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Topic: Fernando Castro-Chavez: Some Implications for the Study of Intelligent Design ...
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posted 08. March 2004 11:02
Some Implications for the Study of Intelligent Design Derived from Molecular and Microarray Analysis
by Fernando Castro-Chavez
Independent Biotechnologist
fdocc@yahoo.com
Abstract: There are several implications for intelligent design of molecular work using microarray analysis. Here I present some of these implications.
To read the entire article, click here.
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nobody
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posted 14. March 2004 12:39
Very good.
I would like to know more about point 2, the "species specific genes".
How many of these have been found so far?
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Fernando Castro-Chavez
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posted 15. March 2004 20:16
Dear Member # 145:
For example, the human genome contains at least 223 genes that do not have "the required predecessors on the genomic evolutionary tree", never transmitted "vertically".
This is "a jump" that does not follow any current "evolutionary theories", according to Steven Scherer, director of mapping of the Human Genome Sequencing Center at Baylor College of Medicine, as a report printed in the journal Nature states.
The Public Consortium Team, conducting a detailed search, found that some 113 genes (out of the 223) are widespread among bacteria, though they are entirely absent, even in invertebrates. An analysis of the proteins that those genes produce showed that out of 35 identified, only ten had counterparts in vertebrates (ranging from cows and rodents, to fish), being 25 of them unique to humans.
A preliminary dig of “species-specific” genes in many other organisms can be done by carefully looking one by one, within the results obtained from nucleotide databases, using the words “species-specific” in a search that provides 7,000 sequence entries:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=species+specific
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Mesk
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posted 15. March 2004 21:42
quote:
Fernando:
For example, the human genome contains at least 223 genes that do not have "the required predecessors on the genomic evolutionary tree", never transmitted "vertically".
This is "a jump" that does not follow any current "evolutionary theories", according to Steven Scherer, director of mapping of the Human Genome Sequencing Center at Baylor College of Medicine, as a report printed in the journal Nature states.
The Public Consortium Team, conducting a detailed search, found that some 113 genes (out of the 223) are widespread among bacteria, though they are entirely absent, even in invertebrates. An analysis of the proteins that those genes produce showed that out of 35 identified, only ten had counterparts in vertebrates (ranging from cows and rodents, to fish), being 25 of them unique to humans.
But these are not "species-specific genes" - they are present in at least two organisms (humans and some bacterial species). And in any case, you should have examined the literature published after 2001, Fernando. The vast majority of the 223 putative examples of bacteria-to-human horizontal gene transfer have since been shown to be methodological artifacts - see this neat little article for a review of this topic:
Genereux, D.P, and Logsdon, J.M. Jr. 2003. Much ado about bacteria-to-vertebrate lateral gene transfer. Trends in Genetics 19(4): 191-195. (PubMed abstract)
This is a classic illustration of the dangers of concluding phylogenetic gaps based on BLAST searches on a sparse dataset. Almost all of the anomalies vanished once a few more eukaryotic genomes were added to the analysis, and most of the remainder disappear as soon as they are exposed to detailed phylogenetic analysis (rather than naive BLAST-based analysis). A grand total of nine genes remain anomalous, and these have not yet been (to my knowledge) actually subjected to detailed analysis at this time.
Even if the genes in question had not been methodological artifacts, it is somewhat difficult to see how they would have represented a challenge for evolutionary theory. Genes present only in vertebrates and humans could represent (a) genes transferred to vertebrates from early-branching eukaryotes, (b) genes lost independently in other eukaryotic lineages, or (c) genes actually transferred to vertebrates from eubacterial organisms. None of these scenarios is inconsistent with modern evolutionary biology.
Finally, it's worth pointing out that the existence of "species-specific genes" is a particularly weak argument for ID for at least three reasons: (1) we can never actually be certain that a putative "species-specific" gene won't actually turn up in other organisms once we have sequenced them, (2) any given "species-specific gene" could simply represent a vertically transmitted gene which has accumulated sufficient mutations to annihilate detectable sequence similarity with its orthologues, and (3) it is likely that at least some genes arise de novo from non-coding sequence, although this is certainly rarer than origin through gene duplication.
