Archive for January, 2018

Jan 30 2018

Gattaca

Published by under General Science

The Human Genome Project was started in 1990 and completed in 2003. It took 13 years, multiple labs around the world, and hundreds of millions of dollars to sequence the human genome – this was more than two years ahead of schedule and millions of dollars under budget.

The reason for exceeding expectations is that the technology for sequence the genome was not static – it progressed throughout the project. DNA contains a code of four letters, the nucleotides indicated by the letters G, T, A, and C. This four-letter alphabet creates 64 different three-letter words, which code for different amino acids or operations that control the conversion of the code into proteins. Sequencing the genome essentially consists of discovering the order of these four letters in the string of a DNA molecule.

In 1997 the movie Gattaca, right in the middle of the genome project, portrayed the near future in which a cheek swab would rapidly yield an individual’s genome. It turns out this is not far fetched at all – we are almost living in Gattaca’s near future, at least in terms of sequencing technology. Scientists have just published a report of the nanopore device, which is a hand-held device capable of sequencing an individual’s genome.

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Jan 29 2018

Shameless Organic Fearmongering

Published by under General Science

I and others have long pointed out that anti-GMO fearmongering was largely created by the organic food lobby as a way of smearing their competitors. The strategy is simple – scare people way from genetically modified organisms (GMOs) and offer organic products as a non-GMO alternative. This is nothing new in advertising, create a fear and then offer your product as a safe haven.

A recent video posted by Stonyfield Organic makes the connection between anti-GMO fearmongering and buying organic explicit, as the screen capture shows.

There are many problems with this short video, not the least of which is that they use young girls to parrot their anti-science. Clearly not aiming for subtlety, the first girl declares that GMOs are “monstrous.” To apparently explain what she means, the second girl says that, “They take a gene from a fish and put it into a tomato.”

No, “they” don’t.

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Jan 22 2018

False Alarm

On January 13 a state-wide alarm was sent out in Hawaii warning of an incoming missile. “BALLISTIC MISSILE THREAT INBOUND TO HAWAII. SEEK IMMEDIATE SHELTER. THIS IS NOT A DRILL,” the emergency alert read. For the next 38 minutes the citizens of Hawaii had the reasonable belief that they were about to die, especially given the recent political face off with North Korea over their nuclear missiles.

However, within minutes the Governor and the Hawaiian government knew that this was a false alarm, resulting from a technician hitting the wrong button. So, there are two massive failures here – sending out the alarm in the first place, and taking 38 minutes to officially send out the correction. (They did tweet that it was a false alarm, but the retraction was not generally known and it wasn’t certain that it was official.)

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Jan 18 2018

The Dangers of Celebrity Culture

Zooey Deschanel has a Facebook page where she gives advice on complex scientific topics. I love Deschanel as an actress and enjoy much of her work (particularly the otherwise mediocre movie version of the Hitchhiker’s Guide), but that does not mean I want to take advice from her on which foods I should eat.

Celebrity culture, in one form or another, has always been part of human society. Even chimpanzees will follow a charismatic leader, and it seems likely that humans are wired also to follow those we admire, and elevate them perhaps a bit too much. There is even research that shows that when we listen to a charismatic speaker the executive function part of our frontal lobes shuts down. We literally turn off our critical thinking when basking in the glow of our glorious leader.

Recognizing that this is part of the human condition is important. First, we need to be vigilant about surrendering our thinking to others. It’s also important to remind ourselves that everyone is a flawed human, and so constantly give those pedestals a reality check.

But that does not meant we should not admire and respect those who deserve it, or even look up to them for wisdom (as long as we maintain our critical eye). It does mean we need to choose carefully those we respect and follow.

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Jan 16 2018

More Mental Illness Denial

Published by under Neuroscience

I was recently pointed to this article by Johann Hari in The Guardian that takes a critical look at depression and the treatment for depression. Unfortunately, it turned out to be nothing more than the usual mental-illness denial talking points, misdirection, and obfuscation.

As you will see if you follow the link above, this is a well-worn topic here. The basics are this – there are those, for various reasons, who are engaged in what I think qualifies as mental-illness denial. They include scientologists, because they push their cult/religion as an alternative to psychiatry. There are also those who follow Szasz who saw psychiatry as a mechanism for political oppression. I also find denial at times among rival professions who want to take psychiatry down a peg or two (often they just confuse their experimental expertise for clinical expertise – always a problem).

