Evolution a hoax?

[Dinwar]

There is absolutely nothing outstanding about fused chromosomes as some sort of evidence for macroevolution.

This is as false as the claim that nostral position is more important than jaw formation in morphology. There are, simply put, some traits which are more significant than others in biology, and randman refuses to acknowledge that.

No, but it's no more and arguably less significant than if humans had 48 chromosomes, or that humans are primates in general and have some shared features such as hands and feet.

A perfect example. The presence of hands and feet IS a useful trait--it's shared by one taxon, and not by others. However, it's useless in comparing two taxa within that larger taxon, as they both have it. There ARE specific criteria, discussed to a great depth in the link to PAST I posted earlier (randman can't see it, but that's his loss), and randman is not using those criteria.

 

[DC]

Oh and ANT, wiki here says we have 2.9 BILLION base pairs, not

http://en.wikipedia.org/wiki/Human_genome

I'll let you do the math and figure out why you are wrong.

Not what? you try to make it look as if Ant claimed something wrong or one of his links, while he did not make a claim regarding the toal number of basepairs.

not what?

 

[randman]

ANT, why don't you bother to read the paper?

Endogenous retroviruses. Endogenous retroviruses (ERVs) have become all but extinct in the human lineage, with only a single retrovirus (human endogenous retrovirus K (HERV-K)) still active24. HERV-K was found to be active in both lineages, with at least 73 human-specific insertions (7 full length and 66 solo long terminal repeats (LTRs)) and at least 45 chimpanzee-specific insertions (1 full length and 44 solo LTRs). A few other ERV classes persisted in the human genome beyond the human–chimpanzee split, leaving ~9 human-specific insertions (all solo LTRs, including five HERV9 elements) before dying out.

http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

my boldd

 

[DC]

ANT, why don't you bother to read the paper?



http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

my boldd

so they have alot shared ERV's and some not shared as if they had a common ancestor and then lived as seperate species for a long time?

what does your fairytale say about this? what's the ID explaenation to this? a creator created them and placed them in those animals?

 

[randman]

Not what? you try to make it look as if Ant claimed something wrong or one of his links, while he did not make a claim regarding the toal number of basepairs.

not what?

Yea, a better rebuttal to ANT and the misguided writer that misinterpreted the study is that the numbers such as 41 refer to families of ERVs, but they didn't get that.

 

[randman]

so they have alot shared ERV's and some not shared as if they had a common ancestor and then lived as seperate species for a long time?

what does your fairytale say about this? what's the ID explaenation to this? a creator created them and placed them in those animals?

ANT quoted a link suggesting nearly 100% of ERVs are in identical loci, which isn't true. Interesting the same guy said if this was not the case, it would be strong evidence against common descent.

I'll let you figure it out.

 

[randman]

This is as false as the claim that nostral position is more important than jaw formation in morphology. There are, simply put, some traits which are more significant than others in biology, and randman refuses to acknowledge that.

A perfect example. The presence of hands and feet IS a useful trait--it's shared by one taxon, and not by others. However, it's useless in comparing two taxa within that larger taxon, as they both have it. There ARE specific criteria, discussed to a great depth in the link to PAST I posted earlier (randman can't see it, but that's his loss), and randman is not using those criteria.

Well, we at least have the same number of feet and hands as chimps. Not so with chromosomes.

 

[DC]

Yea, a better rebuttal to ANT and the misguided writer that misinterpreted the study is that the numbers such as 41 refer to families of ERVs, but they didn't get that.

no you were confused when you read the toal EVR base pairs and then read in another source the total basepairs

 

[Dinwar]

Well, we at least have the same number of feet and hands as chimps. Not so with chromosomes.

This doesn't address my concern. You are not applying standard, or even justifiable, criteria for determining which characters to use in your analysis, either in morphology or in genetics. This is a major concern, as (if you'd read the documents I linked to) you'd see that characters are not chosen randomly, as you seem to believe, but rather very carefully and for sound reasons. You have yet to even attempt a refutation of those reasons--at best, you've provided an article which completely ignores these criteria in terms of comparative morphology.

Secondly, none of the discussion of genetic similarities with chimps means anything without context. What is the outgroup? What are the other taxa used? How similar are these taxa? How robust are the groupings? All of this needs to be addressed.

Finally, even if your argument has some validity it's only applicable to Animalia, and likely only to a subset thereof. You do not give plant reproduction any consideration, and you don't even attempt to delve into bacterea/archea. So even if you're right, it will show that a Designer designed one kingdom, out of many (I'm a splitter when it comes to Protista). So rather than being a refutation of evolution as such, you're actually discussing a relatively narrow part of it and over-extending your results into taxa where you don't even pretend to provide support for your assertions.

You're trying to overturn a PARADIGM. Not just a hypothesis. You should at least present enough data to support the idea that the hypothesis is worth discussing, and thus far you've failed to do so.

 

[A'isha]

You must be misinterpreting the study because 1,608 minus 1,495 is more than 41 by itself alone.

