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Scientists Analyze Chromosomes 2 and 4: Discover Largest "Gene Deserts"
National Human Genome Research Institute ^ | 06 April 2005 | Staff

Posted on 04/13/2005 6:20:23 PM PDT by PatrickHenry

A detailed analysis of chromosomes 2 and 4 has detected the largest "gene deserts" known in the human genome and uncovered more evidence that human chromosome 2 arose from the fusion of two ancestral ape chromosomes, researchers supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported today.

In a study published in the April 7 issue of the journal Nature, a multi-institution team, led by [load of names deleted, but available in the original article].

"This analysis is an impressive achievement that will deepen our understanding of the human genome and speed the discovery of genes related to human health and disease. In addition, these findings provide exciting new insights into the structure and evolution of mammalian genomes," said Francis S. Collins, M.D., Ph.D., director of NHGRI, which led the U.S. component of the Human Genome Project along with the DOE.

Chromosome 4 has long been of interest to the medical community because it holds the gene for Huntington's disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence - a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

One of the central goals of the effort to analyze the human genome is the identification of all genes, which are generally defined as stretches of DNA that code for particular proteins. The new analysis confirmed the existence of 1,346 protein-coding genes on chromosome 2 and 796 protein-coding genes on chromosome 4.

As part of their examination of chromosome 4, the researchers found what are believed to be the largest "gene deserts" yet discovered in the human genome sequence. These regions of the genome are called gene deserts because they are devoid of any protein-coding genes. However, researchers suspect such regions are important to human biology because they have been conserved throughout the evolution of mammals and birds, and work is now underway to figure out their exact functions.

Humans have 23 pairs of chromosomes - one less pair than chimpanzees, gorillas, orangutans and other great apes. For more than two decades, researchers have thought human chromosome 2 was produced as the result of the fusion of two mid-sized ape chromosomes and a Seattle group located the fusion site in 2002.

In the latest analysis, researchers searched the chromosome's DNA sequence for the relics of the center (centromere) of the ape chromosome that was inactivated upon fusion with the other ape chromosome. They subsequently identified a 36,000 base pair stretch of DNA sequence that likely marks the precise location of the inactived centromere. That tract is characterized by a type of DNA duplication, known as alpha satellite repeats, that is a hallmark of centromeres. In addition, the tract is flanked by an unusual abundance of another type of DNA duplication, called a segmental duplication.

"These data raise the possibility of a new tool for studying genome evolution. We may be able to find other chromosomes that have disappeared over the course of time by searching other mammals' DNA for similar patterns of duplication," said Richard K. Wilson, Ph.D., director of the Washington University School of Medicine's Genome Sequencing Center and senior author of the study.

In another intriguing finding, the researchers identified a messenger RNA (mRNA) transcript from a gene on chromosome 2 that possibly may produce a protein unique to humans and chimps. Scientists have tentative evidence that the gene may be used to make a protein in the brain and the testes. The team also identified "hypervariable" regions in which genes contain variations that may lead to the production of altered proteins unique to humans. The functions of the altered proteins are not known, and researchers emphasized that their findings still require "cautious evaluation."

In October 2004, the International Human Genome Sequencing Consortium published its scientific description of the finished human genome sequence in Nature. Detailed annotations and analyses have already been published for chromosomes 5, 6, 7, 9, 10, 13, 14, 16, 19, 20, 21, 22, X and Y. Publications describing the remaining chromosomes are forthcoming.

The sequence of chromosomes 2 and 4, as well as the rest of the human genome sequence, can be accessed through the following public databases: GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of Japan (www.ddbj.nig.ac.jp); and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at EMBL's Nucleotide Sequence Database. [Links in original article.]

NHGRI is one of the 27 institutes and centers at NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.


TOPICS: Culture/Society; Miscellaneous; Philosophy
KEYWORDS: chromosomes; crevolist; dna; evolution; genetics
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To: Fitzcarraldo
Implying that women don't have this protein?

Only if they don't have brains.

251 posted on 04/14/2005 6:32:56 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: furball4paws
This technology also allows us to sequence proteins, which was a real arduous task in the old days

Nope, it only allows the prediction of sequence. If you want to know the actual sequence, you still have to do it the tedious way.

252 posted on 04/14/2005 6:42:26 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: microgood
The fact that we have similar genes with a rat does not mean we evolved from a rat.

Nope, it means that we evolved from a common ancestor.

253 posted on 04/14/2005 6:44:00 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: CJ Wolf
"centromere" I don't use the metric system, what's this about half an inche?