Mesk.
[Edited for clarity.]
[ 17. March 2004, 01:05: Message edited by: Mesk ]
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Fernando Castro-Chavez
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posted 16. March 2004 23:06
Mesk:
>methodological artifacts
It is very important to differentiate them from the real genes, thank you for emphasizing that point. There we have an example and an update on what has been said regarding the human genome.
Dear Member # 145:
For those desiring to dig even deeper in the published history of "Species Specific Genes" and their regulation, the next articles are only some examples of such papers from 1981 to 2003. This is only a preliminary search done in PubMed using the expression "Species Specific Genes" within the title, which provided 43 results (in March 19, 2004):
URL=http://www.ncbi.nlm.nih.gov/entrez
[Edited to to save space, providing details of the original search strategy to verify in situ. Some of those references were commented below by charles d]
Other Searches done (same day):
Using only the two words "Species Specific":
Without field limits: 58603 results;
Putting field limits for title and abstract: 47689 results;
With the title as the limit: 2035 results.
Using the words "Species Specific Gene" within the title only: 123 results, etc.
More quotations below…
[ 19. March 2004, 12:39: Message edited by: Fernando Castro-Chavez ]
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Mesk
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posted 17. March 2004 02:01
Since this point wasn't actually addressed at all in Fernando's (very brief) response to me, I'll try again:
quote:
Fernando's paper:
The discovery of genes expressed only in particular organisms or species
(“species specific genes”) can be emphasized as a product of intelligent design, as
these are not present in any other organism, discarding a continuous evolutionary
way of transmission of genetic material, and enforcing the discontinuous, nonlinear
origin of the genomic organization of living beings.
As I pointed out in my previous post, there are several sound evolutionary explanations for the existance of species-specific genes: for example, extreme sequence changes which obliterate the traces of homology, or (rare but plausible) genuine de novo gene creation from non-coding sequence. Furthermore, if the existence of species-specific genes counts as evidence for intelligent design, wouldn't the fact that the overwhelming majority of genes are not species-specific represent powerful evidence against ID? Given that 99% of human genes have a recognisable orthologue in the mouse, can we be 99% certain that the divergence of primates and rodents was not the result of ID? Or is it that the difference between primates and rodents is 99% due to evolution, and 1% due to ID? ![[Wink]](wink.gif)
Mesk.
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charlie d.
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posted 17. March 2004 10:28
Fernando:
doing a pubmed search for "species + specific" is no way to "dig deeper" into the issue of "species-specific genes" and their evolutionary implications. It's just a way to get a lot of utterly irrelevant stuff, which you seem not to have bothered sorting through yourself, at least judging from the list of titles you posted, most of which have nothing to do with the issue.
For instance:
Heinz S, Haehnel V, Karaghiosoff M, Schwarzfischer L, Muller M, Krause SW, Rehli M.
Species-specific regulation of Toll-like receptor 3 genes in men and mice.
J Biol Chem. 2003 Jun 13;278(24):21502-9. Epub 2003 Apr 02.
This article just deals with regulatory differences of an innate immune system receptor gene which is conserved in human and mouse. That some genes are regulated differently in different species not only is not new, or problematic for evolution, it is indeed one of the major mechanisms by which evolution is thought to occur.
Totmenin AV, Kolosova IV, Shchelkunov SN.
[Orthopoxvirus genes for Kelch-like proteins. I. Analysis of species specific differences by gene structure and organization]
Mol Biol (Mosk). 2002 Jul-Aug;36(4):610-6. Russian.
Shchelkunov SN, Totmenin AV, Kolosova IV, Sandakhchiev LS.
Species-specific differences in the organization of genes encoding kelch-like proteins of orthopoxviruses pathogenic for humans.
Dokl Biochem Biophys. 2002 Mar-Apr;383:96-100. No abstract available.
