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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

Great post PH. Thanks for the ping.


201 posted on 04/14/2005 7:50:21 AM PDT by narby
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To: mc6809e; derheimwill
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.

mc6809e>> What?!?

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.

This is a great example of why it is stupid for believers to interpret Genesis litterally. Evolution is supported by hard facts that can be examined and tested, while faith, by it's very definition, cannot.

When creationists attack evolution, they open themselves up to ridicule and derision. And when young believers enter college and are challeneged with the evidence of evolution that contradicts what they've been taught, some of them will abandon their faith entirely. Any believer who abandons their faith over this silly issue is a tragedy.

The only intellegent solution is for believers to accept that God is powerful enough to have created Evolution, and some, but not all, believers have misinterpreted Genesis to say otherwise.

Problem solved.

202 posted on 04/14/2005 8:04:16 AM PDT by narby
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To: balrog666
The universe-builds-a-bigger-idiot placemarker.

I must say, at least, I admire you for your self-admission. The fact that you blatantly admit it, reinforces its validity.

203 posted on 04/14/2005 8:08:23 AM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: Echo Talon
Well if faith in the bible is a cancer in conservatism count me infected I guess.

I don't think that faith in the Bible is any detriment to conservatisim.

But the rigid interpretation of Genesis that some, but not all, Christians hold that we call "creationism" certianly is a cancer on conservatisim. It damages our credibility, and distracts us (with fights over science classroom content) from working on political goals that are attainable, like proper Supreme Court judges and SS reform.

204 posted on 04/14/2005 8:12:34 AM PDT by narby
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To: AntiGuv

"Can not" <> "Do not"


205 posted on 04/14/2005 8:14:02 AM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: <1/1,000,000th%
This is the usual answer that comes from basic ID theory. It's no surprise that most folks don't have much use for it.

Dunno is infinitely better than your answer to the question appended to dunno.

206 posted on 04/14/2005 8:20:36 AM PDT by jwalsh07
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To: 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 ]

So then, if I get the drift of this correctly...
The Third human on earth DID NOT come from the first two...
Right.?.

207 posted on 04/14/2005 8:42:08 AM PDT by hosepipe (This Propaganda has been edited to include not a small amount of Hyperbole..)
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To: Echo Talon
You keep your faith in man and Scientology and I will keep mine in the Lord.

I don't think that word means what you think it means.

208 posted on 04/14/2005 9:30:09 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
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.

Wow. Not only do you claim to be the final judge of who is and isn't Jewish or Christian, you also claim to be the final arbiter of what the Bible says.

You do know that pride is a sin, right?

209 posted on 04/14/2005 9:35:09 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: AntiGuv

...until you get to Adam: made from dust.


210 posted on 04/14/2005 9:44:53 AM PDT by derheimwill (Love is a person, not an emotion.)
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To: killermosquito
If we evolved from apes why are there still apes?

Because we share an ancestor with today's apes, but we didn't evolve from them.

211 posted on 04/14/2005 9:45:13 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
What's to gain from believing that I evolved from an ape?

You gain an understanding of a certain part of the natural world.

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

You must have a pretty weak faith if you're afraid of a simple scientific theory.

Pretty idiotic to believe in nonsense, whose sole purpose is to undermine the church in the first place.

Hate to rain on your feelings of persecution, but the theory of evolution really has nothing to do with your religion.

212 posted on 04/14/2005 9:48:02 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: frgoff; AndrewC

Thank you both. The things I was taught wrong in school...


213 posted on 04/14/2005 9:50:50 AM PDT by Talking_Mouse (Indeed I tremble for my country when I reflect that God is just... Thomas Jefferson)
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To: Echo Talon
Does it say god created a sea creature that transformed into an ape that evolved into a human? i think not, I believe it says something like 'god created man.'

Genesis simply left out the unimportant details. The process God used to create man isn't in the Bible because it would have been lost on primitive bronze-agers. I imagine God knew that we would eventually be able to fill in the details.

The Bible doesn't deal with very much science. It's a moral guide, not a science textbook.

214 posted on 04/14/2005 9:52:26 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
also strange that humans haven't reverted back... at least in a few births... How come they ALL evolved?

This question is so ignorant that it makes me feel sorry for you.

If you really believe that the theory of evolution calls for humans giving birth to chimps occasionally, there's no point in even discussing this with you.

