Dec 08 2017

In Half a Second

If you have not yet read Daniel Kahneman’s book, Thinking, Fast and Slow, I recommend it. I have discussed its basic principles here many times, and I am reminded of it by a new study that evaluates how we quickly size-up groups of people.

Before we get to the study, here is a quick overview. Kahneman and Tversky did the foundational research into cognitive biases and heuristics – ways in which our thinking is biased or constrained. Kahneman calls this system 1 thinking, or intuitive thinking, which is the fast sort. There is also system 2 thinking, which is slow and analytical.

He admits that these are metaphors, there probably aren’t two distinct biological systems in our brains, but they help us think about the different ways in which we think. Actually, given that our brains are hierarchical, the two-system model may be based in biology to some extent. There are the primitive older parts of our brain that are more system 1 – instinctive, emotional, and fast. Then there is the neocortex – which gives us executive function, and slow deliberative decision-making. I don’t think you can make a clean separation, but it is a useful schematic that is probably more true than not.

In any case, the two systems work together to shape our perceptions and decision-making. The idea is that we evolved rapid-response cognitive systems that makes quick and dirty judgments that are accurate enough and biased in whatever direction favors survival. We can then follow up these quick perceptions with more careful analysis when we have time.

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Dec 07 2017

Alternative Medicine Kills

If the best available evidence is used to determine which treatment strategy for a serious illness has the best survival, than any “alternative” to this evidence-based treatment should, by definition, have a lower survival.

That is a simple and straightforward fact. You have to believe in some twisted conspiracy theory to avoid the obvious conclusion.

But good scientists like to dot all their “i”s and cross all their “t”s. In August Yale researchers published a study in which they looked carefully at the outcomes of cancer patients treated with conventional treatments vs those who opted for so-called alternative treatments. They only considered patient who used alternative treatments instead of proven treatments.

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Dec 05 2017

Plastic Waste

I know, there are already so many things to worry about. It’s almost painful to hear about one more way in which we may be harming the world. Such reports are also often couched in emotional and dramatic terms.

However, it’s important to sift through the rhetoric and evaluate what the science says about what is actually going on. There is increasing reporting about the coming plastic apocalypse. We are dumping massive amounts of plastic into the environment, and some of that plastic is winding up in the world’s oceans. The world produced 343 million tons of plastic in 2014. Only 10% of that plastic was recycled. In total we have produced 8.3 billion metric tons of plastic, which does not biodegrade for hundreds of years.

The fact is, human civilization is big enough that we have to think about the effects of our massive industry. Producing that much plastic will likely have an impact on the environment. The biggest impact may be the percentage that winds up in the oceans – about 10%. Once there is just breaks down into smaller and smaller bits. Many animals accidentally eat the plastic, which can be fatal.

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Dec 04 2017

The Causes of Science Denial

Over the last few decades the challenges we face promoting science and critical thinking have become greater, but so have the tools at our disposal. The “science of anti-science” has been progressing nicely, and we now have a much more nuanced view of what we are up against.

Carl Sagan was fond of saying that, “Pseudoscience is embraced, it might be argued, in exact proportion as real science is misunderstood.” That was the conventional wisdom among skeptics at the time (quote from Demon Haunted World, published in 1997) – that the problem of pseudoscience or science-denial was essentially one of information deficit. Correct the deficit, and the science-denial goes away. We now know that the real situation is far more complex.

To reduce the acceptance of pseudoscience or the rejection of real science, we need to do more than just promote scientific literacy. We also need to understand what is driving the pseudoscience, and we need to give critical thinking skills.

A recent publication of a series of studies looking at the roots of science rejection is a nice cap on this research: Not All Skepticism Is Equal: Exploring the Ideological Antecedents of Science Acceptance and Rejection.

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Dec 01 2017

Liberation Procedure for Multiple Sclerosis – The Final Chapter?

