Archive for the 'General Science' Category

Feb 14 2017

Science – We Have a Reproducibility Problem

Published by under General Science

reproducibility-smallJohn Ioannidis has published an interesting commentary in JAMA about the current reproducibility crisis in basic and clinical scientific research. Ioannidis has built his career on examining the medical literature for overall patterns of quality. He is perhaps most famous for his study showing why most published research findings are wrong.

The goal here is to improve the science of science itself (or “metascience,” like “metacognition”). As science has progressed a few things have happened. The questions are getting deeper, more complex, and more subtle. Research methods have to be more rigorous in order to deal with these more subtle questions.

The institutions of science have also grown. Science is big business, which means that there are “market forces” which push institutions, scientists, and publishers into pathways of least resistance and maximal return. These pathways may not be optimal for quality research, however.

The stakes are also getting higher. We now have professions and regulatory schemes that are supposed to be science-based. If we take medical products, for example, the public is best served is products are safe and effective and truthful in the claims made for them. We need scientific research to tell us this, and we need to know where to set the bar. How much scientific evidence is enough? We can only answer this critical question if we know how reliable different kinds of scientific evidence are.

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32 responses so far

Feb 13 2017

Immigration and Crime

Prevalence-of-CrimeDoes legal or illegal immigration increase crime? That is an empirical question that should be answerable through rigorous research. Whatever the answer, it should inform our policy priorities and decisions. At the very least, if we are going to have a national conversation about immigration, the established facts should serve as common ground.

When you are done laughing (or crying) you might be interested to read about recent research into the correlation between patterns of immigration and various types of personal and property crime. Researchers have previously looked at this question by focusing on individuals – are immigrants more or less likely to commit crimes than native born Americans? Let’s consider that question first.

The research overwhelmingly shows that first generation immigrants, whether legal or illegal, are less likely to commit all types of crime at all ages than the native born. Interestingly, by second generation the statistics look more like native born crime rates, so it does not take long to assimilate in this regard. As an aside, this, of course, does not include crossing the boarder illegally itself, but it has been pointed out that being an undocumented immigrant is not a criminal offense, but a civil offence.

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129 responses so far

Feb 07 2017

New GM Wheat Trials Set

Published by under General Science

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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39 responses so far

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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Oct 31 2016

The Times Gets it Wrong on GMOs

Published by under General Science

Bt BringalIt is unfortunate that so many journalists begin with a narrative and then back fill the facts and points necessary to tell their narrative. I have encountered this many times when being interviewed for an article or documentary – more often than not the reporter or producer is simply hunting for quotes to plug into a story they have already written. I am not giving them information so much as filling a role, which could be that of expert or of token skeptic.

We are all familiar with this phenomenon when reading about political topics in outlets that have a clear editorial policy. If the policy is clear, we don’t even expect objectivity. When reading about non-political topics, however, I do think there is a general expectation of objectivity, but the motivated reasoning can be just as pronounced.

A recent New York Times article, in my opinion, is a good example of what happens when a journalist writes about a complex and contentious topic and allows their narrative to overtake the facts. The article, Doubts About the Promised Bounty of Genetically Modified Crops, declares the narrative in the headline (yes, I know journalists don’t write their own headlines, but they still may accurately reflect the tone of the article, as in this case).

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62 responses so far

Oct 14 2016

Science Is Not Colonialism

science-fallismThis Youtube video is making the rounds. Relax, tape a deep breath, and take a look at the video.

The core point that the primary speaker is making is this: Science is nothing but Western colonialism imposed upon the African people (and presumably others). The only solution is for science to “fall” – she would like to wipe away all of science and start with a blank slate, so that Africans can develop their own knowledge.

She gives as an example that Newton saw an apple fall, made up gravity, wrote down some equations, and now that is scientific truth imposed on the world forever (seriously, I am not exaggerating this one bit).

The other pillar of her position is that in Africa there are practitioners of black magic who can summon a lightening bolt at their enemy. This is not explainable by “Western” science, and yet this is African knowledge, and therefore is an example of Western colonialism suppressing indigenous wisdom.

