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Not Your Father's Genome
familypracticenews.com ^ | 1 January 2008 | GREG FEERO, M.D., PH.D.

Posted on 01/15/2008 7:55:39 PM PST by neverdem

DR. FEERO is a family physician with a doctorate in human genetics from the University of Pittsburgh. He is a senior adviser for genomic medicine in the Office of the Director at the National Human Genome Research Institute.

Our understanding of the genome is changing rapidly and drastically.

For starters, the Human Genome Project has revealed that humans are, on a numerical basis, genetically less complex than a mustard plant (Arabidopsis). In fact, our genome contains between 20,000 and 25,000 sequences suggestive of “genes” encoding proteins, whereas Arabidopsis contains about 27,000. If that doesn't make much sense to you, don't worry, it didn't make any sense to many of the scientists working on the human genome either. Empirically, most of us are far more complicated than a mustard plant. This paradox harkens back to one of the teachings of distant biology and genetic courses, written by our parents' generation. To paraphrase many texts: “About 98% to 99% of the human genome appears to be junk, leftover from evolutionary dead ends.” Any student of biology could spot a problem here: Evolution tends to trim baggage and inefficiencies. Why would we use only 1% of our genetic material after a few billion years of trimming the excess?

Genome scientists recently have completed the first phase of a massive collaborative project, supported by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health, called ENCODE (Encyclopedia of DNA Elements). Initiated in 2003, ENCODE was designed to enhance our understanding of the functional anatomy of the raw DNA sequence revealed by the Human Genome Project.

The first phase focusing on 1% of the genome, completed in June 2007, has shown that all that junk is not junk after all. Our genome is a complex ecosystem with a wide variety of different types of DNA elements, not simply genes encoding proteins. Much of it appears to play a role in determining which genes are expressed, in what order, and at what levels. Substantial portions of our DNA encode information for the production of small RNA molecules that never become translated to proteins, but rather fold up on themselves and act in concert with peptides as regulators of gene expression. Some of these molecules likely act as RNA-based enzymes. Very long stretches of DNA that don't seem to code for any proteins, and therefore would not be predicted by previous models to be highly conserved by evolution, are highly conserved. In contrast, regions that previously would have been predicted to be conserved turn out not to be under as much evolutionary constraint as had been thought.

How about those mustard plants? The emerging model is that human genes don't ascribe to old “one gene, one protein” rule, but are much more akin to Russian nesting dolls. Genes are inside of genes, using alternate promoters, start sites, splicing sites and stop sites. Remember that DNA is double stranded? There is evidence that there are overlapping genes that run on opposite strands, encoding proteins of different functions.

Recall that RNA molecules are translated to form proteins? It turns out that seemingly unrelated RNA molecules can be assembled (trans-spliced) to form templates for entirely new proteins. To further complicate this picture, elements in the DNA known as pseudogenes exist, which, save for minor variations, look exactly like other functional genes.

ENCODE and related results suggest that these pseudogenes are numerous and that they may not be as transcriptionally silent as once believed. Overall, the first phase of ENCODE has demonstrated how little we really know about the human genome. NHGRI has pledged more than $80 million dollars in grant awards to flesh out our understanding of the functional elements in the 99% of the genome not covered in the pilot phase of ENCODE.


TOPICS: Culture/Society; News/Current Events
KEYWORDS: dna; encode; genes; genetics; genome; genomics; godsgravesglyphs; health; helixmakemineadouble; humangenome; humangenomeproject; mattridley; science
For more information about the results of ENCODE, see the free June 2007 issue of Genome Research at www.genome.org/content/vol17/issue6.

What is a gene, post-ENCODE? History and updated definition

1 posted on 01/15/2008 7:55:41 PM PST by neverdem
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To: neverdem

bump


2 posted on 01/15/2008 7:59:33 PM PST by VOA
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To: Mother Abigail; EBH; vetvetdoug; Smokin' Joe; Global2010; Battle Axe; All

If you can use an update in genetics, those links in comment# 1 are FReebies.


3 posted on 01/15/2008 8:00:36 PM PST by neverdem (Call talk radio. We need a Constitutional Amendment for Congressional term limits. Let's Roll!)
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To: neverdem

Well, a plant can’t learn, so much more “instinct” instructions have to be encoded.