In 2009 an Italian neurosurgeon, Paolo Zamboni, published a controversial article in which he claimed that patients with multiple sclerosis (MS) suffered from blockage in the veins that drain blood from the brain, that this correlation was strong and the pattern suggested a causal relationship. He called his newly identified condition Chronic Cerebrospinal Venous Insufficiency (CCSVI). His article concluded:

CDMS is strongly associated with CCSVI, a scenario that has not previously been described, characterised by abnormal venous haemodynamics determined by extracranial multiple venous strictures of unknown origin. The location of venous obstructions plays a key role in determining the clinical course of the disease.

I first wrote about the resulting controversy in 2010. At the time I concluded that there was good reason to be skeptical, that there were many “red flags for crankery”, but that further research should be done to put the question to bed. There were many reasons to be skeptical, not the least of which is that an entirely vascular cause of MS went against decades of research showing that MS is an autoimmune disease. In that first article I also wrote:

Then one of two things will happen: either the new idea or treatment will fade, becoming little more than a footnote in the history of science, or a subculture will persist in believing in the treatment and will dismiss contrary evidence and mainstream rejection as a conspiracy. Which course the new idea will take seems to depend largely on the original scientist – if they accept the new evidence and abandon their claims, it will likely fade. If they refuse to give up in the face of new evidence, then a new pseudoscience will likely be born.

Well, here we are 8 years after Zamboni’s original publication. How has this drama played out?

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Nov 30 2017

Semi-Synthetic Life With Expanded Genetic Code

It’s interesting to follow truly cutting edge research that has the potential to significantly change our world. I include in this category research into brain-machine interfaces, regeneration through stem cells, genetic engineering, and fusion energy. I would also add research into creating synthetic life.

Synthetic life research views living organisms like a technology. It is, in a way, the original nanotechnology, using complex tiny machines to manufacture chemicals, collect and store energy, degrade toxins, and other functions. Scientists have been very successful in tweaking existing organisms to harness them as tiny factories. Many modern drugs are now made in this way, making drugs like insulin widely available.

Some researchers, however, want to go beyond tweaking existing organisms. What if we could create synthetic organisms, even just single cells, entirely from scratch? That is Craig Venter’s dream – to strip down cells to their bare essentials, and then use that as a template to create a completely artificial minimal generic cell. That basic artificial cell, which we understand well because we built it from the ground up, can then be modified to perform endless functions – designer cells.

There is more to this vision, however. Once we free ourselves from the constraints of existing organisms we can explore novel properties that did not happen to evolve. Evolution is powerful, and it has had several billion years to experiment with life, but evolution is also constrained by its own history. For example, all life on earth uses the same genetic code, based upon two pairs of bases in the DNA – cytosine bonds with guanine and thymine bonds with adenine. This produces a 4-letter alphabet for the genetic code (CTAG), and also gives DNA the double-stranded structure and its ability to make copies of itself. The code consists of 64 3-letter words.

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Nov 28 2017

The Pseudoscience of Masaru Emoto

Masaru Emoto thought that emotions can affect inanimate objects. If you are nice to water and then freeze it, it will make pretty happy crystals. If you are mean to water and then freeze it, it will make ugly unhappy crystals. He wrote:

The result was that we always observed beautiful crystals after giving good words, playing good music, and showing, playing, or offering pure prayer to water. On the other hand, we observed disfigured crystals in the opposite situation.

I know – this is ridiculous. Why even bother? Scientific skeptics study pseudoscience for several reasons. What is interesting about Emoto’s research is not the research question he was pursuing (which has close to zero plausibility) but how he had managed to convince himself that his research supported his fantastical notion. Further, he had managed to convince (or at least intrigue) a large segment of the public that he was onto something, and so this presents an opportunity to teach the public about how science works and how we can distinguish it from pseudoscience. Finally, even serious science can fall prey to error and self-deception. Blatant pseudoscience is an excellent opportunity to see pathological science in the extreme, which helps us understand it better phenomenologically, and hopefully then avoid more subtle manifestations elsewhere.