The centromere is the little connecting structure that holds 2 matching chromosomes together (at least, until mitosis or meiosis occurs). When you see a picture of chromosomes that look like X's, the centromere is where the X's cross.

254 posted on 04/14/2005 6:54:47 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: exDemMom
Nope, it means that we evolved from a common ancestor.

Correlation does not equal causation, as you claim it does.
255 posted on 04/14/2005 6:59:14 PM PDT by microgood
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To: Echo Talon
The only thing this "science" does is confuse people about their faith.

I, for one, am not confused. Neither are my colleagues, who practice a variety of faiths. The theory of evolution for us is just a tool, and has nothing to do with faith.

256 posted on 04/14/2005 7:15:05 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: exDemMom
This is a tired argument and your "theory" is just that. Wild speculation and innuendo, assuming this that the other thing draw conclusions only to what you want to believe. As I said before you believe what you want, I will believe what I want. I won't lose any sleep over it.
257 posted on 04/14/2005 7:30:35 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: microgood
Correlation does not equal causation, as you claim it does.

Correlation is a statistical term, and I do not recall using that word today in the context of evolution. Nor did I make a claim about correlation equaling causation, since I do not use the term for that purpose at all (and I do use the term frequently). I'm not even sure how the concept of correlation applies here. We talk about sequence homology--the mouse and rat gene xyz have 97% homology, while the human gene is only 93% homologous to that of mouse or rat, etc. Evolution can be traced by comparing the homology of genes across various species.

258 posted on 04/14/2005 7:32:57 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: PatrickHenry

Biologists...riding in the short bus of science.


259 posted on 04/14/2005 7:34:12 PM PDT by AmishDude (Join the AmishDude fan club: "You are a wise man." -- Torie; "You rock!" -- TonyRo76)
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To: exDemMom

I stand corrected, but the prediction is usually pretty damn good, especially in bacteria (my area).


260 posted on 04/14/2005 7:59:13 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: exDemMom
Evolution can be traced by comparing the homology of genes across various species.

The assumption that because the genetic composition of rats and people are similar that we have a common ancestor is imputing causation to the similar characteristics. It is a logical fallacy to say that. The entire assumption of common ancestry is a logical fallacy.
261 posted on 04/14/2005 9:17:18 PM PDT by microgood
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To: jennyp

I am not lying and I resent your implication that I am.


262 posted on 04/14/2005 9:33:54 PM PDT by Ahban
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To: sakic

His ways are above our ways, which can look like moral relativism to someone who is not willing to know Him.


263 posted on 04/14/2005 9:36:29 PM PDT by Ahban
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To: Chaguito

IF it means what they say, but again it can only show where the cut and paste was done (or something that looks like a c and p). There observations can't say what force did the cutting and pasting.

Besides, they act like it was NOT established before their research, so if they are right then the evos on this board were wrong to claim it was. If they are wrong about the importance of the evidence then why should I believe their evidence?


264 posted on 04/14/2005 9:39:51 PM PDT by Ahban
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To: Ahban
I am not lying and I resent your implication that I am.
Well, I sincerely hope I can apologize for implying that you were lying, but first you'll have to back up this (reckless, IMO) statement of yours:
they write like evolution is a proven fact and to believe otherwise makes you "demon-possessed". If you are a new poster on this board you may not believe that, but that is the term they use to people who fail to interpret the evidence the way they think we should.
Just who is this "they" who use the term "demon-possessed" in referring to you anti-evolutionists? You made a general statement that this is a commonly used term by us. Specifically, that it's common usage, and that it's been used by more than one evolutionist (i.e. not just an individual hotheaded post you once saw).
265 posted on 04/14/2005 10:32:01 PM PDT by jennyp (WHAT I'M READING NOW: my post)
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To: Echo Talon
It was a joke denoted with this ":P" :P HAR HAR

It is a good thing that you put humor tags on your jokes. However the more normal technique to inspire laughter in the reader is to say something funny.

266 posted on 04/15/2005 2:36:41 AM PDT by Thatcherite (Conservative and Biblical Literalist are not synonymous)
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To: Ahban
His ways are above our ways, which can look like moral relativism to someone who is not willing to know Him.

So, what do you think His position is on for example slavery and the stoning of disobedient children? The God of the bible clearly endorsed these practices in the past. Does he still endorse them?

267 posted on 04/15/2005 2:41:18 AM PDT by Thatcherite (Conservative and Biblical Literalist are not synonymous)
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To: Thatcherite
It is a good thing that you put humor tags on your jokes. However the more normal technique to inspire laughter in the reader is to say something funny.

