Pope's astronomer dismisses ID and says Church was "spectacularly wrong" in its treatment of Galileo

[buffalo]

Hello again, buffalo,

What I found bizarre was your citation of only 70 percent similarity. Not even the most hardline creationist organization comes close to that degree of dissimilarity. When I have only your statement to the effect on one hand, and actual, physical measurements on the other, complete with methodologies and analysis, directly contradicting your statement, I can only assume you have been badly misinformed.

Common design is unsatisfying as an explanation as it does not predict these similarities. We have no experience with measuring such design work, nor examples to examine, nor clues on how such design might be implemented. On the other hand, we have abundant evidence of genomes being transmitted across the generations through natural reproductive processes, which is sufficient in itself to explain the similarities we observe. What’s missing is any reason to add a divine submolecular genomic meddler. We know this transmission of similarity occurs naturally. We do not know these natural causes to be insufficient.

And there you have it, an insuperable difficulty in inferring design. Without a basis, some standard by which we can say, “This is what was intended,” no intention can be read from any observation. When “bad” design is interpreted as “intelligent” design, the very idea of design becomes incoherent. More, the suggestion that “bad” design of humans, in the presuppositional framework of humans constructed in the image of the creator itself, strikes me as theologically heterodox for an adherent of any Abrahamic religion.

This is the kind of quagmire that forces me to reject any of these gods, choosing instead a purely natural explanation that bypasses any need to engage in such mental gymnastics. Better an incomplete explanation that makes sense and is open to correction and expansion than a more complete yet fixed explanation which cannot be made to make sense, in my view.

As ever, Jesse

Chimpanzee?

To compare the two genomes, the first thing we must do is to line up the parts of each genome that are similar. When we do this alignment, we discover that only 2400 million of the human genome’s 3164.7 million ’letters’ align with the chimpanzee genome - that is, 76% of the human genome. Some scientists have argued that the 24% of the human genome that does not line up with the chimpanzee genome is useless ”junk DNA”. However, it now seems that this DNA could contain over 600 protein-coding genes, and also code for functional RNA molecules.
Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes.
In the neatly aligned sequences we now find another form of difference, where a single ’letter’ is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%.
We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This ”copy number variation” causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%.
This figure does not take include differences in the organization of the two genomes. At present we cannot fully assess the difference in structure of the two genomes, because the human genome was used as a template (or ”scaffold”) when the chimpanzee draft genome was assembled.
Our new knowledge of the human and chimpanzee genomes contradicts the idea that humans are 98% chimpanzee, and undermines the implications that have been drawn from this figure. It suggests that there is a huge amount exciting research still to be done in human genetics.

Simply put bad design does not preclude bad design. Again, I return to the question, does design exist? How do we know it when we see it?

 

[LittleSoldier]

Here are some of the issues:

---

		**[The Sound of Taxonomy Exploding](http://www.uncommondescent.com/intelligent-design/the-sound-of-taxonomy-exploding/)**

http://www.uncommondescent.com/intelligent-design/the-sound-of-taxonomy-exploding/

OK I looked at the blog. Now can you please give me a definition of species, as the term is used now and tell me the problems with it besides data collection? And what the heck are all those Ac2&*s (I don’t have the correct symbols on my keyboard) scattered through the article (which, BTW, is written by someone who won’t even put his full name on it)?

Of course our current taxonomy is not complete. Many species currently listed are actually extinct, some species which were thought to have been extinct have now been found to have a few member still alive and breathing, and new species are being discovered. But I still see absolutely no problem with the definition of species, unless it has changed within the last thirty years. In fact I think the definition in use when I was in college was an excellent definition.

And if your computer doesn’t have sound, does the missile set off by the White Spy make any noise?

 

[LittleSoldier]

Before genetics it was the best we could do.

Are you a biologist? Were you active in the formation of the system of taxonomy currently in use?

