Jun 05 2017

Minnesota Measles

Measles graph 1There is currently a measles outbreak in Minnesota. This was, unfortunately, entirely predictable – not, of course, that an outbreak would occur specifically in Minnesota, but that we would start to see outbreaks in communities with low vaccination rates.

So far Minnesota has seen 73 cases of measles. This is more than any year in the last 20 years (or more, that is how far back the tables go). In fact, that is more than all Minnesota cases combined in the last 20 years (56).

Nationwide we hit our low point for measles in 2004 with only 37 cases, all imported from other countries. This means that measles we eliminated from the US, with no native reservoir and no endemic cases. Measles, of course, has not been eradicated from the world and so we can still have imported cases. Thirty seven cases is down from the millions that would occur each year prior to the introduction of vaccines. The graph shows reported cases, which were as high as 800 thousand, but the CDC estimates that the real number was much higher as most cases went unreported.

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Comments: 8

Jun 02 2017

The Sixth Extinction

ExtinctThere have been five major extinctions since the evolution of multicellular life on earth. These are events marked by a geologically rapid loss of biodiversity, the most dramatic of which was the end Permian extinction 245 million years ago with 90% species lost. The other four events had between 19-30% species loss. It is interesting and scary to think how close we came to total extinction in the end-Permian event.

The causes of these extinctions vary. Events 1 and 4 were due to volcanic activity. Events 2 and 3 are uncertain but perhaps causes by climate change due to tectonic plate activity. The fifth extinction, the one that wiped out the non-avian dinosaurs 65 million years ago, was mostly due to an asteroid impact.

Many scientists believe we are in the midst of a sixth great extinction event, caused by human activity. It is always difficult to tell when you are in the middle of such an event – it is easier to discern from a perspective after the event is completed. But it’s pretty clear humans are having a dramatic effect on the ecosystems of the world and other species are paying the price.

There have actually been several books titled: The Sixth Extinction. The first, which I read many years ago, is by Niles Eldridge.  Most recently, in 2014, Elizabeth Kolbert published a book: The Sixth Extinction, An Unnatural History.

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Comments: 38

Jun 01 2017

Confirmation Bias vs Desirability Bias

donald-trump-vs-hillary-clinton-top-issuesThe human brain is plagued with cognitive biases – flaws in how we process information that cause our conclusions to deviate from the most accurate description of reality possible with available evidence. This should be obvious to anyone who interacts with other human beings, especially on hot topics such as politics or religion. You will see such biases at work if you peruse the comments to this blog, which is rather a tame corner of the social media world.

Of course most people assume that they are correct and everyone who disagrees with them is crazy, but that is just another bias.

The ruler of all cognitive biases, in my opinion, is confirmation bias. This is a tendency to notice, accept, and remember information which appears to support an existing belief and to ignore, distort, explain away, or forget information which seems to disconfirm an existing belief. This process works undetected in the background to create the powerful illusion that the facts support our beliefs.

If you are not aware of confirmation bias and do not take active steps to avoid it, it will have a dramatic effect on your perception of reality.  Continue Reading »

Comments: 48

May 30 2017

Superantibiotic for Superbug

enterococcus_faecalis-splImagine a day where you get a bacterial infection, and the doctors tell you that there is no antibiotic which is effective against this bug. It is resistant to everything we have. They can give you supportive care, but the infection just has to run its course and may be fatal. For this reason hospitals have to take extreme measures to prevent the spread of infection – disinfecting and wearing disposable protective garments each time they enter a patient’s room. This is already the case for patients with certain kinds of exposures and infections.

This is a serious concern, not hype like most of the doomsday scenarios the press likes to scare you with. Bacteria are slowly (or sometimes not that slowly) evolving resistance to our antibiotics. Even worse, bacteria have loops of DNA called plasmids which they can share with each other. Those plasmids might contain the code for resistance to one or more antibiotics. The more we use antibiotics, the more selective pressure there is for resistance.

