Category Archives: Science

Beautiful Basics of Science

Natalie Angier’s recent book, The Canon, is a great overview of the world of science. The book gets a bit too carried away with being cute (A top-of-the-line radar can pinpoint the whereabouts of a housefly two kilometers away, although clearly this is a radar with far too much time on its hands), but overall is excellent. Such lines are find, in moderation, but this book has too many by a factor of 10 or 100. Some gems from the book:

page 19: Science is not a rigid body of facts. It is a dynamic process of discovery.

page 47: true happenstance bears a distinctive stamp, and until you are familiar with its pattern, you are likely to think it messier, more haphazard, than it is… it often makes people uncomfortable by not looking random enough.

page 92: while the different atoms are all about the same size – a tenth of a billionth of a meter across – they diverge in their mass, in the number of protons and neutrons with which their nucleus is crammed.

page 99: If you drag a comb through your dry hair, the comb will strip off millions of electrons from the outermost shells of the atoms of you coiffure.

The details are great (about a trillion electrons are involved when you get a small static electricity shock) and it is an excellent book for those interested in an overview of science that does not require in depth science education to follow. And yet with a good background in science the material presented is still plenty interesting.

Dolphins Using Tools to Hunt

photo of a dolphin with a sponge it uses to hunt

Photograph of dolphin with a sponge it uses to hunt, courtesy of Ewa Krzyszczyk, PLoS, high resolution.

Cool open access research from PLoS One, Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission.

We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.

The dolphins use the sponge to push along the ocean floor and disturb fish, that are hidden. Once the fish start swimming away the dolphin abandons the sponge and catches and eats the fish. Then the dolphin goes back and gets the sponge and continues.

How Antibiotics Kill Bacteria

Since the first antibiotics reached the pharmacy in the 1940s, researchers discovered that they target various pieces of machinery in bacterial cells, disrupting the bacteria’s ability to build new proteins, DNA, or cell wall. But these effects alone do not cause death, and a complete explanation of what actually kills bacteria after they are exposed to antibiotics has eluded scientists.
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The group found that all bactericidal antibiotics, regardless of their initial targets inside bacteria, caused E. coli to produce unstable chemicals called hydroxyl radicals. These compounds react with proteins, DNA, and lipids inside cells, causing widespread damage and rapid death for the bacteria.
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With the results of these two experiments, the researchers were able to identify three major processes implicated in gentamicin-induced cell death: protein transport, a stress response triggered by abnormal proteins in the cell membrane, and a metabolic stress response.

Poor Reporting and Unfounded Implications

Correlation is not causation. And reporting of the form, “1 time this happened” and so I report it as though it is some relevant fact, is sad. Take any incident that happened and then state random traits you want to imply there is some relevant link to (blue eyes, red hair, people that watch IT Crowd, people that bought a banana yesterday, tall, overweight, did poorly in math…) and most people will know you are ignorant.

Looking at random data people will find patterns. Sound scientific experimentation is how we learn, not trying to find anything that support our opinions. Statistics don’t lie but ignorant people draw faulty conclusions from data (when they are innumerate – illiteracy with mathematical concepts).

It’s not what the papers say, it’s what they don’t by Ben Goldacre

On Tuesday the Telegraph, the Independent, the Mirror, the Express, the Mail, and the Metro all reported that a coroner was hearing the case of a toddler who died after receiving the MMR vaccine, which the parents blamed for their loss. Toddler ‘died after MMR jab’ (Metro), ‘Healthy’ baby died after MMR jab (Independent), you know the headlines by now.

On Thursday the coroner announced his verdict: the vaccine played no part in this child’s death. So far, of the papers above, only the Telegraph has had the decency to cover the outcome.
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Measles cases are rising. Middle class parents are not to blame, even if they do lack rhetorical panache when you try to have a discussion with them about it.

They have been systematically and vigorously misled by the media, the people with access to all the information, who still choose, collectively, between themselves, so robustly that it might almost be a conspiracy, to give you only half the facts.

Science education is important. Even if people do not become scientists, ignorance of scientific thinking is dangerous. The lack of scientific literacy allows scientifically illiterate leaders to make claims that are lacking scientific merit. And results in people making poor choices themselves, due to their ignorance.

Engineers and Scientists in Congress

I started maintaining a list of Congressmen with PhDs and graduate degrees in science, engineering and math awhile back.

Please comment with any additions that you know of.

The following were re-elected:
Vernon Ehlers, Michigan, physics PhD; Rush Holt, New Jersey, physics PhD; John Olver, Massachusetts, chemistry PhD; Brian Baird, Washington, psychology PhD; Bill Foster, Illinois, physics PhD.

Other scientists, engineers and mathematicians that were reelected include: Ron Paul, Texas, biology BS, MD; Jerry McNerney, California, mathematics PhD; Dan Lipinski, Illinois, mechanical engineering BS, engineering-economic systems MS; Todd Akin, Mississippi, management engineering BS;Cliff Stearns, Florida, electrical engineering BS; Louise Slaughter, New York, microbiology BS; Joe Barton, Texas, industrial engineering BS, Pete Stark, California, engineering BS, Mike Honda, California.

Lost: Nancy Boyda, Kansas (BS chemistry).

Newly elected: Bill Cassidy, Louisiana (BS Biochemistry, MD); Pete Olson, Texas (BA computer science); Kurt Schrader, Oregon (Doctor of Veterinary Medicine); Martin Heinrich, New Mexico (BS engineering), Gregg Harper, Mississippi (BS chemistry), Joseph Cao, Mississippi (BA physics); Brett Guthrie, Virginia (BS mathematical economics); Erik Paulsen, Minnesota, mathematics BA; Parker Griffith, Alabama (BS chemistry, MD); Cynthia Lummis, Wyoming (BS animal science and biology).

