Jan 09 2015

Antibiotic Resistance and New Antibiotics

Humans have a massive footprint on our ecosystem. Enough so that we have to think carefully about anything we do on a large scale, such as agriculture, industry, shipping (because of invasive species), and using drugs to fight bacterial infections.

The development of antibiotic resistance is a particular worry of mine, and one that I feel does not get proportional attention in the media. It is quite possible that in the future more people will die from antibiotic resistant bacteria than global warming, food shortages, or disrupted ecosystems (depending on how each of these things develop).

We are already seeing more deaths from drug-resistant bacteria, longer hospital stays, and greater costs. I have seen this change during my career. When I round in the hospital I now have to don protective garments before entering many patient rooms because they are infected or even just colonized with a resistant strain of bacteria.

There is no way around the fact that were are engaged in a war with the subset of bacterial species on this planet that are capable of infecting humans. We have been winning for a while, but the bacteria are now rallying.

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Jan 08 2015

The Science of God

Recently Eric Metaxas wrote an opinion piece in the Wall Street Journal in which he argues that, “Science Increasingly Makes the Case for God.” (Sorry, it’s behind a paywall, but I will quote the salient parts.) Metaxas is an author and speaker, but not a scientist, and it shows in his writing.

His essay is based on two instances of the anthropic principle, which simply notes that in order for life to exist the universe must possess conditions compatible with life. He applies the anthropic principle to the Earth specifically and to the universe as a whole. Starting with the Earth he writes:

As factors continued to be discovered, the number of possible planets hit zero, and kept going. In other words, the odds turned against any planet in the universe supporting life, including this one. Probability said that even we shouldn’t be here.

Today there are more than 200 known parameters necessary for a planet to support life—every single one of which must be perfectly met, or the whole thing falls apart. Without a massive planet like Jupiter nearby, whose gravity will draw away asteroids, a thousand times as many would hit Earth’s surface. The odds against life in the universe are simply astonishing.

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Jan 06 2015

Ancient Indian Airplanes

Being an activist skeptic means being reminded, almost on a daily basis, that there is no idea so absurd that there will not be those who fervently believe it.

At the most recent meeting of the Indian Science Congress Association, Captain Anand J Bodas, apparently under the aegis of Mumbai University, gave a lecture in which he claimed that airplanes existed in India 7,000 years ago, that they were able to fly to different continents, and even to different planets.

These claims are obvious nonsense (although I will link to resources which painstakingly demonstrate this). What is more interesting is that such a talk was able to infiltrate what is apparently a science conference. This is a disturbing phenomenon, all too common, in which rank pseudoscience is able to work its way into the domain of respected science.

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Jan 05 2015

Cancer Risk Largely Bad Luck

This is one of those glass-half-full / glass-half-empty news items. Different headlines reporting on the same study present the results in opposite ways. The BBC, for example, writes, “Life choices ‘behind more than four in 10 cancers.’” Meanwhile the press release from Johns Hopkins states, “Bad Luck of Random Mutations Plays Predominant Role in Cancer, Study Shows.”

The Hopkins headline is more accurate. The BBC headline is not just focusing on life choices vs bad luck, it actually gets the data wrong.

What the researchers did was look at the replication rate of stem cells in different tissue types (they did not include breast cancer and prostate cancer as they could not find published replication rates). They then compared differences in these rates to differences in adult cancer rates in the same tissues. For example, colon cancer is more common than cancer of the small intestine, and colon cells replicate more frequently than small intestine tissue. (In mice, this is reversed, but the correlation holds.)

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Jan 02 2015

How To Create a Fad Diet

Fad diets pop up on a regular basis. I believe that is because they are so easy to manufacture and there is a ready made market for them. Add to that the fact that it is difficult to lose weight. There is also a great deal of misinformation out there about diet and health, so the environment is very friendly to pop pseudoscience.

If you want to create your own fad diet, here is a handy formula. These things pretty much write themselves.

#1 – You need a catchy title, usually taking the form of “The blank Diet.” You can fill in the blank with almost anything. For example, a recent fad diet is called “the bulletproof diet.” This doesn’t say anything about the diet itself, it’s just a catchy phrase, a brand. You can fill in the blank with a title that does reflect the diet itself, but this is optional. Creating a catchy title is actually the most creative work you have to do in making a fad diet.

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Jan 01 2015

2014 Was a Bad Year for Homeopathy

I have been saying for several years that if there is a pseudoscientific medical treatment that is especially vulnerable to critical analysis it’s homeopathy. There’s a lot of nonsense in the world of medicine, but homeopathy takes the prize. First, it is complete and utter nonsense.

