Genetic Future Weblog

What do lightning and bacteria have to do with one another? Quite a bit, it turns out…

Global Gravy

To begin with, lightning and bacteria share the important job of providing the fundamental food for all of life on Earth: fixed nitrogen. Plants eat the nitrogen, animals eat the plants, and then the most barbarous of us animals eat one another. Pull nitrogen out of the pyramid, and the whole thing collapses.

Our atmosphere stores a significant portion of our planet’s reserve of pure nitrogen (N₂). That said, most plants can’t eat nitrogen until it gets fixed in some other compound, such as nitrate (NO₃-), ammonia (NH₃), or urea (NH₂)₂CO. As of today, we only know of two mechanisms in nature that facilitate the creation of these compounds:

• Nitrifying Bacteria – which do the dirty work of turning plant and animal excretions and dead organisms into ammonia. Farther down the line, additional bacteria convert some of this ammonia into nitrites (NO₂-) and nitrates (NO₃-).
• Lightning – which, as it blasts a path through the atmosphere, splits apart nitrogen molecules. The resulting promiscuous nitrogen atoms combine with oxygen to form nitrogen oxides (NO₃-). Rain dissolves these into nitrates, which then wash to the surface of the Earth.

Lightning and bacteria — strange bedfellows, don’t you think? But wait, it gets weirder yet…

Genetic Partners-in-Slime

If the above recapitulation of the Nitrogen Cycle was yesterday’s news for you, then you might find this factoid more interesting: Bolts of lightning appear to be responsible for facilitating gene transfer in soil bacteria. From New Scientist’s website:

Scientists commonly use electricity to increase the permeability of bacterial cell membranes, making it easier to insert DNA. Now Sandrine Demanèche’s team at the University of Lyon has provided the first evidence that nature may have been wise to this trick all along.

The researchers seeded soil samples with the E. coli bacterium, as well as fragments of DNA containing genes for antibiotic resistance. They zapped the soil with a simulated lightning strike, and found that many of the bacteria had acquired the resistance genes.

Bacteria are already known to take up and use foreign DNA released into the environment when other organisms die. Scientists knew this “horizontal gene transfer” occurs naturally in soil, but thought it was relatively rare. However, recent genomic research indicates that this gene take-up is widespread and has played a major role in the evolution of the bacterial genome.

“This result might help explain the discrepancy between the very low observed rates of gene transfer and the apparently wide distribution of DNA sequences among bacteria,” says team member Timothy Vogel.

Yay lightning! Yay bacteria! And yow, what a kick in the pants when you appreciate how little we know about how genes go about spreading themselves. After all, if there is one thing genes “want”, it’s to get Somewhere Else. As such, the kinds of biological mechanisms genes code for will tend to express weirder and weirder means of gene transference as sex and pollination reach their natural limits…

Thanks to j.kimball’s nitrogen cycle summary for the above diagram, and for refreshing my high-school biology understanding on this matter.

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Here’s an article that brings up some tricky cause/effect questions:

Genes May Determine Who Developed Gulf War Syndrome [U. Buffalo news wire, Aug 9 2004]

The research showed that a certain gene predicted whether or not veterans who served in the Persian Gulf War would come with Gulf War Syndrome:

External or environmental factors do play a role in Gulf War Syndrome, said Vladutiu, but likely as triggers in those with a genetic predilection, rather than as the initial cause.

These triggers may be extreme exertion, heat, chemical exposures, infections, multiple vaccinations, emotional stress and a combination of these conditions or something else entirely.

This reminds me of another set of controversial studies, those focusing on people infected with Simian virus 40.

“Simian virus what?” Take note! SV40 is something YOU may have! Simian virus 40 used to be exclusively a Monkey Thing, but during the 1960′s the virus hitched a ride into our species when we had the bright idea to manufacture polio vaccines from ground-up infected monkey kidneys. (Vegans take note.)