The two main things we need to do to avoid a “post-antibiotic era” includes first uses antibiotics as smartly as possible. Use them only when necessary, use narrow-spectrum antibiotics when possible, and complete all courses of antibiotics so all the bacteria are killed.

The second thing we need to do is develop more and better antibiotics. Attacking bacteria using new mechanisms is especially useful. Ideally these antibiotics would be resistant to resistance – they would attack a vulnerability in the bacteria that they cannot easily evolve a defense against.

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Comments: 21

May 26 2017

Pyramid Homology vs Analogy

Pyramid nonsenseI saw this post on the Credible Hulk Facebook page today. It refers to an old claim by proponents of ancient astronaut theories that the fact that there are similar looking pyramids from different locations on Earth proves cultural contamination from an extraterrestrial source.

While this is a silly argument, it is interesting to explore exactly why it is silly. The underlying principles have to do with homology and analogy, and are exactly the same as they are applied in evolutionary theory. The displayed meme implies that because there are step pyramids in Mexico, Egypt, and Indonesia – countries too far removed to have had direct contact with each other – the idea of a step pyramid therefore had a common source.

This is similar to the evolutionary argument that because two structures look similar or serve a similar function, they must have had a common source, which means the feature was derived from a common ancestor. But we know that this is not always true. The wings of bats, birds, and pterydactyls have similar features, but not a common evolutionary origin. The eyes of vertebrates and cephalopods also have features in common, but evolved independently. But giraffes and humans both have seven cervical vertebrae.

So how do evolutionary biologists tell the difference? They try to determine if the features are homologous (derive from a common ancestor) or analogous (independent origins but similar structure). They can do this in a number of ways, either based on direct evidence or inference. Direct evidence would be finding a fossil of a common ancestor with the feature.

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Comments: 15

May 25 2017

Organic Farming is Bad for the Environment

land useMarketing sometimes involves the science of making you believe something that is not true, with the specific goal of selling you something (a product, service, or even ideology). The organic lobby, for example, has done a great job of creating a health halo and environmentally friendly halo for organic produce, while simultaneously demonizing their competition (recently focusing on GMOs).

These claims are all demonstrably wrong, however. Organic food is no more healthful or nutritious than conventional food. Further, GMO technology is safe and there are no health concerns with the GMO products currently on the market.

There is an even more stark difference, however, between beliefs about the effects of organic farming on the environment and reality.  In fact organic farming is worse for the environment than conventional farming in terms of the impact vs the amount of food produced.

First, organic farming may use pesticides. They just have to be “natural” pesticides, which means the ones they use are not chosen based upon their properties. Ideally choice of pesticide and the strategy in using them would be evidence-based and optimized for best effect, minimal impact on health and the environment, cost effectiveness, and convenience.   Organic farming, however, does not make evidence-based outcome choices. Their primary criterion is that the pesticides must be “natural”, even if they are worse in every material aspect. This represents ideology trumping evidence. It is based on the “appeal to nature” fallacy, an unwarranted assumption that something “natural” will be magically better than anything manufactured.

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Comments: 75

May 23 2017

Graecopithecus – Possible Early Human Ancestor from Europe

graecopithecusFinding fossils is like finding pieces to a jigsaw puzzle, although we don’t know what the final picture is, or where the edges are, and the pieces themselves are damaged or partial and so it is not always clear if they fit. A piece may seem to fit in one location, but it actually goes somewhere else. Sometimes one section of the puzzle can come together, but you are still not sure where it fits into the greater puzzle. But eventually a clear picture can emerge.

For the last century paleontologists have been trying to piece together the puzzle of human evolution. It’s hard to say how close we are getting to having a reasonably complete picture, because again we don’t know how big the puzzle is or where the edges are. One way to get a sense of where we are is this – with each new fossil find is the puzzle getting bigger and more complex or are we filling in known gaps? It’s definitely some of both, but mainly the puzzle is still getting bigger. We don’t know yet how much we don’t know. We’re not just connecting the dots, we keep adding new dots.

