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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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Bold and underlining added by me. Everybody be nice.
1 posted on 04/13/2005 6:20:24 PM PDT by PatrickHenry
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To: VadeRetro; Junior; longshadow; RadioAstronomer; Doctor Stochastic; js1138; Shryke; RightWhale; ...
EvolutionPing
A pro-evolution science list with over 260 names. See list's description at my homepage. FReepmail to be added/dropped.

2 posted on 04/13/2005 6:21:59 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

This stuff is way out of my field of knowledge. I'm surprised to learn that we have one less pair of chromosomes than the apes. I would have thought more pairs would be indicative of further evolutionary advancement.


3 posted on 04/13/2005 6:35:40 PM PDT by Dog Gone
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To: PatrickHenry
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.

amazing complexity.

4 posted on 04/13/2005 6:37:35 PM PDT by Cicero (Marcus Tullius)
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To: PatrickHenry
Scientists have tentative evidence that the gene may be used to make a protein in the brain and the testes.

Implying that women don't have this protein?

5 posted on 04/13/2005 6:40:33 PM PDT by Fitzcarraldo
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To: PatrickHenry

Blah blah blah, a bunch of big words perpetuating a lie that we evolved from apes.


6 posted on 04/13/2005 6:43:37 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: PatrickHenry
Everybody be nice.

What's that supposed to mean? I love it when bad logic is portrayed as science. Sure the scientists in question have identified the functions of gene sequences with great precision and skill but, to jump from there to the rest is simply rediculous. Everybody be nice? There's no need to be mean to anyone just for being wrong. It's their God given right :)

7 posted on 04/13/2005 6:49:00 PM PDT by derheimwill (Love is a person, not an emotion.)
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To: PatrickHenry

PH,

Haven't the evos at FR been assuring us for years that the fusion of the two ape chromosomes was a fact? On at least one recent thread they even had pictures pointing to where the centromere would have been. How can these evo scientists just now be announcing proof of what your team has long assured me HAS ALREADY BEEN PROVEN?


8 posted on 04/13/2005 6:51:15 PM PDT by Ahban (PS- they only show where the cut and paste was, not whether ID or evolution did it.!!!!)
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To: PatrickHenry

This wouldn't have happened if Bush had OK'd the Kyoto Protocol!


9 posted on 04/13/2005 6:51:28 PM PDT by Verginius Rufus
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To: Cicero

Yeah, but hardly irreducible even in the wildest fantasy, which is why the ID raconteurs don't torture us endlessly about titin. It basically evolved from a series of gene duplications in tandem with the evolution of multicellularity, giving rise to regularly repeating domain patterns.


10 posted on 04/13/2005 6:53:06 PM PDT by AntiGuv ()
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To: Echo Talon
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.

Blah blah blah, a bunch of big words perpetuating a lie that we evolved from apes.

Yeah, really big words there. Must be all the way up to the 8th grade.

But really, the discovery of a 36,000 base pair sequence is really just a cosmic joke that G-d is playing on us to make us think that evolution happened. At least that is the viewpoint of our creationist "scientists" with their mail order Ph.Ds.

*snicker*

11 posted on 04/13/2005 6:59:49 PM PDT by 2ndreconmarine
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To: AntiGuv

No, I wasn't claiming that it was. What this article says could just as easily be interpreted one way as the other. For instance, if God were designing apes and men, it stands to reason that He would use many of the same materials.

(I'm not saying that's the case, I'm just saying that this doesn't really prove that men evolved from apes. Before Darwin came along, the "great chain of being" that goes back to the ancient Greeks organized the members of the animal and plant kingdoms in much the same way as Darwinists did later. It was understood that there was a hierarchy of complexity, or of lower and higher orders.)


12 posted on 04/13/2005 7:01:00 PM PDT by Cicero (Marcus Tullius)
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To: derheimwill
What's that supposed to mean? I love it when bad logic is portrayed as science. Sure the scientists in question have identified the functions of gene sequences with great precision and skill but, to jump from there to the rest is simply rediculous.

What?!?

Scientists discover we have one fewer chromosome than the apes and then find a large section of one of our chromosomes that looks like it used to be a centromere.

The theory that fusion took place is a good one. It may not be correct, but there is evidence that it is.

It's hardly a ridiculous theory.

Here's an example of a ridiculous theory: the big sky-daddy is testing our faith by planting this genetic evidence.

13 posted on 04/13/2005 7:02:14 PM PDT by mc6809e
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To: Cicero

God would not use materials, he would conjure them. ;^)


14 posted on 04/13/2005 7:04:46 PM PDT by AntiGuv ()
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To: 2ndreconmarine
But really, the discovery of a 36,000 base pair sequence is really just a cosmic joke that G-d is playing on us to make us think that evolution happened.

He's not trying to "make us think" any such thing. Rather, He made us out of the same protiens because he made us out of the same kinds atoms - which work in the same way. Why do some people make things so complicated?