 

[wanstronian]

I do not posit that the designer actively manipulates DNA. (although He could if He wished). IDvolution as you have read by now posits that God “breathed” the language of DNA in the beginning. (think of terraforming ala Star Trek)

Can you describe the process of this ‘breathing’ - how does/did it work? Can you define the ‘kinds?’ When was ‘the beginning?’ Why did God do all this?

Do you actually have a definition of this thing you’ve made up called ‘IDvolution?’ Because the description in your tag line is pretty much the most nebulous and vague definition I’ve ever seen for any process.

 

[rossum]

The CSI formula has to be solved. For example what value do we assign certain attributes?

Here are some answers - (Rome wasn’t built in a day)
Intelligent Design as a Theory of Information

The CSI formula has not been solved yet. Dr Dembski has failed so far to provide a rigorous definition of what is, and what is not, a “specification”. He has also failed so far to solve the question of differentiating between real CSI and apparent CSI. Your reference is dated 1998. Has Dr Dembski made no progress in the last twelve years?

Which scientists are studying CSI in DNA? That is exactly the problem. They are ignoring it because of the implications. I doubt mainstream scientists will risk their careers. This research will be done on the outside until it gains traction. It also takes funding.

By now ID people should have worked out that mainstream scientists are not gong to do their ID research for them. They are going to have to do it for themselves. ID scientists do have funding and labs. I can point to Robert Marks’ Evolutionary Informatics Lab and to the DI’s own Biologic Institute. Funding can be obtained from the DI itself. Why is this work not being done? If ID really wants to be science then it actually has to do the scientific work. If it just wants to look sciency enough for its political purposes then ID can just carry on writing press releases.

I do not posit that the designer actively manipulates DNA. (although He could if He wished). IDvolution as you have read by now posits that God “breathed” the language of DNA in the beginning. (think of terraforming ala Star Trek) We see that all living organisms share the same core genes, 500 or so. The language of DNA is the main driver of adaptations. In other words life is front loaded with the information to necessary to adapt.

Random mutation and natural selection is a process which transfers information from the environment into DNA. If your designer created the environment then there is no requirement for Him to intervene further. He put the information into the environment and evolution copies that information into genomes. Of course the specific designer you are thinking of cannot be mentioned by the DI because that would get in the way of their political objective in the science classroom.

rossum

 

[wanstronian]

edwest2;7117672:

Nice attempt to dodge. An obviously manufactured object, in my example, would contain many parts, likely metallic, and visible examples showing how the parts interact upon disassembly. You are simply refusing to use your imagination. Just a reminder, scientists are spending time and money looking for intelligent signals from space on the assumption that other civilizations at least as advanced as our own, and likely more so, are out there, even though they lack the mechanical object on Mars for evidence that anyone is out there.

Do not presume to understand the motivation for my question. It was asked genuinely. I was curious as to how you would identify something as designed.

You’ve given a few examples of properties of a designed object (one of which clearly doesn’t apply to biological life) - but what’s the process that you follow to determine whether an object is designed? Is it a checklist, a subset of a documented set of properties…what?

No answer, Ed?

 

[buffalo]

OK I looked at the blog. Now can you please give me a definition of species, as the term is used now and tell me the problems with it besides data collection? And what the heck are all those Ac2&*s (I don’t have the correct symbols on my keyboard) scattered through the article (which, BTW, is written by someone who won’t even put his full name on it)?

Of course our current taxonomy is not complete. Many species currently listed are actually extinct, some species which were thought to have been extinct have now been found to have a few member still alive and breathing, and new species are being discovered. But I still see absolutely no problem with the definition of species, unless it has changed within the last thirty years. In fact I think the definition in use when I was in college was an excellent definition.

And if your computer doesn’t have sound, does the missile set off by the White Spy make any noise?

Search on - taxonomic problems.

 

[latin_rite]

Please correct me if i am wrong. But wasn’t the Pope impressed by Galileo’s theory? So impressed, that he urged him to continue with his work on this theory and to share it with his fellow scientist. But not to teach it as fact?

