Archive for the 'General Science' Category

Mar 28 2014

Synthetic Yeast

Published by under General Science

Synthetic biology is an emerging field with incredible potential. The idea is to build genomes from the ground up. Craig Venter made the first breakthrough in synthetic biology four years ago when his team created the first artificial bacterial genome. Now another team has made similar progress with yeast, which is eukaryotic (meaning the cells keep their DNA in a nucleus).

To be clear, these teams have not made life entirely from scratch, not even the genome. In Venter’s case he started with an existing bacterium, and then recreated its genome with some changes, and inserted it into a bacterium whose DNA had been removed.

In the latest research, the scientists have created one of the yeast’s 16 chromosomes. Again, they did not build it from scratch but started with the wild chromosome and then made significant changes. They therefore have 15 chromosomes to go, but there is no reason they should not get there.

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19 responses so far

Mar 14 2014

GMO and Indian Farmer Suicide

Published by under General Science

In 2005 PBS aired a Frontline special: Seeds of Suicide, in which they report:

In recent years, as Heeter finds in the fields of Andhra Pradesh, crop failure can often be traced to Bt cotton, a genetically modified breed that contains a pesticide that naturally occurs in soil rather than plants. Bt technology should, in theory, repel bollworm — cotton’s worst enemy — but some farmers who plant more expensive Bt seeds often wind up worse off than those who don’t. One farmer, Pariki, confides that after he fell into debt, his wife killed herself, leaving him to care for their three small children.

In 2008 Prince Charles, who has campaigned against GM crops, directly blamed a rise in suicides among Indian farmers on the failure of GM crops and the predatory practices of big seed companies. It was reported at the time:

“He called cultivating the modified crops ‘a global moral question’ and ‘a wrong turning on the route to feeding the world.’ He associated the technology with ‘commerce without morality’ and ‘science without humanity.’”

And Prince Charles criticized in a speech:

‘the truly appalling and tragic rate of small farmer suicides in India, stemming… from the failure of many GM crop varieties’.

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14 responses so far

Mar 04 2014


Published by under General Science

A new article published in PNAS warns of, Increasing homogeneity in global food supplies and the implications for food security. They reviewed crop production worldwide over the last 50 years and found that:

“The increase in homogeneity worldwide portends the establishment of a global standard food supply, which is relatively species-rich in regard to measured crops at the national level, but species-poor globally.”

In other words, there has been a globalization of crop production, with more nations looking very similar to each other in terms of which crops they grow in what amounts. This has caused a shift to the major energy-dense crops (wheat, corn, rice, potatoes, and sugar) and a relative reduction in more nutrient dense foods. At the national level, species diversity remains high. However local varieties around the world are being displaced by the same energy dense crops internationally.

This has allowed countries around the world to increase their calorie production to help feed a growing human population. However, the trend also raises several concerns discussed by the authors.

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103 responses so far

Feb 25 2014

Krauthammer’s Global Warming Straw Men

Published by under General Science

A recent column by political commenter, Charles Krauthammer, attacking the notion that global warming is “settled science,” has been getting a lot of attention. Although perhaps he is making a more nuanced argument than most global warming dissidents, Krauthammer is still largely attacking straw men and engaging in tactics of denial. Up front he says he is not a global warming denier nor a believer, but his arguments are certainly mainstream global warming denial.

He begins:

“The debate is settled,” asserted propagandist in chief Barack Obama in his latest State of the Union address. “Climate change is a fact.” Really? There is nothing more anti-scientific than the very idea that science is settled, static, impervious to challenge.

To be fair, Krauthammer is talking about the politics of climate change as much as the science, and politicians often open the door to criticism by overstating the case or glossing over complexity and nuance. That does not, however, justify the same sloppiness by Krauthammer. The language above is virtually identical to that used by creationists to attack the position that evolution is a “settled fact” of science. Both arguments erect a straw man about what we mean by settled.

In both cases (evolution and climate change) there is a core scientific claim that is well-established, with less and less certain details about that basic fact. That life on earth is the product of evolution with common descent is established beyond all scientific doubt, sufficient to be treated as a fact. It would take a great deal of rock-solid evidence to push evolution from its scientific perch.

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123 responses so far

Feb 24 2014

What’s in a Name?

Published by under General Science

Classification systems are important in science. They often reflect our fundamental understanding of nature, and are also important for efficient and unambiguous communication among scientists. But there is also an emotional aspect to the labels we attach to things.

Perhaps the most famous example of this from recent history is the “demoting” of Pluto from planet to dwarf planet in 2006. There was a great deal of hand wringing about this decision, which ultimate was based on a practical operational definition – a planet needs to be in orbit around the sun, be large enough to pull itself into a spherical shape, and have cleared out its orbital neighborhood. Pluto failed the third criterion, and so was reclassified a “dwarf planet.”

It is very telling that most news reports discussing the category change characterized it as “downgrading” or “demoting” Pluto. Clearly people felt that being a planet was more special or prestigious than being a dwarf planet. This is not unreasonable – planets are generally larger and have a more dominant presence in the solar system. There are currently 8 planets, and that number is now very unlikely to change. There are only 5 named dwarf planets, but that number can climb very high as new Kuiper belt objects are discovered and named.

Still, it is interesting that what should be a technical issue appealing to those who love the Dewey Decimal System became such an emotional controversy for the general public.

