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  Topic: FL and gene duplication ala Jerry Bergman< Next Oldest | Next Newest >  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: April 16 2010,11:35   

In a discussion on increases in genetic information on another forum, gene duplication was presented as a means by which non-intelligent intervention can increase genetic information.

Mellotron/FL countered with one of his patented long quotes from YEC Jerry Bergman (italics and bolds (except for the title) mine):
Quote

Does gene duplication provide the engine for evolution?

by Jerry Bergman

....The proposition that large scale evolution has occurred via gene duplication is contradicted by numerous lines of evidence. Little evidence currently exists to support the belief that gene duplication is a significant source of new genes, supporting one University of South Carolina molecular evolutionist’s conclusion that scientists can not ‘prove that [genome duplication] didn’t happen, but [if it did], it didn’t have a major impact. … For me, it’s a dead issue’. (Ref 10)

...
According to Hughes, ‘Everything we’ve looked at [fails to] support the hypothesis.’ (39)

Darwinists promote gene duplication as an important means of evolution, not because of the evidence, but because they see no other viable mechanism to produce the required large number of new functional genes to turn a microbe into a microbiologist.

In other words, evolution by gene-duplication is yet another example of just-so story-telling.

Refs:

(10) Pennisi, E., Gene duplications: the stuff of evolution? Science v294: page2458, 2001.

(30) Behe, M.J. and Snoke, D.W., Simulating evolution by gene duplication of protein features that require multiple amino acid residues, Protein Science 13:2651–2664, 2004; p. 2652.

(39) Pennisi, ref. 1, p. 2460.

So, I read Bergman's article, and I decided to check one of his sources, Googling this article:

Pennisi, E., Gene duplications: the stuff of evolution? Science v294: page2458, 2001.


And darn it if the returns I got were to THIS article:
Quote

Science 21 December 2001:
Vol. 294. no. 5551, pp. 2458 - 2460
DOI: 10.1126/science.294.5551.2458

News Focus

MOLECULAR EVOLUTION:
Genome Duplications: The Stuff of Evolution?

Elizabeth Pennisi
The controversial--and formerly unprovable--proposition that evolution moves forward through duplication of entire genomes is getting support from current advances in molecular biology. The emerging data have not persuaded all of the skeptics, however. They maintain that evolutionary change could have been fueled by duplication of individual genes or perhaps segments of chromosomes--without invoking anything as dramatic as genome duplications.

Note what I underlined -

FIRST - Bergman misrepresents the title - in the Bergman article, in his references, the word "Gene" is in italics, while the rest of the title is not. Interesting...

SECOND - read the abstract. Not only is the article not even really about gene duplications as such, but rather GENOME duplications, the abstract actually indicates that GENE DUPLICATIONS are more likley a cause of evolution!

THIRD - Mellotron/FL, who had originally referred to the Bergman article, claimed that Bergman's manipulation of the title was a mere "typo" of a mere 2 letters, and that my pointing this out was due to my bias against Bergman (I admit, I am biased against any person with a well documented history of lying about and/or misrepresenting all manner of things related to evolution).

THE QUESTION:


Does anyone truly believe:

1. That Bergman's 'error' was a mere typo

2. That Bergman correctly represented the content of the article (judging by the abstract, anyway)

3. Mellotron/FL is not merely engaging in obfuscation to protect one of his YEC hero-sources?

Thanks

p.s. - I should point out that Bergman also claims that Down syndrome is caused by a gene duplication, but it is caused by an extra chromosome....

p.p.s - I should also point out that the above article was the only one I actually checked...


p.p.p.s. - I should also point out that I did contact Bergman about it and he did indeed claim that it was a mere typo and that genome duplications are really just big gene duplications, so his use of quotes about genome suplications supporting his claims about gene duplications is OK.

  
midwifetoad



Posts: 3992
Joined: Mar. 2008

(Permalink) Posted: April 16 2010,11:59   

I'm less inclined to believe it was a typo and more inclined to believe he doesn't know the difference.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: April 16 2010,13:39   

Quote (midwifetoad @ April 16 2010,11:59)
I'm less inclined to believe it was a typo and more inclined to believe he doesn't know the difference.

Could be - he did claim that Down syndrome is 'often' presented as an example of 'gene duplication', though he was unable to provide any examples of this.

Not knowing the difference can explain how he used an article critical of genome duplication as a driving force in evolution to try to dismiss gene duplication, but it was just too much for me to accept that he just happened to mis-type the title of the article, just coincidentally making it look like the article realy was about what his thesis was about.

Of course, what I did not mention is the megths that Floyd Lee aka Mellotron went to to claim that Bergman is correct ion claiming that gene and genome duplication are the same thing - a sampling (he was trying to claim that all sorts of people conflate gene and genome duplication):

Quote
Here's another example:
Quote


Gene & Genome Duplication in Acanthamoeba Polyphaga Mimivirus
Authors: Karsten Suhre (IGS)
(Submitted on 25 May 2005 (v1), last revised 19 Jul 2005 (this version, v3))
Abstract: Gene duplication is key to molecular evolution in all three domains of life and may be the first step in the emergence of new gene function. It is a well recognized feature in large DNA viruses, but has not been studied extensively in the largest known virus to date, the recently discovered Acanthamoeba Polyphaga Mimivirus. Here we present a systematic analysis of gene and genome duplication events in the Mimivirus genome. We find that one third of the Mimivirus genes are related to at least one other gene in the Mimivirus genome, either through a large segmental genome duplication event that occurred in the more remote past, either through more recent gene duplication events, which often occur in tandem. This shows that gene and genome duplication played a major role in shaping the Mimivirus genome.
http://arxiv.org/abs/q-bio/0505049

Once again, there's that same conflation.