The smaller numbers are full-length LTR retrotransposons/retroviruses in the respective genomes (ie, greater than 5000 base pairs), while the larger numbers include solo LTRs and/or fragmented endogenous retroviral sequences (from 80 up through 12,000 base pairs).

I suppose it's a matter of definitions, whether you count fragments as "ERVs", rather than full-length retroviruses in the genome. The paper itself focuses on identifying and classifying full-length chimpanzee ERVs - the larger gap search was to try and identify the proportion of indels that could be attributed even vaguely to ERVs, rather than being caused in the genomes by other mechanisms.

I used the calculation I did because the paper's aforementioned focus on the identification of full-length sequences with classifiable ERVs. And so, when the gap search was run for anything ERV-sequence related, no matter how small and fragmentary (and when you're talking about genomes of 2.9 billion base pairs total in size, 80 base pairs is almost indescribably tiny), there were only 31/41 instances of full-length ERVs that did not have orthologous positions in both genomes.

And there are many more ERVs than 1495.

The authors note that they were focusing only on ERV sequences that they could unambiguously identify. "Using the procedure described above, we identified a total of 425 full-length chimpanzee endogenous retroviruses. This is certainly an underestimate of the number of endogenous retroviruses in the chimpanzee genome because we consciously excluded any sequences that could not be unambiguously identified as an endogenous retrovirus."

 

[A'isha]

ANT, why don't you bother to read the paper?



http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

my boldd

Why don't you bother to read it? Both this paper and the other one are very clear about the distinction between full-length ERVs and solo/fragmentary LTRs. I counted full-length ERVs as "an ERV".

If you don't like it, make your own calculation.

EDIT: The authors of the ERV comparison paper certainly think that the data are consistent between full-length and fragmentary insertions:

Consistent with the copy number of CERV 30 (HERVK10) species-specific full-length insertions (Table ​4), the insertions of solo LTRs from this family were higher in humans (78) than in chimpanzees (43) since they diverged from the common ancestor (Table 5). Apart from CERV 30 (HERVK10) insertions in both the genomes, five other endogenous retroviral families continued to be active in chimpanzees, resulting in solo LTR or fragmented insertions while only one new insertion from MER31B occurred in humans since they diverged from the common ancestor (Table 5).

 

[Wowbagger]

Most ID in biology could work with aliens as the intelligence behind the design of biological life, but doesn't work for ID in physics.

You didn't answer my question.

Someone who is going to try to debunk evolution, and/or promote Intelligent Design should, I hope, be concerned over whether or not life really was designed with the full intention of the Designer, or if we were merely left in His Dust Bin.

Do you have a test by which one can determine this?

 

[randman]

This doesn't address my concern. You are not applying standard, or even justifiable, criteria for determining which characters to use in your analysis, either in morphology or in genetics. This is a major concern, as (if you'd read the documents I linked to) you'd see that characters are not chosen randomly, as you seem to believe, but rather very carefully and for sound reasons. You have yet to even attempt a refutation of those reasons--at best, you've provided an article which completely ignores these criteria in terms of comparative morphology.

Secondly, none of the discussion of genetic similarities with chimps means anything without context. What is the outgroup? What are the other taxa used? How similar are these taxa? How robust are the groupings? All of this needs to be addressed.

Finally, even if your argument has some validity it's only applicable to Animalia, and likely only to a subset thereof. You do not give plant reproduction any consideration, and you don't even attempt to delve into bacterea/archea. So even if you're right, it will show that a Designer designed one kingdom, out of many (I'm a splitter when it comes to Protista). So rather than being a refutation of evolution as such, you're actually discussing a relatively narrow part of it and over-extending your results into taxa where you don't even pretend to provide support for your assertions.

You're trying to overturn a PARADIGM. Not just a hypothesis. You should at least present enough data to support the idea that the hypothesis is worth discussing, and thus far you've failed to do so.

I took you off ignore but it's getting tedious. None of what you wrote is relevant. The simple fact is we have 46 chromosomes and some believe it is due to a human being having a chromosomal fusion and somehow passing that trait down to all of us.

Big deal. It's entirely within the scope of purely human lineage.

What's more interesting is what sort of bottleneck (or was it Adam and Eve... would have created this scenario, but it's still entirely within human lineage.

 

[randman]

You didn't answer my question.

Someone who is going to try to debunk evolution, and/or promote Intelligent Design should, I hope, be concerned over whether or not life really was designed with the full intention of the Designer, or if we were merely left in His Dust Bin.

Do you have a test by which one can determine this?

Personally, I would look a strong version of the anthropomorphic principle in physics to suggest intentionality and some areas outside of biology but you can talk with more IDers and creationists who point to specific evidence in biology all the time.

Once again, isn't this thread supposed to be on evolution?

 

[A'isha]

If you think my full-length to all-length calculation was off-base, here's another for you that I hope eases your apples-to-oranges concerns.

The paper identified 425 full-length ERVs in the chimpanzee genome, spread across 42 "families" (though the family thing isn't important right now). 41 of those full-length ERVs aren't in an orthologous position in the human genome. That means 384 were in an orthologous position in the human genome.

So, if you just compare full-length ERVs, you're still looking at 90.4% of them being in an orthologous position in the genomes of both species.

