Archive for the 'General Science' Category

Mar 30 2015

Peer-Review Scandal

Published by under General Science

Biomed Central, a UK company that publishes 277 peer-reviewed journals, announced that it is retracting 43 articles because of “fabricated” peer-review.

Peer-review is a process that many scientific journals use to vet submitted articles. Typically an editor will review the article but also send it out to two or three experts in the subject matter and have them take a close look at the article to make sure everything is high quality. Most submitted articles will come back with required changes before acceptance. Of course many articles are rejected outright.

The process is not perfect, but it is one critical layer of quality control. The “peer-reviewed literature” is therefore a body of evaluated knowledge that has met at least a minimal standard of quality.

Of course, your mileage may vary. Not all peer-reviewed journals are as rigorous. Also, whenever there is any system in place to separate the wheat from the chaff, someone will try to game the system for their own advantage. There also needs to be some monitoring or policing in place to ensure the integrity of the system.

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Mar 16 2015

FOIA Requests to Biotech Scientists

On the SGU this week we interviewed Kevin Folta, who is a biotechnology scientist at the University of Florida. His specialty is strawberries – he is trying to identify which genes are responsible for the intense flavor of wild strawberry varieties. Some of this flavor was inadvertently lost over decades of cultivating strawberries to be big, attractive, and have a good shelf life. He sent me some of the wild varieties he is working with. They produce small (really small) unattractive strawberries that taste amazing. Ideally he would like to figure out how to combine the incredible flavor of some of the wild strawberries with the marketable cultivated varieties.

Kevin is also a science communicator. He does outreach to help the public understand his science, the science of plant genetics, which includes genetic modification. He is publicly funded and so all of his funding sources are fully disclosed. He has no funding from industry, no conflicts of interest.

However, because he is an outspoken critic of unscientific anti-GMO propaganda he has been targeted by the anti-GMO crowd. Their latest strategy is to go on a fishing expedition using freedom of information act (FOIA) requests. The anti-GMO lobby, of course, is not monolithic, and this is one group who is undertaking this approach – US Right to Know (funded by the Organic Consumers Association). They have issued FOIA requests to obtain all the e-mails of 14 senior biotech scientists.

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Feb 24 2015

Anti-GMO Propaganda

Published by under General Science

There is so much anti-science propaganda out there I often feel like I am emptying the ocean with a spoon. Just today I was faced with an array of choices for my post – should I take on anti-vaccine, anti-GMO, or anti-AGW propaganda? For today, anyway, anti-GMO won. I’ll get to the others eventually.

This was sent to me by a reader – 5 reasons to avoid GMOs.  The content is mostly tired anti-GMO tropes (lies, really) that have been thoroughly debunked, but it is good to address such propaganda in a concise way. Also, it is a useful demonstration of the intellectual dishonesty of the anti-GMO movement. I may not get through all of them today – each one is so densely packed with wrong, and it takes longer to correct a misconception than to create one. Here is point #1 – GMOs are not healthy:

GMOs are unhealthy: Since the introduction of GMOs in the mid-1990s, the number of food allergies has sky-rocketed, and health issues such as autism, digestive problems and reproductive disorders are on the rise. Animal testing with GMOs has resulted in cases of organ failure, digestive disorders, infertility and accelerated aging. Despite an announcement in 2012 by the American Medical Association stating they saw no reason for labeling genetically modified foods, the American Academy of Environmental Medicine has urged doctors to prescribe non-GMO diets for their patients.

The author begins with an assumption of causation from correlation. The increase in food allergies actually does not correlate well with the introduction of GMOs. The correlation between organic food and autism is much more impressive. In fact, the organic food industry has been rising steadily over this same time period, and so one could make the even stronger point that organic food causes all the listed ills.

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Jan 22 2015

Fail Safe for Artificial Life

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In Jurassic Park the scientists who created the dinosaurs from DNA trapped in amber included what they called the “lysine contingency.” They engineered the dinosaurs so that they could not manufacture the amino acid lycine. The dinosaurs could only survive if they were fed lysine by the park staff. Without the supplement they would quickly fall into a coma and then die.

This contingency was a fail safe if any dinosaur ever escaped from their designated areas, or from the park itself. However, the lysine contingency failed. Dinosaurs could survive by eating lysine rich foods, like chickens or soya beans, or other dinosaurs.

