Category Archives: Science

Vaccine For Strep Infections

Engineered Protein Shows Potential as a Strep Vaccine

A University of California, San Diego-led research team has demonstrated that immunization with a stabilized version of a protein found on Streptococcus bacteria can provide protection against Strep infections, which afflict more than 600 million people each year and kill 400,000.
…
Group A Streptococcus (GAS). GAS causes a wide variety of human diseases including strep throat, rheumatic fever, and the life-threatening “flesh-eating” syndrome called necrotizing fasciitis. Studies were performed using M1 protein, which represents the version of M protein present on the most common disease-associated GAS strains.
…
“We created a modified version of M1 with a more stable structure, and found that it is just as effective at eliciting an immune reaction, but safer than the original version of M1, which has serious drawbacks to its use in a vaccine.”

Phun Physics

Coolest science toy ever

Phun is without question the greatest computer toy in the history of the universe, if this had been around when I was a kid I would be a frickin genius by now. You don’t need things any more. It’s extremely easy to use. As a starter tip, turn gravity off when you’re attaching stuff to the background (right click after selecting “affix” tool).

Very cool. Get your Phun (2D physics software) for free. Phun is a Master of Science Theises by Computing Science student Emil Ernerfeldt.

Some other very cool stuff: Cool Mechanical Simulation System – Scratch from MIT – What Kids can Learn – Lego Autopilot First Flight – Awesome Cat Cam

Flint and Steel: What Causes the Sparks?

What many people do not realize is that iron is a pyrophoric material; in the presence of oxygen, iron catches on fire automatically! It just starts burning. “But how can this be?” you may ask. “I can hold a chunk of iron in my hand and it does not burn me”.

The answer lays in the fact that the portion of the iron object in contact with the air and your skin is not pure iron. Rather it has developed a thin coating of iron oxide, or rust, immediately upon contact with the oxygen in the air. This serves to seal off the iron inside from exposure to the air and reduces the rate of further rusting.

Iron, whether man-made objects or naturally occurring in rocks, will rust upon exposure to oxygen in the air. The act of rusting is actually an exothermic reaction called “oxidation”, which is a fancy way of saying when iron touches the oxygen in the air a reaction occurs; the iron rusts (turns into iron oxide) and gives off heat. In other words, it burns. The simplified chemical reaction can be expressed as:

Fe2 + O2 = Fe2O3 + heat

Or in English:

Iron + Oxygen = Rust + Heat

Clouds Alive With Bacteria

Clouds above the Mesa Trail by John Hunter

Earth’s Clouds Alive With Bacteria

Clouds are alive with tiny bacteria that grab up water vapor in the atmosphere to make cloud droplets, especially at warmer temperatures, a new study shows.

The water droplets and ice crystals that make up clouds don’t usually form spontaneously in the atmosphere – they need a solid or liquid surface to collect on. Tiny particles of dust, soot and airplane exhaust – and even bacteria – are known to provide these surfaces, becoming what atmospheric scientists call cloud condensation nuclei (CCN).
…
These microbes could be carried into the atmosphere from an infected plant by winds, strong updrafts or the dust clouds that follow tractors harvesting a field. Christner and others suspect that becoming cloud nuclei is a strategy for the pathogen to get from plant to plant, since it can be carried for long distances in the atmosphere and come down with a cloud’s rain.

The next step in determining how big a role biological particles play in cloud droplet formation is to directly sample the clouds themselves, Christner says.

Pynchonverse Science

Mind-Bending Science in Thomas Pynchon’s Mind-Bending Novel Against The Day: Part I

Pynchon takes the science of this period and incorporates it deeply into the language and structure of Against the Day, more so perhaps than in any of his other novels. Against the Day is suffused with meditations on light, space, and time, and often plays with the tension between different perspectives in math and physics – classical physics versus relativity, Maxwell’s laws of electromagnetism described with the imaginary numbers of quaternions versus the real numbers of vector analysis. This material is not just filler – it’s critical to the core of Against the Day, a fact which has been underappreciated in early reviews of the novel.

