New Genetic Information

[UTEOTW]

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.

CHC17 is bound and regulated by LCa and LCb, whereas CHC22 does not functionally interact with either light chain. The imbalanced interactions between clathrin subunit isoforms suggest a distinct evolutionary history for each isoform pair. Phylogenetic and sequence analysis placed both heavy and light chain gene duplications during chordate evolution, 510-600 million years ago. Genes encoding CHC22 orthologues were found in several vertebrate species, with only a pseudogene present in mice. Multiple paralogons surrounding the CHC genes (CLTC and CLTD) were identified, evidence that genomic or large-scale gene duplication produced the two CHC isoforms. In contrast, clathrin light chain genes (CLTA and CLTB) apparently arose by localized duplication, within 1-11 million years of CHC gene duplication. Analysis of sequence divergence patterns suggested that structural features of the CHCs were maintained after gene duplication, but new interactions with regulatory proteins evolved for the CHC22 isoform. Thus, independent mechanisms of gene duplication expanded clathrin functions, concomitant with development of neuromuscular sophistication in chordates.

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

 

[UTEOTW]

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.

Transcriptional modules of coregulated genes play a key role in regulatory networks. Comparative studies show that modules of coexpressed genes are conserved across taxa. However, little is known about the mechanisms underlying the evolution of module regulation. Here, we explore the evolution of cis-regulatory programs associated with conserved modules by integrating expression profiles for two yeast species and sequence data for a total of 17 fungal genomes. We show that although the cis-elements accompanying certain conserved modules are strictly conserved, those of other conserved modules are remarkably diverged. In particular, we infer the evolutionary history of the regulatory program governing ribosomal modules. We show how a cis-element emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a more ancient cis-element. We suggest that this formation of an intermediate redundant regulatory program allows conserved transcriptional modules to gradually switch from one regulatory mechanism to another while maintaining their functionality. Our work provides a general framework for the study of the dynamics of promoter evolution at the level of transcriptional modules and may help in understanding the evolvability and increased redundancy of transcriptional regulation in higher organisms.

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

 

[UTEOTW]

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.

We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain families are common to all kingdoms of life and account for nearly 50% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different multidomain proteins. The ways in which these domain combinations evolve tend to be specific to the organism so that less than 15% of the protein families found within a genome appear to be common to all kingdoms of life. Recent analyses of completed genomes, exploiting the structural data, have revealed the extent to which duplication of these domains and modifications of their functions can expand the functional repertoire of the organism, contributing to increasing complexity.

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

 

[jcrawford]

Originally posted by UTEOTW:
Two recent papers seem relevent to some of the discussions we have been having...

How are these two papers relevent to neo-Darwinist racial theories of human evolution?

 

[Paul of Eugene]

Who said THIS thread is about human evolution? Its about evolution in general and the opening salvo is against the idea, frequently expressed around here without any theoretical justification, that new information simply cannot arise in a genome. Do you or do you not accept the idea that it is possible for new information to get into a genome by natural means?

 

[jcrawford]

Originally posted by Paul of Eugene:

"Who said THIS thread is about human evolution?"

The first paper did.

"Do you or do you not accept the idea that it is possible for new information to get into a genome by natural means?"

Only if it was part of that genome's original intelligent design to allow it.

 

[UTEOTW]

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.

 

[jcrawford]

Originally posted by UTEOTW:

"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?"

Charles, I'm not trying to derail any thread, let alone "every thread that comes up."

"Your charges make no sense."

Neither do racial DNA theories about the genetic origins of the human race.

"You claim it is some how racist to claim that all humans share a common ancestor."

Not at all, since all humans do share a common human ancestor that didn't share common ancestry with African apes.

"You confuse the physical traits that are used to divide organisms into species with the traits that some use to determine race."

No I don't. It's neo-Darwinist speciators who confuse the varied physical characteristics and traits of the present and past human race with extinct species of Australopithicine apes.

"You bring nothing substantive to the discussion with these constant charges of racism."

