Jul 18 2017

More on Junk DNA

Junk-VennJunk DNA, put simply, is those parts of the genome (human or otherwise) that have no known function. The human genome has about 19,000 genes. A gene is essentially a sequence of base pairs that code for a protein – there are four difference bases with each triplet being a “word” that either codes for an amino acid or tells the process of transcribing the protein to stop.

Even within genes there are noncoding regions, called introns, which have to be removed from the RNA so that the coding regions can be joined together. Between the genes there are also vast non-coding regions. Some of this non-coding DNA is regulatory and structural – it helps regulate when and how much specific genes are transcribed into proteins.

The burning question is, how much of the non-coding regions between the genes serves any function and how much is completely unnecessary, or “junk”? This is an important question for understanding genetics, but also has implication for creationists. Creationists don’t like the concept of junk DNA because it strongly implies an evolutionary history. Why would a designer sloppily insert so much unneeded junk into our pristine genome? Why are genes clogged with non-coding regions that need to be removed? So they claim that all DNA has function, we just don’t know what it is.

ID proponent Stephen Meyer, for example, said:

“For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. “

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Jul 17 2017

The Return of Dr. Gunter

goop screen-shot-2017-07-14-at-10-31-34-amIn my last post I discussed how Paltrow and her people over at goop launched a personal attack against Dr. Jen Gunter, an OB/GYN blogger who has taken the time to point out a lot of the nonsense that goop sells. Goop has been criticized by many science bloggers and mainstream outlets for fearmongering to women in order to sell dubious products.

For some reason “team goop” did not go after Science-Based Medicine, or Tim Caulfield, or Steven Colbert – they went after one humble medical science blogger. This is particularly ironic because Gunter’s blogging career is all about empowering women with science-based information, about advocating for women’s health and autonomy. I can only suppose that goop went after her because they felt particularly stung by her on-target criticism, or perhaps they thought she was an easy target for bullying.

The irony is thickened by including a response from Dr. Steven Gundry, who takes a particularly condescending tone and actually earns the often overused description of “mansplaining.”

The result was the typical litany of alternative medicine tropes, bad logic, and bad science, wrapped in a personal attack against Gunter. But they did leave themselves wide open for poking some additional fun at them, in order to point out how intellectually vacuous and dishonest they are. Dr. Gunter just drove a Mack truck through that opening.

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Jul 14 2017

Goop Strikes Back

goop-kimmelGwyneth Paltrow has been using her celebrity to promote a “lifestyle brand” she calls “Goop.” The site recommends all sorts of medical nonsense, like detox, earthing, putting stuff up your vagina, and the usual scaremongering about “toxins” or whatever. Recently I wrote about Goop’s promotion of magical stickers that are alleged to align and balance your vibrations.

Deservedly she has received push back from science communicators who are trying to raise the level of scientific literacy and critical thinking in the world. The concern is that she is spreading misinformation and pseudoscience, which is increasingly harmful in our modern technological world.

One highly vocal critic has been Dr. Jen Gunter, an OB who is particularly offended by the fact that Paltrow wraps her pseudoscientific misinformation in “female empowerment.” I’m sorry, but taking advantage of women by scaring them and selling them nonsense is not empowering – it’s exploitation. Apparently Goop has been stung by this criticism, and decided to hit back. The results are predictably awful, but do provide an opportunity to deconstruct some popular anti-intellectual nonsense.

“Team goop” begins:

As goop has grown, so has the attention we receive. We consistently find ourselves to be of interest to many—and for that, we are grateful—but we also find that there are third parties who critique goop to leverage that interest and bring attention to themselves.

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Jul 13 2017

The Fragility of Truth

homeopathy5There is a lot to be horrified about regarding the alternative medicine (CAM) industry. The industry largely trades in fraud and misinformation at the expense of the public’s health. But I often find myself most dismayed by what the industry says about the relationship between humans and reality.

I have discussed over the years the many ways, mostly revealed through psychological research, but also with many specific examples, in which people build their narratives about the world and how these narratives trump reality and often even basic logic. If you ever doubt the ability of people to erect a false narrative and worship it as truth, remember that there are people who believe, in the 21st century, that the Earth is flat.

Humans, however, also have science, philosophy, logic, and reason. We have managed, especially in the last few centuries, to collectively crawl out of a deep pit of self-deception and slowly accumulate real knowledge about the universe and how it works. As a species we have this weird dual nature, at times rigorously rational, and at others hopelessly gullible and ideological.

What is perhaps most concerning about the CAM phenomenon is what it tells us about the balance between reason and deception. Sitting on top of the last few centuries of scientific progress, it certainly seems like science and reason are winning. But perhaps this vantage point gives us a biased perspective. Over this period we have largely shifted from a pre-scientific view of the world to a scientific one. Science then showcased its power by picking a lot of the low-hanging fruit – answering the easiest questions to answer.

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Jul 11 2017

No, This Isn’t Amelia Earhart

amelia-earhart-photo2I love a good unsolved mystery as much as anyone. Mysteries provoke curiosity, and challenge our investigative skills. They may also challenge our skepticism and critical thinking.

The story of Amelia Earhart is an iconic mystery, and the inspiration for both legitimate investigation and a lot of nonsense. The story of Earhart is in the news again. The History Channel is promoting a theory that Earhart, and her navigator (Fred Noonan) were captured by the Japanese and later died in prison. Their new alleged evidence for this is the above photograph.

Some Quick Background

Earhart is famous for being a female aviation pioneer.  She had many firsts, including being the first person to fly solo across the Pacific from Honolulu to Oakland, California. This in itself was enough to make her famous, but her disappearance on July 3, 1937 made her legendary. She was attempting to fly around the globe, starting and ending in Miami, Florida. She made it as far as Papua, New Guinea.

