Human Chromosome 2 Question

[Squawk]

It's also consistent with the Intelligent Design hyppthesis as well. The only difference is, the evolutionary explanation has an actual mechanism underlying it, whereas ID can only say that it is conceivable that a designer could have done it.

Give me any idea, on anything, anywhere, that would not be deemed consistent with ID. Ie, show me a falsification point of ID.

HC2 fusion is consistent (and indeed predicted) by evolutionary theory. Non fusion is not.

Fusion or non fusion are both "consistent" with ID, because ID is only ever applied retrospectively.

 

[DWisker]

Give me any idea, on anything, anywhere, that would not be deemed consistent with ID. Ie, show me a falsification point of ID

I think their assertion that complex specified information cannot arise via a Darwin
mechanism of random mutation and natural selection qualifies as a falsifiable claim. Of course, this has been falsified many times, most effectively by the TURF-13 gene in the mitochondrial genome of maize. It is the result of recombination, a cobbling together of non-protein-coding sequences into a novel, functional protein.

 

[Gunboat Diplomat]

Give me any idea, on anything, anywhere, that would not be deemed consistent with ID. Ie, show me a falsification point of ID

I think their assertion that complex specified information cannot arise via a Darwin
mechanism of random mutation and natural selection qualifies as a falsifiable claim. Of course, this has been falsified many times, most effectively by the TURF-13 gene in the mitochondrial genome of maize. It is the result of recombination, a cobbling together of non-protein-coding sequences into a novel, functional protein.

I don't think so. Recall the type of argumentation used by the people for whom this thread is a response. Just because "complex specified information" (whatever that is) could arise from Darwinian mechanisms doesn't mean it did! Life was just mostly intelligently designed and Darwinian evolution is used for microevolution... as per God's design!

 

[DWisker]

This is beginning to remind me of that old joke about philosophers saying "We know it works in practice, but does it work in principle? "

 

[Squawk]

That would qualify as a falsifiable point for evolution, not ID.

 

[DWisker]

I can see that.

 

[TheFlyingBastard]

That's such a silly argument, if someone made everything they designed look the same - they'd lose business.

There's this electronics company from Cupertino, California that wants to speak with you...

 

[ShootMyMonkey]

Of course, this has been falsified many times, most effectively by the TURF-13 gene in the mitochondrial genome of maize. It is the result of recombination, a cobbling together of non-protein-coding sequences into a novel, functional protein.

But with maize, you have the problem that quite a lot of what happened to its genome is the result of humans crossbreeding and selecting for certain traits. While the processes underlying the formation is completely natural, the selection parameters weren't .. so it is ID in a sense, but the "designer" happens to be generations of human farmers. But then, most people if you show them the difference between teosinte grasses and modern maize, they would think it a case of so-called "macroevolution", when it is in fact, technically "micro."

I think the key point that creationists miss about HC2 is how its evidence in support of common descent. Ken Miller, in the video, expressed it correctly. It's not that HC2 proves, by itself, that common descent absolutely MUST be true... but rather that in order for common descent to be true, HC2 MUST be a chromosome fusion. As far as showing that common descent itself is true, it's only one piece of data in a larger context. For instance, the fact that the chromosome fusion itself HAD to be true is the result of a host of other data including the sheer degree of matching DNA between humans and other apes... that too, indicates common descent when put into the context of how much greater a degree of DNA similarity there is on that comparison as opposed to humans and some other group of animals... that too, indicates common descent when put into the context of how the progression of similarity as well as difference shows up across varying degrees of specificity in classification.

 

[DWisker]

Of course, this has been falsified many times, most effectively by the TURF-13 gene in the mitochondrial genome of maize. It is the result of recombination, a cobbling together of non-protein-coding sequences into a novel, functional protein.

But with maize, you have the problem that quite a lot of what happened to its genome is the result of humans crossbreeding and selecting for certain traits. While the processes underlying the formation is completely natural, the selection parameters weren't .. so it is ID in a sense, but the "designer" happens to be generations of human farmers.

Why would the fact that maize is domesticated make any difference? As you said, the processes that created T-URF13 are completely natural. They had nothing to do with any artificial selection for traits. The trait that it is responsible for (cytoplasmic male sterility) is not selected for by breeders. Pointing out that the plant is domesticated as if it makes any difference is exactly what the creationist try and do when confronted by this. Is that what your point was?

But then, most people if you show them the difference between teosinte grasses and modern maize, they would think it a case of so-called "macroevolution", when it is in fact, technically "micro."

Yes, that is one of the best examples of only a few mutations producing macroevolutionary-type change.

