Category Archives: Science

Contradictory Medical Studies

I have written before about false research findings. This is an important topic – we need to remember that the interpritation of one study (or many studies) in not necessarily conclusive. Another article – When Medical Studies Collide:

Two years ago, the headlines blared that echinacea was a bust. Millions of people who believed the best-selling herbal remedy was warding off colds were probably deluding themselves, according to The New England Journal of Medicine. Now echinacea is back in the news. This time, it works! So says a study in The Lancet Infectious Diseases.

How could two studies come to such different conclusions—especially when there have been no new trials of the herb? While the New England Journal reported on one clinical trial, authors of the latest report combined data from previous studies, a controversial approach called a meta-analysis. Its conclusion is dramatically different—not just from that of the New England Journal paper, but also from a review last year of the same studies.
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The problem is, the world of medical and health research is messier than most people realize. Black-and-white answers are rare, even when it comes to a single drug trial.

Just remember those last two sentences. Very simple. And most people would agree if you showed them those two sentences and asked if they agreed. But then they see a headline and away they go… Just force yourself to repeat that idea every time you see a health report. Don’t believe the headline without strong support.

An interesting tidbit from the article. The coneflower is the source of echinacea. I tried to find photos that I am pretty sure I have on my hard drive of the flowers in my back yard, but I couldn’t.

Evolutionary Design

Evolutionary algorithms now surpass human designers by Paul Marks:

Evolutionary Algorithms take two parent designs – for a boat hull, say – and blend components of each, perhaps taking the surface area of one and the curvature of another, to produce multiple hull offspring that combine the features of the parents in different ways. Then the algorithm selects those offspring it considers are worth re-breeding – in this case those with the right combination of parameters to make a better hull. The EA then repeats the process. Although many offspring will be discarded, after thousands of generations or more, useful features accumulate in the same design, and get combined in ways that likely would not have occurred to a human designer. This is because a human does not have the time to combine all the possibilities for each feature and evaluate them, but an EA does.

Evolving new designs is very cool. One point I would like to make (I am biased since my father did a great deal of work in this area) is the power of design of experiments to allow experimenting on multiple factors at once. This is a methodology that is still used far too little. Regardless, evolutionary design is very cool. The Human-Competitive awards highlight some examples.

National Science and Technology Medals

photo of White House Technology Medal Ceremony - July 2007

The 2005 and 2006 National Medals for Science and Technology were awarded at a White House Ceremony this week. The National Science and Technology Medals Foundation web site has photos of each award winner receiving their medals this year and a list of all winners. The National Medal of Science was established by Congress in 1959 as a Presidential award, has recognized 441 of America’s leading scientists and engineers. The evaluation criteria is based on the total impact an individual’s work has had on the present state of physical, chemical, biological, mathematical, engineering, behavioral or social sciences.

The National Medal of Technology was established by Congress in 1980 as a Presidential award, has recognized 146 individuals and 26 companies whose accomplishments have generated jobs and created a better standard of living. Their accomplishments best embody technological innovation and support the advancement of global U.S. competitiveness.

List of all winners from the White House press release: Continue reading →

Time

Newsflash: Time May Not Exist

Planck time—the smallest unit of time that has any physical meaning—is 10-43 second, less than a trillionth of a trillionth of an attosecond. Beyond that? Tempus incognito. At least for now. Efforts to understand time below the Planck scale have led to an exceedingly strange juncture in physics. The problem, in brief, is that time may not exist at the most fundamental level of physical reality.
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Einstein’s theories also opened a rift in physics because the rules of general relativity (which describe gravity and the large-scale structure of the cosmos) seem incompatible with those of quantum physics (which govern the realm of the tiny). Some four decades ago, the renowned physicist John Wheeler, then at Princeton, and the late Bryce DeWitt, then at the University of North Carolina, developed an extraordinary equation that provides a possible framework for unifying relativity and quantum mechanics. But the Wheeler-ÂDeWitt equation has always been controversial, in part because it adds yet another, even more baffling twist to our understanding of time.

“One finds that time just disappears from the Wheeler-DeWitt equation,” says Carlo Rovelli, a physicist at the University of the Mediterranean in Marseille, France. “It is an issue that many theorists have puzzled about. It may be that the best way to think about quantum reality is to give up the notion of time—that the fundamental description of the universe must be timeless.”

