A New Species: The Clean Room Bacteria

A fascinating piece in Scientific American, summarizing how scientists discovered a new species of bacterium in two separate clean room facilities (one at the European Space Agency and the other at Kennedy Space Center):

The researchers named the bacterium Tersicoccus phoenicis. “Tersi” is Latin for clean, as in clean room, and “coccus” comes from Greek and describes the bacterium in this genus’s berrylike shape. “Phoenicis” as the species name pays homage to thePhoenix lander. The scientists determined that T. phoenicis shares less than 95 percent of its genetic sequence with its closest bacterial relative. That fact, combined with the unique molecular composition of its cell wall and other properties, was enough to classify Tersicoccus phoenicis as part of a new genus—the next taxonomic level up from species in the system used to classify biological organisms. The researchers are not sure yet if the bug lives only in clean rooms or survives elsewhere but has simply escaped detection so far, says Christine Moissl-Eichinger of the University of Regensburg in Germany, who identified the species at the ESA’s Guiana Space Center in Kourou, French Guiana. Some experts doubt thatTersicoccus phoenicis would fare well anywhere other than a clean room. “I think these bugs are less competitive, and they just don’t do so well in normal conditions,” says Cornell University astrobiologist Alberto Fairén, who was not involved in the analysis of the new genus. “But when you systematically eliminate almost all competition in the clean rooms, then this genus starts to be prevalent.”

Only the hardiest of microbes can survive inside a spacecraft clean room, where the air is stringently filtered, the floors are cleansed with certified cleaning agents, and surfaces are wiped with alcohol and hydrogen peroxide, then heated to temperatures high enough to kill almost any living thing. Any human who enters the room must be clad head to foot in a “bunny suit” with gloves, booties, a hat and a mask, so that the only exposed surface is the area around a person’s eyes. Even then, the technician can enter only after stomping on sticky tape on the floor to remove debris from the soles of her booties, and passing through an “air shower” to blow dust away from the rest of her. 

As always: life finds a way. Not only was this a discovery of a new species, it was a discovery of a new genus.

The full paper, for those of you interested, is here.

 

The Sports Gene and the New Science of Athletic Excellence

Katie Drummond interviews David Epstein, the author of the recently released The Sports Gene: Inside the Science of Extraordinary Athletic Performance.

The context is fascinating: whether you’re a gym rat or just starting out with an exercise routine, you typically follow the advice you read in magazines, from friends/coworkers, or personal trainers. But in the future, however, you might be able to develop a training plan that has nothing to do with external edicts, generalized principles, or even trial and error. Instead, you’d be training according to your own genetic athletic profile — a sequence of genes that determine what kind of exercise, done for how long and how often, your body will best respond to.

According to Drummond,

Epstein offers a fascinating look at how genetic research is already transforming sports science. Along the way, he digs into controversial questions about gender and race, examines the latest in genetic testing that purports to spot athletic traits, and unravels how some of the world’s best athletes — from Usain Bolt to Michael Jordan — attained the pinnacle of sporting success.

On to the interview questions:

Q: You don’t shy away from controversial topics in the book, including gender and ethnic differences where athletic ability is concerned. You also mention how scientific progress has been hindered because of concerns about sexism or racism creeping into cultural discussions about findings. To what extent, do you think, have those fears held back research on genetics and athleticism?

A: You know, when I went into the book I figured that scientists worked in bubbles to some extent, and that they didn’t decide what to publish based on any external force. In a sense, that they published their data so long as they maintained academic rigor. But in this field, that hasn’t been the case at all: scientists have literally told me that they have data, really great data, that they won’t publish because of how it might be perceived or construed by the public.

The primary instance of this is related to race. Namely, scientists are concerned that data suggesting that black people are predisposed to some athletic superiority will get wound up into this bigoted misconception that athletic ability means someone lacks intellect. That might sound ridiculous, but it’s been a prejudice for some time, and it has really reached deeply into the psyches of some scientists. Where gender is concerned, I had one researcher who has published a huge amount on sex and gender differences tell me that he didn’t publish any findings until he got tenure, because it just threatened to be too controversial. From my perspective, the best way to move the field forward and to help athletes is to collect sound data and then publish it — I was disappointed to see that this hasn’t happened.

Q: As you point out, the relationship between athletics and genetics is really complicated. But where do you see research going in the future, and what will it mean for athletes — elite or otherwise?

A: It is complicated, but we’re already seeing genetic tests trickling out that can hint at different aspects of someone’s athletic ability. Namely we’re seeing gene tests that relate to injury risk — one example is a test for the ApoE gene, which helps determine your vulnerability to brain damage from the hits you take during boxing or playing football, for example. That test is already out there, and it might really make a difference for athletes, how they compete, and what kind of medical treatment they get.