15 posted on 04/13/2005 7:05:15 PM PDT by derheimwill (Love is a person, not an emotion.)
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To: PatrickHenry

Funny that false evidence trail (a pseudo-centromere sequence) would be there if humans and apes are separately created. It's as if someone wanted to fake a chromosome fusion event in the history of humans. </creo-mode>


16 posted on 04/13/2005 7:05:53 PM PDT by VadeRetro (Liberalism is a cancer on society. Creationism is a cancer on conservatism.)
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To: AntiGuv
God would not use materials...

Genesis says otherwise...

17 posted on 04/13/2005 7:07:48 PM PDT by derheimwill (Love is a person, not an emotion.)
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To: VadeRetro
It's as if someone wanted to fake a chromosome fusion event in the history of humans.

Creationism is knowing when not to look.

18 posted on 04/13/2005 7:08:27 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: Ahban
Haven't the evos at FR been assuring us for years that the fusion of the two ape chromosomes was a fact? On at least one recent thread they even had pictures pointing to where the centromere would have been. How can these evo scientists just now be announcing proof of what your team has long assured me HAS ALREADY BEEN PROVEN?

I don't think anything can be proved in science. There are only theories that best fit the evidence.

What's interesting about this, though, is that science predicted fusion, and lo, here we have more evidence for it.

It really is too bad, though, that there isn't some book somewhere that already contains all the answers. Instead, scientists have to constantly check their theories and do research.

19 posted on 04/13/2005 7:09:49 PM PDT by mc6809e
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To: derheimwill

Hmmmm.. I see an awful lot of "let there be"s in my version of Genesis....


20 posted on 04/13/2005 7:09:54 PM PDT by AntiGuv ()
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To: PatrickHenry
These guys make the same mistake as the evolutionists. When an evolutionist states that because past fossils have similar characteristics to supposedly older fossils, they make the HUGE assumption that they have a common ancestor. These people are making the same mistake. The genes may have similar characteristics to apes and portions may be exactly the same, but you cannot conclude that they came from the same place. It is a logical fallacy.

Correlation does not equal causation, but many scientists fall into that trap. Look at all the epidemiological studies and the deception involved in them.
21 posted on 04/13/2005 7:14:22 PM PDT by microgood
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To: 2ndreconmarine
You keep your faith in man and Scientology and I will keep mine in the Lord.
22 posted on 04/13/2005 7:14:43 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: mc6809e

That sounds very reasonable. I hope that you will avail yourself the opportunity to remind some of the evos on this board of that when they become to strident and dogmatic. It seems from behind my keyboard that 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.

In this instance for example, if there was a fusion, and if the fusion point has indeed been found, it only shows where the "cut and paste" was, not whether an ID or blind evolution performed the operation!


23 posted on 04/13/2005 7:16:36 PM PDT by Ahban
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To: PatrickHenry

Considering how little we actually know about the specific proteins coded by DNA in a cell, I don't think it's particularly wise to go around unilaterally declaring all these gene deserts.

I wouldn't be surprised to find that these deserts, much like the tonsils and appendix, aren't as vestigial and unused as biologists currently maintain they are.

Interestingly enough, an evolutionary paradigm led to the wrong conclusions about the appendix and tonsils being vestigial.


24 posted on 04/13/2005 7:18:25 PM PDT by frgoff
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To: mc6809e

PS- even those of us who believe in Revelation as a source for truth believe that our interpretations of those revelations must be examined.


25 posted on 04/13/2005 7:18:32 PM PDT by Ahban
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To: microgood
The genes may have similar characteristics to apes and portions may be exactly the same, but you cannot conclude that they came from the same place. It is a logical fallacy.

So where are all the 500 million year old apes? If there's no relationship between the apes' genes, why do they exist at roughly the same time in history?

26 posted on 04/13/2005 7:19:25 PM PDT by <1/1,000,000th%
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To: microgood
The genes may have similar characteristics to apes and portions may be exactly the same, but you cannot conclude that they came from the same place. It is a logical fallacy.

Where would you propose they came from?

27 posted on 04/13/2005 7:20:01 PM PDT by AntiGuv ()
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To: PatrickHenry

"...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. "

Well, I'll be a monkey's uncle. Where is WJB when you need him?

(could this fusion have created this "gene desert"?)


28 posted on 04/13/2005 7:22:03 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: Echo Talon
Blah blah blah, a bunch of big words perpetuating a lie that we evolved from apes.

If we evolved from apes, what did apes evolve from? I've never had that question answered.

29 posted on 04/13/2005 7:23:13 PM PDT by Cowboy Bob (Question Liberalism)
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To: frgoff

The absence of Open Reading Frames is good evidence for a "desert".

Gene sequencing technology has found many genes that were previously unknown by examining for open reading frames. This technology also allows us to sequence proteins, which was a real arduous task in the old days (sigh... I guess I am getting to the point where I belong with the dinosaurs).


30 posted on 04/13/2005 7:26:23 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: furball4paws
Well, I'll be a monkey's uncle.

Nephew, more likely.

could this fusion have created this "gene desert"?

The gene desert is proof of the Fall. And the Flood. And design. And Darwin's degeneracy.
</creationism mode>

31 posted on 04/13/2005 7:26:31 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; Lijahsbubbe; aculeus; Dataman
"gene deserts"

"Mmmm, jean desserts."

