Posted on 04/08/2008 2:44:28 PM PDT by blam
Scientists find a fingerprint of evolution across the human genome
The Human Genome Project revealed that only a small fraction of the 3 billion “letter” DNA code actually instructs cells to manufacture proteins, the workhorses of most life processes. This has raised the question of what the remaining part of the human genome does. How much of the rest performs other biological functions, and how much is merely residue of prior genetic events?
Scientists from Cold Spring Harbor Laboratory (CSHL) and the University of Chicago now report that one of the steps in turning genetic information into proteins leaves genetic fingerprints, even on regions of the DNA that are not involved in coding for the final protein. They estimate that such fingerprints affect at least a third of the genome, suggesting that while most DNA does not code for proteins, much of it is nonetheless biologically important – important enough, that is, to persist during evolution.
Conservation of genetic information
To gauge how critical a particular stretch of DNA is, biologists often look at the detailed sequence of “letters” it consists of, and compare it with a corresponding stretch in related creatures like mice. If the stretch serves no purpose, the thinking goes, the two sequences will differ because of numerous mutations since the two species last shared an ancestor. In contrast, it’s believed that the sequences of important genes will be similar, or “conserved,” in different species, because animals with mutations in these genes did not survive. Biologists therefore regard conserved sequences as a sign of biological importance.
To test for conservation, researchers need to find matching stretches in the two species. This is relatively easy for stretches that “code” for proteins, where scientists long ago learned the meaning of the sequence. For “noncoding” regions, however, the comparison is often ambiguous. Even within a gene, stretches of DNA that code for pieces of the target protein are usually interspersed with much larger noncoding stretches, called introns, that are removed from the RNA working copy of the DNA before the protein is made.
Signs of splicing
Previous researchers assumed that mutations in the middle of introns do not affect the final protein, so they simply accumulate. In the new work, however, the researchers found signs that evolution rejects some types of mutations even in these regions of the genome. Although the selection is weak, “introns are not neutral,” in their effect on survival, says CSHL professor Michael Zhang, a bioinformatics expert who headed the research team.
To look for selection, CSHL researcher Chaolin Zhang, a doctoral candidate at Stony Brook University, looked in the human genome for a subtle statistical imbalance in how often various “letters” appear. The researchers attribute this imbalance to special short stretches of DNA that mark regions to be removed. Unless these signal sequences are sprinkled throughout an intron, the data suggest, it may not be properly spliced out, with potentially fatal consequences. Other sequences must likewise be preserved in the regions to be retained.
The scientists found a preference for some “letters” across intron regions, and the opposite preference in coding regions. Together, these regions make up at least a third of the genome, which is thus under selective pressure during evolution. The result supports other recent studies that suggest that, although most DNA does not code for proteins, much of it is nonetheless biologically important.
In addition to demonstrating how splicing affects genetic evolution, the statistical analysis identified possible signaling sequences, some that were already known and others that are new. According to co-author Adrian Krainer, a CSHL professor and splicing expert, “the exciting thing will be to experimentally test whether these predicted elements are really true.”
“RNA landscape of evolution for optimal exon and intron discrimination” appears in the April 15, 2008 edition of the Proceedings of the National Academy of Sciences. The paper is available online at http://www.pnas.org_cgi_doi_10.1073_pnas.0801692105.
Source: Cold Spring Harbor Laboratory
And this reductionist view of life promoted by evolutionists has hampered biology for over a century. Besides mRNA, there are a whole slew of non-coding regulatory RNAs. And there has to be to do things like wire up neurons to muscles and senses, and differentiate cell types throughout the body. If DNA is a computer/computer program, then mRNA is simply an output based on a complex instruction set of regulatory RNAs.
But then you are so much smarter than those idiot scientists.
Inasmuch as most of your eagerly cited, even revered 'evolution scientists' have never been deemed by Mensa to have a 160+ I.Q., yes, I am provably alot smarter than the vast, lemming-like bulk of them--who start with a theory and then refer only to that data which supports their ignorant theory. THAT is NOT science, bonehead.
Also, I'm at least smart enough to know that "Hare brained" is TWO words, you ridiculous stupenagle. I'll compromise, n'kay? You probably are closely related to a chimp.
;-/
If Biology has been hampered I would love to see it unfettered. We have learned more in Biology the last 20 years than what was known about Biology in all of human history. If this is your viewpoint (along with calling reasonable Scientists “evolutionists”); I can see there is little common ground on which we can speak because your not living in the same reality that I experience every day.
I’m very sorry about your obvious deficiencies. If it is any interest to you, spell check likes the way I spelled it. Now ask your mother to tuck you in, you are up very late for such a small child.
