Skip to comments.Not Your Father's Genome
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.
If you can use an update in genetics, those links in comment# 1 are FReebies.
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.
Ah, come on Pat! You made that up, didn’t you?
New Bacteria Strain Is Striking Gay Men bug chasers gone wild
FReepmail me if you want on or off my health and science ping list.
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.
Thanks neverdem. Martin, pingworthy?
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$80 million is a tad small a sum for learning more about 99% of human DNA when 1% has proved so complicated.
Worth looking at?
How do you tell whether a chromosome is a boy chromosome or a girl chromosome?
Pull down its genes and look.
"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.
“God don’t make junk.”
Why in the world would we have “left-over” anything?
I think the operative term here is “appears” to be junk.
Of course. Translated loosely, it means, “my OPINION is that it APPEARS to be junk.”
Thanks for putting it into perspective for me! LOL!
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.
That joke was both X-rated and Y-rated.
Besides Chinese food, you mean... ;’)
"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)
Well, that goes without saying. ;o]
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.
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.
It is interesting you use a tomb as your analogy. I'll ponder your meaning with grave consideration.
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.
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.
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