215 posted on 04/14/2005 9:55:35 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: Cicero
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.

Nature is one fast typing monkey!

216 posted on 04/14/2005 9:56:22 AM PDT by bondserv (Alignment is critical! )
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To: Echo Talon
What are you going to do when the lord says "are you questioning my authority"(/cartman voice)... then you get pummeled with a billy club. :D

So God intentionally created evidence pointing to evolution as an attempt to fool humans?

Doesn't sound like the Christian God I'm familiar with. More like Loki, the Norse god of mischief.

217 posted on 04/14/2005 10:03:01 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: AndrewC

It wasn't a quote..


218 posted on 04/14/2005 10:05:04 AM PDT by AntiGuv ()
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To: Dimensio; Strategerist; Echo Talon
Let's allow the Bible to speak for itself:

From another post I made.

The creation of the world and the creation of man are connected repeatedly throughout scripture.

Isa 45:12 I have made the earth, and created man upon it: I, [even] my hands, have stretched out the heavens, and all their host have I commanded.

Zec 12:1 The burden of the word of the LORD for Israel, saith the LORD, which stretcheth forth the heavens, and layeth the foundation of the earth, and formeth the spirit of man within him.

Isa 42:5 Thus saith God the LORD, he that created the heavens, and stretched them out; he that spread forth the earth, and that which cometh out of it; he that giveth breath unto the people upon it, and spirit to them that walk therein:

Isa 45:18 For thus saith the LORD that created the heavens; God himself that formed the earth and made it; he hath established it, he created it not in vain, he formed it to be inhabited: I [am] the LORD; and [there is] none else.

Isa 40:21-22
Have ye not known? have ye not heard? hath it not been told you from the beginning? have ye not understood from the foundations of the earth?

Isa 64:4 For since the beginning of the world [men] have not heard, nor perceived by the ear, neither hath the eye seen, O God, beside thee, [what] he hath prepared for him that waiteth for him.

Again, more passages speaking about Adam being created:

Gen 2:7 And the LORD God formed man [of] the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

Gen 5:1 This [is] the book of the generations of Adam. In the day that God created man, in the likeness of God made he him;

Deu 4:32 For ask now of the days that are past, which were before thee, since the day that God created man upon the earth,

And the myth called Adam lived a specific number of years, then the myth died.

Gen 5:5 And all the days that Adam lived were nine hundred and thirty years: and he died.

It all ties together scripturally.

And no good study of beginnings can go without a passage written by the finger of God on the tablets of stone, which tends to override any scholars desire to reattribute it to the eating of a bad pickle.

Exd 20:8-11
8 Remember the sabbath day, to keep it holy.
9 Six days shalt thou labour, and do all thy work:
10 But the seventh day [is] the sabbath of the LORD thy God: [in it] thou shalt not do any work, thou, nor thy son, nor thy daughter, thy manservant, nor thy maidservant, nor thy cattle, nor thy stranger that [is] within thy gates:
11 For [in] six days the LORD made heaven and earth, the sea, and all that in them [is], and rested the seventh day: wherefore the LORD blessed the sabbath day, and hallowed it.

A direct correlation.

219 posted on 04/14/2005 10:16:34 AM PDT by bondserv (Alignment is critical! )
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To: AntiGuv

I was just noting the potential conflict between a para 2 and para 3 in your green warbler example. The two varieties are the same species.


220 posted on 04/14/2005 10:22:28 AM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: AndrewC

I realize what you're saying and it's an interesting question that I don't know the answer to (i.e., if, for whatever reason, they exchanged gametes would offspring result?) but all other sources I've seen on the Green Warbler aside from the S.F. Chronicle graphic say they cannot interbreed. This may only be due to them not recognizing the mating calls, but there are other clearly different species that "can" in theory interbreed but never will in practice.

In some ways, and I think you already know this, "species" is an arbitrary, problematic concept - designed to assist in our classification of the natural world. The boundaries are frequently fuzzy as one would expect in a backdrop of common descent.


221 posted on 04/14/2005 10:33:34 AM PDT by AntiGuv ()
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To: PatrickHenry
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

Anybody know? Does this mean that the nucleotide sequences in the regions are conserved (wrt what would be expected from selectively neutral evolution) or does it just mean that the size and position of these regions, and/or some other characteristic beyond the primary sequence structure, is conserved?

