Jeffrey Tomkins (creationist) on the chromosome 2 fusion

[atxaxbig...@yahoo.co.uk]

https://answersingenesis.org/genetics/dna-similarities/alleged-human-chromosome-2-fusion-site-encodes-an-active-dna-binding-domain-inside-a-complex-and-hig/

Does anyone know if this been debunked anywhere? I can't seem to find anything on it besides some unconfirmed reports about Ken Miller apparently admitting that Tomkins was right, conveniently in private and with no camera rolling.

[RSNorman]

On Wed, 9 Mar 2016 12:49:46 -0800 (PST), atxaxbig...@yahoo.co.uk
wrote:

>https://answersingenesis.org/genetics/dna-similarities/alleged-human-chromosome-2-fusion-site-encodes-an-active-dna-binding-domain-inside-a-complex-and-hig/
>
>Does anyone know if this been debunked anywhere? I can't seem to find anything on it besides some unconfirmed reports about Ken Miller apparently admitting that Tomkins was right, conveniently in private and with no camera rolling.

There was a recent (March 2) thread on this here titled "Human
Chromosome 2". jillery and I both posted responses which included
debunking cites.

[jillery]

On Wed, 9 Mar 2016 12:49:46 -0800 (PST), atxaxbig...@yahoo.co.uk
wrote:

>https://answersingenesis.org/genetics/dna-similarities/alleged-human-chromosome-2-fusion-site-encodes-an-active-dna-binding-domain-inside-a-complex-and-hig/
>
>Does anyone know if this been debunked anywhere? I can't seem to find anything on it besides some unconfirmed reports about Ken Miller apparently admitting that Tomkins was right, conveniently in private and with no camera rolling.

As I posted here about a week ago:

This point and others are refuted here:

<http://sandwalk.blogspot.com/2015/06/creationists-discover-that-human-and.html>

where Ken Miller posts this comment:

************************************************
I’m happy to be dragged into the discussion!

I exchanged a couple of emails with Tomkins last year, pointing out
the errors in his papers (in creationist journals) on the Chromosome 2
fusion site. As you all know, he’s very excited that he’s found a
“highly-expressed” gene that “spans” the fusion site. This means, he
claims, that the fusion site couldn’t possibly be what it seems.

He’s wrong, and many of the reasons why have already been pointed out
in this discussion. First and foremost, the gene in question (actually
a pseudogene with no known function) is a member of a transcript
family known as DDX11L. Tomkins pointedly ignores the Costa (2009)
paper, which identified 18 members of this gene family. Each of them
is next to a sequence known as “WASH,” which is transcribed in the
opposite direction of the DDX11L pseudogene. And, more to the point,
each and every one of them is located right next to a telomere –
except for one. That’s the DDX11L2 sequence, which is parked right
next to the fusion site. That alone is very strong evidence that site
is exactly what it seems to be – the remnant of a telomere-to-telomere
fusion.

Most of the genome databases show the DDX11L2 sequence as off to one
side of the fusion site, so it really doesn’t span it. However, in
some of the databases there are transcript variants that include the
head-to-head telomere sequence motifs as one of the introns in the
primary transcript. That is basis on which Tomkins claims that the
gene spans the site. But the very same data are easily explained by
variability in the termination of transcription so that occasionally a
somewhat longer RNA is produced. This is exactly what I pointed out to
Tomkins…. So that any claim that I “admitted” he was right about his
interpretation is bogus.

And, if Larry permits me to rant on a bit:

• Tomkins said that “some” chromosome banding patterns were similar
between humans and other great apes. Some? The matches were so
extensive that Yunis & Prakash (1982) were able to align each and
every chromosome from four different species!

• He said there were too few telomere repeats in the fusion site. A
“pristine” site would have 20,000 – 30,000 bases. But the fact is that
“pristine” telomeres would prevent fusion, and treatments that
dramatically shorten telomeres actually cause fusion, which is why
there are so few repeats in chromosome 2. The small number of telomere
repeats is exactly what should be expected at a fusion site.

• Tomkins said that the DDX11L2 gene was unique to humans. Wrong. As
Costa (2009) showed, there are members of this family in chimpanzees
and gorillas. And, as you might expect, they are located right next to
telomeres.

• Finally, Tomkins lays great emphasis on the observation that
transcription factor binding has been found throughout this region.
But simple binding says nothing about the specificity of binding or
its biological importance.

• Tomkins has constructed a straw man in which an authentic fusion
site would have to be an exact replica of the ends of two present day
chimpanzee chromosomes to be valid. What he does not seem to realize
is that the fusion occurred millions of years after our lineage
separated from chimpanzees, and that both lines have continued to
evolve along separate pathways. That accounts for the differences he
regards as so significant.