Where research is concerned, the most progress we’re seeing now is in studies that look at genes related to responses to endurance training — genetic pathways that determine who responds well to cardiovascular exercise, and who doesn’t. That has obvious appeal for athletes, or even people who wish they were athletes: the takeaway is that just because you don’t seem to have this innate, amazing talent, you might have an underlying predisposition to respond much better than you’d expect. The idea of figuring out someone’s training routine based on what they do and don’t respond to is really appealing, and I’d say we’re maybe five or ten years away from getting into that.

And it might also play an important role in personalized medicine: if someone with heart problems can respond well to aerobic activity, then maybe we can prescribe an exercise program instead of medicating them.

Fascinating. I’ve placed The Sports Gene in my to-read queue.

Are Selfish Traits Favored by Evolution?

A recently published paper in Nature argues that it doesn’t pay to be selfish, in terms of maintaining or gaining evolutionary advantage. From the abstract, they used the famous Prisoner’s Dilemma to come to their conclusion:

Zero-determinant strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner’s Dilemma irrespective of the opponent’s strategy (coercive strategies), or else to set the ratio between the player’s and their opponent’s expected payoff (extortionate strategies). Here we show that zero-determinant strategies are at most weakly dominant, are not evolutionarily stable, and will instead evolve into less coercive strategies. We show that zero-determinant strategies with an informational advantage over other players that allows them to recognize each other can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition.

More interestingly, this latest finding is in direct contradiction the findings in a paper published in The Proceedings of the National Academy of Sciences last year, which posited that selfish people could get ahead of more co-operative partners…

The reason that being selfish wouldn’t work in an evolutionary environment is that knowing your opponent’s decision would not be advantageous for long because your opponent would evolve the same recognition mechanism known to you.

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(via BBC News)

The Evolutionary Paradox of Exercise

Slate has an interview with evolutionary biologist Daniel Lieberman, who explains the paradox between exercise being good for us and it feeling like a chore.

Q: What are the consequences of the modern sedentary lifestyle?
DL: It’s hard to think of one disease that is not affected by physical activity. Take the two major killers: heart disease and cancer. The heart requires exercise to grow properly. Exercise increases the peripheral arteries and decreases your cholesterol levels; it decreases your risk of heart disease by at least half.

Breast cancers and many other reproductive tissue cancers also respond strongly to exercise. Other factors being constant, women who have engaged in regular vigorous exercise have significantly lower cancer rates than women who have not. Colon cancer has been shown to be reduced by up to 30 percent by exercise. There are also benefits for mental health—depression, anxiety, the list is incredibly long.

Q: What can we do about our maladaptive traits?
DL: If we want to practice preventive medicine, that means we have to eat foods that we might not prefer, and exercise when we don’t want to. The only way to do that is through some form of socially acceptable coercion. There is a reason why we require good food and exercise in school—otherwise the kids won’t get enough of it. Right now we are dropping those requirements around the world.

Q: Being able to run is one thing—how did we then go on to become endurance athletes?
DL: We evolved from very non-active creatures. A typical chimp will walk 2 to 3 kilometers a day, run about 100 meters and climb a tree or two. Your average hunter-gatherer walks or runs 9 to 15 kilometers per day, and we have all these features in our bodies, literally from our heads down to our toes, that make us really good at long-distance walking and running.

I and my colleagues at the University of Utah, Dennis Bramble and David Carrier, think the key advantage for humans was persistence hunting, whereby you run very long distances to chase animals in the heat and run them into heat stroke. We can run for very long distances, marathons in fact, at speeds at which other animals have to gallop. That’s not an endurance gait for quadrupeds, because they cool by panting—short shallow breaths. You can’t pant and gallop at the same time. If you make an animal gallop in the heat for 15 minutes or so, on a hot day, you’ll kill it.

Q: But we have adaptations for this kind of endurance running?
DL: Yes. Our bodies are loaded with all kinds of features: short toes that require less energy to stabilize and generate less shock when running; the Achilles tendon that stores and releases energy appropriately as we run; the large gluteus maximus muscles that steady the trunk; and stabilization of the head. I’m a middle-aged professor, I’m not a great specimen of an athlete, but I can easily run a marathon at a speed that would cause a dog my size to gallop.