Har har! whoo hoo your a real knee slapper. You must be one devoted atheist for you to be this upset that I don't believe your theory.

268 posted on 04/15/2005 3:36:09 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Ahban

Either you believe the Bible is the literal word of God or not. Do you? If so, you believe that God thinks it fine to own and beat slaves. If not, then you're admitting the Bible is a book written by man.


269 posted on 04/15/2005 4:38:44 AM PDT by sakic
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To: Echo Talon

ID proponents will disagree with you then. You do know that the ID movement believes that the earth is billions of years old, that evolution occurs, and that man and modern apes are descendents of a common ape-like ancestor. Seems like you wouldn't want to associate yourself with the ID movement any more than you would with evolution. The only difference (as far as I can tell) between ID and evolution is that ID adds an intelligent entity to guide the process, while evolution doesn't require any entity outside the living creatures on earth.


270 posted on 04/15/2005 5:16:30 AM PDT by stremba
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To: stremba

well who created the first piece of "mega sperm" that started it all Einstein?


271 posted on 04/15/2005 7:18:32 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: microgood
That is the biggest problem with the scientific community today, whether it be evolution or global warming or epidemiological studies, you claim to know things you do not.

Yet you do the very same thing in your post #231. I don't know if you realize it but you sound just like an evolutionary biologist. ;)

In general, scientists are very aware of the limits of knowledge in their field. However, the media filter makes things sound very strange and there are people with a political agenda who will use anything to get their way. When scientists exact words are quoted here on FR, creationists complain that they use words like "seems to", "it's probable that", or "this evidence suggests". So you can't have it both ways.

In the case of organisms growing arms and legs, Ichneumon's post documents the fossil evidence of this occurring. Alternative points of view to evolution don't address the fossil record. That's why I was being satirical about the previous poster's ID prediction.

The problem for anti-science is that there is an enormous amount of fossil evidence. More than any one individual could view in their lifetime. Creationists can't address it. They're still looking for the origins of seaweed. ID'ers can't address it because they have a rhetorical argument, not a theory. They're still struggling to understand complexity. So they've chosen to pick on something well documented, like the development of flagella or eyes (there are over 3500 different kinds), but have ignored truly complex structures like the brain.

Evolutionary biology is still the best explanation. And our understanding of how this works is growing daily. If we're lucky, we'll be here long enough to see a pill that can grow someone a new kidney. But who knows.

272 posted on 04/15/2005 7:35:02 AM PDT by <1/1,000,000th%
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To: Echo Talon
The bible is very clear that God created man in his image. If you think god is an ape you can believe that.

So, God has two arms, two legs, genitalia and He has to defecate, eat and breathe?

Or, could it be that "made in God's image" means that humans are thinking beings with free will, just like their creator?

273 posted on 04/15/2005 8:20:34 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Echo Talon
well who created the first piece of "mega sperm" that started it all Einstein?

The origins of life is not something the TOE covers.

274 posted on 04/15/2005 8:45:10 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Modernman; Echo Talon
So, God has two arms, two legs, genitalia and He has to defecate, eat and breathe?

I wonder how God did those things before He created a physical universe? Still, at least He didn't look like an ape, or anything disgusting like that.

275 posted on 04/15/2005 8:52:01 AM PDT by Thatcherite (Conservative and Biblical Literalist are not synonymous)
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To: Thatcherite; Echo Talon
I wonder how God did those things before He created a physical universe? Still, at least He didn't look like an ape, or anything disgusting like that.

I wonder what He wore? Or did He strut around naked? What color hair does He have? How tall is He?

Is He a lefty or a righty? Does He have knee and back problems like many humans?

The idea that an all-powerful, all-knowing deity would look anything like the hairless apes He created is laughable.

276 posted on 04/15/2005 8:55:30 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Dimensio
You do know that there are no true Scots?
277 posted on 04/15/2005 9:24:55 AM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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hairless deity placemarker


278 posted on 04/15/2005 9:28:41 AM PDT by js1138 (There are 10 kinds of people: those who read binary, and those who don't.)
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To: Echo Talon
"Genesis is clear as day."

Yup! It clearly is *not* a science text.

279 posted on 04/15/2005 9:30:10 AM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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To: Modernman
you keep saying "He" hmmm are you a sexist along with being an atheist?
280 posted on 04/15/2005 9:37:18 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Echo Talon
you keep saying "He" hmmm are you a sexist along with being an atheist?

"He" refers to the God described in the Bible. You're the literalist, you tell me, is God male or female?

281 posted on 04/15/2005 9:39:43 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Modernman
Your the scientist you tell me.
282 posted on 04/15/2005 9:43:32 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Echo Talon
Your the scientist you tell me.