One reviewer claimed that a new generation of writers has a “grasp of the systems that fascinate Pynchon — science, capitalism, religion, politics, technology — [that] is surer, more nuanced, more adult and inevitably yields more insight into how those systems work than Pynchon offers here.” When it comes to science at least, this claim is not true – Pynchon’s achievement in Against the Day proves that he is peerless as a poet who can mine science for gems of insight and set them into the context of the humanity that is the ultimate concern of his novels.

This great post offers a detailed explanation of some of the science related to Pynchon’s writing.

Placebo Effect

Don’t laugh, sugar pills are the future

In fact the new study added nothing (and it was ridiculously badly reported): we already knew that antidepressants perform only marginally better than placebo, and the National Institute for Health and Clinical Excellence (Nice) guidelines has actively advised against using them in milder depression since 2004. But the more interesting questions are around placebo.
…
Another study from 2002 looked at 75 trials of antidepressants over the past 20 years, but looked only at the response in the placebo arms of the trials, and found that the response to placebo has increased significantly in recent years (as has the response to medication): perhaps our expectations of those drugs have increased, or perhaps, conversely to our earlier example, the trial designs have become systematically more flattering. I’m giving you tenuous data, on an interesting area, because I know you’re adult enough to cope with ambiguity.

At the Heart of All Matter

The hunt for the God particle by Joel Achenbach

Physics underwent one revolution after another. Einstein’s special theory of relativity (1905) begat the general theory of relativity (1915), and suddenly even such reliable concepts as absolute space and absolute time had been discarded in favor of a mind-boggling space-time fabric in which two events can never be said to be simultaneous. Matter bends space; space directs how matter moves. Light is both a particle and a wave. Energy and mass are inter- changeable. Reality is probabilistic and not deterministic: Einstein didn’t believe that God plays dice with the universe, but that became the scientific orthodoxy.
…
Most physicists believe that there must be a Higgs field that pervades all space; the Higgs particle would be the carrier of the field and would interact with other particles, sort of the way a Jedi knight in Star Wars is the carrier of the “force.” The Higgs is a crucial part of the standard model of particle physics—but no one’s ever found it.
…
The Higgs boson is presumed to be massive compared with most subatomic particles. It might have 100 to 200 times the mass of a proton. That’s why you need a huge collider to produce a Higgs—the more energy in the collision, the more massive the particles in the debris. But a jumbo particle like the Higgs would also be, like all oversize particles, unstable. It’s not the kind of particle that sticks around in a manner that we can detect—in a fraction of a fraction of a fraction of a second it will decay into other particles. What the LHC can do is create a tiny, compact wad of energy from which a Higgs might spark into existence long enough and vivaciously enough to be recognized.

Previous posts on CERN and the Higgs boson: The god of small things – CERN Prepares for LHC Operations – CERN Pressure Test Failure – The New Yorker on CERN’s Large Hadron Collider

Funding Medical Research

Cheap, ‘safe’ drug kills most cancers

It sounds almost too good to be true: a cheap and simple drug that kills almost all cancers by switching off their “immortality”. The drug, dichloroacetate (DCA), has already been used for years to treat rare metabolic disorders and so is known to be relatively safe. It also has no patent, meaning it could be manufactured for a fraction of the cost of newly developed drugs.

Evangelos Michelakis of the University of Alberta in Edmonton, Canada, and his colleagues tested DCA on human cells cultured outside the body and found that it killed lung, breast and brain cancer cells, but not healthy cells. Tumours in rats deliberately infected with human cancer also shrank drastically when they were fed DCA-laced water for several weeks.

DCA attacks a unique feature of cancer cells: the fact that they make their energy throughout the main body of the cell, rather than in distinct organelles called mitochondria. This process, called glycolysis, is inefficient and uses up vast amounts of sugar.

Until now it had been assumed that cancer cells used glycolysis because their mitochondria were irreparably damaged. However, Michelakis’s experiments prove this is not the case, because DCA reawakened the mitochondria in cancer cells. The cells then withered and died

The University of Alberta is raising funds to further the research. Some look at this and indite a funding system that does not support research for human health unless there is profit to be made. Much of the blame seems to go to profit focused drug companies. I can see room for some criticism. But really I think the criticism is misplaced.