I think the key point that creationists miss about HC2 is how its evidence in support of common descent. Ken Miller, in the video, expressed it correctly. It's not that HC2 proves, by itself, that common descent absolutely MUST be true... but rather that in order for common descent to be true, HC2 MUST be a chromosome fusion.

Exactly. The problem is, many laypeople on the evo side don't understand the distinction either. We have to be careful to educate these folks as well.

 

[ShootMyMonkey]

Why would the fact that maize is domesticated make any difference? As you said, the processes that created T-URF13 are completely natural. They had nothing to do with any artificial selection for traits. The trait that it is responsible for (cytoplasmic male sterility) is not selected for by breeders. Pointing out that the plant is domesticated as if it makes any difference is exactly what the creationist try and do when confronted by this. Is that what your point was?

Yep. That was the point. That creationists would make the argument that everything that ever happened to maize is the result of "design" since it's a domesticated plant. Or, at best, they might say that because the selection parameters were artificial, the process can't strictly be called "Darwinian," (i.e. not natural selection) in spite of the fact that the effects of selection on domesticated plants and animals was basically what Darwin extended to a capacity within nature.

 

[Dragan Glas]

Greetings,

It's also consistent with the Intelligent Design hyppthesis as well. The only difference is, the evolutionary explanation has an actual mechanism underlying it, whereas ID can only say that it is conceivable that a designer could have done it.

Give me any idea, on anything, anywhere, that would not be deemed consistent with ID. Ie, show me a falsification point of ID.

HC2 fusion is consistent (and indeed predicted) by evolutionary theory. Non fusion is not.

Fusion or non fusion are both "consistent" with ID, because ID is only ever applied retrospectively.

Just commenting on this rather than the "meat" of the topic...

Perhaps the only way to falsify ID - along with Creationism - is to identify something which they can't explain (where "God/Designer did it!" really doesn't look viable) and explain it with evolution.

For example, nylonase and/or other examples of evolution which have happened - are happening! - in our lifetime.

Another type of example would be "junk" DNA: why that amount - no more, no less?

This is the sort of thing that makes ID look empty as a explanation.

Vestigial organs, etc - such as the appendix - are simpler examples of the above why? type of question.

Why can some people wiggle their ears and others can't? Why can some people form their tongue into a tube-shape, whilst others can't? Why can some people taste a bitter compound from tea in a glass of water, whilst others can't?

Both "God did it!" and "Designer did it!" appear - and are - empty explanations of these phenomena.

Kindest regards,

James

 

[Deleted member 619]

Nah, wouldn't work. Over at Ratskep (and formerly at RDF), we have a very special case, name of Robert Byers, who erects some bollocks about 'innate triggers', the idea being that these things were there all along just waiting to be triggered.

Edit: Not that he can be taken seriously, of course. He is the famed source of the idea that polar bears are white because they're scared of humans, and that you can intimidate a predator into running away simply by shaking your car keys at it.

 

[Gunboat Diplomat]

Just commenting on this rather than the "meat" of the topic...

Perhaps the only way to falsify ID - along with Creationism - is to identify something which they can't explain (where "God/Designer did it!" really doesn't look viable) and explain it with evolution.

For example, nylonase and/or other examples of evolution which have happened - are happening! - in our lifetime.

Another type of example would be "junk" DNA: why that amount - no more, no less?

This is the sort of thing that makes ID look empty as a explanation.

Vestigial organs, etc - such as the appendix - are simpler examples of the above why? type of question.

Why can some people wiggle their ears and others can't? Why can some people form their tongue into a tube-shape, whilst others can't? Why can some people taste a bitter compound from tea in a glass of water, whilst others can't?

Both "God did it!" and "Designer did it!" appear - and are - empty explanations of these phenomena.

They're already there...

 

[ShootMyMonkey]

Perhaps the only way to falsify ID - along with Creationism - is to identify something which they can't explain (where "God/Designer did it!" really doesn't look viable) and explain it with evolution.

For example, nylonase and/or other examples of evolution which have happened - are happening! - in our lifetime.

Another type of example would be "junk" DNA: why that amount - no more, no less?

This is the sort of thing that makes ID look empty as a explanation.

Vestigial organs, etc - such as the appendix - are simpler examples of the above why? type of question.

Why can some people wiggle their ears and others can't? Why can some people form their tongue into a tube-shape, whilst others can't? Why can some people taste a bitter compound from tea in a glass of water, whilst others can't?

Both "God did it!" and "Designer did it!" appear - and are - empty explanations of these phenomena.