 

[randman]

If you think my full-length to all-length calculation was off-base, here's another for you that I hope eases your apples-to-oranges concerns.

The paper identified 425 full-length ERVs in the chimpanzee genome, spread across 42 "families" (though the family thing isn't important right now). 31 of those full-length ERVs aren't in an orthologous position in the human genome. That means 394 were in an orthologous position in the human genome.

So, if you just compare full-length ERVs, you're still looking at a 92.7% of them being in an orthologous position in the genomes of both species.

Link.

I think there is some confusion equating a family having an ortholog with all the sequences in that family being an ortholog.

F

orty two families of ERVs were identified in the chimpanzee genome including the discovery of 9 previously unknown families in humans. The vast majority of these families were found to have orthologs in the human genome except for two (CERV 1/PTERV1 and CERV 2) families.

http://smartech.gatech.edu/handle/1853/29789?show=full

 

[DC]

I took you off ignore but it's getting tedious. None of what you wrote is relevant. The simple fact is we have 46 chromosomes and some believe it is due to a human being having a chromosomal fusion and somehow passing that trait down to all of us.

Big deal. It's entirely within the scope of purely human lineage.

What's more interesting is what sort of bottleneck (or was it Adam and Eve... would have created this scenario, but it's still entirely within human lineage.

any indication of the existence of Adam and Eve?

 

[catsmate]

so its pure accident that today we find two chromosome in Chimps that match our fused Chromosome 2?

Obviously god The Designer designed it that way.

 

[Dinwar]

I took you off ignore but it's getting tedious. None of what you wrote is relevant.

The quality of the characters you choose is entirely relevant to a discussion on taxonomy--in fact, I know several people who believe this is the very definition of such a discussion. If you're unwilling to discuss this, you don't want to discuss taxonomy. Period.

You've got a choice to make--do you want us to evaluate your analysis, or not? If not, why bother arguing? If you do, why complain when we do so?

The simple fact is we have 46 chromosomes and some believe it is due to a human being having a chromosomal fusion and somehow passing that trait down to all of us.

No. The simple fact is that you've made several arguments about taxonomy and morphology which, to put it mildly, leave much to be desired. I gave a long post on why your link to the comparative morphology of mosasaurs and cetaceans was garbage, and ANTpogo seems to be doing well showing that your genetic information is equally bad. If we demonstrate that your arguments are bad, we demonstrate that you have nothing to base your conclusion on.

Once again, isn't this thread supposed to be on evolution?

You're proposing a specific mechanism: design. It's perfectly acceptable, and to my mind required, to evaluate that mechanism. If you can't provide a well-supported mechanism, all you have is a string of observations, and any theory you derive from it should justifiable be discarded as inadequately supported at the present time.

 

[A'isha]

Link.

It's in, you know, the paper we've been talking about all this time! This one right here! The one where it says:

Using the procedure described above, we identified a total of 425 full-length chimpanzee endogenous retroviruses. This is certainly an underestimate of the number of endogenous retroviruses in the chimpanzee genome because we consciously excluded any sequences that could not be unambiguously identified as an endogenous retrovirus. The majority of these endogenous retroviruses (395/425 or 93%) were identified directly by LTR_STRUC or by homology to LTR_STRUC-identified elements.

ClustalX [13] was used to build a multiple alignment of the RT domain of these 425 elements together with the RT domains of 16 previously described LTR retrotransposons/retroviruses representative of the three major classes of retroviral elements (Table ​1). Phylogenetic analysis of the RT regions of the 425 full-length elements revealed the presence of at least 42 independent lineages of endogenous retroviruses in the chimpanzee genome that we here define as families (Figure ​1).

Note that I didn't include the 16 previously described LTR retrotransposons/retroviruses, just the 425 identified by the paper's authors. If I do, it'll just make the percentage of ERVs in an orthologous position in the genomes of both species that much higher (well, okay, 90.7% instead of 90.4%, but it's the principle of the thing!).

I think there is some confusion equating a family having an ortholog with all the sequences in that family being an ortholog.

F

http://smartech.gatech.edu/handle/1853/29789?show=full

Which is why I (and the paper's authors) didn't count orthologous families when running a full-length ERV gap search, but only identified individual ERV sequences that either were present or not present. Though the paper does break down the "missing" sequences by which family they belong to.

Of the 41 instances where an endogenous retroviral sequence is present in chimpanzees but lacking in humans, 29 were due to novel insertions in chimpanzees while 12 were deletions in humans (Tables ​3 and ​and 4; Figure ​Figure 6a). Of the 31 instances where an endogenous retrovirus is present in humans but absent in chimpanzees, we found that 8 were due to novel insertions in humans while 23 were deletions in chimpanzees (Table ​4; Figure ​Figure 6b). Of the 29 novel insertions in chimpanzees, 25 belong to the CERV 1/PTERV1 family, 2 to the CERV 2 family, 1 to the CERV 3 (HERVS7 1) family and 1 to the CERV 30 (HERVK10) family whereas all the 8 novel insertions in humans belong to the CERV 30 (HERVK10) family (Tables 3 and ​4).