 

[grannymh]

Please correct me if i am wrong. But wasn’t the Pope impressed by Galileo’s theory? So impressed, that he urged him to continue with his work on this theory and to share it with his fellow scientist. But not to teach it as fact?

I have read similar reports.

Considering that Galileo lived toward the end of the Renaissance amidst the competition between the “universities”, it is common sense that the Pope and a lot of high ranking clergy would be interested in Galileo’s science explorations no matter what. Factor in the Protestant Reformation and normal politics and the pot boils over.

 

[reggieM]

Here’s an interesting thread (the comments section) on measuring CSI. This quoted text is from gpuccio’s response to the challenge about measuring functional information.
The Durston study which is referenced is this:

Measuring the functional sequence complexity of proteins
tbiomed.com/content/4/1/47

Here’s the quoted text from this thread:
uncommondescent.com/intelligent-design/15027/#comments

a) We can compute the global dFSCI of a protein, or better of a protein family. Durston, for instance, computes it for 35 protein families (I am afraid hemoglobin is not in the group). Let’s take for instance his value for Ribosomal S12:

Length: 121 AAs

Functional complexity: 359 Fits

Number of sequences on which the computation has been made: 603

What is the meaning of the value of 359 Fits? It means that according to Durston’s computations, if we had to generate the functional information of that protein in a completely random system, the probablities to get a functional result would be 1: 2^359. That is well beyond my personal threshold for biological systems, which is of 150 bits.

Now, what does it mean “generate the functional information of that protein in a completely random system”? I does not mean, obviously, to pass from one form of Ribosomal S12 in one species to that in another species. Which is the example you suggest for hemoglobin.

No. In Durston’s computation, all the sequences of protein S12 in different species are considered as one family. It is very easy to pass from one to another, and the essential function in preserved (with possible minor tweakings form species to species). That is exactly what microevolution can do (and probably does do): To preserve an existing function by negative selection, and to change the primary sequence inside a functional island by neutral mutations. That’s what the “big bang” theory of proteins, which I often quote, is all about.

But the ID problem is all another matter: the ID problem is: how was the first fuinctional S12 protein generated? IOWs, how was the essential protein domain generated?

Now, as we know that there are in the proteome about 1000 – 6000 individual and unrelated protein domain superfamilies (according to how you do the grouping), it is obvious that if you hypothesize that they did not come out of scratch in a random way (in which case the Durston computation applies perfectly), than each of them must have come out of some unrelated different sequence, through a random walk. And, in that case, the Durston computation applies just the same. because a random walk starting from a completely unrelated sequence is indeed a random search.

b) We can compute the dFSCI of a transition.

So, let’s imagine that you can deconstruct the walk form A to B (where B is our first S12, and A is some pre-existing, unrelated protein domain) in a series of steps, let’s say A1, A2, An. Where each intermediate implies a survival advantage, and therefore can be “seen” by NS. If you could do that (which you can’t), then you would be right to affirm that the transition does not any more imply 369 Fits, because a necessity mechanism (NS) intervenes in each of the n points.

That’s true. Then, we can simply compute the dFSCI implied in each of the n-1 transitions, and sum those values. That is perfectly possible. After you have given the explicit pathway of transitions and intermediates which your model refers to.

 

[Betterave]

Hello Betterave,

The absence of a curriculum could be quite easily contradicted were you to present one. But in fact, among the original objections presented by the biology teachers at Dover was their inability to find material to fill out a curricular unit on the topic. There’s a great deal of wishful thinking among ID opponents that ID actually has positive material to present in support of its case. I suspect your belief that I am “clearly mistaken” about the conceptual structure of ID is a product of a similar faith.

Conceptually, ID is a search for things that cannot be explained. As such, it offers no explanations at all. In fact, I was amused to find that the “journal” you cited earlier as academic support for ID included only one issue, and two papers in total, both of which were objections to biological evolution.

Criticism of the Qur’an is not support for the Bible.