SV40, like HIV, can’t be cured, and it probably spreads through sexual contact. Unlike HIV, it doesn’t seem to harm you on its own. (There’s a little controversy on this issue, however.) Without a doubt, SV40 doesn’t kill you, so the chances are that someday it will become pretty much ubiquitous among humans, as will herpes and a whole host of other non-debilitating viruses.

So here’s the problem with Simian virus 40. While on its own, SV40 may not be harmful to humans, when combined with asbestos, it’s deadly. For a long time, researchers were puzzled by the fact that while some people who had minimal contact with asbestos died of asbestos-related cancer, other people who lived, worked, and breathed asbestos all day long for years never had any such problems. The breakthrough came when we realized that if you carried SV40, this made you susceptible to asbestosis. Our government, which was responsible for infecting millions of its citizens with SV40, tends to be a little hesitant to admit fault in all this. Understandably, there is some concern that people might not look kindly on preventative vaccination practices if this news got a lot of attention.

Anyhow, what’s interesting about both these diseases — Gulf War Syndrome and Asbestosis — is that they seem to express themselves exclusively in the presence of certain environmental conditions. It kind of makes you wonder what other genes we have lurking inside of us, just waiting for the right circumstances for them to expose their secret nature…

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This article is especially interesting to me because of what I feel is a clear and present ethical issue: inadvertent abortions caused by amniocentesis. (Amniocentesis: Test in which fluid surrounding a fetus is analyzed, usually to determine if baby is at risk for birth defects, sometimes to determine sex.)

The issue: This procedure ought to be done later in the pregnancy, but sometimes is done between the 14th and 18th weeks. For these early tests, 1 in 200 procedures result in a miscarriage. 0.5% might not seem like a big risk, but consider these numbers:

If you get pregnant when you’re 37 years old, there is a 0.39% chance that your baby will have down syndrome. It’s a big enough risk that many doctors will insist that clients age 37-plus take this test.

When you multiply out the miscarriage risk of early-term amnio tests against the down syndrome risk for 37 year old women, it turns out that for every 100 fetuses that are diagnosed with down syndrome, 128 healthy fetus are miscarried.

For the time being, disregard the ethical issue of whether or not it’s appropriate to abort a baby because it is likely to develop down syndrome. At the very least, this news article (below) promises to make prenatal testing a bit safer…
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http://www.biomedcentral.com/news/20040707/01

Some worry that mass spec technique described in PNAS could be used for sex selection [Source:The Scientist :: Daily News]

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Welcome one, welcome all to GeneticFuture.org. I’ve been musing and reading about genetics for the past few years, especially as it relates to ethics, medicine, and agriculture. I haven’t been transformed into a “bio-luddite”, nor have I become a transhumanist GMO-munching cheerleader for the wholesale appropriation and rejiggering of the animal and plant genomes around us.

What I have concluded is that genetic engineering is going to be responsible for revolutionizing our economic, environmental, and personal landscapes. Furthermore, it seems clear to me that this is going to happen Real Soon Now, long before most of us have had a chance to understand and weigh the ethical considerations that come with all the goodies locked away in this particular Pandora’s Box.

The purpose of geneticfuture.org is to build a resource which will help to keep us informed about developments in the fields of genetic and genomic research. It’s not meant to be super-technical, nor dumbed down to USA-Today — “MONKEY WITH SUPER BRAIN TO REPLACE HUMANS” — style content.

For the time being, this site will consist of a blog in which I will track the news, organize some of my thoughts, and hopefully engage a number of folks in discussions about ethics, our hopes, our fears, and even the fate of monkeys with super brains. Later on, geneticfuture.org will be the home to something like a full-blown “wiki” which will make it easier for folks to learn more about the background and history of genetics.

For those of you who are curious about the image above, the “bar code” type stuff is what chromosome fingerprinting looks like to your average gene researcher. The lower image is in fact a fish being tagged by some game wardens, but doesn’t it evoke some kind of weird DNA-tangled human manipulation future creepiness?

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