These articles are about species-specific differences between genes in pox viruses, i.e. all pox viruses have the genes (they are shared, not species-specific), but they differ structurally. Are you saying that evolution predicts all pox viruses would display identical genes?
Rodriguez I, Mombaerts P.
Novel human vomeronasal receptor-like genes reveal species-specific families.
Curr Biol. 2002 Jun 25;12(12):R409-11. No abstract available.
This article deals with a large family of odorant receptors, which are encoded by a class of genes shared between many species (the article deals predominantly with mouse and human). Odorant receptors are evolutionarily interesting because a) they are composed of very large structurally- and evolutionarily-related families, and b) some of these families do display characteristic sequence differences between between species (i.e. the proteins are structurally and evolutionarily related, but can be grouped into subsets according to more subtle differences), presumably because requirements for odorant sensitivity also differ. For example, evidence exists for responsiveness of certain families of ORs to specific signals, eg pheromones (which is, luckily, why we don't get aroused when our pets are in heat, and why our pets don't usually waste too much of their time trying to copulate with members of the wrong species). Indeed, humans, which have a much reduced sense of smell compared to other mammals, are chock-full of OR pseudogenes (which makes evolutionary sense, but would be a puzzling feature from a design perspective, I would think).
Cuadrado M, Sacristan M, Antequera F.
Species-specific organization of CpG island promoters at mammalian homologous genes.
EMBO Rep. 2001 Jul;2(7):586-92. Epub 2001 Jul 03.
Similarly to the first article I mentioned, this deals with differences in presumptive regulatory elements (regions of DNA rich in CG) between shared, not species-specific genes.
Singh KV, Malathum K, Murray BE.
Disruption of an Enterococcus faecium species-specific gene, a homologue of acquired macrolide resistance genes of staphylococci, is associated with an increase in macrolide susceptibility.
Antimicrob Agents Chemother. 2001 Jan;45(1):263-6
This one says even in the title that the gene in question has homologues in other bacteria. Nuff said.
Kanaya S, Yamada Y, Kudo Y, Ikemura T.
Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis.
Gene. 1999 Sep 30;238(1):143-55.
This one isn’t even about species-specific genes, but codon usage. That is, some bacterial species' genes tend to preferentially use certain codons rather than others to encode the same aminoacid. The article shows how this is related to the number of genes for individual tRNAs in each species (the higher a tRNA gene's copy number, the more that codon is favored in highly expressed genes, which need to be translated more efficiently). No species-specific genes here either.
Rossi F, Torriani S, Dellaglio F.
Genus- and species-specific PCR-based detection of dairy propionibacteria in environmental samples by using primers targeted to the genes encoding 16S rRNA.
Appl Environ Microbiol. 1999 Sep;65(9):4241-4.
This one is about a PCR assay capable of detecting sequence differences between highly conserved (not species-specific) genes in Propionibacteria species, the bugs which give Swiss cheese its holes.
Grone A, Fonfara S, Markus S, Baumgartner W.
RT-PCR amplification of various canine cytokines and so-called house-keeping genes in a species-specific macrophage cell line (DH82) and canine peripheral blood leukocytes.
Zentralbl Veterinarmed B. 1999 Jun;46(5):301-10.
“Species-specific” in the title here refers to the macrophage cell line (a rather unfortunate usage, if you ask me: how could any cell line not be species-specific?). The cDNAs isolated form the line and dog peripheral white blood cells are from genes that are not species-specific, but shared with other species, including us.
Pan J, Xia L, McEver RP.
Comparison of promoters for the murine and human P-selectin genes suggests species-specific and conserved mechanisms for transcriptional regulation in endothelial cells.
J Biol Chem. 1998 Apr 17;273(16):10058-67.
Waters AP, van Spaendonk RM, Ramesar J, Vervenne RA, Dirks RW, Thompson J, Janse CJ.
Species-specific regulation and switching of transcription between stage-specific ribosomal RNA genes in Plasmodium berghei.
J Biol Chem. 1997 Feb 7;272(6):3583-9.
