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

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Here's another example:
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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.


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The short answer is THIS:
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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.


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Biology professor Andre Cavalcanti wrote:
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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.



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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:

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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:

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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?

  
  11 replies since April 16 2010,11:35 < Next Oldest | Next Newest >  

    


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