They all tend to have in common the core claim that “mental illness” is a fiction. How can thoughts be diseased? This is ultimately a straw man that confuses different types of illness. Some illness is based in biological pathology – cells are damaged, deteriorating, poisoned, genetically flawed, or essentially not functioning within healthy parameters for some reason. You can often see the pathology in a biopsy or measure it with some physiological parameter.

But not all illness is pathological disease. There are also disorders in which some biological function is outside of healthy parameters without clear pathology. The brain in particular is prone to this type of illness, and that is because brain function depends on much more than just the health of its cells (neurons and glia). Even healthy brain cells can be organized in such a way that their neurological function is compromised.

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Jan 15 2018

Oprah Would Be a Disaster

Published by under Culture and Society

I know that Oprah has not stated she is considering running for president in 2020 and the initial buzz about her is just a fantasy. But some of her people have stated that she would consider running, and it is possible that they are testing the waters. Let’s put the idea out there and see how the public responds.

Those who are enthusiastic about Oprah after her rousing speech at the Golden Globes have failed to fully appreciate what the real problem with Trump is (at least from this skeptic’s perspective). This is not about politics, and all the ways that Oprah is different than Trump don’t affect the ways in which she is the same – and those similarities are what I am primarily concerned about.

Marc Fisher, writing for The Citizen, describes what Trump apparently means when he calls himself a genius. Trump thinks that being smart is succeeding without trying. He congratulated himself on getting through school without ever really studying (like those other chumps). He admires instinct, his ability to feel in his gut what the answer is. He criticizes academics, and brags that the most important thing he learned at school was that academics don’t really know anything.

By all accounts that it his approach to the presidency. The very fact that he thought he could be president without any prior relevant experience betrays this attitude. It did not appear to bother him, or even occur to him, that being the executive of a large and complex government might requires skills and experience that he had never honed, or even tested. He thought he could sit in the Oval Office and just shoot from the hip, rely on his gut to divine the right answer to the country’s and the world’s complex problems. He would have a staff of eggheads to worry about the details.

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Jan 11 2018

Fast Radio Bursts – Still Not Aliens

Published by under Astronomy

This is a (sort of) follow up to my previous post. Fast Radio Bursts (FRBs) are a legitimate astronomical mystery, and very interesting. They are very brief (30 microseconds to 9 milliseconds) and very powerful bursts of radio waves. To date about 30 FRBs have been detected. Most of these FRBs are one-offs – they occur once and never repeat (at least so far). There is one exception, however, FRB 121102 (more on that below).

What do we know about FRBs so far? They are isotropic, which means they occur all over the sky. They are not concentrated in the galactic disk. This by itself implies they are extragalactic. But also analysis of the radio bursts indicate that they have traveled through intergalactic plasma, for billions of light years. So they must also be incredibly powerful. The radio waves are broadband, so they are spread throughout the radio wavelengths. They are also highly polarized, which means they were aligned at their creation with a strong magnetic field.

Because they are radio bursts, they are studied by radio astronomers, which includes SETI astronomers, whose primary mission is to survey the sky for possible alien communications. In an SGU interview with SETI astronomer Seth Shostak he indicated that SETI does a lot of non-ET-related astronomy. This is a good example of that – they are helping to detect and analyze FRBs, including analysis of FRB 121102.

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Jan 09 2018

Tabby’s Star Mystery Partly Solved

Published by under Astronomy

It’s not aliens.

So far, no astronomical mystery has turned out to be aliens, although this hypothesis seems to come up every time. The first detections of signals from pulsars were named LGMs for “little green men.”

I’m not really criticizing this – part of me wishes the mystery will turn out to be evidence of an alien technological civilization. I always think of how plausible that is for an explanation. But still it should be last on the list. Chances are overwhelming that we are just seeing some new or unusual natural phenomenon. It’s a big complex universe out there.

In this case astronomers found a genuine mystery – a star that dimmed and brightened over time to a degree never seen before. The star has the designation KIC 8462852, and has been nicknamed “Tabby’s Star” after the astronomer who first described it, Tabetha Boyajian (she actually led a team of 200 astronomers involved in the work).

The intensity of the light coming from the star, which is a little bigger and 4.7 times brighter than our sun and is about 1300 light years away, dims at irregular intervals by as much as 22%. This could not be caused by a planet passing in between us – even a Jupiter-sized planet would only block about 1% of the light from the star. And what’s with the irregular period? Dimming from an object in orbit should be very regular.