As far as evolution is concerned, they, and their moldering opinions, are just more detritus on the scrap-heap of an uncaring universe.
But since you brought it up, where is the fossil-record of the hundreds-of-millions of years of "evolving" eyes? Evolution posits that it took 300-450-million years for eyes to evolve.
Where is the 200-300-million year long fossil record of "partially evolved" eyes?
And given that those eyes need a circulatory system to sustain them, a nervous system to operate them AND the circulatory system, a respiratory system to oxygenate the circulatory vehicle, a musculature to operate the eyes- circulatory-and-respiratory systems, and a skeletal systemn to house it all (exo-or-endo, it matters not), how did all of this eveolve in the first place?
Hmmmmmm...., mutually interdependent, inextricably interwoven systems of unspeakable complexity.
Each of which systems require all of the others in order to exist and to function... especially vis-a-vis the eybeall.
Either they all "evolved" into being at once in an as yet un-hinted-at simultaneous "BIG EVOLUTIONARY BANG", or they were designed and created.
The bloodstream coudn't have evolved first and then waited around for a musculature, respiratory and nervous systenm to evolve for it to work with. The same is true of each of the others.
If the "EVO" scientific community (or its brain-dead acolytes) were able to see the noses on their faces, they would realize and admit this very simple and obvious conundrum.
They might even let the absence of any fossil-record of hundreds-of-millions of years of partially evolved eyes give them a hint.
But, it seems eyes only really work best when one uses them to look, not just to see; and there are none so blind as those who simply refuse to see.
I await your cleverly pointless religion based reparté.
;-/
But, in your eagerness to prove me ignorant, you only showed your own dirty undies.
"The higher the chimp climbs the tree, the more people can see his ass."
;-/
But since you brought it up, where is the fossil-record of the hundreds-of-millions of years of "evolving" eyes? Evolution posits that it took 300-450-million years for eyes to evolve.
Where is the 200-300-million year long fossil record of "partially evolved" eyes?
Creationist claim CB301: The eye is too complex to have evolved.
Creationist claim CB921.1: What use is half an eye?
No doubt our earliest uses of DNA as a computer are rather crude compared to how the bio systems work. At the moment I suspect the DNA computers serve as adjuncts to non-electronic devices somewhere in the cells that send and receive protons.
You did know that we have receptors in our nervous systems that respond to protons, right?!
BTW, you said “most”. My criticism was of “most”, not the process. Until the entire genome has been examined in every particular I don’t think you can say “most”.
Hanging every element of our religion on those stories is ridiculous.
They were placed there as both instruction (God is concerned) and as a tribute to the ancients who thought them worthy of being handed down to their descendants.
10:58 08 April 2008
NewScientist.com news service
Ewen Callaway
A new "Darwin chip" could make evolution as easy as pressing play.
Researchers have created an automated device that evolves a biological molecule on a chip filled with hundreds of miniature chambers.
The molecule, which stitches together strands of RNA, became 90 times more efficient after just 70 hours of evolution.
"It's survival of the fittest," says Brian Paegel, a biochemist at the Scripps Research Institute, in La Jolla, California, who led the study with colleague Gerald Joyce.
The experiment could be used in the future to evolve molecules – or even cells – to sense environmental pollutants, Paegel says.
Dispelling doubts
And by demonstrating natural selection in real-time, the device could also help dispel doubts over evolution in the classroom and beyond, says Joyce. "There's a whole bunch of people who think evolution is only theory, including some former presidential candidates."
While Darwin used natural selection to explain differences between species, his principles also work at the level of molecules.
RNA is usually used to create proteins from genes. But some kinds of RNA can perform tasks similar to protein enzymes. Paegel's team used just such an RNA molecule, or ligase, in their work.
In the process, the ligase sews another strand of RNA to itself and is then duplicated by a pair of proteins.
Because of occasional errors in copying, the new ligase molecule might work differently from its predecessor – sometimes better, and sometimes worse. Paegel's team wanted to see if they could evolve a better ligase by natural selection.
Evolving ability
To do this, they took a form of ligase that is not very good at recognising RNA molecules, and dumped it in a pool of RNA. After letting it duplicate for a while, the researchers gradually reduced the number of RNA molecules in the pool, meaning that only the more efficient copies of the ligase could survive.
All the reactions occurred in a miniature chamber on the "evolution chip". After reaching a specified level of efficiency, a miniature pump automatically sucked up a small amount of the contents and plopped it into a new chamber. This started another round of selection.
