Category Archives: Science

High Resolution Darwin Documents

View high resolution scans of Darwin’s notes and review his thoughts and ideas. Speaking of Faith (American Public Media program) has teamed with Cambridge University Library to present a narrated tour of Darwin’s private notebooks and hand sketches with David Kohn.

Very interesting. I am not thrilled with the usability of the web application but the high resolution images are interesting and the narration is informative.

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.

Researchers Create Molecule-Sized Test Tubes

The test tubes are actually bubble-like nanocontainers that are porous to small molecules. Researchers can easily feed needed ions and other chemicals into the ultra-tiny reaction chambers.

Many scientists say that more can be learned about the dynamics of chemical reactions that power biological processes by studying the behavior of individual molecules rather than observing the collective behavior of many molecules, as scientists do now. But techniques for single-molecule studies are limited and often highly specialized. The new nanocontainers, however, will make single-molecule techniques both more accessible and more powerful
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The researchers say their technique can be easily applied in other laboratories, to enable scientists to study individual molecular reactions free of the complications of analyzing reactions in bulk solution. The new approach also improves on other methods used for observing the behavior of single molecules. One of the most common methods required that single molecules be tethered to a surface. With nanocontainers, however, the vesicles themselves are attached to a surface, meaning the molecules inside do not have to be. This simplifies analysis, because the effects of the surface on the reaction do not have to be taken into account, the researchers said.

To bad I can’t find the article online: I. Cisse, B. Okumus, C. Joo, T. Ha, “Fueling protein-DNA interactions inside porous nanocontainers”, PNAS. The Howard Hughes Medical Institute is doing great things: $600 Million for Basic Biomedical Research – $1 Million Each for 20 Science Educators

Reducing the Impact of a Flu Pandemic

Model for tracking flu progression could reduce flu pandemic’s peril – Engineer who survived pandemic of 1968 focuses on reducing influenza’s death toll:

Nearly 40 years ago, MIT Professor Richard Larson spent a week sick in bed with the worst illness he’d ever had–the particularly virulent strain of flu that swept the globe in 1968. “That was the sickest I’d ever been,” Larson recalled. “I really thought that was the end.” It took him two or three months to recover fully from the illness.

Known as the Hong Kong flu, the virus killed 750,000 people worldwide, the second worst influenza pandemic the world has seen since the infamous 1918-1919 epidemic of so-called Spanish flu.
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The findings strongly suggest that influenza emergency plans should include measures to reduce social contact, such as encouraging people to work from home and avoid large gatherings, Larson said. This is especially important because it generally takes at least six months from the time of an outbreak to develop an effective vaccine.

Tuberculosis Risk

We have posted about the Tuberculosis risks previously: Extensively Drug-resistant Tuberculosis (XDR TB), May 2007 – Deadly TB Strain is Spreading, WHO Warns, Mar 2007 – Tuberculosis Pandemic Threat, Jan 2007 – ‘Virtually untreatable’ TB found, Sep 2006. One USA citizen, while infected with XDR TB, flying to Europe and then to Canada and driving back into the USA has created a huge amount of publicity on this topic in the last week.

The risks are well known, given the extreme mobility in the world today, for TB, and other communicable diseases, becoming more troublesome, costly and deadly – often due to improper antibiotic use. But we continue to avoid giving this risk near the level of attention it seems to deserve. Deaths due to these diseases is likely to be very high in the next 20 years.

In fact there were 1.6 million TB deaths in 2005 (see WHO fact sheet below). Even if you only care about deaths in the USA (I am not advocating such a position, but even for those that hold such a position…) failing to address these issues will greatly increase the odds of large numbers of deaths in the USA (for TB and other diseases that become difficult or impossible to treat with antibiotics).

The current news will do little in my opinion (though it will help raise awareness). It will take a significant number of deaths in the USA, for significant policy changes to be implemented. Luckily scientists and policy makers have been giving these risks thought and so possible actions are already fairly well know. Unfortunately we seem very inclined to ignore problems for those out of sight (either continents away, or in the future) so until the consequences of the current action forces people to confront this issue little has been done (well actually good action is being taken, but much more is left to do).