A good brain that can learn and adapt can take the place of all those genes.


4 posted on 01/15/2008 8:01:06 PM PST by patriciaruth (http://www.freerepublic.com/focus/f-news/1562436/posts)
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To: patriciaruth

Ah, come on Pat! You made that up, didn’t you?


5 posted on 01/15/2008 9:49:31 PM PST by SatinDoll (Fredhead and proud of it!)
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To: martin_fierro

ping


6 posted on 01/15/2008 10:53:14 PM PST by Cacique (quos Deus vult perdere, prius dementat ( Islamia Delenda Est ))
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To: El Gato; Ernest_at_the_Beach; Robert A. Cook, PE; lepton; LadyDoc; jb6; tiamat; PGalt; Dianna; ...
The second link in comment# 1 is a pretty good review article. The more that is discovered, the more questions are raised.

New Bacteria Strain Is Striking Gay Men bug chasers gone wild

Drug Approved. Is Disease Real

Yet another new environmentally friendly product causes problems

FReepmail me if you want on or off my health and science ping list.

7 posted on 01/15/2008 11:14:05 PM PST by neverdem (Call talk radio. We need a Constitutional Amendment for Congressional term limits. Let's Roll!)
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To: neverdem

I taught A&P at a JUCO last year and I had to get a refresher on genetics to be able to teach. I did more studying than when I took the courses the first times because of all of the new information that has been revealed during the past 20+ years. Quite an eye opener to me.


8 posted on 01/15/2008 11:25:44 PM PST by vetvetdoug
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To: neverdem; martin_fierro; blam; StayAt HomeMother; Ernest_at_the_Beach; 1ofmanyfree; 24Karet; ...

· join list or digest · view topics · view or post blog · bookmark · post a topic ·

 
Gods
Graves
Glyphs
Thanks neverdem. Martin, pingworthy?

To all -- please ping me to other topics which are appropriate for the GGG list.
GGG managers are Blam, StayAt HomeMother, and Ernest_at_the_Beach
 

· Google · Archaeologica · ArchaeoBlog · Archaeology magazine · Biblical Archaeology Society ·
· Mirabilis · Texas AM Anthropology News · Yahoo Anthro & Archaeo ·
· History or Science & Nature Podcasts · Excerpt, or Link only? · cgk's list of ping lists ·


9 posted on 01/15/2008 11:32:27 PM PST by SunkenCiv (https://secure.freerepublic.com/donate/____________________Profile updated Sunday, December 30, 2007)
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To: neverdem

$80 million is a tad small a sum for learning more about 99% of human DNA when 1% has proved so complicated.


10 posted on 01/16/2008 1:26:02 AM PST by Jedi Master Pikachu ( What is your take on Acts 15:20 (abstaining from blood) about eating meat? Could you freepmail?)
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To: DaveLoneRanger; Coyoteman

Worth looking at?


11 posted on 01/16/2008 2:58:10 AM PST by MacDorcha (Do you feel that you can place full trust in your obsevations of the physical world?)
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To: SunkenCiv

How do you tell whether a chromosome is a boy chromosome or a girl chromosome?

Pull down its genes and look.


12 posted on 01/16/2008 4:40:34 AM PST by CholeraJoe (The older you are, the easier it is to convince people you are senile and they'll stop bugging you.)
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To: neverdem
Human Gene Count Tumbles Again

"A new analysis, one that harnesses the power of comparing genome sequences of various organisms, now reveals that the true number of human genes is about 20,500, thousands fewer than what is currently listed in human gene catalogs.

13 posted on 01/16/2008 7:02:39 AM PST by blam (Secure the border and enforce the law)
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To: SunkenCiv

“God don’t make junk.”

Why in the world would we have “left-over” anything?


14 posted on 01/16/2008 7:05:22 AM PST by Monkey Face (If you don't have it, you haven't asked for it!)
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To: Monkey Face

I think the operative term here is “appears” to be junk.


15 posted on 01/16/2008 8:45:31 AM PST by D_Idaho ("For we wrestle not against flesh and blood...")
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To: D_Idaho

Of course. Translated loosely, it means, “my OPINION is that it APPEARS to be junk.”

Thanks for putting it into perspective for me! LOL!