222 posted on 04/14/2005 10:36:50 AM PDT by Stultis
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To: AndrewC
I must say, at least, I admire you for your self-admission. The fact that you blatantly admit it, reinforces its validity.

You missed the point again. Somehow I just can't seem to underestimate you.

223 posted on 04/14/2005 11:23:05 AM PDT by balrog666 (A myth by any other name is still inane.)
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To: dread78645

Nanobot placemark


224 posted on 04/14/2005 11:34:44 AM PDT by dread78645 (Sarcasm tags are for wusses.)
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creationist-equivalent-of-corporal-queball PLACEMARKER.


225 posted on 04/14/2005 11:42:15 AM PDT by jennyp (WHAT I'M READING NOW: Mn17#mg 5gu2Ee 0%Ae by Howard & LeBlanc)
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To: balrog666
You missed the point again.

No. You are validating your self-description even more. I ignored your attempted point and highlighted your trolling nature. Or are you going to provide yet even more evidence by trying to defend your comment as a relevant contribution to this thread?

226 posted on 04/14/2005 11:50:26 AM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: AndrewC

Now you're about 0-for-200,000. Go troll somewhere else.


227 posted on 04/14/2005 12:24:00 PM PDT by balrog666 (A myth by any other name is still inane.)
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To: PatrickHenry
"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,"

Ahh, how refreshing. Nice repeatable scientific experimentation with respect to the human genome As a side effect of this science we gain insight into the historical model of the evolution of species. Too bad the later is beyond the scope of the scientific method - and too bad this latter fact is too offensive to the sensibilities of some who like to think they are objective.

228 posted on 04/14/2005 12:35:54 PM PDT by AndyTheBear (Disastrous social experimentation is the opiate of elitist snobs.)
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To: balrog666
Now you're about 0-for-200,000. Go troll somewhere else.

Don't say I didn't warn you.

229 posted on 04/14/2005 12:47:31 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: AndrewC; Admin Moderator
Here's a clue:

Don't post to me. Ever.

230 posted on 04/14/2005 12:55:43 PM PDT by balrog666 (A myth by any other name is still inane.)
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To: <1/1,000,000th%
OK. What process would create apes, then a couple millions of years later, humans with similar genes?

Assuming that your statement about the timing of apes and man is correct, I do not know. But it might be the same process that allowed creatures with arms and legs and brains to come into existence where they previously did not exist (of course I am just speculating here).
231 posted on 04/14/2005 1:01:04 PM PDT by microgood
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To: AntiGuv
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).

Except for the fact that it could have just happened that way. I understand that the historical information may bolster the assumption of common ancestry, but it certainly does not prove the assumption nor is it a testable assumption.
232 posted on 04/14/2005 1:07:24 PM PDT by microgood
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To: microgood

Well that's true, in much that same way that, while the odds that you just so happen for no apparent reason to share many of your father's traits are infinitesimal, they aren't nonexistent.


233 posted on 04/14/2005 1:15:35 PM PDT by AntiGuv ()
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To: Admin Moderator

I expect the same behavior from the individual who posted the order to me and alerted you. Finally, he should consider contributing to the discussion rather than the typical "BWAAHHHHHHAAAAHHHAAHAA" comments and other belittling comments he makes.


234 posted on 04/14/2005 1:26:48 PM PDT by AndrewC (Darwinian logic -- It is just-so if it is just-so)
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To: All
For those who care about the ever-growing List-O-Links, here are a few of the changes made recently:

13Apr: Added section on Eugenics, with three new links
12Apr: Added section on the Cambrian Explosion with three new links
10Apr: Added "Neither intelligent nor designed" to Isn't ID Superseding Evolution? section
01Apr: Added "The Evolution of Man Scientifically Disproved" from 1928 to THEORY IN CRISIS section
31Mar: Noted Link not working for Gould's "Evolution as Fact and Theory"
27Mar: Added section SOME LINKS DEBUNKING "YOUNG EARTH" BELIEFS with three links
26Mar: Added "The Pocket Darwin" to What is Evolution? section
24Mar: Added "Timeline of Evolutionary Thought" to What is Evolution? section
24Mar: Added "History of Science" to Essential Information section
24Mar: Added "The omphalos hypothesis" to section on Epistemological Issues (it's "Last-Thursdayism")

235 posted on 04/14/2005 3:02:54 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

I'm no "evo" but the discovery of the fusion was discovered three years ago. So that indeed is "years" of assurance, if the discovery means what the discoverers say it means.