Biologists have now done Jurassic Park one better. Genetically modified bacteria are extremely useful. Bacteria have been engineered to produce drugs, like insulin, or to eat up spilled toxins or petroleum products, or to make synthetic fuel. There is always a concern, however, that such a synthetic bacteria could get out into the wild with unpredictable effects. Physical containment strategies are therefore used to minimize the chance of this happening.

Research teams at Harvard and Yale have developed a new strategy of containment. The genetic code shared by all life involves a language of 3 nucleotides, of which there are 4 types, resulting in 64 different combinations. Each three letter combination codes for an amino acid, of which there are 20 used by living organisms. This allows for some redundancy, with each amino acid having 2-3 different codes. There are also some regulatory codes, such as stop codons – three letter combinations that tell the machinery to stop making the protein at that point.

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Jan 19 2015

Golden Rice Follow Up

Published by under General Science

There is a major anti-golden rice smear and disinformation campaign underway, spearheaded by Greenpeace with other anti-GMO activists on board. They themselves consider golden rice to be a “Trojan horse” for GM technology in general, so they essentially admit that their motivation is to oppose GM technology, even if that means opposing a technology that can save the sight and lives of poor children.

Golden rice is a genetically modified rice variety with enhanced production of beta carotene, the pro-vitamin of Vitamin A. The name derives from its golden color, provided by the beta carotene, the same thing that makes carrots orange. Carrots, by the way, were originally white and were modified through breeding to produce beta carotene, which was a very successful biofortified campaign in Europe that effectively combated vitamin A deficiency.

In response to my post from last week on biofortified GM crops, one commenter did a large “cut and paste” into the comments (generally considered a comment etiquette no-no, but I let it through because the topic is so important) with essentially the full anti-golden rice propaganda. The commenter seemed to think this constituted a “convincing” argument. Let’s see.

*GR IS STILL NOT READY

While there have been long delays in the development of GR since it was “invented” in 2000 (1), this has not been due to the activities of anti-GMO activists, but to basic R&D problems.

This is confirmed in a statement by the International Rice Research Institute, the main body working on the GR project (2). According to the Institute, the time frame for developing a new product is about 13 years, and GR is “still under development and evaluation”. In September 2013 the IRRI expected GR to take another two years before it was ready.

While this point is essentially correct, it is not an argument against the adoption of golden rice. Golden rice (GR) development began in the 1980s. By 2000 the first GR variety was ready, but it produced too little beta carotene to be effective. GR2, using different genes, was ready by 2005 and contained 23 times as much beta carotene as GR 1. This is enough to effectively combat vitamin A deficiency in cultures that consume rice as their primary staple.

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Jan 12 2015

Another Salvo in the Mammoth Extinction Controversy

Published by under General Science

There are many enduring controversies within science, and they are fun to follow. There are raging debates about the so-called Hobbit or Homo floresiensis, is it a new species or a diseased human? You may be surprised to hear that there is still a controversy over whether or not the dinosaur extinction was due to a meteor impact or other terrestrial factors (although I think this one is heavily tilting toward the impact theory).

One controversy I have been following, here and on the SGU, concerns the Young Dryas and whether or not the cooling characteristic of that period was due to melting glaciers or a local comet impact.

Such controversies always raise a few general issues for me. The first is how the mainstream media covers them, which I always find disappointing. Properly covering genuine scientific controversies is challenging, but that is what science journalists are supposed to do. What I find is that they tend to present each new study in the debate as if it is definitive and has ended the debate, rather than putting it into the proper context of the ongoing controversy.

Another common mistake is to rely on one expert rather than getting a reasonable sample. They tend to weight the story toward the side of the expert on which they relied, and maybe provide only token coverage of other views. There is also, of course, the issue of proper balance. Reporting should reflect the balance of opinion in the scientific community. It’s OK to present minority opinions but they should be presented as such.

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Dec 15 2014

The Mound Builder Conspiracy

Even after a couple of decades as a skeptical activist I can still encounter new dark recesses festering with pseudoscience. The human capacity for nonsense seems endless.

A report in an alternative news outlet from the American Institution of Alternative Archeology (AIAA – the tag “alternative” is a huge red flag) claims that the Smithsonian Institution “destroyed thousands of giant human remains during the early 1900′s.”