16 posted on 01/16/2008 8:47:48 AM PST by Monkey Face (If you don't have it, you haven't asked for it!)
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To: SunkenCiv

As more complications in DNA sequences are discovered, what gets credit for this intricacy? Evolution. It’s funny.

I can imagine stumbling upon the Taj Mahal someday and being amazed at the stunning shape rocks had evolved into... and then as I explore the interior, becoming more in awe of the evolution process. Isn’t it just incredible how something so complex can be put together with just time and environmental change and no outside creative design or intent whatsoever?
Try as I might to understand the formation, I would never get close, and need to constantly change my theories, until I finally acknowledged the fact that the Taj Mahal had a builder, and the builder had a purpose for the building.


17 posted on 01/16/2008 9:12:01 AM PST by ValerieTexas
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To: CholeraJoe

That joke was both X-rated and Y-rated.


18 posted on 01/16/2008 10:05:30 AM PST by SunkenCiv (https://secure.freerepublic.com/donate/____________________Profile updated Sunday, December 30, 2007)
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To: Monkey Face

Besides Chinese food, you mean... ;’)


19 posted on 01/16/2008 10:08:36 AM PST by SunkenCiv (https://secure.freerepublic.com/donate/____________________Profile updated Sunday, December 30, 2007)
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To: ValerieTexas
:')
"For thirty years, nobody disputed this 'fact'. One group of scientists abandoned their experiments on human liver cells because they could only find twenty-three pairs of chromosomes in each cell. Another researcher invented a method of separating the chromosomes, but still he thought he saw twenty-four pairs. It was not until 1955, when an Indonesian named Joe-Hin Tjio travelled from Spain to Sweden to work with Albert Levan, that the truth dawned. Tjio and Levan, using better techniques, plainly saw twenty-three pairs. They even went back and counted twenty-three pairs in photographs in books where the caption stated that there were twenty-four pairs. There are none so blind as do not wish to see." (Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, p 23-24)

20 posted on 01/16/2008 10:09:35 AM PST by SunkenCiv (https://secure.freerepublic.com/donate/____________________Profile updated Sunday, December 30, 2007)
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To: SunkenCiv

Well, that goes without saying. ;o]
*snirt*


21 posted on 01/16/2008 10:12:23 AM PST by Monkey Face (If you don't have it, you haven't asked for it!)
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To: SatinDoll

My lesser genome sized brain figured it out. I’ve been vegetating lately with a cold, but have not yet devolved into a plant.

May not be long. Hope all’s going well for you in the New Year.


22 posted on 01/16/2008 12:30:58 PM PST by patriciaruth (http://www.freerepublic.com/focus/f-news/1562436/posts)
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To: ValerieTexas
"As more complications in DNA sequences are discovered, what gets credit for this intricacy? Evolution."

Or 'Nature.' Sure seem to be a lot of Gaiaists out there....

There was a time when God (appropriately) got the compliments/credit.

Agree with your comment.

23 posted on 01/16/2008 2:57:25 PM PST by Jedi Master Pikachu ( What is your take on Acts 15:20 (abstaining from blood) about eating meat? Could you freepmail?)
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To: ValerieTexas
and the builder had a purpose for the building...

It is interesting you use a tomb as your analogy. I'll ponder your meaning with grave consideration.

24 posted on 01/16/2008 4:57:56 PM PST by bigheadfred (THE SGT. EVAN VELA DEFENSE FUND , (See my FR homepage to help. Donate today!)
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To: patriciaruth

Here’s hoping all goes well for you, too, in the New Year! And watch that cold - some have the nasty habit of evolving into pneumonia.


25 posted on 01/16/2008 8:11:10 PM PST by SatinDoll (Fredhead and proud of it!)
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To: neverdem
If you can use an update in genetics, those links in comment# 1 are FReebies.

Thanks

26 posted on 01/16/2008 9:06:57 PM PST by rdl6989 (FRed Thompson '08)
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To: ValerieTexas
Well said Val.

I'm suspect as time goes by, "science" will experience even greater surprises in the complexities of His creation. Truth be known, if they could see the totality of it all, they would likely be scratching their collective heads wondering why they couldn't see it before.

27 posted on 01/16/2008 10:14:32 PM PST by ForGod'sSake (ABCNNBCBS: An enemy at the gates is less formidable, for he is known and carries his banner openly.)
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