236 posted on 04/14/2005 3:09:36 PM PDT by Chaguito
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To: Chaguito

Yikes! That was the most poorly worded sentence of my career. To many "discover" words. Sorry.


237 posted on 04/14/2005 3:11:15 PM PDT by Chaguito
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To: PatrickHenry

Saving for later. Too long and lots of big words.


238 posted on 04/14/2005 3:15:30 PM PDT by JusPasenThru (http://giinthesky.blogspot.com/)
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To: AntiGuv
Well that's true, in much that same way that, while the odds that you just so happen for no apparent reason to share many of your father's traits are infinitesimal, they aren't nonexistent.

You can make a lot more assumptions about observable events in that you can test your theories. Saying an offspring has the traits of its parent is a little different than saying apes and man share a common ancestor.
239 posted on 04/14/2005 3:24:12 PM PDT by microgood
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To: Thatcherite
I'm cool, I reckon he looks stupider than me to the lurkers.

If he doesn't look stupider than dirt, something's wrong.

240 posted on 04/14/2005 3:54:54 PM PDT by VadeRetro (Liberalism is a cancer on society. Creationism is a cancer on conservatism.)
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To: Modernman
So God intentionally created evidence pointing to evolution as an attempt to fool humans?

I do believe that their are hurdles to test faith. You have read Job haven't you?

241 posted on 04/14/2005 4:27:36 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Modernman
You do know that pride is a sin, right?

Well, I know how to read better than I know how to type :P The bible is very clear that God created man in his image. If you think god is an ape you can believe that.

242 posted on 04/14/2005 4:31:12 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: narby
But the rigid interpretation of Genesis that some, but not all, Christians hold that we call "creationism"

I call it Intelligent Design.

243 posted on 04/14/2005 4:33:03 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: narby
It damages our credibility, and distracts us (with fights over science classroom content) from working on political goals that are attainable, like proper Supreme Court judges and SS reform.

LOL! What a moronic statement. You believe in god thats a distraction that make keeps us from working of SS reform! WAH WAH! OMG!

244 posted on 04/14/2005 4:35:10 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Thatcherite
Are there heathens here? Where? How do you know?

It was a joke denoted with this ":P" :P HAR HAR

245 posted on 04/14/2005 4:37:40 PM PDT by Echo Talon (http://echotalon.blogspot.com)
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To: Ahban
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.

Very true. Evos don't have the scientific evidence available to the Creos who base everything on a book written by men.

Some people swear that the Bible is the Written word of God. Yet, when confronted by passages advocating slave ownership and beating they explain that the "times were different" then.

Hard to think of God as a moral relativist, but what do us Evos know.

246 posted on 04/14/2005 4:43:40 PM PDT by sakic
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To: PatrickHenry

Darwin was just the starting point. The genenome sequencing is going to trash the creationist unbelief.


247 posted on 04/14/2005 4:58:36 PM PDT by bert (Peace is only halftime !)
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To: bert
The genenome sequencing is going to trash the creationist unbelief.

Well, it's certainly a trove of evidence which supports evolution, but we've already accumulated mountains of evidence for the last 150 years, and although the science community is convinced of the theory's value, nothing has made the slightest impression on creationism. I suspect that will continue to be the situation.

248 posted on 04/14/2005 5:06:17 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

Isn't it beautiful?


249 posted on 04/14/2005 5:08:01 PM PDT by firebrand (Member of the proud brotherhood and sisterhood of copyeditors)
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To: <1/1,000,000th%
This is the usual answer that comes from basic ID theory. It's no surprise that most folks don't have much use for it.

Yes but sometimes it is better than saying you know things you don't. 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.

You claim you know how the old the world is and how old rocks are (there are massive assumptions in radiometric dating). You claim to know how life evolved over millions of years(assuming correlation = causation).

You claim all this and yet noone in the evolutionary world can explain how a creature without legs or arms came to have them, except the standard old mutation and natural selection with a bit of punctuated equilibrium added or not, depending on your preference and my all time favorite, which is that an arm or leg had some other function until it finally became an arm.

I think Michael Crighton was right when he said magicians love scientists the most because they are the easiest to fool, because they fancy themselves as being objective.
250 posted on 04/14/2005 6:13:17 PM PDT by microgood
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