Author Archives: curiouscat

Handcrafted Chromosomes

Synthetic DNA on the Brink of Yielding New Life Forms

Scientists in Maryland have already built the world’s first entirely handcrafted chromosome — a large looping strand of DNA made from scratch in a laboratory, containing all the instructions a microbe needs to live and reproduce.

In the coming year, they hope to transplant it into a cell, where it is expected to “boot itself up,” like software downloaded from the Internet, and cajole the waiting cell to do its bidding. And while the first synthetic chromosome is a plagiarized version of a natural one, others that code for life forms that have never existed before are already under construction.
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LS9 Inc., a company in San Carlos, Calif., is already using E. coli bacteria that have been reprogrammed with synthetic DNA to produce a fuel alternative from a diet of corn syrup and sugar cane. So efficient are the bugs’ synthetic metabolisms that LS9 predicts it will be able to sell the fuel for just $1.25 a gallon.

At a DuPont plant in Tennessee, other semi-synthetic bacteria are living on cornstarch and making the chemical 1,3 propanediol, or PDO. Millions of pounds of the stuff are being spun and woven into high-tech fabrics (DuPont’s chief executive wears a pinstripe suit made of it), putting the bug-begotten chemical on track to become the first $1 billion biotech product that is not a pharmaceutical.

Engineers at DuPont studied blueprints of E. coli’s metabolism and used synthetic DNA to help the bacteria make PDO far more efficiently than could have been done with ordinary genetic engineering.

Related: Life-patents – Open-Source Biotech

The State of Physics

The Problem with Physics by Peter Woit

Physics has become obsessed with strings, branes and multiple dimensions, yet the big questions remain fundamentally unanswered. Has the time come to admit these wild conjectures have failed, and move on?
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Fundamental physics now finds itself in a historically unprecedented situation. The multi-decade dominance of string theory, along with its extremely speculative research into the implications of exotic scenarios far removed from any hope of testability, has changed the subject in dramatic and fundamental ways.

What used to be considered part of the dubious fringes of science has now become institutionalised within the mainstream. In physicist Lee Smolin’s recent book, The Trouble With Physics, he characterises the current sociology of the field as dominated by ‘groupthink’, with too few physicists willing to admit how far off the tracks things have gone. The nearly infinite complexity of string theory, M-theory, branes, higher dimensions and the multiverse has led to a vast number of possible challenging calculations for people to do to keep themselves busy, all embedded in a mathematical structure far too poorly understood to ever lead to definitive, falsifiable predictions.

The problems of the Standard Model that faced my colleague and I a quarter of a century ago continue to inspire new generations of young theorists to devote their lives to work that might some day lead to real progress. But these problems remain extremely difficult ones, and we have little in the way of promising ideas, with far too much effort going into the evasion of difficulties and the pursuit of the chimera of unification through ever more complex higher dimensional constructions inspired by string theory.

Superfluid Helium

Once helium is cooled to within 2 degrees above absolute zero helium becomes a superfluid. At that point is has zero viscosity and can do things like rise out of a container – scaling the walls. Graphic from Wikipedia on Superfluid:

Helium II will “creep” along surfaces in order to find its own level – after a short while, the levels in the two containers will equalize. The Rollin film also covers the interior of the larger container; if it were not sealed, the helium II would creep out and escape.

More interesting superfluid traits:

The superfluid component has zero viscosity, zero entropy, and infinite thermal conductivity. (It is thus impossible to set up a temperature gradient in a superfluid, much as it is impossible to set up a voltage difference in a superconductor.) One of the most spectacular results of these properties is known as the thermomechanical or “fountain effect”. If a capillary tube is placed into a bath of superfluid helium and then heated, even by shining a light on it, the superfluid helium will flow up through the tube and out the top as a result of the Clausius-Clapeyron relation. A second unusual effect is that superfluid helium can form a layer, a single atom thick, up the sides of any container in which it is placed.

Strategic Research Plan for Nanotechnology

Productive Nanosystems report for the United States Department of Energy:

This Roadmap is a call to action that provides a vision for atomically precise manufacturing technologies and productive nanosystems. The United States nanotechnology advancement goal should be to lead the world towards the development of these revolutionary technologies in order to improve the human condition by addressing grand challenges in energy, health care, and other fields. The United States can accomplish this goal through accelerated global collaborations focused on two strategies that will offer ongoing and increasing benefits as the
technology base advances:

1. Develop atomically precise technologies that provide clean energy supplies and a cost-effective energy infrastructure.
2. Develop atomically precise technologies that produce new nanomedicines and multifunctional in vivo and in vitro therapeutic and diagnostic devices to improve human health.
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Close cooperation among scientific and engineering disciplines will be necessary because of the nature of the engineering problems involved. This cross-disciplinary collaboration will bring broad benefits through the cross-fertilization of ideas, instruments, and techniques that will result from developing the required technology base.

With international cooperation, the benefits of productive nanosystems will be delivered to the world faster. Coordinating a full international
effort is extremely desirable in order to minimize duplication of effort in smaller national programs conducted independently.

Another Bacteria DNA Trick

A DNA shift never before seen in nature

For several decades, researchers have known that it is possible to modify synthetic oligonucleotides (short strands of DNA) by adding sulfur to the sugar-phosphate DNA backbone as a phosphorothioate. Researchers often use such modifications in the laboratory to make DNA resistant to nucleases (enzymes that snip DNA in certain locations) as a step toward gene and antisense therapies of human diseases.