Interesting. As usual, quantum actions seem bizarre. Related: Quantum Mechanics Made Relatively Simple Podcasts – Physicists Observe New Property of Matter – Particles and Waves – Quantum Theory Fails Reality Checks – Physics Concepts in 60 Seconds

Light-harvesting Bacterium Discovered in Yellowstone

photo of Mammoth Hot Springs, Yellowstone National Park, by John Hunter

Surprising new species of light-harvesting bacterium discovered in Yellowstone

In the hot springs of Yellowstone National Park, a team of researchers has discovered a novel bacterium that transforms light into chemical energy.
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Remarkably, the new genus and species Cab. thermophilum also belongs to a new phylum, Acidobacteria. The discovery marks only the third time in the past 100 years that a new bacterial phylum has been added to the list of those with chlorophyll-producing members. Although chlorophyll-producing bacteria are so abundant that they perform half the photosynthesis on Earth, only five of the 25 major groups, or phyla, of bacteria previously were known to contain members with this ability.

“The microbial mats give the hot springs in Yellowstone their remarkable yellow, orange, red, brown and green colors,” explained Bryant. “Microbiologists are intrigued by Octopus and Mushroom Springs because their unusual habitats house a diversity of microorganisms, but many are difficult or impossible to grow in the lab. Metagenomics has given us a powerful new tool for finding these hidden organisms and exploring their physiology, metabolism and ecology.”
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Unexpectedly, the new bacterium has special light-harvesting antennae known as chlorosomes, which contain about 250,000 chlorophylls each. No member of this phylum nor any aerobic microbe was known to make chlorosomes before this discovery. The team found that Cab. thermophilum makes two types of chlorophyll that allow these bacteria to thrive in microbial mats and to compete for light with cyanobacteria.

This discovery is particularly important because members of the Acidobacteria have proven very hard to grow in laboratory cultures, which means their ecology and physiology are very poorly understood. Most species of Acidobacteria have been found in poor or polluted soils that are acidic, with a pH below 3. However, the Yellowstone environments are more alkaline, about pH 8.5 (on a scale of 1 to 14). Bryant noted, “Judging from their 16S rRNA sequences, the closest relatives of Cab. thermophilum are found around Mammoth Hot Springs in Yellowstone and hot springs in Tibet and Thailand. As we look more closely, we may find relatives of Cab. thermophilum in the microbial mats of thermal sites worldwide.”

Photo of Mammoth Hot Springs, Yellowstone National Park by John Hunter.

Creating a Nation of Wimps

I certainly don’t know if this is true, or the even the consensus of the scientific thought today, but it happens to feel right to me. Not exactly a scientific conclusion but there you go. From, Psychology Today says, A Nation of Wimps:

Parents are going to ludicrous lengths to take the bumps out of life for their children. However, parental hyperconcern has the net effect of making kids more fragile; that may be why they’re breaking down in record numbers.
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In his now-famous studies of how children’s temperaments play out, Harvard psychologist Jerome Kagan has shown unequivocally that what creates anxious children is parents hovering and protecting them from stressful experiences. About 20 percent of babies are born with a high-strung temperament. They can be spotted even in the womb; they have fast heartbeats. Their nervous systems are innately programmed to be overexcitable in response to stimulation, constantly sending out false alarms about what is dangerous.

As infants and children this group experiences stress in situations most kids find unthreatening, and they may go through childhood and even adulthood fearful of unfamiliar people and events, withdrawn and shy. At school age they become cautious, quiet and introverted. Left to their own devices they grow up shrinking from social encounters. They lack confidence around others. They’re easily influenced by others. They are sitting ducks for bullies. And they are on the path to depression.

Well for whatever it is worth I think the article is interesting (I am not exactly sure about the introversion part that doesn’t seem to have a strong ring of truth but I do think it is better to experience real failure and overcome it than be too sheltered and without that you don’t learn confidence you just are kept from having to feel discomfort as long as the adults protect you…) even if it is just because it attacks something I find a bit annoying the increasing tendency to act like mistakes are not mistakes, failure to achieve an objective doesn’t matter, kids should not be challenged… I don’t think coddling is a good way to create confident people that function well in the world.

People need to learn that things often don’t work the way you might think or hope, things are not fair, things can hurt you, you can loose things you care about, if you make a decision you have to live with the consequences… It is not that hard to understand these things. Kids might well prefer to just be handed everything they want without an risk or effort on their part. But I believe they will learn how to cope and take pride in actually doing good stuff. Which will work much better than trying to convince them they should take pride in something even they can probably tell is fake, coddling. Of course I don’t have any kids either so my opinions are not only not put into practice by me. Oh well go read the article if you are interested.

