Archive for the 'General Science' Category

May 08 2015

A Reproducibility Experiment

Published by under General Science

I have been writing quite a bit here and on Science-Based Medicine about metascience – the study of science itself. When you think about it, science is perhaps the most critical and broadly applicable technology of our modern civilization. It is the one endeavor from which all other technologies derive.

It therefore is very important that we understand how the institutions and processes of science are functioning. If there are any inefficiencies or biases in the system they can cause great harm, a waste of resources and a slowing of progress.

A recent metascience project called, The Reproducibility Project: Psychology, asks a very important question:

Do normative scientific practices and incentive structures produce a biased body of research evidence?

The project focuses on one specific aspect of this question – how reproducible are published psychological studies? They looked at 100 studies published in prominent psychology journals with positive results that have been generally accepted. They then crowdsourced scientists conducting replications of these studies, with 270 authors participating.

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May 05 2015

Open Science

Published by under General Science

There is a movement to open access to scientific information, and with the relatively new resources provided by the internet and social media, we may be heading rapidly in that direction. However, I don’t think this will be an easy transition and we should consider the possible unintended consequences.

A 2012 commentary by Nosek and Bar-Anan outlined the changes that would open science:

We call for six changes: (1) full embrace of digital communication, (2) open access to all published research, (3) disentangling publication from evaluation, (4) breaking the “one article, one journal” model with a grading system for evaluation and diversified dissemination outlets, (5) publishing peer review, and, (6) allowing open, continuous peer review. We address conceptual and practical barriers to change, and provide examples showing how the suggested practices are being used already.

The Center for Open Science outlines a similar mission:

1-Increase prevalence of scientific values – openness, reproducibility – in scientific practice
2-Develop and maintain infrastructure for documentation, archiving, sharing, and registering research materials
3-Join infrastructures to support the entire scientific workflow in a common framework
4-Foster an interdisciplinary community of open source developers, scientists, and organizations
5-Adjust incentives to make “getting it right” more competitive with “getting it published”
6-Make all academic research discoverable and accessible

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Apr 30 2015

Neonicotinoids, GMOs, and Colony Collapse Disorder

Published by under General Science

A new propaganda point has entered the anti-GMO repertoire – that GMOs are killing the honey bees. This claim, like many of their claims, is highly misleading, as the actual cause is incidental to the technology of genetic modification or even its use. This hasn’t stopped headlines like this one from organicconsumers.org: GMOs Are Killing the Bees, Butterflies, Birds and . . . ?

This story follows a common strategy among the intellectually dishonest anti-GMO propaganda machine. The fact is, producing enough food to feed over 7 billion people (and growing) is not easy, and requires intensive high-yield farming. Farming, not surprisingly, is having an impact on the ecosystem. Just cutting down forests to make room for crops can have a huge effect, in addition to displacing native species. Perhaps the most challenging aspect of farming’s effect on the environment is that anytime you want to grow millions or even billions of something, critters will evolve to exploit that food source. Any attempt you make to fight back against those critters will inevitably result in resistance.

We face the same challenge with antibiotics. Crowding into cities, and the growing population of humans meant that bacteria who use humans for their lifecycle exploded, leading to outbreaks and epidemics of infectious diseases. Antibiotics have been a powerful weapon against bacterial infections, but evolution is relentless and has led increasingly to antibiotic resistance among bacteria pathogenic to humans and our livestock. This is a genuine dilemma, as we struggle to come up with new antibiotics, and enforce practices that reduce the emergence of resistance.

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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

Published by under General Science

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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