While someone who identifies exclusively with "ID" by name wouldn't be able to claim it, the common argument for this from Judeo-Christian zealots is to say that "we live in a fallen creation, therefore it ended up that way." Of course, there is no model whatsoever, nor is there even the slightest inkling of specificity. It's simply a universal answer that says that anything which isn't quite right is the result of sin.

If you press them to provide exactly how sin causes those specific things, they have no model, but don't really see that as an issue. Now die-hard creationists contend that there is no need for a model in the first place because they're insufferable morons unworthy of drawing even a single breath. IDiots, otoh, feign effort that they are working on such details, but contend that because actual scientists also use the "we're working on it" statement for any unknowns, they're eligible to do the same. What they neglect to mention is that still "working on" a model means they don't have a theory. Sure, there are misnamed things like "M-Theory" which are technically conjectures and not theories in spite of the name, but they are still light years ahead of anything the IDiots have. ID has only an assertion and nothing beyond that point. This is, of course, aside from the fact that IDiots are not actually working on developing a model in any sense -- they're just developing more rehashings of the same old arguments rather than fleshing out the ID concept.

 

[borrofburi]

While someone who identifies exclusively with "ID" by name wouldn't be able to claim it, the common argument for this from Judeo-Christian zealots is to say that "we live in a fallen creation, therefore it ended up that way." Of course, there is no model whatsoever, nor is there even the slightest inkling of specificity. It's simply a universal answer that says that anything which isn't quite right is the result of sin.

Or like tsar say that "intelligent design" doesn't mean "perfect design".

Of course, this plays right into the simple fact that ID is unfalsifiable.

 

[Banana]

Sorry to dig this thread up, but I felt this was relevant.

Some creationist threw this article at me. It looks like total nonsense, but I was wondering if someone more educated in molecular biology could debunk it.

"From a distance humans and chimpanzees look very similar. It is in fact this similarity that prompted Darwin to propose chimpanzees are our closest living relatives with whom we share a common ancestor quite recently. A close up look also reveals many similarities, and the word was man shares 99% of the genetic make up with his chimp cousin. The word was. In 2005 the chimpanzee genome project released the first genetic comparison of man and chimp. With astounding results: Man and chimp share far less sequences than ever expected. Science had to admit recently that the difference between man and chimp is 6.4% [1]. Despite the adjustment by over 5%, it can hardly be the right figure. After the realization of the first chimp-human whole genome comparison in 2005, the Chimpanzee Sequencing and Analysis Consortium stated:

"Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover 2.4 gigabases (Gb) of high quality sequence, including 89 Mb from chromosome X and 7.5 from chromosome Y." [2]

In other words, of the 2.85 Gb (=billion base pairs) human euchromatic DNA only 2.4 Gb formed a match with that of the chimpanzee. DNA sequences that do not match do not match because they are distinct sequences. Over 15% of the sequences do not match! The difference between man and his "closest relative" is now suddenly 15% plus 6.4% is more than 21 percent! Based on this figure, and the fact that man has unique protein-coding [3] and miRNA [4] genes for which standard evolutionary theory hasn't the faintest origin clue, it is logically sound to reject common ancestry with chimpanzees. This also means that the structure and arrangement of human chromosome 2 has to be reinterpreted. The chromosome is said to be a fusion product of two ancestral primate chromosomes that are still separate in chimpanzees and is among the best molecular evidence of Darwinian common descent.

Comparing human and chimpanzee chromosomes its turns out there are 10 major chromosomal differences (5). Intra-chromosomal inversions are identified in nine human chromosomes: 1, 4, 5, 9, 12, 15, 16, 17 and 18. This means that a huge part within the chromosome was inverted head to toe, so that it now has the opposite orientation. In addition, there appears to be a fusion of chimpanzee chromosome 12 and 13, thus producing human chromosome 2 (5). It is this "fusion" located to chromosome 2q13-2q14.1 that has delighted evolutionists, as they claim it proves we have a common ancestor with chimpanzees. But is it compelling?

Remnants of telomeric DNA? In 2002, Fan et al analyzed the structure of >600 kb surrounding the fusion site and closely related sequences on other human chromosomes (6). Their analysis showed, what they call, "multiple subtelomeric duplications to chromosomes 1, 5, 8, 9, 10, 12, 19, 21, and 22" present in the fusion site. The sequences resembling telomeric DNA, which can also be found on several locations elsewhere in the human genome, are compelling evidence for the fusion. Isn't it?

