Jun 15 2017

What Speech is Legally Protected?

free-speech2Ken White, a first amendment attorney and proponent, has an excellent op-ed in the LA-Times about the law and free speech. It’s a necessary read for anyone interested in the ongoing debate about the role and limits of free speech in America.

The article is framed around pointing out common free-speech tropes, which is a good way to communicate about such topics. However, the scope of the article doesn’t really address the debate itself, it only provides a solid logical and legal framework for the debate. This is necessary to get the discussion to the point where it needs to be in order to address the actual issues, without getting distracted by legal myths.

The First Amendment

The First Amendment protection of free speech is based on the principle that a free and open society requires individual citizens to have the space and comfort to express their opinions without fear of oppression. White points out that the courts have generously interpreted this right over the years. Essentially all speech is protected except for very specific exceptions, which he lists as: “obscenity, defamation, fraud, incitement, true threats and speech integral to already criminal conduct. ”

You will notice that “hate speech” is not on the list. The courts have recognized that any speech which might be part of political expression must be protected, and that the speech which most needs protection is that which some or even most people will find objectionable.

Interestingly, the go-to example of not-protected speech that most often comes up, crying “fire” is a crowded theater, is actually protected. The current precedent is that the “incitement” criterion must be direct and immediate – “You, go kill that guy right there,” Indirect or vague incitements, or speech that might inspire someone to do something illegal or harmful, are still protected.

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Jun 13 2017

The CRISPR Controversy

CRISPR-mechanismI suspect that CRISPR is rapidly following the path of DNA in that many people know the abbreviation and what it refers to but not what the letters stand for. Clustered regularly interspaced short palindromic repeats (CRISPR) is a recently developed technology for making precise gene edits. Such technology carries a great deal of promise for treating or even curing disease, for accelerating research, and for genetic modification technology.

However a recent study has thrown some water on the enthusiasm for CRISPR and sparked a mini-controversy. The authors looked at two mice that were treated for blindness with CRISPR-cas9, sequencing their entire genome. They found over 1,500 unintended mutations. That would be bad news for the technology, which is revolutionary partly because it is supposed to be so precise.

For a little background, CRISPR was discovered in bacteria and archea. It is essentially part of their immune system – locating inserted bits of DNA from viruses and clipping them out. Researchers realized they could use this system to target specific sections of a genome to insert or remove a genetic information. The technique is fast, cheap, and convenient.

What this has meant is that genetic modification can now be cheaply available to even small labs. Further, since the technique can be used in living organisms, it could theoretically be used to cure genetic diseases.

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Jun 12 2017

Earliest Modern Human

Published by under Evolution
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Jebel Irhoud skullLast month I wrote about Graecopithecus, a possible human ancestor from just after the split with chimpanzees about 7 million years ago. Also last month it was reported that an analysis of new Homo naledi specimens dates the fossils from as recently as 236 thousand years ago. H. naledi share some primitive features that paleontologists thought would date to about 2 million years old, but they also have some more modern features.

In April I also wrote about the latest study of H. floresiensis (the Hobbit) showing that it is very likely this was indeed its own species.

All of these news items share a theme – that the picture of the evolution of modern humans from our last common ancestor with chimpanzees is likely much more complicated than we currently know and previously suspected. I think the analogy of a jigsaw puzzle is apt. We are trying to piece together this puzzle, but we don’t know what the final picture looks like. We are connecting lines to the pieces we have, but when we find more evidence we are not just filling in the picture, we are expanding it.

Our map of how human evolution proceeded was just a best fit to the existence evidence. We are still in a stage of our discovery where every new major find alters that best fit. This process was inevitable as we started with a maximally simple (and naive) map – a linear progression from apes to humans. Now we know, as with pretty much every other evolutionary tree, the real map is much more bushy. Adaptive radiation lead in multiple directions simultaneously, only one branch of which survived to be modern humans.

Homo Sapiens from Jebel Irhoud Continue Reading »

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Jun 06 2017

The Mechanism of Substitution Heuristic

Kahneman-TverskyHuman thinking is complicated. I further find it ironic that we find it so difficult to think about our own thinking. The reason for this is that we are not aware of all of the processes that go into the workings of our own minds. When you think about it, that makes sense. If we had to monitor the mechanisms by which we process information, and then monitor that monitoring, we would use a lot of mental energy in a potentially endless loop of self inspection. This could easily become paralyzing.

So mostly we engage is automatic subconscious problem solving, which uses simplified algorithms to produce decisions which are fast and good enough, absent awareness of what those algorithms are. When we have the luxury for more introspection we can indulge in some analytical thinking as a check on our intuitions.

Added to this, we have made our own world incredibly complex. In a way we have overwhelmed our own intuitions (what psychologists call system 1 thinking). We are fumbling through complex technological and scientific questions involving a world-spanning civilization with a brain evolved for a much smaller and simpler world. This means we need to rely much more heavily on system 2 thinking – careful analytical thinking. This involves metacognition, or thinking about how we think.

Psychologists Kahneman and Tversky have arguably had the most dramatic effect on the study of decision making starting in 1979. They put forward the whole notion of cognitive biases and heuristics, or mental shortcuts we substitute for careful analytical thought.  Continue Reading »

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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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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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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 »

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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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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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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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