Savon SP, Hakimi P, Crawford DR, Klemm DJ, Gurney AL, Hanson RW.
The promoter regulatory regions of the genes for the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) from the chicken and the rat have different species-specific roles in gluconeogenesis.
J Nutr. 1997 Feb;127(2):276-85.
Scatena CD, Adler S.
Trans-acting factors dictate the species-specific placental expression of corticotropin-releasing factor genes in choriocarcinoma cell lines.
Endocrinology. 1996 Jul;137(7):3000-8.
All these articles deal with differential regulation of conserved, not species-specific genes.
Shall I go on?
Frankly, it seems to me you certainly haven’t read the vast majority of these articles, and most likely not even their abstract or titles. So much for “digging deeper in the published history”. This is the equivalent of strip-mining.
This is not to say that ORFans do not exist, or are not interesting, just that it takes more than a ridiculously superficial look at the published record to try to understand what the issue is about.
[ 17. March 2004, 10:52: Message edited by: charlie d. ]
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Fernando Castro-Chavez
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posted 17. March 2004 19:41
charlie d:
>This is not to say that ORFans do not exist, or are not interesting
That is an excellent statement.
My personal interest on those "species-specific" genes started just recently when, on doing my microarrays in mice, I found a transcript [data not published yet] notably altered, matching in Blast only to Mus musculus at its full length (in 3 nr) and/or almost full (in many ests).
AA185432 (456 letters).
In Blast nr:
gi|1769078|gb|AA185432.1|AA185432 mt61a07.r1
Soares_thymus_2NbMT Mus musculus cDNA clone IMAGE:634356 5'
XM_135913.3| Mus musculus cDNA sequence BC023829 (cDNA clone IMAGE:5343601)
AL672026.10| Mouse DNA sequence from clone RP23-403O11 on chromosome X, complete sequence
Plus hundreds of ests.
-------------------
Mesk
>the difference between primates and rodents is 99% due to evolution, and 1% due to ID?
In Intelligent Design, I don't have a problem understanding that, i.e., if somebody is an intelligent computing engineer, he will use a similar code and related pieces as his "fingerprint" on his several programs, it is like one painter with a unique and characteristic style as his main physical signature ("el Greco" clearly distinguishable from "Botero"), but also adding the specific seal that makes each of his productions different and, in the case of living beings, self-reproducible.
So much emphasis has been put on similarities. I think that now is time to look also at the differences, at those molecular aspects that make a particular organism unique.
The problem is when people puts a lot of weight on imaginary scenarios that, when some new pieces are put together, then it vanishes away, always speculating (on and on), and modifying theoretical models but never reaching any goal, as if wasting a life inside a theory.
I.E., molecular examples depicting a short presence of humans on earth; Gibbons in Science even suggest a calculation of 6,000 years:
From mtDNA:
The small amount of sequence divergence observed in mtDNA from different contemporary human populations, especially in Europe indicates a relatively recent origin of Homo sapiens without admixture of ancient Neandertal sequences (Torroni, A., et al., 1994. Am. J. Hum. Genet. 55, 760-776).
From the Y chromosome:
The Y chromosome, inherited from fathers to sons has a much lower mutation rate than that of mtDNA, inherited from the mother, however Y-chromosome studies support results of recent human origins, as the mtDNA analyses indicate. One study of Y-chromosome variation in a worldwide sample of over 1,000 men determined that Africans and non-Africans shared a common ancestor (Underhill P.A., et al, Y chromosome sequence variation and the history of human populations, 2000, Nature Genetics, 26: 358-361).
From an Intron:
"Nucleotide variation was examined in an 8 kb intronic DNA bordering exon 44 of the human dystrophin gene on Xp21. Thirty-six polymorphisms (substitutions, small insertions/deletions and one (T)n microsatellite) were found using SSCP/heteroduplex analysis of DNA samples from mixed Europeans, Papua New Guineans as well as from six African, three Asian and two Amerindian populations. The data suggest a recent common origin of the African and non-African populations, where a greater geographical isolation of the latter resulted in a smaller number of newly acquired polymorphisms" (Zietkiewicz E, et al, Nuclear DNA diversity in worldwide distributed human populations, 1997, Gene, 205(1-2):161-71).
