May 29 2015

A Chocolate Science Sting

John Bohannon is at it again. In 2013 he published the results of a sting operation in which he submitted terrible papers with fake credentials to 304 open access journals. Over half of the journals accepted the paper for publication. He published his results in Science magazine, and it caused a bit of a stir, although arguably not as much as it should have.

Bohannon was asked to repeat this feat, this time to expose the schlocky science of the diet industry. He was asked to do this for a documentary film which will be release shortly, but he has already published his reveal. You can read his full account for details, but here is the quick summary.

He collaborated with others to perform a real (although crappy) scientific study. His researchers recruited 16 people, with one drop out, the remaining 15 were divided into three groups: low carb diet for three weeks, low carb diet plus daily chocolate for three weeks, and no change in diet. The results were not surprising in that the two diet groups lost 5 pounds on average, while the no diet group did not. However, they also found that the chocolate group lost 10% more weight. He explains:
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May 28 2015

How the Brain Chooses Where to Go

Neuroscientists are making progress mapping out the cortical pathways that allow us to know where we are and navigate to a desired location. A recent study adds another bit of information to this growing picture.

The Nobel Prize for Physiology or Medicine for 2014 was given to several scientists, Dr. John M. O’Keefe, Dr. May-Britt Moser and Dr. Edvard I. Moser, for their collective research in working out the basic neurological function that underlies our ability to place ourselves in our environment and to navigate around. O’Keefe identified place cells. A specific place cell will fire when we are in a specific location. Different patterns of place cells firing represent different locations.

These place cells are found in the hippocampus, specifically area CA1. O’Keefe also found that the place cells have memory function, and are therefore critical to our ability to remember specific locations.

Moser and Moser extended this work by finding grid cells in the entorhinal cortex. This area connects heavily with CA1, and contains cells that behave like the place cells. However, the grid cells are arranged in a hexagonal grid, and they fire in sequence as rats move through their environments. The grid cells therefore seem to be a literal map of the environment, and track our movement through the environment, while the place cells tell us where we are.

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May 26 2015

The Implications of Online Time-lapse

This is very cool – programmers have created a process with which they scour the internet for photographs. They then categorize them by subject matter, and then select groups of photos that are essentially of the same subject over different periods of time. They crop, color correct, and adjust each photo so that it matches a master, and put them together to create a time-lapse video.

The result is thousands of time-lapse videos that might have taken years to otherwise create.

This is a fun demonstration of two technological trends that are worth pondering. The first is the absolute explosion in digital data, including photographs and video. One estimate is that there were 880 billion photos uploaded in 2014. There are 27,800 photos uploaded to Instagram alone every minute. This is partly due to the smartphone revolution – a large portion of the population in developed nations walk around with a camera on them at all times.

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May 22 2015

Creationist Talking Points

Yesterday I wrote about our struggle to promote and defend the teaching of evolution, and good science in general, in the public school science classroom.  My overall point was that, while we are winning on the legal battleground, we are not making much headway in the broader cultural context, and perhaps we need to step back and think about our strategy.

To my delight, Michael Egnor made an appearance in the comments, and it seemed he truly wanted to engage (at least for a while). Dr. Egnor, if you recall, is a neurosurgeon who rejects what he calls “Darwinism.” He blogs on his own blog and for the Discovery Institute, and we have occasionally crossed swords on our respective blogs.

I was also pleased that the conversation remained polite and civil, allowing us to drill down to the core issues. I want to summarize our exchange here and expand on my responses in the comments.

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May 21 2015

Creationism – Are We Winning The Battle and Losing The War?

One of the major ambitions of my life is to promote science and critical thinking, which I do under the related banners of scientific skepticism and science-based medicine. This is a huge endeavor, with many layers of complexity. For that reason it is tempting to keep one’s head down, focus on small manageable problems and goals, and not worry too much about the big picture. Worrying about the big picture causes stress and anxiety.

I have been doing this too long to keep my head down, however. I have to worry about the big picture: are we making progress, are we doing it right, how should we alter our strategy, is there anything we are missing?

The answers to these questions are different for each topic we face. While we are involved in one large meta-goal, it is composed of hundreds of sub-goals, each of which may pose their own challenges. Creationism, for example, is one specific topic that we confront within our broader mission or promoting science.

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May 19 2015

Federal Anti-SLAPP Statute Proposed

Americans cherish our free speech, enshrined in the very first amendment to the Constitution. SLAPP suits (strategic lawsuit against public participation) are a serious threat to that freedom of speech. We desperately need libel reform in the form of effective anti-SLAPP laws.