The best hypothesis was that a swarm or cloud of something was blocking the light. It would have to be a big and dense cloud, however. This hypothesis had problems also, however, because such a cloud should be heated up and glowing in the infrared, but we don’t see it.

The “swarm” idea sparked the notion of a Dyson swarm, which is a hypothesized high-tech structure surrounding a star used to capture the light for energy. An advanced civilization, for example, could power themselves with either a large single structure of solar cells, or a swarm of smaller ones.

No scientists really took the alien megastructure hypothesis seriously, even though it could not be entirely ruled out. It was just way too early to get excited, and it was overwhelmingly likely that a natural explanation was to be found. But scientists love a mystery in any case, and whatever was going on around Tabby’s star was likely to be new and interesting.

What astronomers needed was a lot more data. So Boyajian and others started a kickstarter campaign to fund the telescope time they would need to gather that data. The campaign was successful, exceeding their needed $100,000. Last week they published the result of their analysis and…no aliens.

What they did was look at the different wavelengths of light to see how they were dimmed. If the swarm that is causing the dimming is comprised of solid objects, whether rocks, planetary debris, comets, or solar panels, then all wavelengths should be dimmed equally. That’s not what they found. They found that different wavelengths were dimmed to different degrees at different times.

That is what you would expect to find if the cloud (circumstellar material) blocking the light were comprised of very tiny particles (smaller than a micron), like dust. So that is what they concluded – there is a dense dust cloud around Tabby’s star blocking the light from our perspective. This also makes sense in terms of the variable periods, because different densities in the cloud could cause random fluctuations in the amount of light blocked.

But of course now astronomers just have a new mystery – what caused this massive fine dust cloud around Tabby’s star? Comets are very dusty, and a dust cloud like this could result from a comet – but it’s a lot of dust. It’s also probably close to the star, which means it is also probably a recent phenomenon as a dust cloud would likely not survive long that close to a star that bright. This also still doesn’t explain the lack of an infrared glow from the cloud.

The results also don’t rule out that the star is dimming and brightening on its own, and not just being blocked from view. And of course, some hopefuls have pointed out that it could be a swarm of alien nanobots or similar microscopic technology. Sure.

There is still more science to be done here, but this latest result does add a significant piece to the puzzle. It’s also cool that the research was crowd-funded. That’s a great way to get private citizens involved in science, and to fund more science. That may, in fact, be the bigger story here. Yeah for crowdfunding cool science.

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Jan 08 2018

Nitrite Free Bacon

A Northern Irish food company, Finnebrogue, is offering what it calls “Naked Bacon” – free from chemical preservatives that contain nitrites. But would such bacon actually be more healthful? And what is the deal with nitrites in food?

Sodium nitrite (NaNO2) is a salt containing sodium, one nitrogen, and two oxygen atoms. Nitrate is similar but contains three oxygen atoms (NaNO3). Nitrites are oxidized to nitrates when exposed to the air. Nitrates can also be converted into nitrite in the GI tract. This is why we often talk about the two in food interchangeably.

Sodium nitrite serves a critical function in some foods – it is a good preservative that inhibits the growth of bacteria, specifically C. botulinum, the bacteria that causes botulism. It is therefore incredibly important to food safety, and removing it from meat products could therefore have the unintended consequence of increasing food poisoning.

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Jan 05 2018

The Return of “Traditional” Astrology

Published by under Pseudoscience

I guess this is a theme recently – the return of previous pseudosciences that had been fading into the background. If you type “astrology” into the search window on this blog you get exactly two articles specifically about this topic in the last 10 years. Hopefully this won’t really change and astrology will remain safely on the fringe, an old-school pseudoscience curiosity.

But there are those who are trying to give astrology new respectability. A recent article by Ida Benedetto outlines the strategy, which is two-pronged. First, blame astrology’s poor reputation on modern psychology. Then the fix is an appeal to antiquity – return to the ancient texts. She writes:

“Astrology’s contemporary flavor has a closer relationship with the social science of psychology than the observational science it used to be based upon. If we can set modern judgments aside and learn the language of the ancient astrologers—a language that is now newly available due to the recent revival of classical texts—we may discover lost insights.”

Let’s strangle this infant in the crib, as both prongs of this strategy are nonsense.

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