As ever, Jesse

Hi Jesse,

Conceptually ID is not a search for things that cannot be explained. It’s a search for things that can be best explained by a particular kind of explanation (and, obviously, concomitantly the attempt to work out a robust theoretical framework to specify the nature this kind of explanation, to determine what conditions should be reasonably said to call for an inference to ID - rossum seems to get this, try reading his posts). Again, you clearly misunderstand the conceptual structure of the ID argument.

Dave

 

[Betterave]

You’re rude and irrational. Let me explain:

Yes, very. I have presented the reasons why ID is unscientific. I have presented a list of organisations representing hundreds of thousands of scientists and teachers, who say the same thing. You disagree, and consider those hundreds of thousands of scientists to be wrong, and yourself to be right. It is you who are irrational. You haven’t even presented a defence of ID, all you’ve done is misrepresent and subsequently criticise your straw man representation of my comments.

You attribute to me the claim again that I have declared all these scientists wrong. But I have never done that.

No, just stupidity. The arguments have been made. That you disagree with them - and the vast majority of the scientific community - is not my problem.

If my asking you for a substantive argument is stupidity, that can only be because you are rude and irrational.

No, the FACT that the vast majority of people with a scientific background dismiss ID as unscientific. That fact. No straw men required or invoked. Other than by you, in a desperate attempt to win an argument that you lost several posts ago.

This FACT is irrelevant to my specific objections to your arguments. You would realize this if you weren’t so rude and irrational.

I don’t care whether you think ID is scientific. I think it isn’t, I’ve presented my reasons, and they are reasons consistent with the overwhelming weight of scientific opinion.

I don’t care what either of us thinks, I’m interested in a substantive argument.

ID has been debunked by proper scientists on so many occasions, it’s incredible that anybody still has the courage to defend it. It’s junk science, pure and simple.

Red herring.

Yes, I’d stop now then. Because I’m unlikely to change my position when all the evidence is on my side. I’d be as intellectually bankrupt as you seem to be.

Your position being that you should be rude and irrational, and ignore my actual specific criticism of your views, because, after all, “all the evidence is on your side”? The evidence here is that you are rude and irrational.

I’ve answered all your criticisms - although it has to be said, it really took the form of correcting your misapprehensions of what I originally said. However, as a special concession because you don’t seem to remember this, please present the criticisms again, and I’ll respond.

I refer you to post #264.

Oh, is that the one who got beatified because some deacon recovered from a back operation in two days, which just happens to be the usual time for recovery from that particular operation. Miracle indeed!!

Red herring - again, you are rude and irrational.

 

[lao_tzu]

Chimpanzee?

Hello again, buffalo,

To compare the differences between human and chimpanzee genomes, it’s necessary to examine the primary literature. This is not it. I’ve found your Dr. Buggs, and he’s apparently a perfectly respectable evolutionary biologist specializing in plant evolution, but he doesn’t do research in primate evolution. However, he has religious objections to common ancestry between humans and chimpanzees that have unfortunately allowed him to bypass the care we find in his published literature, care that is notably missing in this monograph.

The most obvious flaw here is the absence of any references for his numbers. There are no citations at all. Fortunately, I’ve managed to find the primary literature, Initial sequence of the chimpanzee genome and comparison with the human genome, and unsurprisingly, it tells a much different story. I strongly suspect the lack of this reference was not merely incidental. It’s not possible to read the actual paper and come away with the impression Buggs’ would like to convey. This is, as it turns out, yet another example of the quote-mining we see so often in creationist literature.

Genome evolution

We set out to study the mutational events that have shaped the human and chimpanzee genomes since their last common ancestor. We explored changes at the level of single nucleotides, small insertions and deletions, interspersed repeats and chromosomal rearrangements. The analysis is nearly definitive for the smallest changes, but is more limited for larger changes, particularly lineage-specific segmental duplications, owing to the draft nature of the genome sequence.

Nucleotide divergence

Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover approx 2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y.

Genome-wide rates. We calculate the genome-wide nucleotide divergence between human and chimpanzee to be 1.23%, confirming recent results from more limited studies 12, 33, 34.