Science cannot, nor does it even attempt to, describe the supernatural.

So, is God male or female? Does He have two legs, two arms and genitalia?

283 posted on 04/15/2005 9:45:19 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Thatcherite
"I'm cool, I reckon he looks stupider than me to the lurkers."

Should we take a poll? ;-)

284 posted on 04/15/2005 9:50:46 AM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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To: Modernman

Not to forget the all-important male nipples and his bellybutton (where mother God had her umbilical cord attached when he still was a fetus-God).


285 posted on 04/15/2005 9:58:11 AM PDT by anguish (while science catches up.... mysticism!)
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To: Modernman
So, is God male or female? Does He have two legs, two arms and genitalia?

You see, theres just some things that I don't care about. You wanna know what gods unit looks like? What an idiot.

286 posted on 04/15/2005 10:25:21 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Modernman
Science cannot, nor does it even attempt to, describe the supernatural.

Which is the precise reason why ID is not science. It attempts to describe the existence of the supernatural.

287 posted on 04/15/2005 10:32:59 AM PDT by narby
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To: Echo Talon
You see, theres just some things that I don't care about. You wanna know what gods unit looks like? What an idiot.

I thought you said we were created in God's image, but now you're telling me that you don't know.

288 posted on 04/15/2005 10:36:42 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: Modernman

Hey, thats what the book says. Mines not to queston why... you know the rest.


289 posted on 04/15/2005 10:38:52 AM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Echo Talon

So, God has a penis?


290 posted on 04/15/2005 10:43:27 AM PDT by Modernman ("I'm in favor of limited government unless it limits what I want government to do."- dirtboy)
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To: PatrickHenry
researchers searched the chromosome's DNA sequence for the relics of the center (centromere) of the ape chromosome that was inactivated upon fusion with the other ape chromosome

Strange, I suddenly feel hungry for a banana.

291 posted on 04/15/2005 10:47:44 AM PDT by colorado tanker (The People Have Spoken)
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To: Thatcherite
I wonder how God did those things before He created a physical universe? Still, at least He didn't look like an ape, or anything disgusting like that.


The Divine Image!?

292 posted on 04/15/2005 11:10:11 AM PDT by balrog666 (A myth by any other name is still inane.)
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To: b_sharp
Should we take a poll? ;-)

So far I am winning 1-0. Hurrah! But everything may hang on which way Ohio jumps.

293 posted on 04/15/2005 11:39:55 AM PDT by Thatcherite (Conservative and Biblical Literalist are not synonymous)
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To: Thatcherite
"So far I am winning 1-0. Hurrah! But everything may hang on which way Ohio jumps."

Do votes from Canada count? Send me a few pounds and I'll vote for you too.

294 posted on 04/15/2005 1:01:19 PM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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To: Modernman
"So, God has a penis?"

Hung like a horse, with giant b**ls. How else would he plant his seed?

295 posted on 04/15/2005 1:03:22 PM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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To: b_sharp

I think I see the signs that this thread is just about played out.


296 posted on 04/15/2005 3:07:06 PM PDT by PatrickHenry (<-- Click on my name. The List-O-Links for evolution threads is at my freeper homepage.)
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To: PatrickHenry
"I think I see the signs that this thread is just about played out"

Great, now I'll get the reputation of killing threads.

297 posted on 04/15/2005 5:38:38 PM PDT by b_sharp (Science adjusts theories to fit evidence, creationism distorts evidence to fit the Bible.)
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To: furball4paws
I stand corrected, but the prediction is usually pretty damn good, especially in bacteria (my area).

Oh, yeah, bacteria. No introns, no exons, no alternate splicing, none of that stuff that makes the study of eukaryotes so durned complicated. So, what kind of bacteria do you study? I take it you are a microbiologist?

298 posted on 04/15/2005 7:00:20 PM PDT by exDemMom (Now that I've finally accepted that I'm living a bad hair life, I'm more at peace with the world.)
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To: jennyp; VadeRetro

Vade, jennyp seems to have forgotton about Morton's demon. Can you assure her that I am in fact "demon possessed"?


299 posted on 04/15/2005 7:16:58 PM PDT by Ahban
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To: Ahban
Vade, jennyp seems to have forgotton about Morton's demon. Can you assure her that I am in fact "demon possessed"?
Oh, Morton's demon. Well, yeah. Of course you're afflicted with that one. OK, I apologize. You're not lying. :-)
300 posted on 04/15/2005 7:23:39 PM PDT by jennyp (WHAT I'M READING NOW: my post)
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