After stating that practitioners can summon lightening, someone in the audience shouted “It’s not true.” While this might be considered rude, it is an understandable impulse. The response of the moderator was illuminating, in my opinion. She stood up, shamed the audience member, lectured him about the fact that he violated their safe space that is supposed to be free of antagonism, and then forced him to apologize.  Continue Reading »

72 responses so far

Oct 13 2016

GMOs and Horizontal Gene Transfer

Published by under General Science

horizontal-gene-transferPeople reject genetically modified organisms as food (GMOs) for a variety of reasons, but the single most cited reason is the false belief that they are unhealthy. That specific belief also represents the single greatest disconnect between the opinion of scientists and of the general public in a 2015 Pew poll, greater than evolution, climate change, or vaccine safety.

The reason for this disconnect is that the public is relying upon their intuition, rather than scientific knowledge, to arrive at their conclusion. Further, that intuition has been hijacked by a deliberate anti-GMO campaign orchestrated by misguided environmentalists and by the organic food lobby to help promote their brand.

As Stefaan Blancke and his coauthors argue in the above article:

This intuitive reasoning includes folk biology, teleological and intentional intuitions and disgust.

One of the primary “folk biology” talking points of the anti-GMO crowd is that it is “unnatural” to place genes from one species into a distant species. No further reasoning is offered to defend this position – just the invocation of what is “natural” seems to be enough. Those who defend the scientific position often point out that this irrelevant, just a manifestation of the appeal to nature fallacy. Whether or not something occurs in nature does not determine if it is good or bad for human health.

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Sep 23 2016

Tardigrade Radiation Shield

Published by under General Science

tardigrade1Tardigrades (also called water bears or moss piglets) are one of the coolest animals on earth. They are microscopic, live pretty much anywhere there is water, and are “extremotolerant.” When they lack water they just dry up, and their dessicated form can survive extremes of temperature, high pressure, and even the vacuum of space. Just add water back, and they plump up and go about their business.

They are also very tolerant to radiation, an enviable property. Recently scientists studied the tardigrade genome – more specifically, R. varieornatus, which is one of the hardiest species. There are about 1000 known species of tardigrades and probably a couple thousand more waiting to be described. They had a couple of questions.

First, they wanted to follow up on prior research showing that tardigrades have an extremely high percentage of genes acquired through horizontal transfer from bacteria. This result was not replicated in the current study, which found a very low amount, only about 1.3%. The higher result had already been called into question by other researcher, and this it pretty much the final nail in the coffin.

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13 responses so far

Sep 16 2016

Bayer Buys Monsanto

Published by under General Science

bayer-monsantoGerman company Bayer has successfully bid to buy Monsanto for $66 Billion. This merger represents the latest in the consolidation of the biotech industry that has been going on feverishly in the last few years.

I have more questions than opinions about this merger, but there are some points worth discussing.

Consolidation

Every article and opinion I have read about the merger characterizes it as a bad thing, as a symptom of a dropping agricultural market. The story being told is this: as crop production has increased, the price of major crops in the market has decreased. This has squeezed farmers, who in turn buy less biotech products, which squeezes the seed and fertilizer companies.

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36 responses so far

Sep 15 2016

Congressman Lamar Smith and the Union of Concerned Scientists

smith-house-science-committee-1200Lawrence Krauss recently wrote an editorial in The New Yorker about how Lamar Smith, a congressman from Texas and chairman of the House Committee on Science, Space, and Technology, is harassing scientists who are providing data on global warming.

The story that Krauss tells is very clear – Smith is a Republican who receives more money from the oil industry than any other industry, he is a Christian Scientist, and he is a global warming denier. Last year the National Oceanic and Atmospheric Administration (NOAA) published a paper in Science in which they show data that indicates there never was a global warming pause and that the world is continuing to warm.

The response of Lamar Smith was to accuse the scientists of lying, of altering the data to suit the political agenda of the administration, and to subpoena their internal communication (they had already turned over their data). In the subpoena Smith writes: Continue Reading »

82 responses so far

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