Category Archives: Research

Interesting Lobsters

Lobsters sometimes bury their food and eat it over several days. They use teeth located in their stomachs, eat their molted shells (full of calcium) and can shed appendages if attacked, wounded or surprised, only to regenerate them later. Finally, lobsters live in a hierarchy and it’s the females who do the courting.

But there’s one lobster fact that trumps them all: lobsters show no apparent signs of aging. They don’t slow down or become weaker or more susceptible to disease. They don’t get infertile — older lobsters are actually more fertile than younger ones. Most lobsters seem to die because of something inflicted upon them and not because a body part failed or broke down. They’re such hardy creatures that scientists aren’t even sure how old lobsters can get. Add in that lobsters grow throughout their lives, and one has to ask: Is possible that a lobster born before Napoleon and as heavy as an NFL lineman is chowing down on the seafloor?

Single Electron on Video

Researchers Catch Motion of a Single Electron on Video

Maris and Wei Guo, a doctoral student, took advantage of the bubbles that form around electrons in supercold liquid helium. Using sound waves to expand the bubbles and a coordinated strobe light to illuminate them, Guo was able to catch their movements on a home video camera.

A free electron repels the atoms that surround it, creating a small space, or bubble, around itself. In conventional liquids, the bubble shrinks to nothing because the surface tension of the liquid works against the repulsive force. Superfluid helium has very little surface tension, so the bubble can become much larger. The two opposing forces balance when the diameter of the bubble is about 40 angstroms – still far to tiny to see.

The researchers used a planar transducer – basically, a loudspeaker that produces flat, not focused, sound waves – to pummel the whole volume of liquid helium with sound. As each wave overtook an electron bubble, it alternately increased and decreased the surrounding pressure. Under negative pressure, the bubbles expanded to about eight microns, the size of a small speck of dust, then shrank again as the next wave of high pressure washed over them. A strobe light, synchronized to the sound pulse, illuminated the bubbles without overheating the chamber.

Running a camcorder in “super night mode,” Guo and Maris were able to record the approximately 2,000 photons they estimate were scattered by the expanded bubbles, producing a series of electron-bubble images on each frame of videotape.

Pretty amazing. My pictures are of a bit larger things.

Singapore Research Fellowship

Singapore National Research Foundation Research Fellowship (updated link which was broken – why can’t web site stop breaking links?) offers complete freedom and a 3-year research grant of up to US$1.5million, with possible extension for another 3 years for talented scientists and researchers at or under the age of 35 years at the date of application. This is another example of Singapore investing in creating a scientific and engineering community to strengthen their economy.

Howard Hughes Medical Institute Takes Big Open Access Step

HHMI Announces New Policy for Publication of Research Articles that will require

its scientists to publish their original research articles in scientific journals that allow the articles and supplementary materials to be made freely accessible in a public repository within six months of publication.

Great news. Some, including me, would prefer a shorter time but this is the limit on the slowest time that will be acceptable not a goal. I don’t know but I wouldn’t be surprised if HHMI is the largest source of research funds outside of the federal government in the USA. This is one more sign the tactics of the old school journals are failing.

HHMI and Public Access Publishing policy

The Howard Hughes Medical Institute has long viewed the sharing of research materials and tools as a fundamental responsibility of scientific authorship. That principle also extends to ensuring that original, peer-reviewed research publications and supplemental materials are freely accessible within six months of publication

Well put; it is amazing how out of touch with the basic concepts of advancing scientific ideas the old style journals are.

Evo-Devo

Sean B. Carroll discusses the science of evolution and the field of evo-devo in this New York Times Video. Learn more in this extensive article – From a Few Genes, Life’s Myriad Shapes:

evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.