I do want to emphasize that I have no problem with Emoto researching this question (as long as he was not wasting limited public research funds). Exploring seemingly wacky ideas may bear unforeseen fruit. The probability is low, but that is the nature of exploratory research. Fringe research is a good way to keep us on our toes, keep us from getting too complacent or narrow in our view. And very occasionally, we may just get surprised. Even if the hypothesis itself turns out to be hopelessly wrong, we may find something unexpected along the way.

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Nov 27 2017

Renewed Antiscience Legislation

The fight over science in public education continues, and if anything picked up considerably in 2017. Earlier in the year Nature reported on various state laws designed to water down science education or allow for equal time to be given to unscientific views. They report:

Florida’s legislature approved a bill on 5 May that would enable residents to challenge what educators teach students. And two other states have already approved non-binding legislation this year urging teachers to embrace ‘academic freedom’ and present the full spectrum of views on evolution and climate change. This would give educators license to treat evolution and intelligent design as equally valid theories, or to present climate change as scientifically contentious.

New Mexico took a more direct approach – simply scrubbing “controversial” ideas from the state’s science standards. The standards no longer mention “evolution”, human contributions to climate change, or even mentioning the age of the Earth. This is not a back door approach – this is straight-up censorship of accepted scientific facts.

A new Florida bill also includes this problematic language:

Controversial theories and concepts must be taught in a factual, objective, and balanced manner.

This is part of the latest strategy. First, don’t mention any one theory (like evolution) by name. That is likely to trigger a constitutional challenge. Second, make the bill sound like it is promoting something positive, like academic freedom, democracy, or just being fair and balanced.

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Nov 24 2017

Evolution Observed in Darwin’s Finches

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galapagos finchJust two weeks ago I wrote about “Evolution Caught in the Act” – I was writing about fossils that are clearly transitional and occur within a major evolutionary change, like a land animal adapting to aquatic life. Now we have another report that justifies the same title, although this one is in living species.

For this observation we go back to the beginning, to the Galapagos where Darwin made observations critical to his development of evolutionary theory. The Galapagos are a chain is relatively young volcanic islands, far enough from the mainland to provide relative isolation, but close enough for life to find its way there. Most famously, some ancestral finch species found its way to the island. Their descendants then adapted to a variety of food sources, most obvious in the change in beak size and shape, optimized for its new use.

What Darwin observed is that the Galapagos finches filled many of the same niches as other bird families in other parts of the world. He had to puzzle out why on the Galapagos all those niches were filled by finches. He figured out that they must be descended from an ancestral finch, which also means that they have speciated into a large number of different finch species as they adapted to different islands and different food sources.

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Nov 21 2017

How Wikipedia Tackles Fringe Nonsense

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wikipedia2Wikipedia is an interesting experiment in amateur crowdsourcing of information. I think it is a massively successful experiment, but it faces specific challenges. This page on Wikipedia discusses their approach to what information they allow to remain in their pages. They have a number of policies and practices that are meant to act as a quality control filter.

In my opinion they have settled upon a reasonable approach that might even be used as a model in other contexts. They begin with a completely open model – anyone can become a contributor and add information to Wikipedia. This is the crowdsourcing angle – many hands make light work. There are currently approximately 5,505,947 articles on the English language version of wikipedia. Wikipedia was founded on January 15, 2001, so that is almost 17 years. It is hard to imaging creating a reference with that much information by any other method in that much time.

So the wiki model is ideal for quantity, but what about quality. From the beginning there were concerns about the quality of the information – if anyone can post information, how can we know how accurate it is? A 2008 study comparing Wikipedia to other references for historical articles found Wikipedia to have an 80% accuracy rating, compared to 95-96% for other references. However, a 2005 Nature study of science entries found that Wikipedia was almost as good as Brittanica online – with no differences in major errors, and with an average of 4 errors total per article for Wikipedia, and 3 per article for Brittanica.

There haven’t been many studies since then, but a 2012 small follow up study found no significant difference between Wikipedia and other sources. Wikipedia has tightened its editorial policies over that time, so the improvement makes sense.

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