On the contrary, since any discussion about how and why neo-Darwinist race theorists divide the ancestors of the human race into different and separate 'species' is hugely substantive.

"Even if evolution were the most racist theory ever, that really has nothing to do with whether it is correct or not."

If true, you would have to logically show or physically demonstrate how "the most racist theory ever," could possibly be either scientifically or politically "correct."

"You present no new ideas nor do you force us to confront any holes in the theory of evolution."

Not true, since neo-Darwinist theorists must explain and justify their dividing our human ancestors into different 'species' for any other purpose than associating the first 'species' of human beings with the ancestors of African apes in order to satisfy Darwin's thesis in "Origin of Species," and his racial assumptions in "Descent of Man."

"Nor do you offer any better explanation for what we see."

Lubenow's assessment of the human fossil record offers a better explanation and account of our human origins, than any neo-Darwinist theory about the origins of the human race out of the ancestors of some 'species,' or race, of monkeys.

"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."

It is the right of every human being on earth to trash all forms of neo-Darwinist racial theories, even when such 'scientific' theories are cloaked in the garb of 'scientific' genetics.

"I think there is a term for that on the internet."

A term for what? Neo-Darwinist racial theories or our civil rights to oppose and resist them?

 

[UTEOTW]

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.

Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBGF, for Neuroblastoma Breakpoint Gene Family, because one of its members is disrupted by a chromosomal translocation in a neuroblastoma patient. The NBGF genes have a repetitive structure with high intragenic and intergenic sequence similarity in both coding and non-coding regions. These similarities might expose these genomic regions to illegitimate recombination, resulting in structural variation in the NBGF genes. The encoded proteins contain a highly conserved domain of unknown function, which we have named the NBGF-repeat. In silico analysis combined with the isolation of multiple full-length cDNA clones showed that several members of this gene family are abundantly expressed in a large variety of tissues and cell lines. Strikingly, no discernable orthologues could be identified in the completed genomes of fruitfly, nematode, mouse or rat, but sequences with low homology could be isolated from the draft canine and bovine genomes. Interestingly, this gene family shows primate-specific duplications that result in species-specific arrays of NBGF homologous sequences. Overall, this novel NBGF family reflects the continuous evolution of primate genomes that resulted in large physiological differences, and its potential role in this process is discussed.

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

 

[jcrawford]

Originally posted by UTEOTW:
[QB] It also allows comparisons of this chromosomal region between humans and other primates further cementing their common ancestry.

Scientific tests in support of neo-Darwinist racial theories of the entire human race's origins, common ancestry and reproductive descent from "other" African primates only proves one thing. Lubenow's thesis is scientifically correct while the African Eve Model of human origins out of Africa is only socially expedient and politically correct.

 

[UTEOTW]

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.

 

[jcrawford]

Originally posted by UTEOTW:
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.

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

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.

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

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.

You're the only one saying that. BTW, How do neo-Darwinist theorists account for the existence and origins of trolls, besides just labeling them and classifying them as such?

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

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.

 

[Travelsong]

jcrawford why don't you believe in the Bible?

 

[UTEOTW]

"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.

 

[UTEOTW]

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.

BACKGROUND:
Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear.

RESULTS:
We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection.

CONCLUSIONS:
Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with.

You can read the whole paper here.

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

 

[jcrawford]

Originally posted by Travelsong:
jcrawford why don't you believe in the Bible?

What's the Bible got to do with neo-Darwinist racial theories about the first race of African people descending from ancestral African apes in accordance with neo-Darwinst racial theories of natural selection and genetic mutation?

 

[jcrawford]

QUOTE = Originally posted by UTEOTW:

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.

No one is posting replies "solely for the purposes of distracting, derailing, hijacking and being annoying," since followers of, and believers in, scientific Lubenowism, merely wish to consider and include scientific concepts and observations of neo-Darwinist racial theories in these discussions.

YOu are hijacking the thread. You're a troll.

