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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: PatrickHenry

"centromere" I don't use the metric system, what's this about half an inche?


51 posted on 04/13/2005 7:50:56 PM PDT by CJ Wolf
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To: ndt
Don't leave me in suspense, whats the punchline??

That wasn't a joke, it was haploid for thought. Think about it. :-}

52 posted on 04/13/2005 7:51:21 PM PDT by jwalsh07
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To: Echo Talon
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.

There are a great many Christians and Jews that would disagree with you.

53 posted on 04/13/2005 7:51:56 PM PDT by Strategerist
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To: ndt

Yeah, yeah. I heard you the first time.


54 posted on 04/13/2005 7:52:38 PM PDT by jwalsh07
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To: ndt

I think he starts feeling the most delicious parts and moves on from there.

Or how about "Hot Mama"?


55 posted on 04/13/2005 7:55:51 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: Strategerist
There are a great many Christians and Jews that would disagree with you.

It doesn't matter if they disagree with me or not, they disagree with the Bible.

56 posted on 04/13/2005 7:56:57 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Strategerist; Echo Talon
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.

There are a great many Christians and Jews that would disagree with you.

Pope John Paul II being one of them.

“[N]ew findings lead us toward the recognition of evolution as more than a hypothesis. In fact it is remarkable that this theory has had progressively greater influence on the spirit of researchers, following a series of discoveries in different scholarly disciplines. The convergence in the results of these independent studies—which was neither planned nor sought—constitutes in itself a significant argument in favor of the theory.”

“A theory is a meta-scientific elaboration, which is distinct from, but in harmony with, the results of observation. With the help of such a theory a group of data and independent facts can be related to one another and interpreted in one comprehensive explanation. The theory proves its validity by the measure to which it can be verified. It is constantly being tested against the facts; when it can no longer explain these facts, it shows its limits and its lack of usefulness, and it must be revised.”

         -- Pope John Paul II, 23 October 1996.

57 posted on 04/13/2005 7:58:33 PM PDT by AntiGuv (™)
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To: Strategerist
You forget: anyone who does not share his interpretation of the Old Testament in every identical way is actually a godless atheist.

It's easy to claim to be right by simply redefining any counterexamples out of existence.
58 posted on 04/13/2005 7:58:44 PM PDT by Dimensio (http://angryflower.com/bobsqu.gif <-- required reading before you use your next apostrophe!)
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To: Echo Talon; Strategerist

"It doesn't matter if they disagree with me or not, they disagree with the Bible"

I guess that's settled and we can all go home now.


59 posted on 04/13/2005 7:59:15 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: jwalsh07
"Yeah, yeah. I heard you the first time."

Sorry, computer freaked out on me :) One reboot later.....

"That wasn't a joke, it was haploid for thought."

OK, this haploid walks into a bar ya see...

So are you trying to point out haploid breeding issues then? I'm feeling a little dense this evening, throw me a bone.
60 posted on 04/13/2005 8:01:29 PM PDT by ndt
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To: ndt

fb4p's proverbs:

III - Beware the humorless man.


61 posted on 04/13/2005 8:02:28 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: AntiGuv
I'm not Catholic
62 posted on 04/13/2005 8:04:57 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: ndt
jw's proverb:

Beware the faux libertarian sucking on the public teat.

63 posted on 04/13/2005 8:06:02 PM PDT by jwalsh07
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To: Echo Talon

Last I checked, Catholics are Christian.


64 posted on 04/13/2005 8:08:31 PM PDT by AntiGuv (™)
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To: CJ Wolf

"centromere" I don't use the metric system, what's this about half an inche?"

Let's see:

Centro - probably something 100
Mere - has to be merely, what else?

So maybe "Merely a hunnert footes or maybe a couple dozen rods or sumpin'"

Hope that helps


65 posted on 04/13/2005 8:13:19 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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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?

"It's been so long since I've replicated, I didn't know they moved it!"

66 posted on 04/13/2005 8:22:50 PM PDT by dread78645 (Sarcasm tags are for wusses.)
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To: derheimwill

"He made us out of the same protiens because he made us out of the same kinds atoms - which work in the same way."

Perhaps derheim will take a chemistry course some day and realize how silly this statement is.


67 posted on 04/13/2005 8:24:21 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: Dog Gone
I guess sometimes less is better. LOL!
68 posted on 04/13/2005 8:24:59 PM PDT by Empireoftheatom48 (God bless our troops!! Our President and those who fight against the awful commie, liberal left!!)
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To: Echo Talon
... Not sure if they allow for that sort of thing in scientology but im sure they do.

Huh?

69 posted on 04/13/2005 8:26:18 PM PDT by dread78645 (Sarcasm tags are for wusses.)
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To: dread78645

There's a lot of "huh's" tonight.


70 posted on 04/13/2005 8:27:57 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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Comment #71 Removed by Moderator

To: AntiGuv
Last I checked, Catholics are Christian.