A recent analysis of one potential hominin makes the picture more complex still. Graecopithecus is known from a lower jaw and an upper pre-molar. That is not much, which is why the papers on this fossil all describe is at a “possible” early human ancestor. If Graecopithecus turns out to be legit, then it would be the oldest human ancestor after the split with chimpanzees, and it would move the likely location for that split from sub-Saharan Africa to the Mediterranean.

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Comments: 261

May 22 2017

The Smart Meter Hubbub

smart-meter-exampleSame story, different day.

While the details of specific topics change, people are the same. They commit the same fallacies and errors in thinking, and so the patterns of arguments tend to be the same.

Many power companies are replacing the old analogue meters with digital smart meters – devices that measure how much electricity you use and therefore need to be billed for. The newer meters are able to gather more information about electricity usage, not just overall usage. They can measure when you are using electricity throughout the day, for example. They can also communicate this information to the power company wirelessly, eliminating the need to have someone come to your home to read the meter.

There is an obvious efficiency to this increased data and communication. Further, one of the most challenging aspects of power production is balancing production and demand. Demand also tends to peak at certain times, which means that power companies need to have a lot of extra capacity that kicks in just for peak usage. Peak power production tends to be the least efficient and most expensive.

One hope is that smart meters will allow for peak shaving – giving customers information they can use to shift their energy usage off peak.

So what’s the controversy? The same litany of mostly made up complaints and conspiracy theories that seem to crop up for any new technology. Just about every complaint about smart meters has an analogy with vaccines and GMOs, for example, and generally the same crowd are complaining.  Continue Reading »

Comments: 27

May 19 2017

Young Earth Creationists and the Grand Canyon

Andrew Snelling is a young-earth creationist with a PhD in geology who wants to study the Grand Canyon. The National Park Service (NPS), which regulated who gets to do science in Grand Canyon National Park, turned down his application. You can probably guess what happened next.

Snelling is now suing the NPS and the Department of Interior for religious discrimination. He claims his application was turned down because of his religious views. That does not seem to be the case. The NPS had experts review his application. They determined that his science was not valid, and that the rocks he wanted to remove from the park could be found elsewhere. The NPS is particularly careful about any research that involves removing material from parks.

It seems clear to me that the NPS is on solid ground (heh). They already have a process in place to determine if scientific applications are for worthy science and if they justify the removal of material from a park. They did proper peer-review and abided by the recommendations of their experts. This does not appear to have anything to do with what Snelling believes, but the quality of his science.  Snelling is now being a whiny b**ch. He also appears to be using this for propaganda purposes, which may have been the whole idea from the beginning.

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Comments: 22

May 18 2017

Follow Up on Bem’s Psi Research

telepathyAn interesting article in Slate by Daniel Engber reviews the story of Daryl Bem and his psi “Feeling the Future” research. If you are interested in this sort of thing the entire article is worth a read, but I want to highlight and expand upon the important bits.

For review, in 2011 Bem published a series of 10 experiments in the Journal of Personality and Social Psychology (JPSP). I wrote about the research at the time, and wasn’t impressed. I wrote:

“In the final analysis, this new data from Bem is not convincing at all. It shows very small effects sizes, within the range of noise, and has not been replicated. Further, the statistical analysis used was biased in favor of finding significance, even for questionable data.”

Bem had taken standard social psychology experimental protocols, mostly dealing with priming, and did an interesting thing – he reversed the order of the experiment so that the priming came after the subjects were tested. For example, he would give subjects a memory test and then let some of them study the material. He claimed that the studying had an effect backward in time to allow subjects to perform slightly better.

For experienced skeptics, this was not much of a surprise. When dealing with claims that have a vanishingly small prior probability, you need extraordinary evidence to be taken seriously, and this wasn’t it. We were already very familiar with these kinds of results – if you squint just right there is a teeny tiny effect size. But we already knew that experiments are easy to fudge, even unwittingly, and it would therefore take a lot more to rewrite all the physics textbooks. (What is more likely, that the fundamental nature of reality is not what we thought, or Bem was a little sloppy in his research?) The key (as acknowledged by Bem himself) would be in replication.  Continue Reading »

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