There is no need to equivocate. Homeopathy violates basic scientific knowledge in physics, chemistry and biology. It is transparent witchcraft that cannot possibly work by any known or even semi-plausible mechanism. Further, clinical studies unsurprisingly show that it does not work, for anything.

And yet the public does not generally understand what homeopathy actually is. The most common belief is that homeopathy is natural or herbal medicine. Rather, homeopathy is based upon several dubious notions. The first is that like cures like, and idea based on sympathetic magic and not science or any knowledge of the real world. Further, the actual starting ingredients are based upon a fanciful and often absurd interpretation of this dubious notion, leading to things like using duck liver to treat the flu.

None of this actually matters, however, because most homeopathic remedies are diluted beyond the point that there is any chance of a single molecule of starting ingredient remaining. All of this is supposed to work, however, because the potion is “activated” by shaking it.

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Dec 30 2014

Detecting Life Through Motion

Living things move. In fact our visual system uses the way things move to decide whether or not an object has agency and is able to move on its own. In the pre-technological world only things that are alive have agency, but in the technological era we have animatronics and animated video that can mimic the movement of living things and trick our brains into treating objects or representations as if they are alive.

There are several applications for detecting the signatures of life. So far such efforts have focused mainly on chemical signatures – looking for the products of biochemistry. Researchers publishing in PNAS, however, have taken a new approach.  They are trying to detect the motion signatures of life at a microscopic scale.

They use nanoscale motion detectors that are actually tiny cantilevers. Even a single bacterium twirling its flagella can cause the cantilever to move. Lasers then detect the motion of the cantilever, and that motion is analyzed for the signatures of life. The researchers tested their setup on soil and pond water, and found that it accurately detected microscopic life. They then used drugs to kill any living cells, and the detection stopped. 

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Dec 29 2014

Pertussis Evolving

New evidence suggests that strains of the bacterium, Bordetella pertussis, which is responsible for whooping cough, may be evolving to evade immune protection afforded by the pertussis vaccine.

The research, led by Dr Andrew Preston from the University of Bath, evaluated surface proteins from the 2012 whooping cough outbreak. They found that surface proteins that are included in the acellular pertussis vaccine were evolving faster than surface proteins not included in the vaccine. The authors point out that this was happening even prior to the introduction of the vaccine, but has accelerated since the vaccine.

It is not yet clear what, if anything, this means for the effectiveness of the acellular pertussis vaccine. However, the concern is that circulating strains of B. pertussis will continue to evolve, diminishing the protection provided by existing vaccines.

Whooping cough is a potentially serious illness, primarily affecting infants. There was an outbreak in the UK in 2012 with 10,000 confirmed cases and 14 infant deaths. In the US that same year there were over 48,000 cases reported (not necessarily confirmed) and 20 deaths.

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Dec 25 2014

Io Saturnalia

Seasons Greetings, Happy Holidays, Happy Festivus, Have a wonderful Winter Solstice, and Merry Christmas.

This is the time of year that many cultures in the northern hemisphere celebrate the return of the sun, celebrate family and life while facing the long dark of winter, and engage in superstitious rituals to help them survive the cold and hunger that mark that season. All of that is the real reason for the season.

In western culture the celebration has been largely “Christianized” into the holiday of Christmas, but the secular aspects of Christmas, from gift giving to the Christmas tree, all have non-Christian origins.

For me, though, it all doesn’t matter. It’s a great time of year to take a break from the usual grind and spend time with family and friends, reminding everyone how much we mean to each other. In the darkest part of the year (again, with apologies to my southern hemisphere friends) we spread a little light and warmth to those in our lives.

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Dec 23 2014

A New Wrinkle in Quantum Mechanics

The press release of this news items proclaims: “Quantum physics just got less complicated.” I’m not sure I agree. Perhaps in the minds of physicists who actually understand quantum mechanics (as well as it currently can be understood). To the rest of us this new finding is just as strange and incomprehensible as QM itself.

QM describes the universe at the atomic and subatomic levels. At that scale nature behave very differently from what we are used to at the macroscopic level, which is often referred to as the realm of classical physics. The dividing line between the quantum world and the classical world remains a matter of research and debate, but it is somewhere at the level of molecules.

There are several aspects to QM which essentially describe the results of careful experiments. We don’t currently have a proven theoretical framework to explain why the universe behaves this way – that is a breakthrough waiting to happen.

One aspect of QM is known as wave-particle duality. When particles, such as photons, shine through two narrow close slits (the famous double slit experiment) the pattern of light that hits the wall (or film or detector) behind the slits is in a light and dark banded pattern that resembles the interference pattern that results when two waves intersect. The light is clearly traveling as a wave through the two slit and those waves are interfering on the other side.

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