One huge issue is quarantine. Personally, I try to use as a guide that people have the right to do what doesn’t infringe upon others rights. This allows plenty of room for debate about what level of trade-off is acceptable but I find it a useful guide to shape my thoughts. People don’t have the right to drive drunk and endanger others. People don’t have the right to pollute the air of others by smoking (or polluting the air with dangerous chemicals, CO2…). People don’t have the right to expose others to dangerous communicable diseases. Doctor’s don’t have the right to proscribe antibiotics when not medically justified (creating risks to those in the future)… But how society decides to define the social contract that everyone must agree to (rather that a way I find useful to help me analyze what is reasonable) is in need of some increased clarity in the light of health care issues today.

World Health Organization fact sheet on Tuberculosis:
Continue reading →

BumpZee Science and Engineering Communities

Bumpzee communities provide topic focused blog feeds, tools for blogs and more. I have created communities for science and for engineering. They offer some of the common tools such as highlighting posts community members have voted up (bumped). Blog owners can add there blogs to bumpzee and the communities. Bumpzee offers tools to track blog statistics (others offer similar things, of course, for example: mybloglog, google analytics, feedburner) with interactive features (like showing what Bumpzee members are viewing the blog, most popular posts on your blog, most poplular posts in your community…).

Radical Life Extension

The near-term inevitability of radical life extension and expansion by Ray Kurzweil:

It took 15 years to sequence HIV and from that perspective the genome project seemed impossible in 1990. But the amount of genetic data we were able to sequence doubled every year while the cost came down by half each year.
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If we think linearly, then the idea of turning off all disease and aging processes appears far off into the future just as the genome project did in 1990. On the other hand, if we factor in the doubling of the power of these technologies each year, the prospect of radical life extension is only a couple of decades away.

KurzweilAI.net includes many articles on Kurzweil’s ideas, by him, and others. Major topic areas include: Nanotechnology, Will Machines Become Conscious? and Singularity. The ideas can seem crazy but as Kurzweil discusses the ability to predict with the tremendous increase in the power of technology. I still think many things like radical life extension is unlikely so soon but the ideas presented are interesting and worth thinking about.

Inner Life of a Cell: Full Version

This is an extremely cool 8 minute movie on the inner workings of a Cell. The earlier version we posted about back in September of last year has been one of our most popular posts – see our most popular posts. They have added the scientific explanation that I mentioned I would love to see in the last post.

update: Unfortunately Harvard seems to want to prevent people from seeing this educational webcast. Why they don’t want to promote science education is beyond me. I guess they have better uses for their $35 billion endowment than promoting science. I sure wish they would hurry up and realize this isn’t the 18th century. They say their mission is “The advancement of all good literature, arts, and sciences; the advancement and education of youth in all manner of good literature, arts, and sciences; and all other necessary provisions that may conduce to the education of the … youth of this country…” (Jun 2008). You don’t have to just educate a few privileged soles in ivy covered buildings. You can do that any provide great education material for others around the globe.

Animation created for Harvard’s Molecular and Cellular Biology program:

Harvard University selected XVIVO, LLC, a Connecticut based scientific animation company, to customize and develop an animation that would propel Harvard’s Molecular and Cellular Biology program to the next level of undergraduate education. XVIVO’s recently completed animation, titled “The Inner Life of the Cell”, has already won awards. The eight minute animation transports Harvard Biology students into a three-dimensional journey through the microscopic world of a cell.

DNA Repair Army

Analysis Reveals Extent of DNA Repair Army

Elledge’s group studied human cells in culture and mapped their response to ionizing radiation and ultraviolet light. Specifically, the group looked to see which proteins in the cell were chemically altered by the enzymes ATM and ATR, finding 900 sites on 700 proteins that changed in response to DNA damage. The discovery that so many proteins are involved in the process, Elledge said, was a big surprise.

Also see: Cell Cycle Regulation and Mechanisms of DNA Repair:

Despite the abuse our DNA endures, our individual genomes usually stay basically intact because DNA has a remarkable capacity for repair. Our cells have built-in, highly efficient machinery that finds and fixes “genetic typos.”
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Researchers have learned much about the complex genetic machinery that cells deploy to fix broken, cut, mutated, and misplaced genetic materials. Out of that evolving understanding has emerged a deeper awareness that DNA is truly dynamic and that responses to genetic damage are nearly as fundamental to life—and health—as is the genetic code itself.