Category Archives: Research

Life-patents

ETC is right in suggesting Venter might become “Microbesoft”–controlling operating system for anyone who wants to build an organism from scratch. Other researchers, such as Keasling, are promoting a different way of doing synthetic biology–what they call open source biology. Scientists and their students are amassing an open inventory of parts that anyone can use to design organisms of their own. And it’s open source biology, these researchers argue, that will provide the best protection against any evil uses of synthetic biology. Instead of being hidden behind patents, the information about these parts would be available to everyone, and collectively solutions could be found. As this debate starts to unfold, I think open source biology will keep it from becoming nothing but deja vu.

I support keeping science open. Patents are a tax on society that the government grants inventors for their efforts, in order to benefit society, by encouraging the inventors to innovate. The end is benefiting society. The means is granting a right of the patent holder (a right they do not have without patent law) that will encourage them to make the effort to innovate. I support the proper use of patents, but we have perverted the patent process into something that harms society. The system needs to be fixed. And the whole area of patents on life I find very questionable.

Open Access and PLoS

In An Open Mouse, Carl Zimmer discusses the conflict between closed journals and those that support open access.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it.

His post mentions the recent bad publicity Wiley received. It seems to me the Journals still don’t understand that their copyright of research results paid for by public funds are not going to continue. And that open access science is clearly the way of the future that their continued failure to deal with is increasing the odds monthly that they will find themselves on the outside of those practicing science in the 21st Century.

PLoS on the other hand recently hired Bora Zivkovic as PLoS ONE Online Community Manager. He will be great and continue to build PLoS into an organization supporting free and open science. I loved PLoS proactive action recounted by Bora, he posted that he was interested in the job:

Next morning, I woke up to a comment by the Managing Editor of PLoS ONE asking if my blog-post should be considered as a formal job application. My comment in response was a Yes.

Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.

Finding Open Scientific Papers

Sandra Porter has posted a series of posts on finding scientific papers for free: A day in the life of an English physician – What’s the best way to find free scientific publications? – My new favorite method – one more experiment

via: Finding scientific papers for free

CERN Prepares for LHC Operations

A Giant Takes On Physics’ Biggest Questions

The physicists, wearing hardhats, kneepads and safety harnesses, are scrambling like Spiderman over this assembly, appropriately named Atlas, ducking under waterfalls of cables and tubes and crawling into hidden room-size cavities stuffed with electronics.

They are getting ready to see the universe born again. Again and again and again – 30 million times a second, in fact.

Starting sometime next summer if all goes to plan, subatomic particles will begin shooting around a 17-mile underground ring stretching from the European Center for Nuclear Research, or CERN, near Geneva, into France and back again – luckily without having to submit to customs inspections.

Crashing together in the bowels of Atlas and similar contraptions spaced around the ring, the particles will produce tiny fireballs of primordial energy, recreating conditions that last prevailed when the universe was less than a trillionth of a second old.

Wow that sounds impressive. Oh yeah, it is impressive. Good writing too.

Treadmill Desks

Treadmill desks cut obesity

The participants were able to use the computer while walking without falling or injuring themselves. In fact, they enjoyed it so much, they wanted to keep the walking desks even after the study ended.
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Findlay got the idea from Mayo Clinic researcher James Levin, a co-author of the BJSM study who has been touting the benefits of his walking desk for years.

I must admit I like to think this idea would be work, but am a bit skeptical. I did switch to a job a few years back where I really just sat at my desk all day and would get tired. Previously I had walked around a fair amount going to see people… Someone suggested that getting some activity at lunch would help me feel more energized. It worked. If nothing else walk around at lunch.

Well, most of us in the corporate world feel like rats on a treadmill, so we might as well make the figurative literal…

Great comment on the post. Many of the other comments state categorically this cannot work. I wonder why they think they know what will work for everyone? I am skeptical but that is not the same thing as being sure this can’t work – I think being open to testing out ideas (especially ones that already have studies that claim they work) is a good thing. I would love to try it out myself (though given my skepticism I wouldn’t want to pay up to buy the equipment 🙂 ).

New Yorker on CERN’s Large Hadron Collider

Can a seventeen-mile-long collider unlock the universe?

A proton is a hadron composed of two up quarks and one down; a neutron consists of two downs and one up.) Fermions also include neutrinos, which, somewhat unnervingly, stream through our bodies at the rate of trillions per second.
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The L.H.C., Doser explained, relies on much the same design, and, in fact, makes use of the tunnel originally dug for LEP. Instead of electrons and positrons, however, the L.H.C. will send two beams of protons circling in opposite directions. Protons are a good deal more massive than electrons—roughly eighteen hundred times more—which means they can carry more energy. For this reason, they are also much harder to manage.

“Basically, what you must have to accelerate any charged particles is a very strong electric field,” Doser said. “And the longer you apply it the more energy you can give them. In principle, what you’d want is an infinitely long linear structure, in which particles just keep getting pushed faster and faster. Now, because you can’t build an infinitely long accelerator, you build a circular accelerator.” Every time a proton makes a circuit around the L.H.C. tunnel, it will receive electromagnetic nudges to make it go faster until, eventually, it is travelling at 99.9999991 per cent of the speed of light. “It gets to a hair below the speed of light very rapidly, and the rest of the time is just trying to sliver down this hair.” At this pace, a proton completes eleven thousand two hundred and forty-five circuits in a single second.

Being Bad is Best for Bacteria

That conclusion is based on the first experiments investigating how natural selection influences the transmission of infectious disease. The outcome of those experiments defies old assumptions that pathogens evolve to become less infectious
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The scientists analyzed the patterns of disease transmission and found that strains of bacteria with the greatest damage to their virulence genes were slowest at spreading from one host to another. The strain of pathogen with all of its virulence genes intact spread the fastest. Strains of pathogen lacking the ability to inject any proteins into the host were completely unable to spread between hosts, suggesting that these swapped virulence genes are essential for spread.

Why do We Sleep?

Study puts us one step closer to understanding the purpose of sleep:

Sleep remains one of the big mysteries in biology. All animals sleep, and people who are deprived of sleep suffer physically, emotionally and intellectually. But nobody knows how sleep restores the brain.
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Although an electronic power-napper sounds like a product whose time has come, Tononi is chasing a larger quarry: learning why sleep is necessary in the first place. If all animals sleep, he says, it must play a critical role in survival, but that role remains elusive.

Based on the fact that sleep seems to “consolidate” memories, many neuroscientists believe that sleeping lets us rehearse the day’s events.

Tononi agrees that sleep improves memory, but he thinks this happens through a different process, one that involves a reduction in brain overload. During sleep, he suggests, the synapses (connections between nerve cells) that were formed by the day’s learning can relax a little.

Hacking Your Body’s Bacteria

Hacking Your Body’s Bacteria for Better Health by Brandon Keim

In sheer numbers, bacterial cells in the body outnumber our own by a factor of 10, with 50 trillion bacteria living in the digestive system alone, where they’ve remained largely unstudied until the last decade. As scientists learn more about them, they’re beginning to chart the complex symbiosis between the tiny bugs and our health.

“The microbes that live in the human body are quite ancient,” says NYU Medical Center microbiologist Dr. Martin Blaser, a pioneer in gut microbe research. “They’ve been selected (through evolution) because they help us.” And it now appears that our daily antibacterial regimens are disrupting a balance that once protected humans from health problems, especially allergies and malfunctioning immune responses.