Category Archives: Science

DNA Seen Through the Eyes of a Coder

Great paper looking at DNA from the perspective of a computer programmer. DNA seen through the eyes of a coder by Bert Hubert:

The language of DNA is digital, but not binary. Where binary encoding has 0 and 1 to work with (2 – hence the ‘bi’nary), DNA has 4 positions, T, C, G and A. Whereas a digital byte is mostly 8 binary digits, a DNA ‘byte’ (called a ‘codon’) has three digits. Because each digit can have 4 values instead of 2, an DNA codon has 64 possible values, compared to a binary byte which has 256.

A typical example of a DNA codon is ‘GCC’, which encodes the amino acid Alanine. A larger number of these amino acids combined are called a ‘polypeptide’ or ‘protein’, and these are chemically active in making a living being.
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Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called ‘exons’. The comments, that come ‘inbetween’ are called ‘introns’.

Problems with Scientific Research Funding

The Wired blog proposes the following, Vote for the Biggest Problems with Scientific Research Funding

The cost of the wars in Iraq and Afghanistan, which could exceed $1.2 trillion, are particularly appalling when compared to the measly $6.43 billion requested by the National Science Foundation and $28.6 billion requested by the National Institutes of Health for supporting nationwide research in 2008.

Join us in complaining about the many problems with research funding in the voting widget below.

Some of the current leading problems: Defense Contractors Get More Tax Dollars than Medical Researchers, Keep the masses uneducated = some Republicans don’t believe in evolution, The Science of Global Warming, No Federal Funding for Embryonic Stem Cell Research. Those may or may not serious problems but they do seem to show a tendency for certain constituencies to be vocal online.

I don’t think this voting is actually very insightful. But it is at least raising two issues I have been raising a bit more lately: science funding (our newest category) and politics and science (Science and Engineering in Politics – Politics and Science Research).

Young Geneticists Making a Difference

After an early phase of discouragement, Johannes Krause was able to follow his long interest in genetics and even link it to another passion of his, paleoanthropology. Krause initially chose to study biochemistry at the University of Leipzig. But “I was almost about to quit” at the frustration of learning much more about basic chemistry than biology, he says. However, in the third year of his bachelor’s degree, he took some specialised courses in genetics as an Erasmus student at the University College Cork in Ireland that revived his interest for the field.

Back in Leipzig, a summer internship on comparing gene expression between humans and chimpanzees at the Max Planck Institute for Evolutionary Anthropology sparked Krause’s enthusiasm for good. He stayed on in the lab as a research assistant for 2 years before graduating in 2005. While there, Krause helped develop a biological method to read large pieces of ancient DNA, sequence the complete mitochondrial genome of the mammoth from fossil samples, and place it in the context of evolution. “Johannes has great technical skill and the judgment to distinguish a good project from a blind alley. Like few others he can see the interesting pattern that can hide in sometimes confusing data,” Svante PÃ¤Ã¤bo, his principal investigator, writes in an e-mail to Science Careers.

Cu₂C0₃(OH)₂

Photo of Malachite, Cu₂C0₃(OH)₂, copper(II) carbonate hydroxide, at the Smithsonian Natural History Museum in Washington DC, by John Hunter. Related: United States Botanical Garden photos – Science and Engineering Web Search

Smart Squirrels Sneaky Snake Strategy

Squirrels Use “Snake Perfume” to Fool Predators

To mask their odor from rattlesnakes, California ground squirrels and rock squirrels chew on sloughed-off snake skin and smear it on their fur, according to a new study. The act most likely persuades the predators that another snake, not a squirrel, is in the area.

“To our knowledge this is the first case where [this idea] has been tested systematically and shown to have an anti-predator function—protecting the squirrel from rattlesnake predation,” said study lead author Barbara Clucas.Rattlers and other snakes usually prey on baby squirrels, because the adults have proteins in their blood that make them immune to snake venom.

Pups, on the other hand, aren’t big enough to resist the poison. Clucas and colleagues therefore think that adult female and juvenile squirrels spend more time applying snake scent to their bodies. “Adult females actively protect their pups … and share their burrows with juveniles,” Clucas said.