What I learned when I became the target of a SLAPP suit (that is still ongoing) is that anyone with money can take away your free speech at will. It works like this: if you express an opinion publicly that someone else doesn’t like because it is critical of them, their beliefs, their business, etc. then they can hire a lawyer and send you a cease and desist letter. You are now faced with a dilemma – take down your blog, article, podcast, video, or whatever and allow your free speech to be suppressed, or potentially face tens and perhaps hundreds of thousands of dollars in legal fees.

Except for those few states with effective anti-SLAPP laws (California, Washington, Oregon, Nevada, Texas and the District of Columbia – Florida just passed one which has not yet gone into effect), if you refuse to remove your free speech and you get sued, then expect to spend large sums of money and years of your life defending your rights. Here’s the thing – even if the case against you has zero merit and no chance of winning in the end, the lawsuit is a financial game of chicken. There is no way to shut the case down early. There is no bar for meritless cases.

The net effect of this is that if someone has money they can shut down your free speech at will. This, of course, has a chilling effect on free speech that can go way beyond the one instance of speech being targeted.

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May 18 2015

Ex Machina and AI

I saw Ex Machina this weekend. If you haven’t seen the movie yet, mild spoiler alert – I will try to avoid any major reveals, but I will be discussing major aspects of the movie.

First, it’s an excellent film. I highly recommend it. It was both entertaining and thought provoking. Writer/Director Alex Garland clearly understands the topic of artificial intelligence (AI), and is also a talented filmmaker. I was particularly impressed by how much he accomplished with such a sparse film. The majority of the film takes place in one location and with three characters, but he quickly established those characters and the primary tensions that drive the film.

He also manages to weave in a fairly deep commentary on the nature of consciousness and creativity, the nature of AI, and all with a subtext of oppression, misogyny and male-female relationships. I still feel like I am missing a lot of subtext in this film, which will require at least a second viewing and a lot more thought.

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May 15 2015

The Meddling Prince

Context is important. If a celebrity promotes a good cause, such as Michael J. Fox raising awareness about Parkinson’s disease, then that is considered altruism and charity. If, however, they promote something with which you disagree, then they are exploiting their celebrity.

I find this analogous to many legal and political claims. In the legal context, if you can’t win on the merits, then argue the law. In politics, if you oppose a law then you can challenge it based on state’s rights or as a constitutional purist. I am not opposed to these concepts – I just want to point out that often such arguments are used selectively when it is really the substance that is unwanted.

I am not decrying the use of celebrity itself. Celebrities have a right to advocate for whatever they want, and their celebrity will lend power to their advocacy. I do think that in general the public should not give weight to celebrity itself. They should be, in fact, more skeptical if celebrity is being used to support a claim. I also respect celebrities who use their power for good, and I am free to publicly criticize those who use it for “evil.” Indulge me while I engage in the latter.

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May 14 2015

Why Is the Public So Wrong?

I had hoped that the advent of the internet would have a positive effect on public access to information, and perhaps it has. The problem is that it also facilitates access to misinformation. I also wonder to what extent people are availing themselves of this easy access to information (or are they just watching cat videos?).

I now frequently have the experience of being in a discussion with someone and arriving at a disagreement over a specific fact. Pre-internet we would not be able to resolve the difference, we would agree to look it up later, and usually would never do so. Now we can whip our our smartphones and within a minute or two find references to the correct fact.

Despite this there remains a disturbing gap between public perception and reality on many important issues. I discussed previously the recent survey showing significant differences between public attitudes towards certain scientific issues and the attitudes of science. The biggest difference was for the statement that it is, “safe to eat genetically modified food.” While 88% of scientists agreed with this statement, only 37% of the public did.

The gap is not limited to scientific issues, but spans the spectrum of civil issues as well. For example, 68% of Americans believe crime is worsening nationally, and 48% believe it is worsening locally, while crime has been steadily decreasing for the last two decades.

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May 12 2015

In Defense of Prior Probability

This post is a follow up to one from last week about reproducibility in science. An e-mailer had a problem with the following statement:

“I tend to accept claims based upon published rigorous evidence that shows a consistent robust result with reasonable effect sizes with evidence in proportion to the plausibility. “

In response they wrote:

“I think this might open up for arbitrary amounts of discrimination based on gut feelings. As an example, if it really was so that aliens regularly conducted semi-stealthy visits to planet earth (as the proponents seems to suggest), we might actually never realise so, because there could be a double standard demanding arbitrarily high levels of evidence based on gut feelings about prior probability.

Allowing prior conceptions this power could even open up for psychological effects such as post hoc adapting the prior judgement such that it is just low enough to allow to discard the presented evidence.”

This is a common reaction, especially when prior probability is used as part of an argument for rejecting a scientific claim (to be clear, I don’t think the e-mailer is doing this, they just seem to have an honest question). I am a strong proponent of prior probability, used as part of a Bayesian analysis. That is, in fact, at the heart of the difference between science-based medicine (a term I coined to reflect my approach) and evidence-based medicine.

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