Also, depicting a global reduction of humans in the past (the bottleneck):
One of the most significant findings to come out of human mtDNA studies is that non-Africans show genetic signs of a severe reduction in population size, a "bottleneck", some time in the past, followed by a population expansion (Ingman M., et al, Mitochondrial genome variation and the origin of modern humans, 2000, Nature, 408: 708-713).
'Living humans are strangely homogeneous genetically, presumably because … their ancestors underwent a population bottleneck that wiped out many variations' (Kahn, P. and Gibbons, A., 1997. DNA From an extinct human. Science, 277:176-178)"
Homo sapiens populations plummeted to near extinction and then for some unknown reason bounced back in full force. This population bottleneck is viewed as being responsible for the high degree of genetic uniformity among modern humans (on: Christopher Stringer and Robin McKie, African Exodus. The Origins of Modern Humanity, 1996, NY: Henry Holt and Company, pp. 155-159)
'Using the new clock, 'Eve' would be a mere 6000 years old' (Gibbons, A., 1998. Calibrating the mitochondrial clock. Science, 279, p. 28).
[ 20. March 2004, 08:43: Message edited by: Fernando Castro-Chavez ]
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nobody
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posted 17. March 2004 22:07
quote:
Dear Member # 145:
For example, the human genome contains at least 223 genes that do not have "the required predecessors on the genomic evolutionary tree", never transmitted "vertically".
Thanks!
Everybody else just calls me "nobody".
![[Smile]](smile.gif)
Now here's one of my patented stupid questions: Would these 223 genes you mention be enough to explain the difference between humans and chimps?
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charlie d.
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posted 17. March 2004 23:23
quote:
Nobody:
quote:
------------
Dear Member # 145:
For example, the human genome contains at least 223 genes that do not have "the required predecessors on the genomic evolutionary tree", never transmitted "vertically".
-----------------
Thanks!
Everybody else just calls me "nobody".
Now here's one of my patented stupid questions: Would these 223 genes you mention be enough to explain the difference between humans and chimps?
Nobody:
if you read Mesk's post, you'd find out that those genes were not specific to human, but seemed initially shared only between human and bacteria (they were thought to have arisen by HGT). They would explain the differences between us and chimps only under the assumption that we are significantly more prokaryotic than them. Of course, as Mesk also pointed out, the number of those genes is down to a few, as more eukaryotic genome sequences entered the database.
I also doubt that any specific, complete catalog of gene differences between humans and chimpanzee exists, since the chimp genome has not been completely analyzed yet (the draft sequence only came out a couple of months ago).
[ 17. March 2004, 23:25: Message edited by: charlie d. ]
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nobody
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posted 18. March 2004 22:17
So are there species-specific genes, or not?
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Mesk
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posted 18. March 2004 23:31
Nobody,
Yes, there are almost certainly species-specific genes, but they're extremely rare and it's essentially impossible to know exactly which genes they are (as I said above, unless we have complete genome sequences from every living organism, we can't be sure that a gene is genuinely found in only a single organism). It's worth pointing out that the absence of species-specific genes would actually be evidence against MEB, since the evolution of new genes must occasionally occur if the organisms we see today evolved from simpler common ancestors. I'm still not 100% sure eaxctly why Fernando sees them as evidence against MEB - but hopefully he'll explain himself more clearly in some future post.
Fernando,
You say:
quote:
In Intelligent Design, I don't have a problem understanding that, i.e., if somebody is an intelligent computing engineer, he will use a similar code and related pieces as his "fingerprint" on his several programs, it is like one painter with a unique and characteristic style as his main physical signature ("el Greco" clearly distinguishable from "Botero"), but also adding the specific seal that makes each of his productions different and, in the case of living beings, self-reproducible.
