Feb 07 2017

New GM Wheat Trials Set

Wheat-field-against-blue-sky-1200x600Right now there are no genetically modified (GM) cultivars of wheat that are approved and on the market, so essentially there is no GM wheat. Wheat is an important staple crop responsible for about 21% of total calories consumed by humans in the world. Improving net yields of wheat could therefore have important impacts on our food production.

GM Wheat

Over the last century agricultural experts have used conventional breeding, including hybrids, to increase yields of major crops. Apparently conventional breeding is running up against diminishing returns, and some believe we are at or approaching the limit of wheat yield with conventional techniques.

However, improving the efficiency of photosynthesis, the process by which plants turn sunlight into biomass, is an unexploited strategy. Researchers are now applying for field trials of a GM variety of wheat that incorporates genes from  a closely related grass, the stiff brome.

Professor Christine Raines, Head of the School of Biological Sciences at the University of Essex and principal investigator for this research project, described the current modification:

 “In this project we have genetically modified wheat plants to increase the efficiency of the conversion of energy from sunlight into biomass. We have shown that these plants carry out photosynthesis more efficiently in glasshouse conditions. One of the steps in photosynthesis shown to limit this process is carried out by the enzyme. sedoheptulose-1,7-biphosphatase (SBPase). We have engineered GM wheat plants to produce increased levels of SBPase by introducing an SPBase gene from Brachypodium distachyon (common name stiff brome), a plant species related to wheat and used as a model in laboratory experiments.”

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Feb 06 2017

Why Are We Conscious?

Dennet-Book 2017In Daniel Dennett’s latest book,From Bacteria to Bach and Back: The Evolution of Minds, Dennett explores a number of issues surrounding consciousness. I have not yet completed the book and so may come back to it again, but wanted to discuss one topic that Dennett covers – why are we conscious in the first place?

Dennett makes a distinction between competence and comprehension. Competence is the ability to perform some task, while comprehension is understanding the task and the process. The former is unconscious, while the latter is conscious.

This touches on Chalmers’ “P-zombie” problem – if we can imagine an organism that can do everything a human does without experiencing its own existence (a philosophical zombie), then why did consciousness evolve at all? There are several possible solutions to this problem. The first is that humans were “designed” to be conscious by whatever agent made us. This introduces unnecessary elements and contradicts established science, so I think we can set that aside.

The second solution is that consciousness is an epiphenomenon. We don’t need to be conscious, but we evolved consciousness as an evolutionary accident. This may be true, but is unsatisfying as it just side-steps the question of what use is consciousness.

The third solution, which I find compatible with the evidence and compelling, is that consciousness is inherent to the functioning of our brains and brings with it specific advantages.

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Comments: 231

Feb 03 2017

Pew Vaccine Survey – Some Good and Bad News

Pew recently published a surveyvaccines-Pew-2017 looking at the attitudes of Americans regarding the safety and effectiveness of vaccines. The results are not surprising, but there are some interesting bits in the data.

The headline main results are that 88% of those surveyed thought that the benefits of vaccines outweigh the risks, while only 10% thought the risks outweigh the benefits. Further, 82% supported mandatory vaccinations for healthy school children.

This is both good and bad news. It means a solid majority of Americans understand that vaccines are safe and effective. However, the minority who doubt the safety of vaccines are enough to cause problems. Also, those numbers are a bit worse when you dig into the data.

Parents of young children, age 0-4, were more negative about vaccines, with only 81% stating that the benefits outweigh the risks, compared to 91% of those with older children and 90% of those with no children.  Parents of young children are the ones deciding if they get vaccinated. The reason for this is likely that parents with young children are facing the decision of whether or not to vaccinate and are looking for information online. They are therefore more likely to come across anti-vaccine propaganda. Parents of young children may also be easier to scare than more experienced parents.