Nonsense. You have no more scientific evidence of that claim than you do for supporting racial neo-Darwinist theories about African people sharing common ancestry with African apes.

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.

So you would include Australopithicine chimpanzees in your human lineage and deny your own European or Near East ancestry. No problem. Just don't include the rest of us in your peculiar family tree.

Now this thread is about how new genes and functions come about in contrast to the assertions of YEers.

So you don't really mind YEC's replying to your discovery of new genes and functions, I assume.

If you have something related to that to say, please join in.

Thank you for the special invitation.

If you are merely going to continue to spread your silly, empty assertions, please take it to a thread where it is on topic.

Who's to say what's on topic? You, geneticists or Civil Rights workers?

 

[UTEOTW]

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.

Exonization of Alu retroposons awakens public opinion, particularly when causing genetic diseases. However, often neglected, alternative "Alu-exons" also carry the potential to greatly enhance genetic diversity by increasing the transcriptome of primates chiefly via alternative splicing.Here, we report a 5' exon generated from one of the two alternative transcripts in human tumor necrosis factor receptor gene type 2 (p75TNFR) that contains an ancient Alu-SINE, which provides an alternative N-terminal protein-coding domain. We follow the primate evolution over the past 63 million years to reconstruct the key events that gave rise to a novel receptor isoform. The Alu integration and start codon formation occurred between 58 and 40 million years ago (MYA) in the common ancestor of anthropoid primates. Yet a functional gene product could not be generated until a novel splice site and an open reading frame were introduced between 40 and 25 MYA on the catarrhine lineage (Old World monkeys including apes).

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

 

[UTEOTW]

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.

BACKGROUND:
Sodium bicarbonate cotransporter (NBC) genes encode proteins that execute coupled Na+ and HCO3- transport across epithelial cell membranes. We report the discovery, characterization, and genomic context of a novel human NBC-like gene, SLC4A9, on chromosome 5q31.

RESULTS:
SLC4A9 was initially discovered by genomic sequence annotation and further characterized by sequencing of long-insert cDNA library clones. The predicted protein of 990 amino acids has 12 transmembrane domains and high sequence similarity to other NBCs. The 23-exon gene has 14 known mRNA isoforms. In three regions, mRNA sequence variation is generated by the inclusion or exclusion of portions of an exon. Noncoding SLC4A9 cDNAs were recovered multiple times from different libraries. The 3' untranslated region is fragmented into six alternatively spliced exons and contains expressed Alu, LINE and MER repeats. SLC4A9 has two alternative stop codons and six polyadenylation sites. Its expression is largely restricted to the kidney. In silico approaches were used to characterize two additional novel SLC4A genes and to place SLC4A9 within the context of multiple paralogous gene clusters containing members of the epidermal growth factor (EGF), ankyrin (ANK) and fibroblast growth factor (FGF) families. Seven human EGF-SLC4A-ANK-FGF clusters were found.

CONCLUSION:
The novel sodium bicarbonate cotransporter-like gene SLC4A9 demonstrates abundant alternative mRNA processing. It belongs to a growing class of functionally diverse genes characterized by inefficient highly variable splicing. The evolutionary history of the EGF-SLC4A-ANK-FGF gene clusters involves multiple rounds of duplication, apparently followed by large insertions and deletions at paralogous loci and genome-wide gene shuffling.

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

 

[Gup20]

While I don't have time to get into this now (just about to leave on vacation), I would ask what assumptions have been made here.

For example, have all the genes been taken into consideration, or just the ones which code for proteins? Since it has been discovered that DNA formerly thought to be junk actually performs functions such as gene activation, this is important. Also, the paper noted that some of the genes already contained nitralese genes - how do we know this information isn't ALREADY present? Next, there is a lot of mention of plasmid DNA rather than nuclear DNA. How do we know these aren't designed to dynamicly adapt under pressure and then disable when the plasmids are de-activated in the abcense of pressure (such as in the case of the nylon eating bacteria).

Seems pretty unsubstantial to me.