The organizations for which curing cancer is the partial aim (rather than making money) say government (partial aim or public health…), public universities (partial aim of science research or medical research…), foundations, cancer societies, private universities… should fund such efforts, if they have merit. Universities have huge research budgets. Unfortunately many see profit as their objective and research as the means to the objective (based on their actions not their claims). These entities with supposedly noble purposes are the entities I blame most, not profit focused companies (though yes, if they claim an aim of health care they I would blame them too).

Now I don’t know what category this particular research falls into. Extremely promising or a decent risk that might work just like hundreds or thousands of other possibilities. But lets look at several possibilities. Some others thoughts on where it falls: Dichloroacetate to enter clinical trials in cancer patients, from a previous post here – Not a Cancer Cure Yet, The dichloroacetate (DCA) cancer kerfuffle, CBC’s ‘The Current’ on dichloroacetate (DCA), Dichloroacetate (DCA) Phase II Trial To Begin (“Like hundreds (if not, thousands) of compounds being tested to treat cancer, DCA was shown by Michelakis’ group earlier this year to slow the growth of human lung tumors in a preclinical rodent model.”).
Continue reading →

Your Inner Fish

photo of Neil Shubin

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin. A great piece from the University of Chicago, Fish out of Water, provides a good preview to the book:

What are the leading causes of death in humans? Four of the top ten causes—heart disease, diabetes, obesity, and stroke – have some sort of genetic basis and, likely, a historical one. Much of the difficulty is almost certainly due to our having a body built for an active animal but the lifestyle of a spud.
…
The problem is that the brain stem originally controlled breathing in fish; it has been jerry-rigged to work in mammals… This works well in fish, but it is a lousy arrangement for mammals.
…
The example from microbes is not unique. Judging by the Nobel Prizes awarded in medicine and physiology in the past 13 years, I should have called this book Your Inner Fly, Your Inner Worm, or Your Inner Yeast. Pioneering research on flies won the 1995 Nobel Prize in medicine for uncovering a set of genes that builds bodies in humans and other animals. Nobels in medicine in 2002 and 2006 went to people who made significant advances in human genetics and health by studying an insignificant-looking little worm (C. elegans). Similarly, in 2001, elegant analyses of yeast (including baker’s yeast) and sea urchins won the Nobel in medicine for increasing our understanding of some of the basic biology of all cells. These are not esoteric discoveries made on obscure and unimportant creatures. These discoveries on yeast, flies, worms, and, yes, fish tell us about how our own bodies work, the causes of many of the diseases we suffer, and ways we can develop tools to make our lives longer and healthier.

Two of my more controversial posts have been: Evolution is Fundamental to Science and Understanding the Evolution of Human Beings by Country. Evolution is not controversial scientifically. Just as gravity is not. Obviously this understanding is far from universal however.

But it is just a matter of time: similar to Galileo Galilei and heliocentric cosmology. See: Galileo’s Battle for the Heavens – Copernican System – Galileo). We now sit maybe 100 years after Galileo’s death (based on the evidence available in support of each scientific theory). At some point the evidence is accepted and life continues. Though I must admit it, I find it a bit disappointing how long it is taking for some people to accept the evidence of evolution. But I probably need to learn to be more patient – I have been told that more than once. All I can do is try to help present some small amount of the great work so many scientists have done to advance our knowledge. And here I am talking about evolution – for the 28% of those in the USA that couldn’t provide the answer that earth revolves around the sun, in 1998, well, they need much more help than I can provide.

Bacteria Can Transfer Genes to Other Bacteria

From page 115 of Good Gems, Bad Germs:

Microbiologists of the 1950’s did not appreciate the stunning extent to which bacteria swap genes… In 1959 Japanese hospitals experience outbreaks of multidrug-resistant bacterial dysentery. The shigella bacteria, which caused the outbreaks, were shrugging off four different classes of previously effective antibiotics: sulfonamides, streptomycins, chloramphenicols, and tetracyclines… In fact, the Japanese researches found it quite easy to transfer multidrug resistance from E. coli to shingella and back again simply by mixing resistant and susceptible strains together in a test tube.