These numbers are important because of herd immunity – if enough of the population is vaccinated, then a disease outbreak cannot find enough susceptible hosts to spread and will therefore peter out quickly. This will keep the disease from being endemic, meaning that it is self-sustaining in the population. Continue Reading »

Comments: 20

Feb 02 2017

What Is Normal?

normal-spider-flyOne of the main themes of this blog is metacognition – thinking about thinking. This is a critically important topic because much of our thinking is subconscious, or it is not explicit. This means we are not aware of exactly how our brains process information and come to certain conclusions or decisions. In fact, we may have false beliefs about how we arrive at our decisions.

Cognitive psychologists study how people think, and knowledge of this field can help us become more aware of the otherwise unrecognized assumptions or processes in our decision-making.

Take an apparently simple concept such as “normal.” What does it actually mean and how do we use this concept to think about the world? (“Normal” has a specific mathematical definition, as in “normal distribution,” but I am not talking about that here.) A dictionary definition might be, “conforming to a standard; usual, typical, or expected.” This doesn’t quite tell us how we decide what is “normal.”

In medicine use of the term “normal” has fallen out of favor, because it is imprecise, and also because it may contain a moral judgment. We still use it when referring to numbers, such as normal blood pressure, but even then it is not conceptually precise. Normal may be different for different people in different situations. When we are making an effort to be clear in our language we will use terms such as “healthy” or “physiological” (which is distinguished from pathological).

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Comments: 15

Jan 31 2017

Are We Close to a Flying Car?

flying carThere is a good rule of thumb that whenever a headline is phrased as a question the answer is, “No.” This headline is no exception. You might not think this from reading a recent AP article titled: “A commuter’s dream: Entrepreneurs race to develop flying car.”

I am old enough now where I can say that I have been reading such headlines for literally decades. Since I was a nerdy teenage technophile I have been reading about, and dreaming about, flying cars. They are undeniably cool – one of the holy grails of future technology.  I still sometimes imagine myself rising above the congested roads during particularly bad traffic and flying to my destination unhindered.

The AP article, however, is an excellent example of the overhyped future technology trope. Often a dramatic new technology, like flying cars, requires that several different component technologies all work sufficiently so that the application is feasible. Skyscrapers could not be built until the elevator was invented. It didn’t matter if engineers had perfected ways of supporting really tall buildings if no one could get to the upper floors.

I have discussed this idea with batteries many times. A useful battery has to simultaneously have multiple properties: good energy density and capacity, stability, sufficiently rapid charge and discharge rates, many charge-discharge cycles, and be made of material that is not too expensive, heavy, rare, or toxic. There also has to be a way to economically mass produce them. Missing even one property can be a deal-killer.

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Comments: 28

Jan 30 2017

Anti-Evolution Bills Continue to Evolve

teacherclassroomstudents01272017gettyAs we enter a new legislative session in many states we are also faced by a new wave of anti-evolution bills. Creationists have been trying to undermine the teaching of evolution in public schools since Scopes in the 1920s. They have essentially been unsuccessful legally but successful culturally. For the first half of the 20th century they made the “e” word too controversial for textbooks. Since then they have provided cover for teachers in the Bible Belt to teach creationism or falsely criticize evolution.

In a 2011 survey, only 28% of high school biology teachers reporting following National Research Council and National Academy of Sciences recommendations in teaching evolution, and 13% reported that they openly advocated creationism.

This, of course, refers only to public schools. Private schools can openly teach creationism, which is exactly why Trump’s pick for education secretary, Betsy DeVos, has spent so much effort and money promoting school vouchers and private schools.

Legally anti-evolution efforts have consistently run up against that pesky First Amendment, which guarantees religious freedom. The Supreme Court has interpreted this to mean that the government (Federal or State) cannot promote any specific religion or religious belief. Creationism is a religious belief, not science, no matter how creationists try to dress it up, therefore it doesn’t fly.

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Comments: 272

Jan 27 2017

Scientists Create Metallic Hydrogen

jupiter-magnetic-fieldIt was just announced that for the first time scientists were able to create a small amount of metallic hydrogen in the lab. This is a significant breakthrough, and is sure to lead to further discovery, although it remains to be seen what specific practical applications may emerge.

Hydrogen, as most people know, is a gas at familiar temperatures and pressures. The universe is comprised of about 90% hydrogen. There is very little free hydrogen on the Earth, since it is a very light gas, but there is lots of hydrogen bound up in molecules, such as water.

