Regression with Gnumeric

A test regression (linear equation) using Gnumeric.

Finally, I’ve found a spreadsheet application (Gnumeric) with a reliable Solver for doing regressions. And it’s free. The only tricky part is that there’s no native port for Macs; you have to use a command line package manager to install it (I used Fink).

Gnumeric, however, seems to be an excellent tool for data analysis.

Sending Invasive Species to Mars

George Dvorsky summarizes a new study showing six types of bacteria found in Siberia are able to survive, and even thrive, under Mars-like conditions.

The researchers took these cultures [from Siberian permafrost] and exposed them to similar conditions found on Mars, including a severe lack of oxygen, extreme cold temperatures, and very low pressure (about 150 times lower than the Earth’s, about 7 millibars). The experiment was run over the period of 30 days. Over 10,000 isolates were exposed to these conditions — and they all died.

Except six.

And in fact, these six surviving microbes actually did better under these conditions. Surprised by the result, the researchers took a closer look at the survivors, and following a genetic analysis concluded that they all came from the same genus: an extremely hardy extremophile called Carnobacterium.

— Dvorsky (2012): Scientists show that microbes from Earth can survive conditions found on Mars in io9.

So now we have to wonder if we’ve already, inadvertently, sent life to Mars.

Horizontal Gene Transfer: Plasmids

Peter Eisler has a somewhat scary article on the development of drug resistance in bacteria at the University of Virginia Medical Center. The bacteria were resistant to all of their antibiotics. Everything. And the bacteria were able to pass the genes that gave them their resistance to other bacteria: not just to their offspring, but horizontally to other species of bacteria by exchanging bits of DNA called plasmids.

One bacteria cell passes a piece of DNA (called a plasmid) to another. From USA Today — Image links to more complete information.

When genes are passed on from parent to offspring, or even from one microbe to another by cell splitting, it’s called vertical gene transfer. Horizontal transfer, on the other hand, involves different individual organisms passing genes from one to the other. It would be as if two people could exchange genes by shaking hands.

When the doctors began analyzing the bacteria in their first patient, who’d transferred from a hospital in Pennsylvania, they found not one, but two different strains of CRE bacteria. And as more patients turned up sick, lab tests showed that some carried yet another.

“We were really frustrated; we hadn’t seen anything like this in the literature,” says Costi Sifri, the hospital epidemiologist. “The fact that we had different bacteria told us these cases were not related, but the shoe leather epidemiology suggested to us that all these (infections) came from the same patient. … We realized we might be seeing a mobile genetic event.”

In other words, it looked like a single resistance gene was jumping among different bacteria from the Enterobacteriaceae family, creating new bugs before their eyes.

— Eisler 2012: Deadly ‘superbugs’ invade U.S. health care facilities in USA Today.

The really scary part:

There is little chance that an effective drug to kill [drug resistant] CRE bacteria will be produced in the coming years. Manufacturers have no new antibiotics in development that show promise, according to federal officials and industry experts, and there’s little financial incentive because the bacteria adapt quickly to resist new drugs.

Breeding Drug Resistant Bacteria at Farms

Modern commercial farming uses a lot of antibiotics, and, as a consequence, we’re beginning to see them breeding drug resistant bacteria (see here for exponential growth demo). Jeremy Laurance reports on one bug (MRSA ST398) now being found in milk.

Three classes of antibiotics rated as “critically important to human medicine” by the World Health Organisation – cephalosporins, fluoroquinolones and macrolides – have increased in use in the animal population by eightfold in the last decade.

The more antibiotics are used, the greater the likelihood that antibiotic-resistant bacteria, such as MRSA, will evolve.

The MRSA superbug can cause serious infections in humans which are difficult to treat, require stronger antibiotics, and take longer to resolve. Human cases of infection with the new strain have been found in Scotland and northern England

— Laurance (2012): New MRSA superbug strain found in UK milk supply in The Independent.

Note that consumers of milk don’t have to worry because the milk is pasteurized.

A Global Warming Primer

The Discovery Channel has an interesting series of videos about the effects of global warming on: polar bears; the Antarctic Ice Sheets; the Amazon rainforest; and the Great Barrier Reef. They also have a nice bit on what goes into the average American carbon footprint.

Natural Selection and Polar vs. Grizzly Bears

What I end up seeing, in this quintessentially 21st century creature, is a glimpse of the future.

— Gamble (2012): One, two, three, er…many. in The Last Word on Nothing.

The effect of rapid Arctic warming on polar bears has been a theme this year in Environmental Science, so this article on the hybridization of polar bears and grizzly bears caught my eye.

As caribou migration routes have moved North, grizzlies have followed and started mating with polar bears. Not only have they produced hybrid young, but those young are fertile. Polar bears and grizzlies only diverged about 150,000 years ago and haven’t developed many genetic differences, despite quite dramatic visual dissimilarities. Second-generation hybrids have now been confirmed in the wild.

This article is also of note to my Middle School science class because we’ve talked about speciation — the divergent evolution of two populations into separate species — before when we looked at the phylogenetic tree and bison evolution in particular. This seems to be a re-convergence after separation. As the climate warms the grizzly bears are able to range further north, while the polar bears are more restricted to the shores by the melted sea ice, so the two populations encounter each other more and more. Thus polar bears, may eventually disappear as they are re-incorporated into the grizzly population.

The author, Jessa Gamble, thinks this is a glimpse of things to come.

The Dish.