After 70 hours and billions of duplications, Paegel's team stopped the reaction and analysed the last few batches. The ligase molecules they pulled out were able to find and stitch RNA molecules 90 times more efficiently than the ligase the team started with.
'Tasty potato'
Other researchers have created similar evolution machines, but few as fast and simple as the automated chip. "It's a big technical advance,” says Jack Szostak, a biochemist at Harvard University. Other labs are likely to follow, he says. "It doesn't look that difficult to do."
The device might be able to evolve better sensors to detect environmental pollutants such as lead, Paegal says. Just as his team reduced the number of RNA molecules in the reaction to select for a better ligase, cutting the level of lead would select an improved lead sensor.
Paegel also hopes to use the Darwin chip to make molecules with new chemical properties, not just improved editions of old molecules.
"We took a potato and made a really tasty potato," says Pagael. "But we would really like to discover broccoli – something completely different."
Journal reference: PLoS Biology (DOI: 10.1371/journal.pbio.0060085)
Cool!
Scientists had been guessing wrongly about the human appendix for decades, likewise claiming that the appendix was evolutionary residue; a subtle way for atheists and secularists to try to sweep God under a carpet. But scientists have now discovered God's purpose for the appendix.
Appendix not evolutionary residueWhere so-called genome residue is concerned, given that scientists have bills to pay like everybody else, I suspect that scientists are again willing to pimp out their credentials, lending their reputations to politically correct agendas in exchange for funding.
The Scars of Evolution:"The most remarkable aspect of Todaro's discovery emerged when he examined Homo Sapiens for the 'baboon marker'. It was not there... Todaro drew one firm conclusion. 'The ancestors of man did not develop in a geographical area where they would have been in contact with the baboon. I would argue that the data we are presenting imply a non-African origin of man millions of years ago.'"
What Our Bodies Tell Us
About Human Origins
by Elaine Morgan
Primary Literature by Jonathan Marks
Benveniste, Raoul E. and Todaro, George J. (1976) Evolution of type C viral genes: Evidence for an Asian origin of man. Nature, 261:101-107. This study also applied DNA hybridization to the apes. They found a 3-way split.
socrates.berkeley.edu/~jonmarks/biblio.html
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There have been a few pseudogenes that have been assigned putative function based upon their evolutionary conservation. This was because they DID do a genome wide survey of pseudogenes and saw a few that stood out against the background because these lucky few WERE evolutionarily conserved. What they might do, or why they show conservation has yet to be determined; but the fact is that MOST pseudogenes change at the neutral mutation rate because they do not perform a function and so are ‘neutral’ to selective pressure.
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates.Khelifi A, Meunier J, Duret L, Mouchiroud D.
Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard-Lyon 1, 16 rue Raphael Dubois, 69622 Villeurbanne Cedex, France. khelifi@biomserv.univ-lyon1.fr
Processed pseudogenes are generated by reverse transcription of a functional gene. They are generally nonfunctional after their insertion and, as a consequence, are no longer subjected to the selective constraints associated with functional genes. Because of this property they can be used as neutral markers in molecular evolution. In this work, we investigated the relationship between the evolution of GC content in recently inserted processed pseudogenes and the local recombination pattern in two mammalian genomes (human and mouse). We confirmed, using original markers, that recombination drives GC content in the human genome and we demonstrated that this is also true for the mouse genome despite lower recombination rates. Finally, we discussed the consequences on isochores evolution and the contrast between the human and the mouse pattern.
PMID: 16752212 [PubMed - indexed for MEDLINE]
grow up
Just like the rest of the Evo crowd, you make a few denigrating remarks about Christians and Creationists, and act as though that covers the blatant ignorance of your indefensible beliefs and their exploded Theory.
It does not.
You claim not only the intellectual high-ground, but also that your faith-based Theory is correct, but when assailed by someone with only a high-school education (me), the best you can do is post a picture of a Bible and two non-sequiturs which don't even address my posting;
I said nothing at all about the complexity of the eyeball. You genius. Do you really even fool yourself with this crap?
I rather referred to the inextricability of the many interdependent systems all of which are needed for the eye to function.
The distinction is not really all that subtle, yet you, who claim the intellectual high-ground can't even see that, so blinded are you by your faith in Darwin's Sour Grapes Mtyth.
You may fool yourself, but you don't fool me. Answer my questions utilizing the brilliance you feign, or admit your fraud, one or the other,
You Evo hucksters have gotten off easy for too long, spreading your lies and deceiving all who don't know any better than to be impressed by your hollow claims of intelligence.
Nothing but the spawn of chimps doing tricks.
;-)
I wish I could be a smart as these Evos...
;-)
Yummy!
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