It sounds awfully like your argument is based on a loose analogy between human design and some of the features we see in living organisms. Unfortunately argument from loose analogy does not constitute scientific evidence, and your argument is further undermined by the fact that modern evolutionary theory can explain species-specific genes very well indeed, as I explained above.
But perhaps I have misunderstood you. Could you please spell out for me exactly why you see species-specific genes as evidence for ID and against modern evolutionary theory?
Now, onto the next topic you raise. You are being exceptionally selective in your references to the literature on human genetic history. It is important to remember that not all of the genetic material in modern humans is the same "age" - some parts of it (e.g. the Y chromosome and mitochondrial genome) are relatively young, while other regions (e.g. most autosomal nuclear genes, and most notably some chromosomal segments containing immune system genes) are absolutely ancient. The reasons for this are complicated, but partly boil down to population size. In a small population, everyone will (on average) share a more recent common ancestor than will people in a large population. Since the effective population size of the Y chromosome and mtDNA is 25% and 50%, respectively, of the effective population size of most other genetic regions, population genetics predicts that they will have a much more recent coalescence time (that is, a younger "age"). And while there are a few genetic regions which can be analysed in such a way as to obtain coalescence times in the thousands of years, the vast majority of loci produce ages in the hundreds of thousands to millions of years. In the case of regions containing certain immune system genes such as MHC loci, which are under powerful balancing selection which maintains genetic variation over long periods of time, coalescence times go back tens of millions of years - in some cases, prior to the divergence of the human and mouse lineages ~70-100 million years ago.
Only by very carefully cherry-picking through the data can one even attempt to argue for a "young age" (in the thousands of years) for modern humans - any balanced analysis will always point to a very ancient genetic history. The extent to which you are actually cherry-picking the data can be easily illustrated by quoting from the abstract (which I'm sure you've read?) of one of the articles you cited in support of a recent human origin:
"...contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago." (Underhill P.A., et al. 2000. Y chromosome sequence variation and the history of human populations. Nature Genetics 26: 358-361.)
Remembering that the Y chromosome lineage (called the "patrilineage," since it descends only through males) is always significantly younger than the remainder of the human genome, this puts the claims for a young human genetic origin in a more realistic light. And one need only take a look at the wealth of literature on large-scale human genetic analyses over the four years since the publication of this article (which you appear not to have done) to realise that this is not an isolated finding - it is now fairly widely accepted that all modern humans are descended from a common ancestral population which lived in Africa somewhere between 100,000 and 200,000 years ago. Human genetic history in Africa can be traced back much further, with some genetic regions being dated back millions of years. The recent publication of the genome sequence from our closest living relative, the chimpanzee, will help us explore even further back into our evolutionary history.
There are some good recent reviews of the subject of human genetic history, which I would strongly recommend you take a look at - this article would be an excellent starting point.
Mesk.
[ 18. March 2004, 23:34: Message edited by: Mesk ]
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Mesk
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posted 19. March 2004 00:39
quote:
charlie d.:
I also doubt that any specific, complete catalog of gene differences between humans and chimpanzee exists, since the chimp genome has not been completely analyzed yet (the draft sequence only came out a couple of months ago).
The comprehensive catalogue of chimp-human differences certainly hasn't been written yet, but most of the required information is already available for anyone who wants to take a look. The UCSC Genome Browser has added the chimp genome sequence to its database and aligned it to the human genome. This means you can examine any region of the human genome using the Browser, and can immediately see all of the differences between human and chimp (both substitutions and indels).
Mesk.
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Fernando Castro-Chavez
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posted 19. March 2004 13:09
Mesk:
Ashley Montagu, M. F. Man: His First Million Years, 2nd edition. Signet Science Library, 1962. p. 58:
"It is important to note that the dating of these samples has been problematic, [more recent] specimens [are] not covered by the 14C and potassium-argon dating techniques, dates estimated for have been [also] estimated using the newly developed luminescence and electron spin resonance techniques [and] must be regarded as estimates, at best."
