In the new study, scientists ordered 101 DNA fragments, encompassing the entire Mycoplasma genome, from commercial DNA synthesis companies. These fragments were designed so that each overlapped its neighboring sequence by a small amount; these overlapping stretches stick together, thanks to the chemical properties of DNA. Researchers then bound the fragments piece by piece, eventually generating the full 582,970 base pair Mycoplasma sequence.

Scientists have been warning for years that overfishing is degrading the health of the oceans and destroying the fish species on which much of humanity depends for jobs and food. Even so, it would be hard to frame the problem more dramatically than two recent articles in The Times detailing the disastrous environmental, economic and human consequences of often illegal industrial fishing.

Sharon LaFraniere showed how mechanized fishing fleets from the European Union and nations like China and Russia – usually with the complicity of local governments – have nearly picked clean the oceans off Senegal and other northwest African countries. This has ruined coastal economies and added to the surge of suddenly unemployed migrants who brave the high seas in wooden boats seeking a new life in Europe, where they are often not welcome.

The second article, by Elisabeth Rosenthal, focused on Europe’s insatiable appetite for fish – it is now the world’s largest consumer. Having overfished its own waters of popular species like tuna, swordfish and cod, Europe now imports 60 percent of what it consumes. Of that, up to half is contraband, fish caught and shipped in violation of government quotas and treaties.

The measured effects today should be enough for sensible people to realise the tragedy of the commons applies to fishing and obviously governments need to regulate the fishing to assure that fishing is sustainable. This is a serious problem exacerbated by scientific and economic illiteracy. The obvious scientific and economic solution is regulation. Determining the best regulation is tricky (and political and scientific and economic) but obviously regulation (and enforcement) is the answer.

“The results were pretty astounding. All non-bacterial life on Earth – called eukaryotic life – can now be divided into four main groups instead of the five groups that we have been working with up to now,” says Kamran Shalchian-Tabrizi, an associate professor from the University of Oslo’s Department of Biology
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All life on Earth can be divided into two essentially different life forms—eukaryotes and prokaryotes. The eukaryotes gather their genetic material in a nucleus, while the prokaryotes (bacteria and archaea) have their genetic material floating freely in the cell. Eukaryotic organisms—such as humans—can, as a result of the new findings, be divided into the following four categories:

• Plants (green and red algae, and plants)
• Opisthokonts (amoebas, fungi, and all animals—including humans)
• Excavates (free-living organisms and parasites)
• SAR (the new main group, an abbreviation of Stramenophiles, Alveolates, and Rhizaria, the names of some of its members)

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Three billion years ago, there was only bacteria and Archaea. Eukaryotic life, which comprises all multi-celled organisms, developed in the sea—probably between 1.2 and 1.6 billion years ago. It was not before about 500 million years ago that the first creatures crept onto land.

For decades, the theory that lowering cholesterol is always beneficial has been a core principle of cardiology. It has been accepted by doctors and used by drug makers to win quick approval for new medicines to reduce cholesterol.

But now some prominent cardiologists say the results of two recent clinical trials have raised serious questions about that theory — and the value of two widely used cholesterol-lowering medicines, Zetia and its sister drug, Vytorin.
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“The idea that you’re just going to lower LDL and people are going to get better, that’s too simplistic, much too simplistic,” said Dr. Eric J. Topol

Legislation in the form of the America Competes Act was passed in the House and Senate in 2007, and it appeared the United States was finally going to move forward after years of neglect to increase investment in math, science and basic research. All parties agreed that our competitiveness in the 21st century was at stake and we needed to act.

So much for political will.

The recent budget deal between Republicans and Democrats effectively flat-funds or cuts funding for key science agencies. Excluding “earmarks,” the Department of Energy funding for fiscal year 2008 is up only 2.6 percent, thus losing ground to inflation. The National Science Foundation is up 2.5 percent, with the same result. The National Institute of Standards and Technology is up 11 percent, however the labs where research happens only get 2.3 percent, again losing ground to inflation.
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What are they thinking? When will they wake up? It may already be too late; but I genuinely think the citizenry of this country wants the United States to compete. If only our elected leaders weren’t holding us back.

Over the last few years we have noticed worrisome trends in CS education. The following represents a summary of those trends:
1. Mathematics requirements in CS programs are shrinking.
2. The development of programming skills in several languages is giving way to cookbook approaches using large libraries and special-purpose packages.
3. The resulting set of skills is insufficient for today’s software industry (in particular for safety and security purposes) and, unfortunately, matches well what the outsourcing industry can offer. We are training easily replaceable professionals.
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As faculty members at New York University for decades, we have regretted the introduction of Java as a first language of instruction for most computer science majors. We have seen how this choice has weakened the formation of our students, as reflected in their performance in systems and architecture courses.
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Every programmer must be comfortable with functional programming and with the important notion of referential transparency. Even though most programmers find imperative programming more intuitive, they must recognize that in many contexts that a functional, stateless style is clear, natural, easy to understand, and efficient to boot.

An additional benefit of the practice of Lisp is that the program is written in what amounts to abstract syntax, namely the internal representation that most compilers use between parsing and code generation. Knowing Lisp is thus an excellent preparation for any software work that involves language processing.

Dewar, a professor emeritus of computer science at New York University, believes that U.S. colleges are turning out programmers who are – there’s no nice way to say this – essentially incompetent.

Dr. Jeff Brooks has been director of the UCSF lab for 29 years, and has watched with a mixture of fascination and dread how bacteria once tamed by antibiotics evolve rapidly into forms that practically no drug can treat.
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“We are on the verge of losing control of the situation, particularly in the hospitals,” said Dr. Chip Chambers, chief of infectious disease at San Francisco General Hospital. The reasons for increasing drug resistance are well known:
– Overuse of antibiotics, which speeds the natural evolution of bacteria, promoting new mutant strains resistant to those drugs.
– Careless prescribing of antibiotics that aren’t effective for the malady in question, such as a viral infection.
– Patient demand for antibiotics when they aren’t needed.
– Heavy use of antibiotics in poultry and livestock feed, which can breed resistance to similar drugs for people.
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Terry Hazen, senior scientist at Lawrence Berkeley National Laboratory and director of its ecology program, is not at all surprised by the tenacity of our bacterial foes. “We are talking about 3.5 billion years of evolution,” he said. “They are the dominant life on Earth.”

Bacteria have invaded virtually every ecological niche on the planet. Human explorers of extreme environments such as deep wells and mines are still finding new bacterial species. “As you go deeper into the subsurface, thousands and thousands of feet, you find bacteria that have been isolated for millions of years – and you find multiple antibiotic resistance,” Hazen said.

In his view, when bacteria develop resistance to modern antibiotics, they are merely rolling out old tricks they mastered eons ago in their struggle to live in harsh environments in competition with similarly resilient species.