No, it is not compelling at all. In 2005, Hillier et al published the molecular sequence of human chromosome 2 and 4. The paper demonstrated that human chromosome 4 also has a 1.1 Mb (1.1 million base pairs) subtelomeric region (4q26) showing an abundance of subtelomeric duplications to human chromosomes 1-9, 11, 16, 19 and 20. Similar "not highly conserved" sequences could also be demonstrated in the mouse genome, but without "conclusive evidence" for an ancient fusion, (6; p729-730). Remarkably, chromosome 4 shows another region resembling non-functional subtelomeric sequences (4q32.3) that is highly conserved in mice (6; p730).

What do these data mean? As a matter of fact it means nothing at all with respect to common descent. The sequences will, of course, be interpreted by our dear Darwinian opponents as the result of common ancestry with chimpanzees, but the fact that subtelomeric regions can be found also in other parts of the human and other genomes makes the conclusion merely conclusion jumping, not compelling at all. The fact that subtelomeric repetitive regions can be found scattered throughout the human genome merely reflects the nature of repetitive sequences, i.e. they easily duplicate and translocate. Why than do the sequences present in chromosome 2 qualify as evidence for a chromosome fusion, while similar sequences in chromosome 4 do not? Because it fits the Darwinian presupposition of an ancient fusion. We call this selective data interpretation.

And how do our Darwinian friends explain the conserved ancient subtelomeric sequences? As they are what Darwinians claim, remnants of ancient fusion sites, how could these sequences be conserved if they do not have an apparent function in humans?

Remnants of a centromere? Molecular biologists know that a fusion of two ancestral chromosomes would have produced human chromosome 2 with two centromeres. Currently, human chromosome 2 has only one centromere, so there must be molecular evidence for remnants of the other. In 1982, Yunis and Prakash studied the fusion site of chromosome 2 with a technique known as fluorescence in situ hybridization (FISH) and reported signs of the expected centromere (5). In 1992, another study also reported signs of the centromere (7). In 2005, after the complete sequencing of human chromose 2, we would have expected full, watertight proof of the ancestor's centromere. However, even after intense scrutiny there are still only signs of the centromere. If signs of the centromere were already observed in 1982, why can it not be proved in the 2005 sequence analysis? Apparently, the site mutated with such high pace it is no longer recognizable as a centromere:

"During the formation of human chromosome 2, one of the two centromeres became inactivated (2q21, which corresponds to the centromere of chromosome 13) and the centromeric structure quickly deteriorated".(6)

Why would it quickly deteriorate? Why would this region deteriorate faster than neutral? Did the centromere actively attract mutations? A close up scrutiny in 2005 showed the region that has been interpreted as the ancestor's centromere to be built from sequences present in 10 additional human chromosomes (1, 7, 9, 10, 13, 14, 15, 18, 21 and 22) as well as a variety of other genetic repeat elements that were already in place before the alleged fusion occurred (6).

The fusion site revisited. The chimpanzee and human genome projects demonstrated that the fusion did not result in loss of protein coding genes. Instead, the human locus contains approximately 150 thousand additional base pairs not found in chimpanzee chromosome 12 and 13 (now also known as 2A and 2B). This is remarkable because why would a fusion result in more DNA? We would rather have expected the opposite: the fusion would have left the fused product with less DNA, since loss of DNA sequences is easily explained. The fact that humans have a unique 150 kb intervening sequence indicates it may have been deliberately planned (or: designed) into the human genome. It could also be proposed that the 150 kb DNA sequence demarcating the fusion site may have served as an adaptor sequence for bringing the chromosomes together and facilitate the fusion in human.

Another remarkable observation is that in the fusion region we find an inactivated cobalamin synthetase (CBWD) gene (8). Cobalamin synthetase is a protein that, in its active form, has the ability to synthesize vitamin B12, a crucial cofactor in the biosynthesis of nucleotides, the building blocks of DNA and RNA molecules. Deficiency during pregnancy and/or early childhood results in severe neurological defects, because of an impaired development of the brain. The Darwinian assumption is that the cobalamin synthetase gene was donated by bacteria a long time ago and afterwards it was inactivated. Nowadays, humans must rely on microorganisms in the colon and dietary intake (a substantial part come from meat and milk products) for their vitamin B12 supply. It is also of note that humans have several copies of inactivated cobalamin-synthetase-like genes on several locations in the genome, whereas chimpanzees only have one inactivated cobalamin synthetase gene. That the fusion must have occurred after man and chimp split is evident from the fact that the fusion is unique to humans:

"Because the fused chromosome is unique to humans and is fixed, the fusion must have occurred after the human-chimpanzee split, but before modern humans spread around the world, that is, between 6 and 1 million years ago." [8]

The molecular analyses show we are more unique than we ever thought we were and this is in complete accordance with creation. We propose the fusion, if it really was a fusion after all, may have resulted from an intricate rearrangement or activation of repetitive genetic elements after the fall (as part of or executors of the curse following the fall) and inactivated the cobalamin synthetase gene (after the fall we had to eat meat!). The inactivation of the gene may have reduced people's longevity in a similar way as the inactivation of the GULO gene which is crucial to vitamin C synthesis [9].