Then my comment is that the errors in the calculation of "great antiquity" for Neandertal bones that were buried side by side with humans underlies in the dating methodologies used. All "dating" systems are based in imaginary assumptions of its inventors, and of course none of them includes in their equation the presence of water covering all earth, which can even explain the existence of petrified forests and of the human "bottleneck" discovered by scientists (some references to it provided in my 17 March 2004 19:41 posting).
Science 2001 May 25; 292: 1481 (in News Focus)
Putting Limits on the Diversity of Life
Richard A. Kerr:
"25 paleontologists demonstrate a fresh approach to extracting a history of life from an imperfect fossil record imperfectly sampled by paleontologists for 180 years. Preliminary results contradict previous studies that showed biodiversity increasing over time. Although far from the last word, the method marks a turning point in the study of paleontological databases, the researchers say." [Quoted Article: PNAS 2001 98: 6261-6266]
To see a link to the original article, or to comment on this outstanding study that depicts the two explosions of life and the interval of destruction, with all the animal life on the ocean appearing at the same time in each explosion, without any "gradual increase in biodiversity" nor any "gradual appearing of new kinds of organisms", go to:
http://www.iscid.org/boards/ubb-get_topic-f-18-t-000034.html
Fragment of: "Chapter 1: "Darwinism in an Age of Molecular Revolution ("Evolution and the Molecular Revolution", Charles R. Marshall & J. William Schopf (eds.), 1996, Jones and Bartlett Publishers, Inc.)":
"A delightful example of the limits on variation is Wayne's (1986) study of variation in domestic animals. There are a great many types of domestic dogs, ranging from great danes to pugs, but there is much less diversity among domestic cats". "During its development, the relative proportions of a dog's skull change dramatically. Young dogs have broad and short skulls in comparison with those of adult dogs. In cats, however, the proportions of the face and head remain essentially constant during their growth to adulthood. This simple observation suggests that if there are large differences between the morphologies (the shape and form) of juveniles and adults in a species, a relatively greater range of varieties can be generated. This rule also holds for horses, the skulls of which show relatively little change of shape during growth and of which there are relatively few domestic varieties. On the other hand, pigs show dramatic face changes during their development and there are hundreds of different breeds. Wayne's analysis suggests that certain types of cat and horse skull morphologies are essentially impossible, not because they would be disadvantageous, but because the development of cats and horses proceeds in such a way that a whole suite of shapes simply cannot be readily generated. Clearly, the range of variation that can be produced by nature is not random with respect to the range of shapes and forms that can be imagined by humans!" [Quoted Article: Wayne, R.K. 1986. Cranial morphology of domestic and wild canids: The influence of development on morphological change. Evolution 40: 243-261]
Li TX, Wang J, Bai Y, Sun X, Lu Z. Links
A novel method for screening species-specific gDNA probes for species identification.
Nucleic Acids Res. 2004 Mar 01;32(4):e45
"The screened unique gDNA fragments can be used as species-specific probes to differentiate the species they represent from all other species."
Krcmar P, Rencova E.
Identification of species-specific DNA in feedstuffs.
J Agric Food Chem. 2003 Dec 17;51(26):7655-8
"A sensitive method for the identification of bovine- and ovine- and also swine- and chicken-specific mitochondrial DNA sequences based on Polymerase Chain Reaction (PCR) has been developed." "The identity of a sample containing 0.1% of bovine, ovine, swine, and chicken meat-and-bone meal has further been confirmed by sequencing."
Charlebois RL, Clarke GD, Beiko RG, St Jean A.
Characterization of species-specific genes using a flexible, web-based querying system.
FEMS Microbiol Lett. 2003 Aug 29;225(2):213-20
"We describe a query-based web-accessible system (www.neurogadgets.com/bws.php)" "We illustrate with a characterization of species-specific protein-coding genes (so-called "ORFans")" "Using a dual-threshold approach, we conclude that these are characteristics of true species-specific genes, rather than artifacts of mis-annotation"
Rodriguez MA, Garcia T, Gonzalez I, Asensio L, Mayoral B, Lopez-Calleja I, Hernandez PE, Martin R.