Take note of the “2.4 gigabases.” This is apparently the source of Buggs’ "2400 million of the human genome’s 3164.7 million ’letters’ and his calculation of 76 percent. It doesn’t, however, represent a measure of how much of the genomes can be aligned. What Buggs has calculated here is not a measure of our genomic differences, but rather how much of the draft chimpanzee genome represents high quality sequence. This draft is based on the whole-genome-shotgun method, and so differing segments of the derived sequence are of differing qualities.

The following paragraph gives an actual comparison of genome-wide differences, finding the nucleotide differences measure about 1.23 percent, confirming previous results.

See also the cited previous results:

Genomewide Comparison of DNA Sequences between Humans and Chimpanzees

Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees

Construction and Analysis of a Human-Chimpanzee Comparative Clone Map

Simply put bad design does not preclude bad design. Again, I return to the question, does design exist? How do we know it when we see it?

I’d imagine then that we’ve left the question of whether evolution is empirical science behind. It really is extremely simple to demonstrate this.

A better question, for me, would be whether a good designer would engage in bad design. Or, alternatively, given only the bad design to examine, we could infer anything more than a bad designer. Certainly, we can recognize design, at least when it comes to designs created by the living beings around us. Having seen a spider spinning a web, we don’t need to see the spider to recognize that the next spiderweb we encounter was also designed. We can recognize the design of natural objects as well, such as crystals in snowflakes or minerals if — and that’s a very big if — we can recognize the natural processes behind their creation.

Intelligent design proponents lack any process to explain the designs they’d like to believe are the work of an intelligent designer. We don’t have the supernatural tools to examine. We can’t establish purposes. They can’t do science on this, nor are they attempting to do so. They begin by assuming an intelligent designer, and then proceed to look for evidence. Science proceeds by following the evidence, and simply can’t be forced into the path of any one supposition, no matter how beloved of any particular group of religious adherents.

As ever, Jesse

 

[grannymh]

Before this thread closes, I hope that readers realize that science matters are different than theological matters at least in the Catholic Church. It is the difference between the created and the Creator.

Blessings,
granny

John 3: 16&17

 

[cassini]

Please correct me if i am wrong. But wasn’t the Pope impressed by Galileo’s theory? So impressed, that he urged him to continue with his work on this theory and to share it with his fellow scientist. But not to teach it as fact?

Correct Latin. But to understand the context of Pope Urban VIII’s view as a cardinal one has to know some background. Copernicus’s inspiration for a heliocentric world came from hermetism, a system of knowledge that emerged after 1000 years in 1460 and led to the Renaissance.
Copernicus’s heliocentricism first emerged in 1524 when he privately distributed an unsigned and untitled manuscript later called Commentariolus or ‘Little Commentary.’ This book died a death and Copernicus hung up his heliocentric hat. Then along came the Lutheran Rheticus who rersurrected *De Revolutionibus * from the shelf and brought it to a Protestant enclave to get it published.

In April 1543, the first edition of De Revolutionibus emerged from the press and both Rheticus and Copernicus received a copy. Copernicus, in the throes of death, had his copy placed on his bed but he died without comment. Rheticus however, opened it up only to find a preface not of his or Copernicus’s writing, the famous To the Reader Concerning the Hypothesis of this Work, otherwise known as the ‘***Ad lectorem’ ***introduction.

‘Since the newness of the hypothesis of this work –which sets the earth in motion and puts an immovable sun at the centre of the universe- has already received a great deal of publicity, I have no doubt that certain of the savants have taken grave offence and think it wrong to raise any disturbance among liberal disciplines which have had the right set-up for a long time now. If, however, they are willing to weigh the matter scrupulously, they will find that the author has done nothing that merits blame…
This artist is markedly outstanding in both these respects for it is not necessary that these hypotheses should be true, or even possible; but it is enough if they provide a calculus which fits the observations…And if it constructs and thinks up causes - and it has certainly thought up a good many - nevertheless it does not think them up in order to persuade anyone of their truth but only in order that they provide a correct basis for calculation…Maybe the philosopher demands probability instead; but neither of them will grasp anything certain or hand it on, unless it has been divinely revealed to him

Written by another Protestant, Osiander, this preface set the limits permitted by both Catholics and Protestants, the conditions required by the Catholic Church thereafter. Thus scientific investigation could continue while adhering to the revealed truth of geocentrism.