References:
1) Cohen J. Relative differences: The Myth of 1%. Science 2007, 316:1836.

2) The Chimpanzee sequencing and Analysis Consortium. Nature 2005, 437: p71.

3) The chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, volume 437, pages 69-87.

4) Berezikov, E., Fritz, T., van Laake, L.W., Kondova, I., Bontrop, R., Cuppen, E. and Plasterk, R.H.A. Diversity of microRNAs in human and chimpanzee brain. Nature Genetics 38:1375-1377, 2006.

5) Yunis J.J. and Prakash O. The origin of man: a chromosomal pictorial legacy. Science. 1982, 215:1525-30.

6) Hillier LW, et al. Generation and annotation of the DNA sequences of humans chromosomes 2 and 4. Nature 2005, 434:724-731.

7) IJdo JW, et al. Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proc Natl Acad Sci U S A 1991, 88:9051-9055.

8) Fan Y, et al. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and paralogous regions on other human chromosomes. Genome Research 2002, 12:1651-1662.

9) Borger P, Truman R. Why the GULO genes in primates cannot be taken as evidence for common descent. J Creation 2008 (in press).
"

 

[Master_Ghost_Knight]

Easy, just quote the bible. "Thou shal not lie".
And do the simple task of reading the papers and see what it actualy says.
Check also if the papers are reliable, hint: publishers like the Journal of Creationism are very likely to have nothing but bunk.

 

[Squawk]

I'll get to it shortly, but there's a hell of a lot of bs in there, so perhaps you could pick out a couple of key points you want debunking to start off with and I'll focus on that. Very much like the gish gallop when they post so much bs packed into one article.

 

[Banana]

He keeps referencing these two sections:

"Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover 2.4 gigabases (Gb) of high quality sequence, including 89 Mb from chromosome X and 7.5 from chromosome Y." [2]

In other words, of the 2.85 Gb (=billion base pairs) human euchromatic DNA only 2.4 Gb formed a match with that of the chimpanzee. DNA sequences that do not match do not match because they are distinct sequences. Over 15% of the sequences do not match! The difference between man and his "closest relative" is now suddenly 15% plus 6.4% is more than 21 percent! Based on this figure, and the fact that man has unique protein-coding [3] and miRNA [4] genes for which standard evolutionary theory hasn't the faintest origin clue, it is logically sound to reject common ancestry with chimpanzees. This also means that the structure and arrangement of human chromosome 2 has to be reinterpreted. The chromosome is said to be a fusion product of two ancestral primate chromosomes that are still separate in chimpanzees and is among the best molecular evidence of Darwinian common descent.

and

No, it is not compelling at all. In 2005, Hillier et al published the molecular sequence of human chromosome 2 and 4. The paper demonstrated that human chromosome 4 also has a 1.1 Mb (1.1 million base pairs) subtelomeric region (4q26) showing an abundance of subtelomeric duplications to human chromosomes 1-9, 11, 16, 19 and 20. Similar "not highly conserved" sequences could also be demonstrated in the mouse genome, but without "conclusive evidence" for an ancient fusion, (6; p729-730). Remarkably, chromosome 4 shows another region resembling non-functional subtelomeric sequences (4q32.3) that is highly conserved in mice (6; p730).

What do these data mean? As a matter of fact it means nothing at all with respect to common descent. The sequences will, of course, be interpreted by our dear Darwinian opponents as the result of common ancestry with chimpanzees, but the fact that subtelomeric regions can be found also in other parts of the human and other genomes makes the conclusion merely conclusion jumping, not compelling at all. The fact that subtelomeric repetitive regions can be found scattered throughout the human genome merely reflects the nature of repetitive sequences, i.e. they easily duplicate and translocate. Why than do the sequences present in chromosome 2 qualify as evidence for a chromosome fusion, while similar sequences in chromosome 4 do not? Because it fits the Darwinian presupposition of an ancient fusion. We call this selective data interpretation.

 

[Squawk]

Ok, without actually even starting to research I can already tell you that half the issue is with a misrepresentation of genetic polymorphism. Not inclined to do research that will take me a couple of hours at nearly midnight though.