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Author | Topic: PROOF against evolution | |||||||||||||||||||||||
Mammuthus Member (Idle past 6496 days) Posts: 3085 From: Munich, Germany Joined: |
quote: To nitpick, introns are also "expressed" i.e. transcribed, but are spliced out as a posttranscriptional modification. Also, not all exons make it into the protein for example the prion gene has 2-3 exons, the entire ORF contained ona single exon. re chimp-human sequence divergence, there was a recent paper that suggested a much higher divergence in sequences when indels are taken into account. This will have to be factored in once the chimp genome sequence is completed. Proc Natl Acad Sci U S A. 2002 Oct 15; 99(21): 13633-5. Epub 2002 Oct 04. Related Articles, Links Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Britten RJ. California Institute of Technology, 101 Dahlia Avenue, Corona del Mar, CA 92625, USA. rbritten@cco.caltech.edu Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by REPEATMASKER (http://ftp.genome.washington.edu/RM/RepeatMasker.html).
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DNAunion Inactive Member |
quote: quote: You’re right. (Also, I wasn't talking about historically: "related", with a "d", was a typo: I meant relate but didn't go back and proofread my post very well: so I might have confused things even more). Exons and introns are terms that relate directly to RNA since for a primary RNA transcript, EXons are EXpressed sequences (they remain in the RNA after splicing has occurred) and INtrons are INtervening sequences (they are excised from the primary RNA transcript). Off the top of my head, I thought that referring to the DNA regions that map to RNA exons and introns as being actual exons and introns was informal, since the excision of introns and splicing together of exons occurs in RNA, not in DNA (and thus, supposedly, the terms would technically refer only to RNA). However, I checked and found I was wrong: the terms exons and introns refer to either the RNA or the DNA regions, without the latter being informal usage.
quote: quote: Sorry, but I’m going to have to deny your nitpick. I didn’t say introns weren’t transcribed, I said they weren’t expressed. It is clear from my last sentence in the quote that I am quite aware that introns are found in RNA (having been transcribed from corresponding DNA regions, of course). So it’s clear that what you meant by expressed is not what I meant by expressed: hence, nitpick rejected. In fact, as I will show below, biology texts often times state what I did: that exons are expressed while introns are intervening sequences. But first, let’s also look at the overall context. A primary RNA transcript has regions that are EXcised and regions that are left IN. So obviously, EXons are the regions that are EXcised and INtrons are the regions left IN. Right? Wrong. That’s completely backwards. The original poster was offering a way for someone to remember whether exons or introns are excised: I offered another way, one that is often times mentioned in biology texts. So the context is that we were after a simple way to remember which-is-which, and, EXons are EXpressed and INtrons are INtervening sequences: that works, and is used by many biology texts.
quote: quote: PS: Thanks for the additional info on human vs. chimp DNA similarity that included indels. [This message has been edited by DNAunion, 01-19-2004]
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sfs Member (Idle past 2554 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:Yeah, that was the paper I was referring to when I mentioned indels. I was just too lazy to look it up.
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Mammuthus Member (Idle past 6496 days) Posts: 3085 From: Munich, Germany Joined: |
Hi DNAunion
There are in some cases, expressed introns DNA Res. 2000 Feb 28; 7(1): 27-30. Related Articles, Links mRNAs encoding zinc finger protein isoforms are expressed by alternative splicing of an in-frame intron in fission yeast. Okazaki K, Niwa O. Kazusa DNA Research Institute, Kisarazu, Chiba, Japan. kokazaki@kazusa.or.jp We report here that a gene encoding a protein with three zinc fingers is expressed predominantly to produce a protein containing only two zinc fingers in the fission yeast Schizosaccharomyces pombe. A third zinc finger resides within the in-frame intron that is normally spliced out. By RT-PCR analysis, we detected a minor transcript encoding a protein with three zinc fingers. Such alternative splicing for assortment of zinc finger domains have been reported in animals and implicated in switching of the target genes expressed specifically during development. This is the first report of the occurrence of such zinc finger assortment in lower eucaryotes. Another issue, if one studies gene expression, one can examine total RNA or mRNA. Total RNA will measure transcripts containing introns which have been expressed, hence gene expression. This is different from actually making a protein which does not necessarily correlate all that well with total mRNA levels in any case. There are even functional genes in introns Biochem J. 2002 Aug 1; 365(Pt 3): 833-40. Related Articles, Links An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease. Cioffi AV, Ferrara D, Cubellis MV, Aniello F, Corrado M, Liguori F, Amoroso A, Fucci L, Branno M. Biochemistry and Molecular Biology Laboratory, Stazione Zoologica A. Dohrn, Villa Comunale 80121 Naples, Italy. Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1. RNA. 2000 Apr; 6(4): 616-27. Related Articles, Links Expression of the Naegleria intron endonuclease is dependent on a functional group I self-cleaving ribozyme. Decatur WA, Johansen S, Vogt VM. Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA. NaSSU1 is a complex nuclear group I intron found in several species of Naegleria, consisting of a large self-splicing group I ribozyme (NaGIR2), which itself is interrupted by a small, group I-like ribozyme (NaGIR1) and an open reading frame (ORF) coding for a homing endonuclease. The GIR1 ribozyme cleaves in vitro transcripts of NaSSU1 at two internal processing sites about 400 nt downstream of the 5' end of the intron, proximal to the endonuclease ORF. Here we demonstrate that self-cleavage of the excised intron also occurs in vivo in Naegleria gruberi, generating an ORF-containing RNA that possesses a short leader with a sequence element likely to be involved in gene expression. To assess the functional significance of self-cleavage, we constructed a genetic system in Saccharomyces cerevisiae. First, a mutant yeast strain was selected with a mutation in all the rRNA genes, rendering the rDNA resistant to cleavage by the Naegleria endonuclease. Active endonuclease, which is otherwise lethal, could be expressed readily in these cells. Endonuclease activity also could be detected in extracts of yeast harboring plasmids in which the endonuclease ORF was embedded in its native context in the intron. Analysis of the RNA from these yeast cells showed that the excised intron RNA was processed as in N. gruberi. A mutant intron constructed to prevent self-cleavage of the RNA failed to express endonuclease activity. These results support the hypothesis that the NaGIR1-catalyzed self-cleavage of the intron RNA is a key event in expression of the endonuclease. The problem with science textbooks is they are too general and usually take to long to update given the rapid pace of science and the near futility of keeping up with the primary literature. RE: chimp human comparisons, as I understand it, how the comparisons are made is still controversial. Some only compare expressed sequences like EST sequences. Whether the initial studies will include transposons, HERVs, microsatellites, etc. is not clear..but inclusion will be essential ultimately in getting an accurate measure of the human-chimp genomic differences.
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sonicxp Inactive Member |
you do know that oxygen is a prime component of chlorophyll
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NosyNed Member Posts: 9003 From: Canada Joined: |
And your point is?
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Coragyps Member (Idle past 755 days) Posts: 5553 From: Snyder, Texas, USA Joined: |
you do know that oxygen is a prime component of chlorophyll
In what way? Five atoms of oxygen out of about 135 total in chlorophyll a; one as a ring ketone, the others in ester linkages on side chains. How is that a "prime component?" Oh, and hello, new person! [This message has been edited by Coragyps, 02-11-2004]
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NosyNed Member Posts: 9003 From: Canada Joined: |
Ah, I get it. Welcome sonicxp.
I think you are confused about free oxygen and oxygen bound in any chemicals. There was no free oxygen until living things formed it. There was, obviously, lots of oxygen in various compounds.
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sonicxp Inactive Member |
Thought that one would get your attention.
Then tell if oxygen is found in other molecules eg. h20. then tell me the way I did my chemistry, the way to get a ketone is to allow a alcohol to semi-oxidise. if you know another way. please tell. if you read that article closely, they only produced very few amino acids in very small quantities, the other products were destructive to the amino acids so they couldn't exist without human influence to isolate the amino acids. Thanks for greeting me too.
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AdminNosy Administrator Posts: 4754 From: Vancouver, BC, Canada Joined: |
(sory should have been NosyNed)
I've only been half following this. It would be helpful to back up and summarize where we are at. [This message has been edited by AdminNosy, 02-12-2004]
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NosyNed Member Posts: 9003 From: Canada Joined: |
This thread was, once upon a time in a galaxy far away, "proof against evolution". However, the poster who opened it was aptly named.
If you are actually arguing something about abiogenesis rather than evolution you could tidy up with a new thread.
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sonicxp Inactive Member |
Excuse me, but were you there - if you were actually there it would be called science. but if you weren't, it is called a religion - you believe that that is the way the world was.
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crashfrog Member (Idle past 1487 days) Posts: 19762 From: Silver Spring, MD Joined: |
Excuse me, but were you there No, but the rocks we're looking at were. It's called "evidence", and it's how courts are able to convict people of crimes that were not witnessed. You don't have to have been there, because you can be there where the evidence is.
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sonicxp Inactive Member |
have you read your 'scientific method' lately. Just in case heres a link:
http://teacher.nsrl.rochester.edu/...ppendixE/AppendixE.html For something to be science, it must be observable.
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crashfrog Member (Idle past 1487 days) Posts: 19762 From: Silver Spring, MD Joined: |
For something to be science, it must be observable. uh, yeah. I know. And processes happening in the past leave evidence that you can observe, in the present. If I hold a rock in front of your face, and do tests on it right in front of you, what's not observable about that? You've observed the whole damn thing!
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