Quote
The short answer is THIS:
Quote

What is a gene and genome?
A genome is all genetic data of a single cell. That includes the genes in the nucleus, but also that of mitochondrial DNA.
A gene is a section of the genome which codes for one protein. It consists of various codons.
http://wiki.answers.com/Q/What_is_a_gene_and_genome

So indeed, we have a situation analogous to the book and page gig discussed earlier. After all, a gene IS a section of a genome. One DOES include the other.


Quote
Biology professor Andre Cavalcanti wrote:
Quote

Duplications can involve parts of genes, a complete single gene, part of a chromosome (called block duplication), an entire chromosome, or the whole genome (Li, Molecular Evolution, 1997 Sinauer).
http://pages.pomona.edu/~ac044747/aroc/Duplications.htm

Hmm. Imagine that. Book and page, Derwood. Book and page.



Quote
Beginning with a single universal ancestor, the magnificent diversity of life has come about through a series of branchings of new species, which eventually gave rise to the major branches of the living kingdoms and the hundreds of millions of separate species that have graced the earth. A similar series of branchings, but this time within genomes?—?gene duplications?—?has spawned the large and diverse population of clusters of genes that constitutes the modern genome.


I liked this one, too:

Quote
Quote
Gene duplication is believed to play a major role in evolution; this stance has been held by members of the scientific community for over 100 years. Susumu Ohno was one of the most famous developers of this theory in his classic book Evolution by gene duplication (1970). Ohno argued that gene duplication is the most important evolutionary force since the emergence of the universal common ancestor. Major genome duplication events are not uncommon. It is believed that the entire yeast genome underwent duplication about 100 million years ago. Plants are the most prolific genome duplicators. For example, wheat is hexaploid (a kind of polyploid), meaning that it has six copies of its genome.

They don't even mind saying gene-dup and genome-dup in the same paragraph, the same **process** , like I said earlier.


Does the Wiki article REALLY claim that gene and genome duplication are the same process?

No, not at all.  It does ambiguously state that gene duplication "is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.[1] "  Their reference 1 is to this paper:
[url=Evolution by gene duplication: an update]Evolution by gene duplication: an update

and in that paper, while it is stated that gene duplications can occur via chromosomal duplications (probably where Bergman got his 'definition' from), when one reads the paper, one sees that that statement is one of those 'overly broad introductory' type statements, for the authors then go on to differentiate each type of duplicate, and they make it quite clear that chromosomal duplications occur by mechanisms other than those in which gene duplication occurs - same process?  Hardly:

Quote

Gene duplication can result from unequal crossing over
(Fig. 1a), retroposition (Fig. 1b), or chromosomal
(or genome) duplication, the outcomes of which are quite
different. Unequal crossing over usually generates tandem gene duplication; that is, duplicated genes are linked in a chromosome (Fig. 1a). Depending on the position of crossing over, the duplicated region can contain part of a gene, an entire gene, or several genes. In the latter two cases, introns, if present in the original genes, will also be present in the duplicated genes. This is in sharp contrast to the result from retroposition (Fig. 1b). Retroposition occurs when a message RNA (mRNA) is retrotranscribed to complementary DNA (cDNA) and then inserted into the genome. As expected from this process, there are several molecular features of retroposition: loss of introns and regulatory sequences, presence of poly A tracts, and presence of flanking short direct repeats, although deviations from these common patterns do occasionally occur [17].
Another major difference from unequal crossing over is that a duplicated gene generated by retroposition is
usually unlinked to the original gene, because the insertion of cDNA into the genome is more or less random. It is also impossible to have blocks of genes duplicated together by retropositionunless the genes involved are all in an OPERON.
Only those genes that are expressed in the germ line are
subject to heritable retroposition. Because promoter and
regulatory sequences ofagenearenot transcribedandhence
not duplicated by retroposition, the resulting duplicate often lacks necessary elements for transcription and thus
immediately becomes a pseudogene. Nevertheless, several retroposition-mediated duplicate genes are expressed, probably because of the chance insertion of cDNAinto a genomic location that is downstream of a promoter sequence [17].
Chromosomal or genome duplication occurs probably by a
lack of disjunction among daughter chromosomes after DNA replication. Substantial evidence shows that these large scale duplications occurred frequently in plants but
infrequently in animals [10]. Recent human genome
analysis reveals another type of large-scale duplication,
segmental duplication, which often involves 1000 to
.200 000 nucleotides [18]. That most segmental duplications do not generate tandem repeats suggests that unequal crossing over is probably not responsible,
although the exact duplication mechanism is unclear [18].



