ID proponents. If you’ve read ID material, you would know that. Since it’s off-topic, I won’t get into it here. Maybe you can get Jason to start a thread along that line.
Interesting post, Jason.
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May 2, 2010 at 6:27 am
“I guess it wasn’t designed.”
I think you mean to say that while the computer was designed, it clearly wasn’t designed well. That’s ok to say about flawed human designers, but it’s an odd thing to say about a perfect, all-powerful creator. I once heard an ID proponent say that while the Ford Pinto was badly designed, it was still designed. Great. Now we’re comparing God to the guy who build an exploding car.
“If you’ve read ID material, you would know that.”
I’ve read the ID material (see Ford Pinto above). Their answer to questions like this explains why ID is of no value. In short, it’s not testable. There is no possible observation that can disprove the idea, so if it’s wrong, there’s no way to know that it’s wrong. Doesn’t matter if something looks good or looks bad, it’s all designed. Nothing can count against the idea.
Now, if you wish to stay on topic, perhaps you can explain to me why the difference in the Y chromosome in chimps versus humans can’t be the result of natural changes occurring over a 7 million year period of time.
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May 2, 2010 at 11:17 am
Very interesting post. Those percentages make the idea of common descent sound ridiculous.
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May 2, 2010 at 12:30 pm
Philip says,
No, that isn’t what I meant to say; and your statement is all that is needed to demonstrate you do not understand the ID reply. I suggest you do what you recommended to Jason: Read more.
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May 2, 2010 at 1:03 pm
Scalia,
“No, that isn’t what I meant to say.”
If I misinterpreted, feel free to explain what you meant. What is the ID reply? You can even give me a link. Unlikely Jason, I’ll read a link if it isn’t book-length.
You said, “Any idea why a computer isn’t working properly? I guess it wasn’t designed.”
I assumed that you were making a comparison to the Y chromosome. So, you were saying that while the Y chromosome “isn’t working properly”, that doesn’t matter, because it’s still designed like a computer is designed. Yes? You’re saying that bad design is still design, yes?
RB,
“Those percentages make the idea of common descent sound ridiculous.”
Why?
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May 2, 2010 at 1:07 pm
Scalia,
Oops, forgot something. You wanted me to stay on topic. So, perhaps you can explain to me why the difference in the Y chromosome in chimps versus humans can’t be the result of natural changes occurring over a 7 million year period of time.
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May 2, 2010 at 1:29 pm
“RB,
“Those percentages make the idea of common descent sound ridiculous.”
Why?”
For years I’ve heard comments like “97% similar”. These percentages show us that the similarities are no where near what they wanted us to believe.
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May 2, 2010 at 1:40 pm
Philip wrote
You did; and since you continue to play this cat and mouse game with Jason on the other thread, I’m in no mood to indulge your request. It is obvious you know very little about ID. Your “bad designer” objection is one of the most common we hear and has been answered time and again. So long as you keep up this “please define X, please read Y, do you have a degree?” stuff, it’ll get thrown back at you. Read more ID material and you’ll get your answer.
Why would I do that when I’ve never made that claim? Moreover, even that isn’t the topic of this thread. All Jason asserts in his opening remarks is the chimp-human disparity “is counter-intuitive to Darwinian expectations.” The fact it is counter-intuitive does not make it impossible. If Jason wants to take this thread into other areas, that’s his prerogative as the moderator, but I won’t do so.
There are other threads raising this topic and if you care to post there, perhaps we can continue; but my history on this site demonstrates I rarely take a thread beyond its scope (only when I forget!). 🙂
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May 2, 2010 at 1:57 pm
Scalia,
“You did (misinterpret); and since you continue to play this cat and mouse game with Jason on the other thread, I’m in no mood to indulge your request. “
Well, if you choose not to clarify your remarks, that’s your choice. It’s not very helpful, but it’s your choice.
Actually, I did google “dysteleology”, I clicked on the third link down, that link took me to Evolution News and Views, and there I found the following… “As Dembski says in response to the “Incompetent Design” song, “yes, the performance is poor, but poor design is not the absence of design.”
Isn’t that what I said the ID answer was? Bad design is still design? That’s the answer, right?
“It is obvious you know very little about ID. Your “bad designer” objection is one of the most common we hear and has been answered time and again. “
Oh, I know the ID answer, but as previously stated, the problem is that the answer demonstrates why ID is untestable and of little value.
So long as you keep up this “please define X, please read Y, do you have a degree?” stuff, it’ll get thrown back at you.
Sorry, but my “define this” request is absolutely essential to the discussion on another thread. Please explain how I can show someone something if I don’t know what that something is. It’s not a game, it’s an essential part of the answer. You can’t show someone that something has, in fact, been observed until we have a definition of what it is we’re looking for. I’ve found from past experience that such definitions are essential to a meaningful discussion of the topic.
“The fact it is counter-intuitive does not make it impossible. “
Thank you. I don’t think it’s all that “counter-intuitive”, but I’ll settle for what you said.
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May 2, 2010 at 1:58 pm
Scalia,
Oh, and I’m not sure that “cat and mouse” describes my approach on the other thread when I’ve provided links to research that answers Jason’s questions. It’s Jason who’s choosen not to read the answers provided.