Stephen Hawking Joins Attack on Science Cuts

Stephen Hawking joins attack on science cuts

The Council, which funds public research in particle physics and astronomy, has to save Â£80 million over the next three years because of lack of Government funding. To add insult to injury, Nature reports that the Government has also raided a similar amount – Â£93 million – from the money raised from patents by the Medical Research Council, an act which has been condemned as a “breach of faith” by the Royal Society.

The newest category I added was for funding a month ago. This is another example of the important role funding plays in science. And is a reminder that political realities affect government funding science will receive. As I said earlier this month: If the science and engineering community are not well represented to our representatives the interests of the science and engineering community will get short changed. Many working is science don’t want to be involved in the political debate but those who are involved play an important role.

Africa Turning to China and India for Engineering and Science Education

‘Browning’ the technology of Africa by G. Pascal Zachary

The sudden influx of Chinese and Indian technologies represents the “browning” of African technology, which has long been the domain of “white” Americans and Europeans who want to apply their saving hand to African problems.

“It is a tectonic shift to the East with shattering implications,” says Calestous Juma, a Kenyan professor at Harvard University who advises the African Union on technology policy. One big change is in education. There are roughly 2,000 African students in China, most of whom are pursuing engineering and science courses. According to Juma, that number is expected to double over the next two years, making China “Africa’s leading destination for science and engineering education.”

China’s technology inroads are usually less dramatic, but no less telling. In African medicine, Chinese herbs and pharmaceuticals are quietly gaining share. For example, the Chinese-made anti-malarial drug artesunate has become part of the standard treatment within just a few years. Likewise, Chinese mastery over ultra-small, cheap “micro-hydro” dams, which can generate tiny amounts of electricity from mere trickles of water, appeals to power-short, river-rich Africans. Tens of thousands of micro-hydro systems operate in China, and nearly none in Africa.

Science Explained: What The Heck is a Virus?

What The Heck is a Virus? [removed broken link]

A virus is not strictly alive.. nor is it strictly dead… A virus has some fundamental information (genes made of DNA or RNA) which allows it to make copies of itself. However, the virus must be inside a living cell of some kind before the information can be used. In fact, the information won’t be made available unless the virus enters a living cell. It is this entrance of a virus into a cell which is called a viral infection. Too, the virus is very, very small relative to the size of a living cell. Therefore, the information the virus can carry is actually not enough to allow it to make copies (replicate). The virus uses the cell’s machinery and some of the cell’s enzymes to generate virus parts which are later assembled into thousands of new, mature, infectious virus which can leave the cell to infect other cells.

Bigger Impact: 15 to 18 mpg or 50 to 100 mpg?

This is a pretty counter-intuitive statement, I believe:

You save more fuel switching from a 15 to 18 mpg car than switching from a 50 to 100 mpg car.

But some simple math shows it is true. If you drive 10,000 miles you would use: 667 gallons, 556 gallons, 200 gallons and 100 gallons. Amazing. I must admit, when I first read the quote I thought that it must be an wrong. But there is the math. You save 111 gallons improving from 15 mpg to 18 mpg and just 100 improving from 50 to 100 mpg. Other than those of you who automatically guess that whatever seems wrong must be the answer when you see a title like this I can’t believe anyone thinks 15 to 18 mpg is the change that has the bigger impact. It is great how a little understanding of math can help you see the errors in your initial beliefs. Via: 18 Is Enough.

It also illustrates that the way the data is presented makes a difference. You can also view 100 mpg as 1/100 gallon per mile, 2/100 gallons per mile, 5.6/100 gpm and 6.7 gpm. That way most everyone sees that the 6.7 to 5.6 gpm saves more fuel than 2 to 1 gpm does. Mathematics and scientific thinking are great – if you are willing to think you can learn to better understand the world we live in every day.

Great Physics Webcast Lectures

One great example of MIT’s Open Course Ware initiative is Physics I: Classical Mechanics. This course features lecture notes, problem sets with solutions, exams with solutions, links to related resources, and a complete set of videotaped lectures. The 35 video lectures by Professor Lewin, were recorded on the MIT campus during the Fall of 1999. These are some great lectures by a entertainer and educator. Some lecture topics: Newton’s Laws, Momentum – Conservation of Momentum – Center of Mass, Doppler Effect – Binary Stars – Neutron Stars and Black Holes, The Wonderful Quantum World – Breakdown of Classical Mechanics. What a wonderful web it is.