Quantum Random Number Generator

Quantum Random Bit Generator Service:

The work on QRBG Service has been motivated by scientific necessity (primarily of local scientific community) of running various simulations (in cluster/Grid environments), whose results are often greatly affected by quality (distribution, nondeterminism, entropy, etc.) of used random numbers. Since true random numbers are impossible to generate with a finite state machine (such as today’s computers), scientists are forced to either use specialized expensive hardware number generators, or, more frequently, to content themselves with suboptimal solutions (like pseudo-random numbers generators).
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To achieve high availability of the service, several network access modes are developed, or shall be developed. These include transparent acquisition of random numbers using C/C++ libraries, web services (access over the SOAP protocol), and Mathematica/MATLAB client add-ons.
To enable high security, in future, SSL protocol shall be supported, i.e. all data shall be encrypted, at users request, with user/service certificates.
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We use ‘Quantum Random Bit Generator’ (QRBG121), which is a fast non-deterministic random bit (number) generator whose randomness relies on intrinsic randomness of the quantum physical process of photonic emission in semiconductors and subsequent detection by photoelectric effect. In this process photons are detected at random, one by one independently of each other. Timing information of detected photons is used to generate random binary digits – bits.

Second Life for Scientist

A farewell to academia and hello to Second Life – a professor of Physics and Astronomy moves on the the second act of his professional career.

Loved the teaching. Loved the science. Couldn’t take the politics. Couldn’t take the tenure stress. That about sums it up.

It is a very good post that spells out several important points that should be addressed including:

Many people have noted that it’s getting harder to get null results published, and that it’s very difficult to get “credit’ for having done good science if you produce a null result… even though such things really should be the bread and butter of what scientists do, if we really believe all the things we say all the time about how science works, and about how the process of science is an honest, open, and objective process.

Lifestyle Drugs and Risk

I see taking drugs as risky. Certain drug have long histories and seem safe and even seem to have positive side effect like Aspirin (though even it is not without risks – see below). Even if a drug has a good chance of a positive result in treating some medical condition – assuming it is otherwise safe is not wise. I believe you have have a significant positive known benefit to consider taking drugs given the unknown problems that are likely to be lurking. I find the pop a pill culture for anything that might be a minor annoyance to be foolish – taking risks without consideration. Taking drugs entails taking a risk and the more you take the risks of interactions and cumulative effects increase the risks to you. Business Week (somewhat surprising given the huge amount drug makers pay to advertise lifestyle drugs) has a decent article pointing out some of the foolishness involved in the Lifestyle Drug Binge:

The renewed excitement is most evident in four treatment areas that account for the bulk of lifestyle-drug sales: weight loss, hair loss, sleep, and sexual dysfunction.

This trend is surprising because such treatments can expose patients to risks, sparking criticism of drug companies at a time when patient safety is already under a spotlight. Lifestyle drugs are defined loosely as products used to treat conditions that are not life-threatening. Because people take them over long periods of time, sometimes on a daily basis, they may be more dangerous than they first appear.

We have found amazingly helpful and useful drugs. This is great. But people need to remember these drugs are not without potential negative consequences. Take advantage of them when appropriate but don’t forget the risks each instance has for negative side effects. Related: health care improvement articles – health care blog posts
Continue reading →

Evolution at Work – Blue Moon Butterfly

Butterfly shows evolution at work

The tropical Blue Moon butterfly has developed a way of fighting back against parasitic bacteria. Six years ago, males accounted for just 1% of the Blue Moon population on two islands in the South Pacific. But by last year, the butterflies had developed a gene to keep the bacteria in check and male numbers were up to about 40% of the population.

Scientists believe the comeback is due to “suppressor” genes that control the Wolbachia bacteria that is passed down from the mother and kills the male embryos before they hatch. “To my knowledge, this is the fastest evolutionary change that has ever been observed,” said Sylvain Charlat, of University College London, whose study appears in the journal Science.
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“We’re witnessing an evolutionary arms race between the parasite and the host. This strengthens the view that parasites can be major drivers in evolution,” Mr Charlat said.

It makes a great deal of sense that evolution would have such bursts under the right conditions. This seems an nearly perfect example of such conditions – if males can be produced they are going to have a large opening to reproduce and rapidly pass on a new tool to fight the bacteria. The University of California – Berkeley has a good site on understanding evolution (with lesson plans for k-16 and information for anyone interested in science).

Relates: Two Butterfly Species Evolved Into Third – Evolution in Darwin’s Finches – Evolution In Action – Evo-Devo