Before you leap to the conclusion that scientists are taking over Congress, remember 2 things: 1) I have probably been missing plenty that were in congress already and 2) this is still a total of less than 10% with even a BS in science, math or engineering. I attempted to determine the status of all those newly elected this year.

Please comment, if you know of others in Congress with science and engineering backgrounds. If we get this list to be relative close to accurate then we can start tracking the total representation in congress and see if it is increasing, decreasing or randomly fluctuating over time.

Compounding is the Most Powerful Force in the Universe

A talking head with some valuable info. I remember my father (a statistics professor) getting me to understand this as a small child (about 6 years old). The concept of growth and mathematical compounding is an important idea to understand as you think and learn about the world. It also is helpful so you understand that statistics don’t lie but ignorant people can draw false conclusions from limited data.

It is unclear if Einstein really said this but he is often quoted as saying “compounding is the most powerful force in the universe.” Whether he did or not, understanding this simple concept is a critical component of numeracy (literacy with numbers). Also quoted at times as: “Compound interest is the eighth wonder of the world.” My guess is that people just find the concept of compounding amazing and then attribute quotes about it to Einstein.

I strongly encourage you to watch at least the first 2 segments (a total of 15 minutes). And then take some time and think. Take some time to think about compounding in ways to help you internalize the concepts. You can also read his book: The Essential Exponential For the Future of Our Planet by Albert Bartlett.

Britain’s Doctors of Innovation

Susannah Fleming, a PhD student at the University of Oxford life sciences interface doctoral training centre. She is developing a monitoring system to assess children when they first present to medical care. Source

Minister of State for Science and Innovation, Lord Drayson, announced the Â£250million (about $370 million) initiative which will create 44 training centres across the UK and generate over 2000 PhD students. They will tackle some of the biggest problems currently facing Britain such as climate change, energy, our ageing population, and high-tech crime.

17 of the centers will put specific emphasis on integrating industrial and business skills with the PhD education. This approach to training has been extensively piloted by EPSRC through a small number of thriving Engineering Doctorate Centres and Doctoral Training Centres in Complexity Science, Systems Biology and at the Life Sciences Interface. This new investment builds on the success of these and will establish a strong group of centres which will rapidly establish a pre-eminent international reputation for doctoral training.

The multidisciplinary centres bring together diverse areas of expertise to train engineers and scientists with the skills, knowledge and confidence to tackle today’s evolving issues. They also create new working cultures, build relationships between teams in universities and forge lasting links with industry.

As I have said before I think countries are smart to invest in their science and technology futures. In fact I believe creating centers of science and technology excellence is a key to future economic wealth.

Full press release: Â£250 Million to Create New Wave of Scientists and Engineers for Britain

Harnessing Light to Drive Nanomachines

A team led by researchers has shown that the force of light indeed can be harnessed to drive machines – when the process is scaled to nano-proportions. Their work opens the door to a new class of semiconductor devices that are operated by the force of light. They envision a future where this process powers quantum information processing and sensing devices, as well as telecommunications that run at ultra-high speed and consume little power.

The energy of light has been harnessed and used in many ways. The “force” of light is different — it is a push or a pull action that causes something to move. “While the force of light is far too weak for us to feel in everyday life, we have found that it can be harnessed and used at the nanoscale,” said team leader Hong Tang, assistant professor at Yale. “Our work demonstrates the advantage of using nano-objects as ‘targets’ for the force of light – using devices that are a billion-billion times smaller than a space sail, and that match the size of today’s typical transistors.”

Full Press release

2,000 Species New to Science from One Island

photo of squat lobster

Photograph by Dr Tin-Yam Chan, University of Keelung

153 scientists from 20 countries fanned out across the remote South Pacific island of Espiritu Santo, examining mountains, forests, caves, reefs, and water for all living organisms. In five months, they collected 10,000 species. Some 2,000 of these may be new to science.

This squat lobster, found in waters 150 meters (492 feet) deep, is one of the new species. Eighty percent of the world’s species remain to be discovered, notes French scientist Philippe Bouchet, one of the expedition’s leaders.

A World of Crabs from One Tiny Island

About 600 of these were crab species. The two-horn box crab is able to crack and peel open snails’ shells using a sharp “tooth” on its right claw to cut open shells and long, slender “fingers” on the left claw to yank out its prey.

HHMI on Science 2.0: Information Revolution

The Howard Hughes Medical Institute does great things for science and for open science. They have an excellent article in their HHMI Bulletin – Science 2.0: You Say You Want a Revolution?

Cross-pollination among research disciplines is in fact at the core of many other popular science blogs. Michael Eisen, an HHMI investigator at the University of California, Berkeley, is an avid blog reader who particularly enjoys John Hawks’ site on paleoanthropology, genetics, and evolution. A recent post there discussed a new sequencing of Neanderthal mitochondrial DNA. “It’s like a conduit into another whole world,” says Eisen.
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The current extreme of collaboration via Science 2.0 is OpenWetWare.org. Begun in 2003 by Austin Che, who was then a computer science and biology graduate student at MIT, this biological-engineering Website uses the wiki model to showcase protocols and lab books: everything is open and can be edited by any of its 4,000 members.
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“Most publishers wish open access would go away,” says Brown. It won’t. Major research-funding organizations, including NIH, HHMI, and the Wellcome Trust, now require their grantees to post their findings on openaccess Websites such as PLoS or PubMed Central within 12 months of publication in traditional journals. Publishers are pushing back, however, and in September, the House Judiciary Committee began holding hearings on whether the federal government should be allowed to require grantees to submit accepted papers to a free archive.