The evidence for a chromosomal fusion in the ancestry of our species
is on very solid ground, and has been greatly strengthened by the very
research he wishes to use against this idea.
***************************************************

--
This space is intentionally not blank.

[atxaxbig...@yahoo.co.uk]

On Wednesday, March 9, 2016 at 10:13:49 PM UTC, jillery wrote:
> On Wed, 9 Mar 2016 12:49:46 -0800 (PST), atxaxbig...@yahoo.co.uk
> wrote:
>
> >https://answersingenesis.org/genetics/dna-similarities/alleged-human-chromosome-2-fusion-site-encodes-an-active-dna-binding-domain-inside-a-complex-and-hig/
> >
> >Does anyone know if this been debunked anywhere? I can't seem to find anything on it besides some unconfirmed reports about Ken Miller apparently admitting that Tomkins was right, conveniently in private and with no camera rolling.
>
>
> As I posted here about a week ago:
>
> This point and others are refuted here:
>
> <http://sandwalk.blogspot.com/2015/06/creationists-discover-that-human-and.html>
>
> where Ken Miller posts this comment:
>
> ************************************************
> I'm happy to be dragged into the discussion!
>
> I exchanged a couple of emails with Tomkins last year, pointing out
> the errors in his papers (in creationist journals) on the Chromosome 2
> fusion site. As you all know, he's very excited that he's found a
> "highly-expressed" gene that "spans" the fusion site. This means, he
> claims, that the fusion site couldn't possibly be what it seems.
>
> He's wrong, and many of the reasons why have already been pointed out
> in this discussion. First and foremost, the gene in question (actually
> a pseudogene with no known function) is a member of a transcript
> family known as DDX11L. Tomkins pointedly ignores the Costa (2009)
> paper, which identified 18 members of this gene family. Each of them
> is next to a sequence known as "WASH," which is transcribed in the
> opposite direction of the DDX11L pseudogene. And, more to the point,

> each and every one of them is located right next to a telomere -

> except for one. That's the DDX11L2 sequence, which is parked right
> next to the fusion site. That alone is very strong evidence that site

> is exactly what it seems to be - the remnant of a telomere-to-telomere

> fusion.
>
> Most of the genome databases show the DDX11L2 sequence as off to one
> side of the fusion site, so it really doesn't span it. However, in
> some of the databases there are transcript variants that include the
> head-to-head telomere sequence motifs as one of the introns in the
> primary transcript. That is basis on which Tomkins claims that the
> gene spans the site. But the very same data are easily explained by
> variability in the termination of transcription so that occasionally a
> somewhat longer RNA is produced. This is exactly what I pointed out to

> Tomkins.... So that any claim that I "admitted" he was right about his

> interpretation is bogus.
>
> And, if Larry permits me to rant on a bit:
>

> * Tomkins said that "some" chromosome banding patterns were similar

> between humans and other great apes. Some? The matches were so
> extensive that Yunis & Prakash (1982) were able to align each and
> every chromosome from four different species!
>

> * He said there were too few telomere repeats in the fusion site. A
> "pristine" site would have 20,000 - 30,000 bases. But the fact is that

> "pristine" telomeres would prevent fusion, and treatments that
> dramatically shorten telomeres actually cause fusion, which is why
> there are so few repeats in chromosome 2. The small number of telomere
> repeats is exactly what should be expected at a fusion site.
>

> * Tomkins said that the DDX11L2 gene was unique to humans. Wrong. As

> Costa (2009) showed, there are members of this family in chimpanzees
> and gorillas. And, as you might expect, they are located right next to
> telomeres.
>

> * Finally, Tomkins lays great emphasis on the observation that

> transcription factor binding has been found throughout this region.
> But simple binding says nothing about the specificity of binding or
> its biological importance.
>

> * Tomkins has constructed a straw man in which an authentic fusion

> site would have to be an exact replica of the ends of two present day
> chimpanzee chromosomes to be valid. What he does not seem to realize
> is that the fusion occurred millions of years after our lineage
> separated from chimpanzees, and that both lines have continued to
> evolve along separate pathways. That accounts for the differences he
> regards as so significant.
>
> The evidence for a chromosomal fusion in the ancestry of our species
> is on very solid ground, and has been greatly strengthened by the very
> research he wishes to use against this idea.
> ***************************************************
>
> --
> This space is intentionally not blank.

Awesome rundown. That's exactly the kind of thing I needed to know and then some. Thanks muchly!

[atxaxbig...@yahoo.co.uk]

On Wednesday, March 9, 2016 at 10:03:49 PM UTC, RSNorman wrote:
> On Wed, 9 Mar 2016 12:49:46 -0800 (PST), atxaxbig....@yahoo.co.uk

Thanks! That's a great help. And apologies for the rookie mistake of not scrolling down far enough.