Why The Cockroach Baits Aren’t Working

A fascinating discovery was recently published in the magazine Science on perhaps the world’s most adaptable insect: the cockroach. From the abstract:

In response to the anthropogenic assault of toxic baits, populations of the German cockroach have rapidly evolved an adaptive behavioral aversion to glucose (a phagostimulant component of baits). We hypothesized that changes in the peripheral gustatory system are responsible for glucose aversion. In both wild-type and glucose-averse (GA) cockroaches, D-fructose and D-glucose stimulated sugar–gustatory receptor neurons (GRNs), whereas the deterrent caffeine stimulated bitter-GRNs. In contrast, in GA cockroaches, D-glucose also stimulated bitter-GRNs and suppressed the responses of sugar-GRNs. Thus, D-glucose is processed as both a phagostimulant and deterrent in GA cockroaches, and this newly acquired peripheral taste sensitivity underlies glucose aversion in multiple GA populations. The rapid emergence of this highly adaptive behavior underscores the plasticity of the sensory system to adapt to rapid environmental change.

As The New York Times notes, what this means is that the cockroach has somehow evolved a way to make glucose smell/taste bitter to it, and it can thus avoid modern-day traps that use glucose as a primary ingredient. Instead of taste buds, roaches have taste hairs on many parts of their bodies. The three North Carolina researchers concentrated on those around the mouth area and on two types of nerve cells that sense tastes and respond by firing electrical signals to the brain. One responds only to sugars and other sweet substances; the other responds only to bitter substances. Whenever a molecule of something sweet attaches to a sweet detector, it fires electrical impulses and the roach brain senses sweetness, which makes it want to eat whatever it is tasting. Whenever a molecule of something bitter attaches to the bitter detector, that cell fires and the brain senses bitterness, which makes the roach want to avoid that substance.

Evolutionary advantages like this have helped the cockroach endure for millions of years. Fascinating.

 

The Uner Tan Syndrome, or The Case of The Bear Walking Family

I’d never heard of the Uner Tan Syndrome before reading this article. It is named after a Turkish scientist who discovered a family who walk on all fours:

The subject of bear crawling hibernated for many decades until a couple of Turkish doctors, in 2004, made a discovery that was more science fiction than science. In a rural village, they happened upon a group of siblings who had never stood up. Members of a family with 19 children, all of whom bear-walked in their infancy, these five brothers and sisters had never lifted up off their hands. They had walked like bears all their life. The siblings actually wrist-walked, with their palms pressed flat against the ground. (Think of someone doing the downward-facing dog yoga pose while walking.) No one had ever seen an adult human move like this before.

The siblings were able to stand upright if they really concentrated on it, an early report on them noted, “but they become unsteady if they try to walk bipedally, and soon go down onto their hands.” They were quadrupeds. To help support the family, the lone male bear crawler ranged as far as a mile from home collecting cans and bottles. While bear-crawling, he was indefatigable. “This contrasts markedly with normal adult humans,” the report noted, “who find such a gait—if and when they try it—tiring and uncomfortable even after practice.”

 

I’d also never heard of the term “reverse evolution,” but that is the phrase that was used in this academic paper on the syndrome.

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More: a documentary on the bear-walking family.

The Life and Death of Words

An intriguing new paper by Alexander M. Petersen et al. presents the findings of Google’s digitization project (scanning millions of books). From their abstract:

We analyze the dynamic properties of 107 words recorded in English, Spanish and Hebrew over the period 1800–2008 in order to gain insight into the coevolution of language and culture. We report language independent patterns useful as benchmarks for theoretical models of language evolution. A significantly decreasing (increasing) trend in the birth (death) rate of words indicates a recent shift in the selection laws governing word use. For new words, we observe a peak in the growth-rate fluctuations around 40 years after introduction, consistent with the typical entry time into standard dictionaries and the human generational timescale. Pronounced changes in the dynamics of language during periods of war shows that word correlations, occurring across time and between words, are largely influenced by coevolutionary social, technological, and political factors. We quantify cultural memory by analyzing the long-term correlations in the use of individual words using detrended fluctuation analysis.

How many words are in the English language? The paper gave the best-yet estimate of the true number of words in English—a million, far more than any dictionary has recorded (the 2002 Webster’s Third New International Dictionary has 348,000). More than half of the language, the authors wrote, is “dark matter” that has evaded standard dictionaries.

The paper also tracked word usage through time (each year, for instance, 1% of the world’s English-speaking population switches from “sneaked” to “snuck”). It also showed that we seem to be putting history behind us more quickly, judging by the speed with which terms fall out of use. References to the year “1880” dropped by half in the 32 years after that date, while the half-life of “1973” was a mere decade.

Finally, the authors identified a universal “tipping point” in the life cycle of new words. Roughly 30 to 50 years after their birth, words either enter the long-term lexicon or fall off into oblivion. How that’s for a half-life?

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(via Wall Street Journal)