 

[Betterave]

‘Since the newness of the hypothesis of this work –which sets the earth in motion and puts an immovable sun at the centre of the universe- has already received a great deal of publicity, I have no doubt that certain of the savants have taken grave offence and think it wrong to raise any disturbance among liberal disciplines which have had the right set-up for a long time now. If, however, they are willing to weigh the matter scrupulously, they will find that the author has done nothing that merits blame…
This artist is markedly outstanding in both these respects for it is not necessary that these hypotheses should be true, or even possible; but it is enough if they provide a calculus which fits the observations…And if it constructs and thinks up causes - and it has certainly thought up a good many - nevertheless it does not think them up in order to persuade anyone of their truth but only in order that they provide a correct basis for calculation…Maybe the philosopher demands probability instead; but neither of them will grasp anything certain or hand it on, unless it has been divinely revealed to him

Written by another Protestant, Osiander, this preface set the limits permitted by both Catholics and Protestants, the conditions required by the Catholic Church thereafter. Thus scientific investigation could continue while adhering to the revealed truth of geocentrism.

Interesting post and interesting to note that the *only *purpose of a ‘scientific’ theory is to “provide a calculus which fits the observations” - in other words, it seems that the ‘true’ doctrine of geocentrism, which does not pursue this end (observation-calculus) and is taken to be independent from it, must not, in this context, be understood to be proffered as a truth of empirical science, but rather as some kind of ‘spiritual’ truth.

 

[grannymh]

Hello again, buffalo,

To compare the differences between human and chimpanzee genomes, it’s necessary to examine the primary literature.

Thank you for the links. I have started to work my way through them. However, my questions would not be addressed to the physical position of earth in the universe nor to Intelligent Design but to evolutionary biology and its methods and materials.

That kind of subject which pertains to the origin of the human species belongs in the Back Fence Forum due to the current ban in Philosophy Forum. See sticky at the top of the Philosophy Forum.

Please see if the following thread would interest you.

forums.catholic-questions.org/showthread.php?t=478146

Blessings,
granny

The quest for knowledge is worthy of the adventures of the journey.

 

[lao_tzu]

Thank you for the links. I have started to work my way through them. However, my questions would not be addressed to the physical position of earth in the universe nor to Intelligent Design but to evolutionary biology and its methods and materials.

That kind of subject which pertains to the origin of the human species belongs in the Back Fence Forum due to the current ban in Philosophy Forum. See sticky at the top of the Philosophy Forum.

Please see if the following thread would interest you.

forums.catholic-questions.org/showthread.php?t=478146

Blessings,
granny

The quest for knowledge is worthy of the adventures of the journey.

Thank you, granny.

I saw you post a link to that thread earlier, and was on the verge of responding to your questions about mitochondrial eve in the OP when I realized I’d need to cover the next 11 pages of posts in order to find a way to insert it back into the conversation. I was daunted. Perhaps I’ll try again to read what’s already been posted there, and join you.

As ever, Jesse

 

[buffalo]