Why i said, i'm not catholic is first of i'm not but also because I dont believe one man(The Pope) can speak for a whole faith. He is just a man and men make mistakes. His states the theroy is possible, he doesnt say he believes it.

72 posted on 04/13/2005 8:34:59 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Dog Gone
I'm surprised to learn that we have one less pair of chromosomes than the apes.

Yeah, I think we lost the "hair all over" gene ...

73 posted on 04/13/2005 8:37:23 PM PDT by 11th_VA (Stop the Immoral Illegal Invasion - Secure the Borders)
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To: 11th_VA
Yeah, I think we lost the "hair all over" gene ...

I figured we'd lost the 'fling feces as a show of dominance' gene, but that was before I listened to Al Franken.

74 posted on 04/13/2005 8:39:10 PM PDT by Wormwood (Iä! Iä! Cthulhu fhtagn!)
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To: Echo Talon

As far as the Catholic Church is concerned, the Pope is infallible (I'm more likely to agree with you that he is just a man, but a special sort of man).

The Pope never says or writes anything without thorough study and making sure it fits the faith. The fact that he said or wrote those words above, means that he believed it and that it is now officially a piece of the Catholic faith.

So you are now in open conflict with JP II. Do you have the credentials and the years of thorough study to stand up to his words? You may not like them, but to question him is to question one of the great theologians of the 20th century. Is that reason to question your conclusions?

And, before you ask, I am also not a Catholic.


75 posted on 04/13/2005 8:47:57 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: furball4paws

Like I said i have no problems being in disagreement with a man, I do not have a disagreement with the bible. Genesis is clear as day.


76 posted on 04/13/2005 8:49:50 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Fitzcarraldo
Implying that women don't have this protein?

I thought of a couple ways to respond to your question, but couldn't bring myself to post them.

77 posted on 04/13/2005 8:52:56 PM PDT by GoLightly
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To: Echo Talon

Well I congratulate you for your chutzpah, but it can also be a form of self-induced blindness.


78 posted on 04/13/2005 8:54:55 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: PatrickHenry

"Creationism is knowing when not to look."

Evolution is thinking you know all the answers when you don't. Of course you could say the same thing about creation.

I'll give you evolutionists a head start. Cut off all of your fingers and toes. Surely some of you will grow new fingers and toes or perhaps your fingers and toes will grow new evolutionists.

I admire your faith.


79 posted on 04/13/2005 9:02:45 PM PDT by killermosquito (Hillary, go back to the little rock you crawled out from under!)
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To: AntiGuv; PatrickHenry

Hey AntiGuv, keep this JP II quote handy. He does a great job defining "theory" and how theories are "supported" by observations. Maybe some of the creationoids will read his words while they would just ignore PH's list of links.


80 posted on 04/13/2005 9:03:30 PM PDT by furball4paws (Ho, Ho, Beri, Beri and Balls!)
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To: PatrickHenry
Creationism is knowing when not to look.

What happened to, Everybody be nice.?

81 posted on 04/13/2005 9:06:45 PM PDT by GoLightly
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To: <1/1,000,000th%

If we evolved from apes why are there still apes?


82 posted on 04/13/2005 9:08:07 PM PDT by killermosquito (Hillary, go back to the little rock you crawled out from under!)
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To: furball4paws
As far as the Catholic Church is concerned, the Pope is infallible (I'm more likely to agree with you that he is just a man, but a special sort of man).

Sorry to disagree with you but the Pope is not infallible at all times. He only speaks infallibly when speaking ex cathedra (from the chair). In the last century the Pope has only spoken infallibly twice. Neither of these times was he discussing evolution.
83 posted on 04/13/2005 9:14:42 PM PDT by Talking_Mouse (Indeed I tremble for my country when I reflect that God is just... Thomas Jefferson)
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To: furball4paws
Well I congratulate you for your chutzpah, but it can also be a form of self-induced blindness.

Blind from what? What's to gain from believing that I evolved from an ape? The only thing this "science" does is confuse people about their faith. Thats it. Am I going to go ask an ape for reparations... What? you tell me... Pretty idiotic to believe in nonsense, whose sole purpose is to undermine the church in the first place.
Read this especially the things about the Church and family

84 posted on 04/13/2005 9:15:50 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Cicero
For instance, if God were designing apes and men, it stands to reason that He would use many of the same materials.

Clearly He did so, but the mechanism of reuse is what's in contention.

85 posted on 04/13/2005 9:22:51 PM PDT by El Gato (Activist Judges can twist the Constitution into anything they want ... or so they think.)
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To: Ahban
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.

Now now, Ahban. No need to resort to lies. You're better than that.

86 posted on 04/13/2005 9:22:52 PM PDT by jennyp (WHAT I'M READING NOW: Mn17#mg 5gu2Ee 0%Ae by Howard & LeBlanc)
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To: PatrickHenry; Michael_Michaelangelo
bolding/underlining omission.

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.