Identification of goose, mule duck, chicken, turkey, and swine in foie gras by species-specific polymerase chain reaction.
J Agric Food Chem. 2003 Mar 12;51(6):1524-9
"The different sizes of the species-specific amplicons, separated by agarose gel electrophoresis, allowed clear identification of goose, mule duck, chicken, turkey, and swine in foie gras."
Kopp E, Mayr B, Schleger W.
Species-specific non-expression of ribosomal RNA genes in a mammalian hybrid, the mule.
Chromosoma. 1986;94(5):346-52
"The expression of nucleolus organizer activity in diploid cells was investigated in a model system for mammalian hybrids, the horse-ass cross (mule)." "As a rule we found species-specific non-expression of the horse-derived NOR chromosomes in the mule, whereas the ass-derived NOR chromosomes were active."
Scholz M, Bachmann L, Nicholson GJ, Bachmann J, Giddings I, Ruschoff-Thale B, Czarnetzki A, Pusch CM.
Genomic differentiation of Neanderthals and anatomically modern man allows a fossil-DNA-based classification of morphologically indistinguishable hominid bones.
Am J Hum Genet. 2000 Jun;66(6):1927-32. Epub 2000 Apr 27.
"When hybridized with genomic DNA of either human or Neanderthal origin, DNA extracted from two Neanderthal finds-the Os parietale, from Warendorf-Neuwarendorf, Germany, and a clavicula, from Krapina, Croatia-was shown to yield hybridization signals that differ by at least a factor of two compared to the signals obtained with the use of fossil DNA of an early Homo sapiens from the Vogelherd cave (Stetten I), Germany." "The genome of Neanderthals is expected to differ significantly from the genome of anatomically modern man, because of the contrasting composition of repetitive DNA. These data support the hypothesis that Neanderthals were not ancestors of anatomically modern man."
[ 25. March 2004, 09:32: Message edited by: Fernando Castro-Chavez ]
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Fernando Castro-Chavez
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posted 24. March 2004 12:42
charlie d,
The next expressions summarize some of our personal research concerns:
“The proteome is astoundingly more complex than the genome. And it is not just the numbers, though they are staggering: 30,000 genes could well translate into one million proteins.” "We have to remember," says Marc Vidal, assistant professor of genetics, Dana Farber Cancer Institute in Boston, "that the proteome is vast. It's like terra incognita.... We have a few settlers, we have to explore a huge amount of space." "If you know what the binding partners [of a protein] were, and when it and neighboring genes were expressed, and if in addition you know the phenotype of the loss of function of these genes, then you can start building models of what those genes might do and also how they do it." “You want to know when [a molecular finding] is surprising, when it makes you think differently." (The Scientist 16[8]:28, Apr. 15, 2002).
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A figure on the limits of variability (Taken from: Roberts, Genet. Res. 8:361-375, 1966):
http://personales.com/mexico/guadalajara/RV1960/robertsgraph.gif
FIGURE 1. Long-Term Responses to Selection of the CL (long mice) and CS (small mice) Lines.
Note on Figure 1: A similar graphic was previously described by Falconer (Falconer, D. S. Selection for Large and Small Size in Mice. J. Genet. 51:470-501, 1953) for the big line NF, that attained a limit of 28 g after 52 generations and the small line NS, that attained a limit of 11 g after 42 generations.
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From the most repetitive sequences that Victor Velculescu reported in his 1999 Nat. Genet. Letter, using his patented methodology SAGE, we can see that amazingly those sequences are only present in humans. It seems that some signaling of specificity are they also providing...
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The knowledge of the RNA Assembly (RNA Editing, RNA Splicing, RNA Trans-Splicing, RNA Post-Transcriptional Modifications, etc…) can help us understand the Abundance and Types of mRNA in the Cell. The Nucleic Acids: DNA and RNA are the Biological Software, you can see that there was a designer of them.
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