Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

Evolution is Fundamental to Science

Evolution is absolutely fundamental to scientific thinking. Any country, or part of a country (or those wishing to lead a country) that teaches evolution as though it is some alternative way of looking at the facts (that can be compared to creationism/intelligent design, as science, for example) is an embarrassment. Unfortunately the United States is home to far too much of this thinking – which explains why scientific literacy is so low. Luckily there are also plenty in the USA that understand science. The National Academy of Science has published, Science, Evolution, and Creationism, in which a

group of experts assembled by the National Academy of Sciences and the Institute of Medicine explain the fundamental methods of science, document the overwhelming evidence in support of biological evolution, and evaluate the alternative perspectives offered by advocates of various kinds of creationism, including “intelligent design.” The book explores the many fascinating inquiries being pursued that put the science of evolution to work in preventing and treating human disease, developing new agricultural products, and fostering industrial innovations. The book also presents the scientific and legal reasons for not teaching creationist ideas in public school science classes.

The scientific theory of evolution still has details that can be debated – which is what the scientists should and will do (seeking out evidence to support such details). The idea that people today can question evolution is beyond amazing to me. It is much easier to understand some people thinking you would sail off the edge of the earth 500 years ago than anyone in the USA thinking there is any serious debate about evolution (there are parts of the world where the educational system does not give everyone a chance to see the available evidence, so I can forgive some in the world for being ignorant – not having been exposed to the evidence). And I guess there are parts of the USA educational system that are nearly so poor also where a gullible student could not see the truth. But in the USA the evidence is easily at hand – you have to intentionally remain ignorant to somehow not understand the truth of evolution.

What Everyone Should Learn:

Dr. Vincent Cerf: “I would want people to really understand the theory of evolution and the origin of species. The power of cumulative, adaptive change in the genome, over the course of billions of years and changing conditions, is hard for many people to fully appreciate.”

Robot Fly

Tinker, Tailor, Robot, Fly

Designing an automated fly implied having the ability to make lightweight, miniature working parts, a process that Wood says took up the bulk of his doctoral study, because of the lack of any previous research on which to draw. “For years, the thrust of our work was ‘How do we do this?'” says Wood. “There was no existing fabrication paradigm, given the scale we were operating on, the speed we wanted to operate with, and things like cost, turnaround, and robustness.” His research group developed and fabricated a laser carving system that could meticulously cut, shape, and bend sheets of carbon fiber and polymer – both strong but lightweight materials – into the necessary microparts.

And how to power those wings to beat 120 times per second? To keep this 60-milligram robot (the weight of a few grains of rice) with a 3-centimeter wingspan to a minimal size and weight, Wood says, you can’t simply use a shrunken version of the heavy DC (direct current) motors used in most robots. So he and his team settled on a simple actuator: in this case, a layered composite that bends when electricity is applied, thereby powering a micro-scale gearbox hooked up to the wings. Wood says the actuator works even better than its biological inspiration. The power density – a measure of power output as a function of mass – of a fly’s wing muscles is around 80 watts per kilogram; Wood’s wing design produces more than 400 watts per kilogram.

The first takeoff occurred late one evening last March, as Wood worked alone in his office, his colleagues gone for the evening. As the fly rose, Wood jumped up in celebration, quickly verified that his camera had captured the flight, and let out a sigh of relief.

Geothite

Photo of Geothite, FeO(OH), Hydrated Iron Oxide, at the Smithsonian Natural History Museum in Washington DC, by John Hunter. Related:Science and Engineering Web Search – Boston Science Museum photos

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’.

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

New Drug Targets May Fight Tuberculosis in Novel Way

New Drug Targets May Fight Tuberculosis and Other Bacterial Infections in Novel Way

“We have developed the first inhibitor of a key small molecule from Mycobacterium tuberculosis and Mycobacterium leprae (which causes leprosy) utilized to subvert human host’s defenses and damage and invade human host’s cells during infection,” explains study senior author Dr. Luis Quadri, Associate Professor of Microbiology and Immunology at Weill Cornell.
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“We are moving beyond antimicrobials such as antibiotics, which kill the bacterium directly, to anti-infectives, that may have no effect against the pathogen in the test tube but which do compromise its ability to infect and spread in the host,” he explains. “We believe that the expansion of the drug armamentarium to include such anti-infective drugs could help the fight against multi-drug resistant infection that has become such a challenge today.”
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“I believe that drugs targeting virulence factors are just one component of the paradigm shift in the antimicrobial drug discovery for the 21st century—one that will offer patients more options in the fight against truly global killers,” he says.

Molecular Bioengineering and Dynamical Models of Cells

Study Maps Life in Extreme Environments, Creating Potential for Molecular Bioengineering and Dynamical Models of Cells

The researchers focused on a little studied organism that can survive high salt, radiation, and other stresses that would be deadly to most other organisms. By focusing on such an organism the researchers were able to show definitively that they could understand and model the circuit controlling the cell directly from experiments designed to measure all genes in the genome simultaneously. These are called systems-biology experiments. This scholarship is part of a new scientific field, systems biology, which examines how genes influence each other via extremely large networks of interaction and how these networks respond to stimuli, adapting over time to new environments and cell states.
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“This is also a good model to explain how, in general, cells make stable decisions as they move through time scales,” added Bonneau, who is part of an NYU research group that handled the analysis of this genome. “If you want to understand how cells respond to their environments, the model offers a clearer window than previously existed for this domain of life.” The collaboration between Baliga’s and Bonneau’s research groups represents a type of partnership becoming more essential to biological and biomedical research: biologists and computer scientists teaming up to design experiments and analysis that synergize to decipher living systems, resulting in ever more complex and accurate models of the cell.

Science Explained: Genetics

The latest 1 page summary of a science topic from Seed Magazine – Genetics cribsheet:

The field of genetics deals with the way living things store and use information required for their development and behavior. This Cribsheet covers the basics of molecular genetics: DNA replication, the genetic code, and gene expression. In addition, we tell you how genome sequencing has progressed over the last decade and what researchers hope to accomplish with synthetic biology.

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.