32 posted on 04/13/2005 7:28:28 PM PDT by Thinkin' Gal
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To: <1/1,000,000th%
So where are all the 500 million year old apes? If there's no relationship between the apes' genes, why do they exist at roughly the same time in history?

Because they came into existence from the same or similar mechanism or process. The fact that we have similar genes with a rat does not mean we evolved from a rat. We could have come into existence via a similar process.
33 posted on 04/13/2005 7:28:53 PM PDT by microgood
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To: PatrickHenry
the medical community

It was most recently the medical industry, but now has become incorporated into the State as the Medical Institute. As soon as somebody damanded the right to medical care the game was over.

34 posted on 04/13/2005 7:29:41 PM PDT by RightWhale (50 trillion sovereign cells working together in relative harmony)
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To: Dog Gone; Ichneumon
Ichneumon has an image (4th graphic down) in his thermo-nuclear evo post. -- a copy here
35 posted on 04/13/2005 7:32:36 PM PDT by dread78645 (Sarcasm tags are for wusses.)
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To: Cowboy Bob

tree shrews -> lemurs -> tarsiers -> apes* -> humans

* The earliest apes differentiated from ancestral haplorhines during the early Miocene Epoch, about 18-22 million years ago.

PS. Keep in mind that the modern critters listed above are just approximations of the ancestral creatures, as the extant species have also continued to evolve, though with lesser divergence. Note that monkeys diverged down their own path from tarsiers, and so apes did not evolve from monkeys, contrary to popular cliché.


36 posted on 04/13/2005 7:33:03 PM PDT by AntiGuv ()
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To: PatrickHenry

Rollin' Rollin' Rollin'
Keep the Luddites rollin'
Rawhide

Ya can't understand 'em
Just rope, tie and brand 'em
Soon they'll be at the end of their line.

.
.
.
rawhide

(sorry Clint)


37 posted on 04/13/2005 7:33:33 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: AntiGuv
Where would you propose they came from?

I am not sure. Of course the point is neither are they though they make the claim(erroneously). The process or mechanism that apes came into existence from could be similar or the same as the one that allowed humans to come into existence.
38 posted on 04/13/2005 7:34:47 PM PDT by microgood
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To: microgood
Because they came into existence from the same or similar mechanism or process.

OK. What process would create apes, then a couple millions of years later, humans with similar genes?

39 posted on 04/13/2005 7:37:12 PM PDT by <1/1,000,000th%
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To: microgood

The problem with convergence theory in this sense is that these features that are deemed emblematic of common ancestry are to a degree arbitrary. There is no reason for them to have emerged independently with precisely this arrangement (or even close to it, in the traits discussed above).


40 posted on 04/13/2005 7:38:20 PM PDT by AntiGuv ()
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To: PatrickHenry

I wonder how much of the "desert" genes relate to the fact that genes can also be read by RNA three dimentionally. Protein production is not always linear along a DNA strand like we see on simple TV animations.


41 posted on 04/13/2005 7:42:03 PM PDT by longtermmemmory (VOTE!)
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To: Cowboy Bob
If we evolved from apes, what did apes evolve from? I've never had that question answered.

Dont ya know, they say we came from some slimy thing from the ocean... and just poof the human body had morphed into the great body that we have today. pretty amazing really...

42 posted on 04/13/2005 7:42:59 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: AntiGuv

How do you supppose that first 23 Chromosomer haploid felt when he met his female counterpart, the 24 Chromosomer haploid?


43 posted on 04/13/2005 7:43:13 PM PDT by jwalsh07
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To: Echo Talon

Pond Scum Alert


44 posted on 04/13/2005 7:44:46 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: Echo Talon

"You keep your faith in man and Scientology and I will keep mine in the Lord."

If you think Scientology has anything to do with science, Tom Cruise would like to speak to you.


45 posted on 04/13/2005 7:44:51 PM PDT by ndt
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To: <1/1,000,000th%
What process would create apes, then a couple millions of years later, humans with similar genes?

Dunno.

What process would create mice with human neurons?

46 posted on 04/13/2005 7:46:01 PM PDT by jwalsh07
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To: jwalsh07

very kinky


47 posted on 04/13/2005 7:48:32 PM PDT by AntiGuv ()
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To: jwalsh07

"How do you supppose that first 23 Chromosomer haploid felt when he met his female counterpart, the 24 Chromosomer haploid?"

Don't leave me in suspense, whats the punchline??


48 posted on 04/13/2005 7:49:10 PM PDT by ndt
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To: ndt
If you think Scientology has anything to do with science, Tom Cruise would like to speak to you

Well, if you believe that we evolved from the ocean into an ape and then into a human, you sure as heck aren't a Christian or Jew. Not sure if they allow for that sort of thing in scientology but im sure they do.

49 posted on 04/13/2005 7:49:43 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: jwalsh07

"How do you supppose that first 23 Chromosomer haploid felt when he met his female counterpart, the 24 Chromosomer haploid?"

Don't leave me in suspense, whats the punchline??


50 posted on 04/13/2005 7:50:04 PM PDT by ndt
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