In 1935, physicists Eugene Wigner and Hillard Bell Huntington hypothesized that under extreme pressure hydrogen atoms may form into a metal – metallic hydrogen. The point at which this happens was named the Wigner-Huntington transition, which explains the title of the recent paper. Metallic hydrogen can further be a liquid, in which the electrons and protons are free flowing, or they can form a crystalline structure and be a solid.

Astronomers infer that the core of Jupiter may be hot liquid hydrogen. We know that Jupiter is made mostly of hydrogen, and we can calculate that the pressure deep in Jupiter’s core must have millions of times the pressure on the surface of the Earth. That is sufficient pressure, according to theory, to compress hydrogen into its metallic form.

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Jan 24 2017

More Evidence Autism Rates Not Truly Increasing

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autism-organicOne of the pillars of the anti-vaccine movement over the last two decades is that we are in the midst of an “autism epidemic” because autism incidence has dramatically increased over this time. This increase calls for an explanation, which, of course, they believe must have something to do with vaccines.

Like all beliefs and movements disconnected from real science, this is a simplistic and invalid approach to a complex science, in this case epidemiology.

In medicine we are very interested in how disease rates change over historical time, and among various locations and demographics. Such information provides critical clues to the etiology (causes) of disease and the effects of various risk factors and treatments. There are many things that can change the incidence (new diagnoses over time) and prevalence (number of people with a diagnosis at any one point in time) of a disease, including the way we make and record such diagnoses.

This is always the critical question when following disease incidence over time – are there any artifacts in how we are collecting data. Are the changes in the numbers reflecting a real biological change in the population, or just a change in the behavior of physicians?

Those who warn about an “autism epidemic” are not asking these questions. They are taking the numbers at face value, because they serve a rhetorical purpose.

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Comments: 448

Jan 23 2017

Acupuncture for Infantile Colic

crying+babyRecently scientists published initial results from an ambitious project to reproduce the results of 50 influential cancer studies. The first five studies resulted in one clear failure to replicate, two partial replications, and two with uninterpretable results.

This is how science works. No one study is definitive, because there are simply too many ways to generate spurious results (even without fraud and with the best intentions). Replication is the final arbiter – any result that is real should consistently reproduce. Results that are spurious will be inconsistent.

These are the core lessons that I have been repeating here and on SBM – most studies are flawed and their results are unreliable. Most false studies are false positive. Even experienced and well-meaning researchers can fall victim to p-hacking and other subtle errors. You can only arrive at a reliable conclusion by looking at a mature and robust research program involving numerous studies and replications. The various replication projects that are under way are confirming this overall impression.

Let’s turn to one of my favorite examples: acupuncture. Acupuncture involved sticking thin needles into specific areas of the body in order to provoke specific clinical benefit, such as pain reduction. There have been several thousand studies of acupuncture. When you review all the research you find, put simply, that acupuncture does not work, for anything. There is no specific effect here, one that is reliably found when appropriately controlled for. The entirety of the research is highly consistent with the conclusion that acupuncture is nothing more than a theatrical placebo.

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Comments: 7

Jan 20 2017

Questions on GMOs

gmo-cartoons-good-fat-100Genetically Modified Organisms (GMOs) remain the one issue on which there is the greatest disparity of opinions between scientists and the general public. Even among self-identified skeptics, people who make a genuine effort to align their opinions with the scientific evidence, there remains great distrust of GMOs and the companies who produce them (such as Monsanto).

This disparity is partly due to the decades-long campaign by Greenpeace and the organic lobby to demonize GMOs. It is much easier to fearmonger than to reassure. I think we have started to crawl back toward reality on this issue, but we have a long way to go. We started with the low-hanging fruit, correcting the outright lies.

It is much more difficult to dispel the vague sense that there is something menacing about GMOs. We have a deep emotional connection to food that we perhaps don’t even recognize. It is easy to trigger our emotion of disgust, and we have apparently evolved to err on the side of avoiding anything that may be tainted. The image of unnatural “frankenfood” still clings to our culture and is hard to dispel.

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