New Genetic Information

Two recent papers seem relevent to some of the discussions we have been having...

The first is the case of producing new genetic sequences through duplication and mutation. "In humans, there are two isoforms each of clathrin heavy chain (CHC17 and CHC22) and light chain (LCa and LCb) subunits, all encoded by separate genes. CHC17 forms the ubiquitous clathrin-coated vesicles that mediate membrane traffic. CHC22 is implicated in specialized membrane organization in skeletal muscle." As it turns out, there is good evidence that these genes were produced both by the duplication of single genes and by the duplication of large segments of DNA, possibly the entire genome.

So this is an example of a couple of ways in which the evidence shows how new genetic sequences arise.

Wakeham et al (2005), Clathrin heavy and light chain isoforms originated by independent mechanisms of gene duplication during chordate evolution, PNAS Vol 102 no.20, 7209-7214.

http://www.pnas.org/cgi/content/full/102/20/7209

 

From the same issue of PNAS...

The second example involves regulatory genes. This may have some bearing on some of the claims of irreducible complexity that come along.

In this case, one regulatory mechanism was replaced by another through a gradual process in which a key part was able to maintain its function through the change.

Tanay et al, Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast, PNAS Vol 102 no.20, 7203-7208.

http://www.pnas.org/cgi/content/abstract/102/20/7203

 

Carrying on with the theme, as scientists decode the genomes of more and more organisms, they are finding over and over that most genes fall into a relatively few number of "families" that appear to have come about through duplication and mutation of other genes. While some continue to claim that there is no method for making new genes or new "information" (forever undefined), science is uncovering the truth of how these things happen.

Orengo & Thornton (2005), 'Protein Families and Their Evolution - A Structural Perspective', Annu Rev Biochem. 2005 Jul 7;74:867-900.

 

Karl

Could you stick to making these vacuous charges on the thread you started for this purpose instead of trying to derail every thread that comes up? Please?

Your charges make no sense. You claim it is some how racist to claim that all humans share a common ancestor. You confuse the physical traits that are used to divide organisms into species with the traits that some use to determine race. You bring nothing substantive to the discussion with these constant charges of racism. Even if evolution were the most racist theory ever, that really has nothing to do with whether it is correct or not. You present no new ideas nor do you force us to confront any holes in the theory of evolution. Nor do you offer any better explanation for what we see.

And I really don't know why to picked a thread on genetics to continue spreading this drivel except that you wish to halt all real discussion on all threads. I think there is a term for that on the internet.

 

From just this month....

After that distraction, let's get back to the subject.

This is another example of a gene family that has been evolved through duplication and mutation. It this case, repeated duplication events have yielded genes that have a repetitive pattern including in the introns. That the repeats extends to the non-coding regions is further proof that the gene family was produced through duplication and mutation. It also allows comparisons of this chromosomal region between humans and other primates further cementing their common ancestry. Furthermore, the members of the family are expressed in a wide variety of tissue type showing that the duplication and mutation process can lead to novel genes with significantly different function.

Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F., A Novel Gene Family NBGF: Intricate Structure Generated by Gene Duplications during Primate Evolution, Mol Biol Evol. 2005 Aug 3.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16079250&query_hl=1

 

I have asked, please, if you are going to make your vacuous claims of racism, can you at least do it on the thread which has that as a topic. This thread is about evidence that shows how new genes are created as a response to the oft made claim by YEers that new "information" cannot be created by evolutionary processes.

Going aroung trying to hijack every thread with your silly allegations only reinforces that opinion that you are interesting in nothing other than being a troll.

And speaking of the other thread, would you mind going over there and supporting your claims about Neanderthals instead of merely making unsupported assertions.

 

"Are you saying that no one else can post on a thread which features "vacuous" claims of geneticists?"

I have posted abstracts and links and full references. If you think that the reveiwers missed something, feel free to contanct the editors of the journals and tell them what the mistakes were. And could you copy that information here, too, please.

Any who wishes can post here but I am making the request that replies be somewhat on topic and not unsubstantiated assertions made solely for the purposes of distracting, derailing, hijacking and being annoying.

"And you want to tell YEC's that they can't reply to your 'superior' genetic threads?"

They can reply all they want. I want them too, I really do. But you are not replying to the topic. YOu are hijacking the thread. You're a troll.

"There's no scientific reason that our Neandertal ancestors couldn't have evolved into modern people of European and Near Eastern descent, other than racist neo-Darwinist theories of genocide which posit that they were somehow exterminated and 'replaced' by 'ape-like' descendents of African Eve."

No one said "couldn't." But they did not. The genetic testing of Neanderthal remains show them to be well outside the range of modern humans and their morphology shows them to be substantially different than modern humans.

Now this thread is about how new genes and functions come about in contrast to the assertions of YEers. If you have something related to that to say, please join in. If you are merely going to continue to spread your silly, empty assertions, please take it to a thread where it is on topic.

 

Trying once again to get back on topic, here is another example of scientists figuring out how a gene family evolved including the specific areas of the gene that were under selective pressure. It also shows how such processes led to a novel metabolic pathway.

You can read the whole paper here.

http://www.biomedcentral.com/content/pdf/1471-2148-5-42.pdf

 

I should have learned by now that it is a mistake to feed the trolls. All you do is encourage bad netiquette by responding to them at all.

Back to our theme.

YEers often claim that there is no way to produce new "information" through evolutionary processes. Up until now, I have been focusing on processes that have used some variation of duplication and mutation to produce new genes. Now I wish to turn to a different method.

Genes are often broken into pieces called exons with bits of non-functional DNA called introns in between. To make the final gene, the introns must be stripped out and the exons joined together. This process allows for a mechanism called alternative splicing to create new genes by making different combinations of the exons into genes. In that manner, a existing gene can remain unchanged while one of its exons is combined with a different set of exons to make a new gene. We are going to examine a variation of this.

There are segments of DNA called retroposons which are easily duplicated and inserted into the genome at diverse places. In humans and other primates there is a particular family of these called Alu sequences. There are very, very many Alu insertions in the human genome. It is possible for these Alu inserts to mutate until they present the proper genetic sequence to mark them as an exon. They can then be spliced into genes potentially making novel and useful genes.

The paper here discusses a particular Alu insertion that occurred all the way back in the basal ancestor of anthropoid primates. The changes that happened to the Alu sequence through time is then charted by looking at the same sequence in various descendents. Eventually mutation caused the sequence to become an exon which was then used in a novel gene p75TNFR in the ancestor of old world monkeys and apes.

This case is of particular problem for YEers because we see a useless insert spread throughout the primates and as various lineages split off, we can trace its change to something useful.

Singer SS, Mannel DN, Hehlgans T, Brosius J, Schmitz J., From "junk" to gene: curriculum vitae of a primate receptor isoform gene, J Mol Biol. 2004 Aug 20;341(4):883-6.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15328599&query_hl=1

 

Sticking with the theme of alternative splicing, here we present a specific case where alternative splicing leads to a variety of genes. In this case, 23 exons form 14 different isoforms. Included here is a variation in the splicing where new sequences are produced by alternatively including or excluding section of DNA from within a given exon. It also provides another method of generating novelty by including expressions of Alu, LINE and MER repeats very similar to the expressed Alu sequence in the previous post.

Lipovich L, Lynch ED, Lee MK, King MC., A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31, Genome Biol. 2001;2(4)

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11305939&query_hl=1