Why would they do this? The AIAA has an unconventional view of human history. Apparently based on mention in the bible that giants once walked the earth, they believe that the mound building cultures of the Americas were not the product of early Native Americans but rather an earlier race of technologically advanced giants. Reading the comments after the article, it also seems that the belief these giants were white and Aryan is popular.

This is an excellent example of how a narrative develops from a combination of religious beliefs and cultural biases, and then history is rewritten and conspiracy theories woven out of whole cloth in order to support the preferred narrative. Science and evidence do not guide the narrative, but rather it is the other way around – a hallmark of pseudoscience.

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Oct 24 2014

The Many Interacting Worlds Hypothesis

Published by under General Science

Howard Wiseman, a theoretical quantum physicist at Griffith University in Brisbane, Australia, and his colleagues have come up with an entirely new theory to explain the weird behavior of particles at the quantum level. The idea is that quantum effects result from classical universes interacting with each other.

Classical physics is essentially the physics of Newton and describes the macroscopic world. In classical physics particles have a definitive location and momentum. At the scale of fundamental particles, however, the world behaves very differently.

At this so-called quantum level, particles move in waves but then interact as particles. They have only a probabilistic location and cannot be nailed down specifically. There is a minimum amount of uncertainty when trying to measure any linked properties, such as location and momentum. Even more bizarre is quantum entanglement in which particles have linked properties, even when separated across the universe.

The bottom line is that we do not really know why the quantum world behaves as it does. We have experimental data, such as the double-slit experiments, that show consistent results. When light beams shine through two close narrow slits they interfere with each other as if they are moving like waves, even when the beams are so faint that only one photon will be passing through the silts at a time. One photon can apparently cause a wave interference with itself. But when those same photons strike a film plate or detector, they behave like a particle.

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Sep 22 2014

Vandana Shiva and GMOs

Published by under General Science

A recent New Yorker article by Michael Specter does an excellent job of putting the activism of anti-GMO campaigner, Vandana Shiva, into perspective. Shiva has since written a very critical response to Specter, and The New Yorker has responded to Shiva. The exchange is very enlightening.

Shiva is a dedicated anti-GMO activist, perhaps the most widely known and successful in the world. Specter paints a picture of Shiva as more than an ideologue – a “demagogue” who has created a dramatic narrative that is meant to frighten the public about GMOs, but has little to do with reality. For Shiva, her anti-GMO stance is part of a broader economic and social ideology. In her vision of the world, local farmers would feed the world with organic farming, without fertilizer or corporate involvement. The actual science about GMOs seems to be irrelevant to her narrative.

Specter illustrates several example. There are definitely religious undertones to her activism. For example, Specter quotes her from a speech earlier this year:

“G.M.O. stands for ‘God, Move Over,’ we are the creators now,”

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Sep 19 2014

How To Be a Science Denier

This Week Louisiana Governor Bobby Jindal gave an excellent lesson on how to be a science denier. Unfortunately, this was not a faux demonstration, he was sincere.

If you recall, in 2012, Jindal advised Republicans to stop being “the stupid party.” This was a provocative statement. I wondered at the time if this signaled a shift in the party away from having anti-science on their platform. Had party insiders finally realized they can’t hang their political future on denying undeniable science, that they need to embrace reality and stop fighting against it?

Alas, it seems that a more cynical interpretation is closer to the truth – that Jindal was simply worried about damage to the Republican brand caused by Republicans saying “offensive, bizarre” comments, but not by the substance of their positions on scientific issues.

At a recent breakfast hosted by the Christian Science Monitor, Jindal was introduced as a Brown graduate at the age of 20 with a biology major, then a Rhodes Scholar at Oxford, and having a 2 year stint as the president of the University of Louisiana, along with many other accomplishments. So he is a scholar and, to some extent, an academic, with advanced study in biology specifically.

During the breakfast, which included journalists, Jindal was asked about global warming. In response to this issue, Jindal performed a very deft dance. He said, “Let the scientists decide,” referring to whether or not global warming is happening. This, of course, is a clever denialist tactic. The hidden premise here is that the scientists have not already spoken with a unified and loud voice. They have decided – it is clear that human activity is increasing greenhouse gases in the atmosphere and warming the climate.

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