Dedon said he and his co-workers were surprised to discover that a group of bacterial genes, known as the dnd gene cluster, gives bacteria the ability to employ the same modification on their own. “It turns out that nature has been using phosphorothioate modifications of DNA all along, and we just didn’t know about it,” he said.
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He theorizes that the modification system might serve as either protection against foreign (unmodified) DNA, or as a “bookmark” to assist with transcription or replication of DNA.

Bacteria really are amazing. I am starting to read more about bacteria and virus so maybe I will post more on these topics over the next few months.

Orcas Create Wave to Push Seal Off Ice

Pretty amazing footage. From Nature News, Unique orca hunting technique documented:

Ingrid Visser of the Orca Research Trust in New Zealand and her colleagues report on six further observations of the animals using group hunting behaviour to divide ice floes, push them into open water, and create waves to wash animals off them into their waiting jaws.

Engineering for a Changing World

This interesting and long report (I have not finished reading it yet – 120 pages) has been completed by the President Emeritus of at The University of Michigan (and current University Professor of Science and Engineering): Engineering for a Changing World by James J. Duderstadt.

The fundamental knowledge undergirding engineering practice increasingly requires research at the extremes, from the microscopic level of nanotechnology to the mega level of global systems such as civil infrastructure, energy, and climate change as well as the mastery of new tools such as cyberinfrastructure and quantum engineering. It also requires far greater attention by government and industry to the support of the long-term basic engineering research necessary to build the knowledge base key to addressing society’s needs.
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It is similarly essential to elevate the status of the engineering profession, providing it with the prestige and influence to play the role it must in an increasingly technology-driven world while creating sufficiently flexible and satisfying career paths to attract a diverse population of outstanding students. Of particular importance is greatly enhancing the role of engineers both in influencing policy and popular perceptions and as participants in leadership roles in government and business.
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The inability of engineering to attract the best and brightest, as it does in most other nations, is due in part to the way engineering is perceived by prospective students, teachers, parents, and society more broadly (NSB, 2007). Society at large simply does not have an accurate perception of the nature of engineering. While the public associates engineers with economic growth and national defense, they fail to recognize the role of engineering in improving health, the quality of life, and the environment. They are relegated to the role of technicians rather than given the respect of other learned professions such as medicine and law. In sharp contrast to most other nations, one rarely finds engineers in leadership roles in business or government and hence they have relatively inadequate impact on the key strategic issues facing our nation and world.

Turning Trash into Gas

Frank Pringle has found a way to squeeze oil and gas from just about anything

Everything that goes into Frank Pringle’s recycling machine—a piece of tire, a rock, a plastic cup—turns to oil and natural gas seconds later.
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The machine is a microwave emitter that extracts the petroleum and gas hidden inside everyday objects—or at least anything made with hydrocarbons, which, it turns out, is most of what’s around you. Every hour, the first commercial version will turn 10 tons of auto waste—tires, plastic, vinyl—into enough natural gas to produce 17 million BTUs of energy (it will use 956,000 of those BTUs to keep itself running).
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Or rather, he had extracted it. Petroleum is composed of strings of hydrocarbon molecules. When microwaves hit the tire, they crack the molecular chains and break it into its component parts: carbon black (an ash-like raw material) and hydrocarbon gases, which can be burned or condensed into liquid fuel. Pringle figured that some gases from his microwaved tire had lingered, and the cold air in the shop had condensed them into diesel. If the process worked on tires, he thought, it should work on anything with hydrocarbons. The trick was in finding the optimum microwave frequency for each material—out of 10 million possibilities.

Long-Eared Jerboa

photo of a long eared jerboa

Mysterious mammal caught on film, the link has videos too:

The long-eared jerboa, a tiny nocturnal mammal that is dwarfed by its enormous ears, can be found in deserts in Mongolia and China.
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Until now, the creatures had proven extremely difficult to study, thanks to their minuscule size, nocturnal nature and the harsh desert environment that they inhabit.
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“These creatures hop just like a kangaroo; it is amazing to watch. Little hairs on their feet, almost like snow shoes, allow them to jump along the sand,” he explained.
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The expedition formed part of ZSL’s Edge programme, which focuses its efforts on conservation plans for animals that are both endangered and evolutionary distinctive. The long-eared jerboa is one of 10 species that the programme is looking at this year.

The Zoological Society of London Evolutionarily Distinct and Globally Endangered (EDGE) web site is a great source of all sorts of information. Including more on the Long-Earned Jerboa in the Gobi Desert. Great stuff, they have done a very nice job with their web site – even if they do force people to download the flash player for some material.

Genomics Course For College Freshman Supported by HHMI at 12 Universities

HHMI Selects 12 Institutions to Launch Nationwide Science Education Experiment

The Howard Hughes Medical Institute (HHMI) has selected 12 colleges and universities to participate in a nationwide genomics course that will involve first-year college students in authentic research. The new course is the first major initiative from HHMI’s Science Education Alliance, which seeks to enhance the teaching of science and inspire new generations of scientists.

In Fall 2008, first-year students at the six undergraduate institutions and six research-intensive institutions will take part in a year-long research course — the Phage Genomics Research Initiative – which is being developed by the Science Education Alliance (SEA). The SEA, headquartered at HHMI’s Janelia Farm Research Campus in Northern Virginia, will foster the development of a national network of scientists and educators who work collaboratively to develop and distribute new materials and methods to the education community.
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HHMI is committing a total of $4 million over the first four years of the program.
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Approximately 20 students at each institution will participate in the two-semester phage genomics research course, in which they will be taught to use sophisticated research techniques. Students will isolate bacterial viruses (phages) from their local soil, prepare the viral DNA for sequencing, and annotate and compare the sequenced genome. The goal is to immerse students in the process of doing science, and equip them with the critical thinking and communication skills necessary for successful research careers.