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Feb 18 2014

GM Potatoes and Disease Resistance

Published by under General Science

The issue of genetically modified food is an excellent one for skeptics – it is a complex question that mostly revolves around scientific data, popular beliefs are rife with myths, misconceptions, and ideology, there are active and well-funded campaigns of misinformation regarding GM, and it is a hugely important topic for society. The topic is too big to cover in one blog post, which is why I have been writing about it sporadically to cover different angles of this issue (see here, here, here, and here). I also was recently interviewed for Mother Jones, with the result in both article and podcast form. The comments after the article are especially revealing.

Much of the discussion around GMO involves the two most common GM traits, pesticide(Bt) production and herbicide resistance. While these traits can be very useful when used intelligently, the potential for GM technology is perhaps much greater in other realms, including disease resistance. Late blight alone, a disease that affects potatoes and tomatoes, is estimated to cost 3-5 billion dollars per year in the US, Europe, and developing countries, through the cost of fungicide use and crop loss.

A three year trial of a new GM potato variety has just concluded, demonstrating impressive resistance to late blight. The researchers took a gene (Rpi-vnt1.1) isolated from a wild relative of potato, Solanum venturii, and placed in into the potato variety known as Desiree. The results:

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108 responses so far

Feb 13 2014

P-Hacking and Other Statistical Sins

Published by under General Science

I love learning new terms that precisely capture important concepts. A recent article in Nature magazine by Regina Nuzzo reviews all the current woes with statistical analysis in scientific papers. I have covered most of the topics here over the years, but the Nature article in an excellent review. It also taught be a new term – P-hacking, which is essentially working the data until you reach the goal of a P-value of 0.05. .

The Problem

In a word, the big problem with the way statistical analysis is often done today is the dreaded P-value. The P-value is just one way to look at scientific data. It first assumes a specific null-hypothesis (such as, there is no correlation between these two variables) and then asks, what is the probability that the data would be at least as extreme as it is if the null-hypothesis were true? A P-value of 0.05 (a typical threshold for being considered “significant”) indicates a 5% probability that the data is due to chance, rather than a real effect.

Except – that’s not actually true. That is how most people interpret the P-value, but that is not what it says. The reason is that P-values do not consider many other important variables, like prior probability, effect size, confidence intervals, and alternative hypotheses. For example, if we ask – what is the probability of a new fresh set of data replicating the results of a study with a P-value of 0.05, we get a very different answer. Nuzzo reports:
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62 responses so far

Feb 04 2014

The GMO Controversy

Published by under General Science

The controversy surrounding genetically modified organisms (GMO) has intrigued me for some time, and recently I have been reading everything I can on the topic. It is an excellent topic for skeptics – it is mainstream (not a fringe topic), it has real importance for society, there are complex scientific and logical issues to sort through, and the topic is rife with misinformation and motivated reasoning.

I wrote recently about the fact that beliefs concerning GMO tend to be dominated by two opposing narratives: GMO critics despise corporate control and greed, and fear the unnatural, while GMO advocates see this technology as an example of the triumph of human ingenuity and science. I admit that with regard to this issue my bias is toward the latter narrative, however, I can understand caution regarding huge corporations (the tobacco industry comes to mind).

But, as a skeptic I have really tried to follow a critical thinking process and pull back from my initial gut reactions. Here, then, is my overview of the issues regarding GMO.

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153 responses so far

Jan 30 2014

Nutritional Content of Produce

Published by under General Science

This is a frequent question I receive that I have yet to address – is the nutritional content of our produce diminishing over time? The claim that our produce is less nutritious is often used as a reason to justify routine vitamin supplementation, and various other dubious health claims, or recommendations to eat locally or eat organic.

The answer is a clear, “it depends” followed by, “it’s complicated.”

There are three levels to this question I want to address: is the nutritional content of produce decreasing over time; if so, what’s the cause; and what should we do about it?

The most often study I see cited is this 2004 study by Davis et al – they examined the nutrient content of 43 crops from 1950 to 1999. They found:

As a group, the 43 foods show apparent, statistically reliable declines (R < 1) for 6 nutrients (protein, Ca, P, Fe, riboflavin and ascorbic acid), but no statistically reliable changes for 7 other nutrients. Declines in the medians range from 6% for protein to 38% for riboflavin. When evaluated for individual foods and nutrients, R-values are usually not distinguishable from 1 with current data. Depending on whether we use low or high estimates of the 1950 SEs, respectively 33% or 20% of the apparent R-values differ reliably from 1. Significantly, about 28% of these R-values exceed 1.

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23 responses so far

Dec 10 2013

Do Seed Companies Restrict Research?

Published by under General Science

Well, yes and no. Such questions are often complex. With some exceptions, we generally do not live in a world with cartoon heroes and villains. Rather we live with people who have conflicting perspectives and priorities. Yet we have a universal human desire for simplicity and the sense of control, so we often reduce the horrific complexity of the world to white hats and black hats.

This tendency makes my job difficult, although also useful – specifically whenever I attempt to wrap my head around a controversial issue, such as GMO crops and agritech, I have to wade through tons of ideological propaganda in order to dig down to some clear information.

In the world of GMO, anti-GMO activists have generally made Monsanto (and big agritech generally) into the cartoon villain. Many of the claims made by critics against Monsanto, however, turn out to be gross distortions. They don’t sue companies for accidental contamination, only deliberate piracy, for example. Pointing this out does not make one a Monsanto shill.

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