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article imageOp-Ed: Just Genes? Rethinking the basics of genetics, as genes mean more than genes

By Paul Wallis     Nov 11, 2008 in Science
We’re just getting used to the ideas of genetics. Now, geneticists are being forced to completely reinvent the old ideas of how genes work. Apparently the old concepts are now being proved to be too simple to explain everything genes do, and can do.
The New York Times:
They no longer conceive of a typical gene as a single chunk of DNA encoding a single protein. “It cannot work that way,” Dr. Prohaska (bioinformatician at the University of Leipzig in Germany) said. There are simply too many exceptions to the conventional rules for genes.
It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but another chemical known as RNA. The familiar double helix of DNA no longer has a monopoly on heredity. Other molecules clinging to DNA can produce striking differences between two organisms with the same genes. And those molecules can be inherited along with DNA.
Well, nobody but physicists ever said biology was simple. Which is ironic if you consider that physics is currently trying to find 75% of the universe and prove it exists, while biology is merely revolutionizing our whole concept of life.
100 years ago, according to NYT, the inventor of the genetic concept said the word “gene” was “completely free from any hypothesis”. I think we can now say that’s no longer the case. The poor little word has now been subjected to moral, metaphysical, professional, religious, economic, sociological and political hypotheses.
Maybe it’s due for a return to the relative safety of incomprehensibility.
The post Human Genome era in genetics has been a volcano of discovery that could give lessons to Krakatoa. It has already completely altered everyone’s perspective in terms of medicine, industry, economics, and food supply, in a few years.
The really good news about this rethink of the gene is that it’s a good case of reliable scientific principles at work. Theories wear out. Information doesn’t match results.
Even getting the information organized isn’t exactly easy. There’s a thing called the Encyclopedia of Genetic Elements or Encode:
One of the biggest of these projects is an effort called the Encyclopedia of DNA Elements, or Encode for short. Hundreds of scientists are carrying out a coordinated set of experiments to determine the function of every piece of DNA in the human genome. Last summer they published their results on 1 percent of the genome — some three million “letters” of DNA. The genetic code is written in letters, like the title of the movie “Gattaca,” with each letter standing for a molecule called a base: guanine (G), adenine (A), thymine (T), cytosine (C). The Encode team expects to have initial results on the other 99 percent by next year.
Encode’s results reveal the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be. “These are not oddities — these are the rule,” said Thomas R. Gingeras of Cold Spring Harbor Laboratory and one of the leaders of Encode.
This is fascinating stuff, and it’s also a good example of what happens to new scientific ideas: They become old scientific ideas.
The genes are showing alternate lines of heredity, different ways of a single gene producing different proteins, and different transcriptions of the same gene by different cells.
Or, if you interpret all this as a GPS direction, “Get working on the new formulae before the next off ramp.”
There’s now a thing called the Epigenome, a sort of genetic memory aid:
All of the molecules that hang onto DNA, collectively known as epigenetic marks, are essential for cells to take their final form in the body. As an embryo matures, epigenetic marks in different cells are altered, and as a result they develop into different tissues. Once the final pattern of epigenetic marks is laid down, it clings stubbornly to cells. When cells divide, their descendants carry the same set of marks. “They help cells remember what genes to keep on, and what genes can never be turned on,” said Bradley Bernstein of Harvard University.
Scientists know much less about this “epigenome” than the genome.
Things they might like to know are how does it work, why is it there, what happens when you play around with it, and how many patents you can get out of it, and how many lawyers you can fit in a laboratory.
So far they’ve discovered it does, definitely, have a role in heredity and apparently does operate in evolutionary changes.
Oh, yeah, and epigenetic markings in male rats predisposed to disease turns off female rats for at least three generations.
Other than that, they’re guessing.
Not quite trivial, given the occasional mild interest in evolution lately.
Get the impression that what we thought was the great leap forward in genetics is actually an impressive hop?
Oh, and there are “undead pseudo genes”, and we’ve had viral genes rotting around in our genome for millions of years. They’re real problems, except the ones that have evolved into RNA we can use.
That’s about it, really.
We can forgive NYT columnist Carl Zimmer for obviously enjoying his work, all four pages of methyl caps, rats, and the history of the science.
Even science news has a genetic sense, obviously. Now, let’s hope the science catches up to the enthusiasm.
This opinion article was written by an independent writer. The opinions and views expressed herein are those of the author and are not necessarily intended to reflect those of DigitalJournal.com
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