I have to wonder if they think that refusing to admit error on something so clearly wrong makes them look smart or something?

  
sledgehammer



Posts: 533
Joined: Sep. 2008

(Permalink) Posted: April 16 2010,19:11   

Not to mention that it isn't even necessary to prove that functional mutations on duplicate genes/genomes actually happened.  As long as it is possible in principle that  information in the genome (by whatever definition) can be generated by this process, than the "no significant info increase without intelligence" ID mantra is falsified, even with the "significant" caveat, since the process can be repeated as often as necessary to achieve "significance".

Ain't that right, Joe?

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: April 17 2010,04:41   

[url=http://en.wikipedia.org/wiki/Copy_number_variation[/url]Copy number variations are pretty common in humans:
Quote
The fact that DNA copy number variation is a widespread and common phenomenon among humans was first uncovered [5][6]  following the completion of the human genome project. It is estimated that approximately 0.4% of the genomes of unrelated people typically differ with respect to copy number.[7]  De novo CNVs have been observed between identical twins who otherwise have identical genomes. [8]

I wonder, how do you explain copy number variation without duplication?
How can duplication be in most cases detrimental (as Bergman claims) if it is so wide spread?
Of course, this doesn't prove that genes with new functions arose via duplication but the "raw material" is clearly there.
BTW, IMO Bergman conflates gene and genome duplication on purpose (or he's so clueless that he shouldn't write articles about it). Another example from his article:

Quote
Artificial gene duplication for experimental purposes has been developed in mice, but it has not provided any evidence for evolution because it is lethal:

   ‘The production of tetraploid (4n) embryos has become a common experimental manipulation in the mouse. Although development of tetraploid mice has generally not been observed beyond mid-gestation [i.e. it is fatal], tetraploid:diploid (4n:2n) chimeras are widely used as a method for rescuing extra-embryonic defects [i.e. a genetic defect that is normally fatal can be artificially made to survive in the chimera].’22

Here, he provides whole genome duplication as "evidence" for his claim that gene duplication is normally detrimental.

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: April 17 2010,06:28   

Quote (JLT @ April 17 2010,04:41)
Here, he provides whole genome duplication as "evidence" for his claim that gene duplication is normally detrimental.

I missed that one - I wonder how Floyd will spin that to try to rescue his hero...

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: April 17 2010,07:20   

To answer your original question, no, I don't think it is a typo. I don't think he retyped the citation in toto, people cut and paste. Otherwise you'd have to argue he made the typo once and then cut and pasted the typo later.

However, there is also the argument that he doesn't know the difference. In the quoted paragraph, Bergman attempts to support a position about gene duplication with a quote about genome duplication.

Are gene duplication and genome duplication the same thing? Obviously not, since they happen by different processes and at different rates. FL's analogy fails, or fails to realize that a book is more than a stack of pages.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: April 17 2010,07:54   

Also the same thing: gnome duplication.

We know it happens:



And we know how it happens:



--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Reciprocating Bill



Posts: 4265
Joined: Oct. 2006

(Permalink) Posted: April 17 2010,07:55   

(Also same as post duplication)

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Dr.GH



Posts: 2113
Joined: May 2002

(Permalink) Posted: April 17 2010,12:31   

Quote (SLP @ April 16 2010,09:35)
[quote]
Does gene duplication provide the engine for evolution?

by Jerry Bergman

....The proposition that large scale evolution has occurred via gene duplication is contradicted by numerous lines of evidence. Little evidence currently exists to support the belief that gene duplication is a significant source of new genes, supporting one University of South Carolina molecular evolutionist’s conclusion that scientists can not ‘prove that [genome duplication] didn’t happen, but [if it did], it didn’t have a major impact. … For me, it’s a dead issue’. (Ref 10)

<snip>

Good catch Scott. YECs lie reflexively.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
MichaelJ



Posts: 462
Joined: June 2009

(Permalink) Posted: April 18 2010,18:44   

FL should realise that if he quotes a creationist he should check the facts as they invariably lie.

I see that FL has run away

  
SLP



Posts: 136
Joined: Dec. 2002

(Permalink) Posted: April 19 2010,06:39   

Quote (MichaelJ @ April 18 2010,18:44)
FL should realise that if he quotes a creationist he should check the facts as they invariably lie.

I see that FL has run away

It is certainly a form of lying - Bergman went to great lengths to "prove" that gene and genome duplication are the same thing (if only via the most simpleminded 'logic' - the same sort of logic that dictates that a single rain drop is the same thing as a torrential downpour), but using an article that in fact indicated that gene duplication was MORE involved in evolution that whole genome duplication as a source indicting gene duplication is just insane.

I expect such things from Bergman and the 'professional' YECs, but Mellotron/Floyd went way over the top in his defense of Bergman that it just floored me.  He thinks he has proved Bergman correct by quoting peope who merely mention both gene and genome duplication in the same paragraphs, regardless of the context, as indicating that Bergman was right - seemed to me that if they were the same thing, then there is no need to name them independantly -  and THAT is a bit disturbing to me that someone in this world actually thinks and and acts that way.


And votes.

  
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