87 posted on 04/13/2005 9:24:33 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: PatrickHenry

Thanks for the ping!


88 posted on 04/13/2005 9:25:18 PM PDT by Alamo-Girl
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To: frgoff
Interestingly enough, an evolutionary paradigm led to the wrong conclusions about the appendix and tonsils being vestigial.

I had always been told that they were vestigial. What is your evidence that they are not? I have not seen any (not that I have looked hard), so I am rather interested.
89 posted on 04/13/2005 9:26:20 PM PDT by Talking_Mouse (Indeed I tremble for my country when I reflect that God is just... Thomas Jefferson)
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To: furball4paws
There's a lot of "huh's" tonight.

<sigh> that's fer shure.

90 posted on 04/13/2005 9:31:27 PM PDT by jennyp (WHAT I'M READING NOW: Mn17#mg 5gu2Ee 0%Ae by Howard & LeBlanc)
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To: AntiGuv
Wonder what a tarsier looks like?
91 posted on 04/13/2005 9:32:49 PM PDT by El Gato (Activist Judges can twist the Constitution into anything they want ... or so they think.)
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To: Talking_Mouse; frgoff
I had always been told that they were vestigial. What is your evidence that they are not?

Immune system

The immune system includes organs and tissues in which lymphocytes predominate as well as cells that circulate in peripheral blood. Lymphoid organs includes: lymph nodes and vessels, spleen, tonsils, adenoids, appendix, bone marrow, thymus, and intestinal lymphoid tissue. The bone marrow and thymus play a role in developing the primary cells of the immune system: B cells and T cells.

92 posted on 04/13/2005 9:33:40 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: killermosquito
If we evolved from apes why are there still apes?

If America was once part of England why is there still an England?

93 posted on 04/13/2005 9:34:44 PM PDT by jennyp (WHAT I'M READING NOW: Mn17#mg 5gu2Ee 0%Ae by Howard & LeBlanc)
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To: Echo Talon

Clearly your complete and total inability to grasp scientific evidence is on display for all to see.

I am sure you see electricity as magic and that when lightning strikes it is "God is Angry."

How you reconcile wireless connections is beyond me but I suspect it is something like "invisible angels move bits from place to place." I guess you pray to these invisible angels to keep your radio and TV connections going daily.

I am sure toilet flushing is beyond your ability to reckon. Just write it up to more magic.


94 posted on 04/13/2005 9:39:20 PM PDT by freedumb2003 (First you get the sugar, then you get the power, then you get the women (HJ Simpson))
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To: jennyp
If America was once part of England why is there still an England?

Because it was part of England.

95 posted on 04/13/2005 9:39:27 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: El Gato
Wonder what a tarsier looks like?
Tarsiers are really cute, in their way. But they sorta look like what that mouse/human chimera would look like if they took that experiment too far!
96 posted on 04/13/2005 9:39:33 PM PDT by jennyp (WHAT I'M READING NOW: Mn17#mg 5gu2Ee 0%Ae by Howard & LeBlanc)
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To: Echo Talon
Blind from what? What's to gain from believing that I evolved from an ape?

Accuracy.

The only thing this "science" does is confuse people about their faith.

Ah... So you're going to turn your computer back in and communicate via smoke signals?

97 posted on 04/13/2005 9:42:11 PM PDT by Ichneumon
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To: Wormwood
I figured we'd lost the 'fling feces as a show of dominance' gene, but that was before I listened to Al Franken

Or the average corporate or governmental middle manager. Although the way I've most often heard their behavior described was as a P**ing contest, to see who could reach higher on the wall, and thus earn the favor of the Alpha above them. :)

98 posted on 04/13/2005 9:42:14 PM PDT by El Gato (Activist Judges can twist the Constitution into anything they want ... or so they think.)
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To: freedumb2003
Clearly your complete and total inability to grasp scientific evidence is on display for all to see.

We must first determine what we are talking about when we use the terms "Science" and "Evolution"

I. Science. According to the Oxford Dictionary science is "A branch of study which is concerned either with a connected body of demonstrated truths or with observed facts systematically classified and more or less colligated by being brought under general laws, and which includes trustworthy methods for the discovery of new truth within its own domain."

For a postulate to qualify as a scientific theory is must fulfill three basic criteria.

1. The postulate must be observable.

2. The postulate must be capable of repeatable experimental verification.

3. The postulate must withstand a falsifiability test, or an experiment must be conceived the failure of which would disprove the postulate.

Neither evolution nor creation can meet the above three criteria and thus are not theories but postulates. In fact neither are fully capable of becoming theories because of the limits of observing events that happened many years in the past.

99 posted on 04/13/2005 9:43:06 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Echo Talon
I do not have a disagreement with the bible. Genesis is clear as day.

Which translation? They don't all agree in every detail and nuance.

100 posted on 04/13/2005 9:44:07 PM PDT by El Gato (Activist Judges can twist the Constitution into anything they want ... or so they think.)
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