For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison.

via: Justin Hunter (Justin and me in Madison) 🙂 Related: Opossum Genome Shows ‘Junk’ DNA is Not Junk – science webcast directory – Learning About the Human Genome – Curious Cat Science and Engineering Search

Tracking the Ecosystem Within Us

Gut Check: Tracking the Ecosystem Within Us

For more than 100 years, scientists have known that humans carry a rich ecosystem within their intestines. An astonishing number and variety of microbes, including as many as 400 species of bacteria, help humans digest food, mitigate disease, regulate fat storage, and even promote the formation of blood vessels. By applying sophisticated genetic analysis to samples of a year’s worth baby poop, Howard Hughes Medical Institute researchers have now developed a detailed picture of how these bacteria come and go in the intestinal tract during a child’s first year of life.
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Before birth, the human intestinal tract is sterile, but babies immediately begin to acquire the microbial denizens of the gut from their environment — the birth canal, mothers’ breast, and even the touch of a sibling or parent. Within days, a thriving microbial community is established and by adulthood, the human body typically has as many as ten times more microbial cells than human cells.
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The results, said Palmer, were striking: the group found that the intestinal microbial communities varied widely from baby to baby – both in terms of which microbes were present and in how that composition changed over time. That finding, she said, is important because it helps broaden the definition of healthy microbial colonization in a baby.

Another intriguing observation, Palmer noted, was a tendency for sudden shifts in the composition of the infants’ intestinal microbial communities over time as different species of bacteria ebbed and flowed.

I find this area and this study fascinating. I’m not exactly sure why this study and the incredibly significant positive bacteria for human life news doesn’t get more notice. Oh well I guess there are not cool pictures of robots or scary stories of potential threats to those reading which makes the news less interesting to some. Still I find this stuff amazing: Energy Efficiency of Digestion – Beneficial Bacteria – Skin Bacteria – Hacking Your Body’s Bacteria for Better Health – Where Bacteria Get Their Genes

Training Grants a Boon to Research and Scientists

Training grants a boon to research, scientists:

According to Petra Schroeder, assistant dean of the Graduate School, there are approximately 30 training grants available at UW–Madison. Most are funded by the National Institutes of Health (NIH), and they direct about $17 million each year toward the training of future researchers.

Each training program has its own specific mission, but most foster interdisciplinary research, providing students with valuable experience in a setting likely to mirror their first job environment. Those involved in the Biotechnology Training Program (BTP) are taught to do research at the juncture of the biological and physical sciences.
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LiGreci is interested in bioremediation, putting microbes to use in cleaning up toxic waste. BTP thrust her into a soil science laboratory on campus. Though LiGreci considers herself primarily a microbiologist, her research lies far outside the comfort zone of most of her peers, involving soil science, chemistry and geology.

According to LiGreci, the exposure she gets to novel lab techniques is eye opening. She learned new modes of culturing bacteria and other lab skills unique to microbiology, expanding her toolkit as a bench scientist. This summer, she will branch out further into the realms of genomics and the intersection between computing and biology when she joins the Joint Genome Institute at Lawrence Livermore National Laboratory as an intern. There, she will work on projects to assemble genomes of soil bacteria.

Self Healing Plastic

Plastic That Heals Itself

The first self-healing material was reported by the UIUC [University of Illinois at Urbana-Champaign] researchers six years ago, and other research groups have created different versions of such materials since then, including polymers that mend themselves repeatedly when subject to heat or pressure. But this is the first time anyone has made a material that can repair itself multiple times without any external intervention, says Nancy Sottos, materials-science and engineering professor at UIUC and one of the researchers who led the work.
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the researchers bend it and crack the polymer coating. The crack spreads down through the coating and reaches the underlying microchannel. This prompts the healing agent to “whip through the channels and into the crack,” Sottos says. There, it comes into contact with the catalyst and, in about 10 hours, becomes a polymer and fills in the crack. The system does not need any external pressure to push the healing agent into the crack. Instead, the liquid moves through the narrow channels just as water moves up a straw.

Life-patents

New Life, New Patent by Carl Zimmer:

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.