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Jul 10 2017

Why Are We Conscious?

brain3While we are still trying to sort out exactly what processes and networks in the brain create consciousness, we are also still uncertain why we are conscious in the first place. A new study tries to test one hypothesis, but before we get to that let’s review the problem.

The question is – what is the evolutionary advantage, if any, of our subjective experience of our own existence? Why do we experience the color red, for example – a property philosophers of mind call qualia?

One answer is that consciousness is of no specific benefit. David Chalmers imagined philosophical zombies (p-zombies) who could do everything humans do but did not experience their own existence. A brain could process information, make decisions, and engage in behavior without actual conscious awareness, therefore why does the conscious awareness exist?

This idea actually goes back to soon after Darwin proposed his theory of evolution. In 1874 T.H. Huxley wrote an essay called, “On the Hypothesis that Animals are Automata.”  In it he argued that all animals, including humans, are automata, meaning their behavior is determined by reflex action only. Humans, however, were “conscious automata” – consciousness, in his view, was an epiphenomenon, something that emerged from brain function but wasn’t critical to it. Further he argued that the arrow of cause and effect led only from the physical to the mental, not the other way around. So consciousness did nothing. We are all just passengers experiencing an existence that carries on automatically.

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Jul 07 2017

Conspiracy Thinking and the Need for Certainty

conspiracy1The world is horrifically complicated and humans have developed a number of strategies to deal with that complexity. These strategies are necessary but imperfect. There is also always a trade-off, sacrificing detail and nuance for understandability.

One such strategy I have written about often is the need for simplicity. A saying, attributed to Albert Einstein with good references, goes: “Everything should be as simple as it can be, but not simpler.” He was talking about the art of making complex scientific knowledge accessible without making it wrong. Unfortunately, the desire for simplicity often leads to oversimplification, with important details and concepts lost or distorted.

There is another related strategy psychologist call the need for cognitive closure. One reference defines this need as:

“As a dispositional construct, the need for cognitive closure is presently treated as a latent variable manifested through several different aspects, namely, desire for predictability, preference for order and structure, discomfort with ambiguity, decisiveness, and close-mindedness.”

It is easy to see the trade-offs here. On the one hand it is good to be intellectually flexible, open-minded, and comfortable with ambiguity and uncertainty. Yet, this disposition can predispose one to indecisiveness, the “paralysis of analysis.” At some point we have to commit, even if tentatively. Structure and order in thought can also be positive things.

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Jul 06 2017

The Brain’s Wiring

connectome5Cardiff University has released its latest scans of the wiring of the human brain. This now adds to a similar project in the US funded by the NIH.

The result is a stunning image of all the axons in the human brain – the wires that conduct signals and form networks and connections to other parts of the body. In addition to these wires there are also the neurons, which are the cell bodies of which the axons are part, and the glia, which are other cells in the brain that serve support functions but also play a role in modulating neuronal function.

These wiring images are part of various connectome projects – attempts at fully mapping all the connections within the human brain and their functions. These latest images from Cardiff are the result of the Siemens 3 Tesla Connectome MRI system. Essentially we are seeing the result of advances in both hardware and software technology.

The MRI scanners themselves are on the more powerful side. The “3 Tesla” refers to the power of the magnet. A typical hospital MRI scanner operates at 1.5 Tesla or 3 Tesla. There is a 10.5 Tesla MRI unit at the University of Minnesota which is used for the NIH connectome project. So 3 Tesla is a powerful MRI scanner, but no more so than the more powerful typical clinical MRI scanners.

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Jul 03 2017

Eroding Science Education in Florida

periodicFlorida just passed a bill designed to challenge the teaching of evolution, climate change, and other “controversial” science in the classroom. This represents the evolution of such laws promoted by those opposed to the teaching of evolution.

In the past century there have been a number of such state laws passed in the US, most of which have been struck down by Federal courts, including The Supreme Court, as a violation of the separation of church and state. These including banning the teaching of evolution, requiring the teaching of “creation science”, teaching the controversy, and teaching creationism’s alter-ego, Intelligent Design.

Essentially these are all attempts to force or allow schools to determine what is taught in the public school science classroom not by the current scientific consensus but by the prevailing religious beliefs of the community. The string of legal defeats has not stopped efforts to oppose the teaching of evolution. Rather deniers have simply tried to craft laws to get around the pesky first amendment.

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Jun 27 2017

Sleep

poor-sleepSleep is essential and yet many people get insufficient sleep or have poor sleep quality. A recent review gives the following stats:

Population studies show that sleep deprivation and disorders affect many more people worldwide than had been previously thought. A recent study found 20% of 25–45 year-olds slept “90 minutes less than they needed to be in good shape”. Insomnia is the most common specific sleep disorder, with ‘some insomnia problems over the past year’ reported by approximately 30% of adults and chronic insomnia by approximately 10%. Prevalence of obstructive sleep apnoea, characterized by respiratory difficulties during sleep, is also very high with estimates of 9–21% in women and 24–31% in men.

The CDC considers poor sleep a public health problem. As a practicing physician these statistics also match my experience. Poor sleep is comorbid with many neurological conditions I treat, such as migraine. What I find interesting is how many patients I see who are having frequent migraines, they have fatigue, have difficulty with weight control, and are having difficulty with concentration and short-term memory. Further, when asked they report having terrible sleep, and yet they did not volunteer this information or make any connection to their other symptoms.

What this tells me is that people under-appreciate the importance of sleep and the negative consequences of chronic poor sleep. In fact, many patients are initially dismissive of the idea that poor sleep could be a major explanation for their symptoms. They are used to having poor sleep and that is now their normal.

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