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May 2, 2010 at 2:21 pm
“For years I’ve heard comments like “97% similar”. These percentages show us that the similarities are no where near what they wanted us to believe.”
Well, first, the percentages given always depend on what we’re counting. Are we counting chromosome numbers, gene families in common, homologous genes in common, base pairs in common, etc.? The percentage will be different for each choice. So, depending on what you count, you can get answers like 99% or 97% or 95 %, etc. It all depends on what, exactly, you’re measuring. The point about ape and human chromosomes is that there is no need for there to be such a high degree of similarity, especially with respect to the ORDER of the genes on the various chromosomes, and if that similarity did NOT exist, this could call evolution into question. But it does exist.
It’s not that the similarities conclusively prove for all time that apes and humans shared a common ancestor, although it does support this conclusion. Rather, sequencing genomes offered the possibility of disprove of common ancestry. Before we sequenced the genomes, we didn’t know what we’d find. The sequences could have been different from what we found and could have disproved common ancestry. Instead, the sequences supported common ancestry.
Second, even when you count the differences in the Y chromosomes, it doesn’t change the overall percentage very much, because the sex chromosomes are just one of twenty-three pairs, and the Y chromosome doesn’t have as many genes as most of the other chromosomes.
Did you read the link Jason provided? Here what is says about Chromosome Pair 21. “If you’re marching along the human chromosome 21, you might as well be marching along the chimp chromosome 21. It’s like an unbroken piece of glass,” says Page.” That statement can be applied to pretty much all of the chromosomes except the Y chromosome. So, yes, the percentages are still close to what “they wanted us to believe”.
Scientists have known that Y chromosomes are odd ducks for some time now. Even within the human population, there is probably more variation among the Y chromosomes of different men than among any other chromosome you chose to compare. I’ve read from time to time about the hypothesis that the Y chromosome is going to continue to lose genes and may one day be nearly gone. Now, you can find references to this hypothesis dating back many years, so scientists have been aware of the Y chromosome’s tendency to lose genes for some time. Thus, the observation that the chimp Y chromosome has lost more genes than the human Y chromosome isn’t nearly as “shocking” as some would have you believe.
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May 2, 2010 at 3:17 pm
Philip, this will be my final word on this thread, so you get the last one, if you so choose.
A discussion site isn’t a battle of links. I can just as easily insist, since Jason has recently summarized two books (written by Behe and Meyer, respectively), that you read both of them before replying; and since they answer all your objections, I win (unless you read them and tell me why they’re wrong). I don’t think there is anything wrong with providing a link (I’ve used them myself), but that is no substitute for discussion.
If you are a scientist or have a degree in science (what field?), there’s no need for you to provide links, unless you’re asked for sources. I have disagreed with Jason numerous times, but I’ve never used a link in lieu of discussion.
What I would expect from somebody with your alleged qualifications is an analysis of Jason’s remarks. They stand or fall on their own merit. His education has nothing to do with the validity of his claims. If you have experience in this field (as you imply), it is easy to clear a definitional fog. You can say, “ID defenders use the word ‘new’ in different ways. In no case does their conclusion follow because of…” Alternatively, you can side-step that altogether and simply say, “When evolutionists say new we mean…” It is then up to your debating partner to either agree with your definition of the relevant term or affirm a different meaning. This, “Do you have a degree, or did you read these books?” smacks of arrogance (I’m smarter than you, so you’re not qualified). It’s cat-and-mouse because all I need to say is, “Since you haven’t read Behe & Meyer, you’re not qualified to comment under this thread. Go someplace else.”
Moreover, you introduce material that is not only irrelevant, you do not understand it; but whether or not you understand the “flawed design” argument, continuing to introduce irrelevant material makes you look like a troll. Instead of this stuff about design, all you needed to do was point out the referenced articles do not imply the impossibility of Y chromosome disparity under the common ancestor paradigm. You could have then reproduced a couple of relevant remarks from that material in support of your rebuttal.
Jason recently reviewed a book I didn’t read. I stated up front I did not intend to read that book. We had a very long discussion and while we disagreed with one another, it was respectful. There was none of this, “I’ve read/know/seen more than you” stuff. Jason respects reasoned discourse, and he isn’t above admitting he is wrong. I hope you will refine your comments on the other thread. Irrelevant material aside, you’ve done a better job under this one.
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May 2, 2010 at 4:46 pm
Scalia,
I understand what you are saying, and I can agree with some of what you are saying. I’ve been crankier than I should have been.
However, when Jason makes a postive statement such as “this find is counter-intuitive to Darwinian expectations” or “mutation can’t produce new genes”, the burden is on him to show that he understands what he is saying and that he can support the assertion. In general, this is what I’ve asked him to do. That doesn’t seem too unreasonable to me.
Also, I’ve played this game in the past, and whenever I show someone a new gene by mutation, they want to play word games like “that’s an altered gene, not a new gene” or “that’s a loss of information”, all the while, refusing to define what these words mean. So, I’ve learned to get defintions first. I’m leery of spending too much time trying to explain things when there’s a good chance that that my “partner” will play games with words.
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October 17, 2010 at 9:23 pm
can we change genetic nature of human gene?
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October 18, 2010 at 10:44 am
What do you mean by changing the genetic “nature”? And are you referring to specific genes, or the human genome?
Jason
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