Hello again, buffalo,

As ever, Jesse

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

The chimpanzee ampliconic regions are particularly massive (44%
larger than in human; Fig. 1b) and architecturally ornate, with 19
palindromes (compared to eight in human) and elaborate mirroring
of nucleotide sequences between the short and long arms of the
chromosome, a feature not found in the human MSY (Fig. 3 and
Supplementary Fig. 11). Of the 19 chimpanzee palindromes, only 7
are also found in the human MSY; the other 12 are chimpanzee specific.
Unlike the human MSY, nearly all of the chimpanzee MSY
palindromes exist in multiple copies (Supplementary Fig. 11), so that
each palindrome arm has potential partners for both intra- and interpalindrome
gene conversion (non-reciprocal transfer)22. This may
help explain why arm-to-arm nucleotide sequence divergence in
some chimpanzee MSY palindromes (as much as 0.5%; Supplementary
Figs 12 and 13) is more pronounced than in human
MSY palindromes (,0.06%)13.
Gene conversion may also account for the relatively low density of
retrotransposable elements in ampliconic regions. In the chimpanzee
and human MSYs, retrotransposon content is markedly lower in
ampliconic than in X-degenerate regions—41% versus 63% in
both species (P,0.000001, Z-test; Supplementary Fig. 1i and Supplementary
Table 2). Although it is possible that retrotransposons
preferentially integrate in X-degenerate sequences, this seems
unlikely given the similarity in C1G content and gene density in
ampliconic and X-degenerate regions (Supplementary Table 2 and
Supplementary Fig. 1h). An alternative explanation is that gene conversion
between amplicon copies removes retrotransposons, especially
recently integrated ones. Tellingly, an endogenous retrovirus
that colonized the chimpanzee genome after the chimpanzee–human
split23 is present in 23 copies in the chimpanzee MSY, but only two of
these copies are located in ampliconic regions (14.7 Mb), whereas 21
copies are located in X-degenerate regions (8.6 Mb; P,0.000001,
chi-square test; Supplementary Fig. 14). These findings offer counterpoint to models of unchecked retrotransposon integration as
a driving force in Y-chromosome evolution17,24.
Despite the elaborate structure of the chimpanzee MSY, its gene
repertoire is considerably smaller and simpler than that of the human
MSY (Table 1) as a result of gene loss in the chimpanzee lineage and
gene acquisition in the human lineage. For example, we previously
discovered that the chimpanzee X-degenerate regions had lost 4 out
of 16 genes through inactivating mutations, whereas the human
X-degenerate regions had not lost any genes since the time of the last
common ancestor9. We also reported that two X-transposed genes in
the human MSY had been acquired since the time of the last common
ancestor13.

Unbelievable Y chromosome differences between humans and chimpanzees

Holy ****!Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation.
So much for 98 percent. Let me just repeat part of that: humans and chimpanzees, “comparable to the difference … in chicken and human”.
This is from a new paper that’s just shown up in the Nature advance publication zone. The authors are Jennifer Hughes and colleagues, and the subject is the first complete sequencing of the chimpanzee Y chromosome. “MSY” stands for “male-specific region of the Y chromosome” – it’s most of the Y, aside from a small fraction that recombines with the X chromosome.

more…

 

[lao_tzu]

“MSY” stands for “male-specific region of the Y chromosome” – it’s most of the Y, aside from a small fraction that recombines with the X chromosome.

Hello again.

This is fairly embarrassing. As gently as possible, I recommend that you actually read the paper before trying to analyze it, and certainly before posting a link allowing others to do so in your stead. There is no suggestion of a contradiction with other researchers here.

We conclude that, since the separation of the chimpanzee and human lineages, sequence gain and loss have been far more concentrated in the MSY than in the balance of the genome. … In this respect, the MSY differs radically from the remainder of the genome, where < 2% of chimpanzee euchromatic sequence lacks a homologous, alignable counterpart in humans, and vice versa 15.

(Reference 15 is the primary research I linked to earlier, by The Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005).)

As the human Y-chromosome is composed of some 60 million of our 3165 million bases, or 1.9 percent, and the MSY region is only a fraction of this, I invite you, before boldly making claims that can be contradicted by arithmetic, to first do the math. The Y-chromosome, our smallest chromosome, principally a degenerate X-chromosome, is in a land of its own. The MSY does not represent the remaining 98 percent of the genome. By the paper you have yourself cited, it is instead “radically different.” As the MSY region retains about 70 percent similarity between chimps and humans, your “so much for 98 percent” is a reference to differences found in only 30 percent of 2 percent of our genome, or 0.6 percent.

As ever, Jesse