Jan 27 2015

Disneyland Measles Outbreak Hubbub

This is an ongoing story that isn’t over yet. As it has been raging for days now, most people have probably heard that there is a big measles outbreak starting in Disneyland in California. There are now 87 confirmed cases of measles, 50 of which can be directly linked to Disneyland. Of the 42 people so far whose vaccination status is known, 34 were unvaccinated, 3 were partially vaccinated, and 5 were fully vaccinated.

Yes, this is caused by those who are not vaccinated

One thing is absolutely certain from these numbers – this outbreak has largely been caused by those who are not vaccinated. As you can see, most of those affected are unvaccinated. The vaccination rate for MMR is about 90% in the US. This means those who are unvaccinated were about 67 times more likely to be infected with measles in this outbreak than those fully vaccinated.

If vaccination rates were higher, then herd immunity could have stopped or severely limited the spread of the disease. That is the point of herd immunity – if enough people are protected then the virus is less likely to find a vulnerable host and continue the spread. The vaccine is about 97% effective in those fully vaccinated, which is why there were a few vaccinated people who contracted the disease.

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Jan 26 2015

The Brains of Lucid Dreamers

Lucid dreaming is a very interesting phenomenon that perhaps gives us a peek into the inner workings of the human brain. I have had about a dozen lucid dreams in my life that I can remember. Normally while dreaming we are not aware of the fact that we are dreaming. Our dreaming selves accept the reality of the dream. During a lucid dream we become aware that we are dreaming, but we do not wake up. This state is inherently unstable and often results in actually waking up or dreaming that we wake up, which ends the lucidity.

The phenomenon of lucid dreaming was originally known from self report, but was first verified in a 1981 study in which subjects consciously gave a signal while lucid dreaming – they carried out predetermined actions in their dreams that resulted in “observable concomitants.”

One of the goals of lucid dreaming research is to determine what exactly is happening in the brains of those who are lucid while dreaming. One hypothesis is that part of the frontal lobes may be more active, allowing for greater self-reflection and reality-testing while dreaming. Preliminary studies, for example using EEG to look at brain activity during wakefullness, normal REM sleep, and lucid dreaming, suggested that lucid dreaming is a hybrid state between fully awake and REM sleep.  The frontal lobes are more active in lucid states than normal REM, but not as active as fully awake.

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Jan 23 2015

Phishing Techniques Studied

Don’t click it. If you ever get e-mailed a link, no matter how authentic the e-mail looks or from whom it appears to be, don’t click it. If you feel you need to respond to the e-mail, then type the URL of the website directly into your browser. But never click it.

As simple as that rule sounds, it’s difficult for everyone to remember the rule all the time. One lapse of attention, and you can find yourself the victim of identify theft, have your credit card numbers stolen, or even all your passwords. Unfortunately there is a lot of money to be made in identity theft and there are many criminals out there.

So-called “phishing” scams involve sending out spam e-mails that are designed to provoke the reader into clicking a link which goes to a dummy website that will load malware on your computer that will mine it for passwords, identity information, and credit card information. Such scammers are getting better and better and provoking the click. 

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Jan 22 2015

Fail Safe for Artificial Life

In Jurassic Park the scientists who created the dinosaurs from DNA trapped in amber included what they called the “lysine contingency.” They engineered the dinosaurs so that they could not manufacture the amino acid lycine. The dinosaurs could only survive if they were fed lysine by the park staff. Without the supplement they would quickly fall into a coma and then die.

This contingency was a fail safe if any dinosaur ever escaped from their designated areas, or from the park itself. However, the lysine contingency failed. Dinosaurs could survive by eating lysine rich foods, like chickens or soya beans, or other dinosaurs.

Biologists have now done Jurassic Park one better. Genetically modified bacteria are extremely useful. Bacteria have been engineered to produce drugs, like insulin, or to eat up spilled toxins or petroleum products, or to make synthetic fuel. There is always a concern, however, that such a synthetic bacteria could get out into the wild with unpredictable effects. Physical containment strategies are therefore used to minimize the chance of this happening.

Research teams at Harvard and Yale have developed a new strategy of containment. The genetic code shared by all life involves a language of 3 nucleotides, of which there are 4 types, resulting in 64 different combinations. Each three letter combination codes for an amino acid, of which there are 20 used by living organisms. This allows for some redundancy, with each amino acid having 2-3 different codes. There are also some regulatory codes, such as stop codons – three letter combinations that tell the machinery to stop making the protein at that point.

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Jan 20 2015

False Confessions

When a suspect confesses to a crime, that is a powerfully persuasive piece of evidence. People assume (reasonably) that no one would confess to a crime they didn’t commit, extrapolating from the conviction that they would never do so themselves.

Of course there are legal reasons why someone accused of a crime would confess to guilt, in order to plea to a lesser charge or sentence and avoid the risk of a much more serious sentence. It is an unfortunate reality that innocent people can be wrongly convicted, and therefore an innocent person might confess in order to avoid the worst consequences of such a wrongful conviction.

Would, however, someone confess not to secure a plea bargain but simply because they are being aggressively interrogated? New research suggests that it is possible to form false memories of having committed crimes that one never committed. This is not surprising given all the previous memory research showing  how easy it is to form false memories.

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Jan 19 2015

Golden Rice Follow Up

There is a major anti-golden rice smear and disinformation campaign underway, spearheaded by Greenpeace with other anti-GMO activists on board. They themselves consider golden rice to be a “Trojan horse” for GM technology in general, so they essentially admit that their motivation is to oppose GM technology, even if that means opposing a technology that can save the sight and lives of poor children.

Golden rice is a genetically modified rice variety with enhanced production of beta carotene, the pro-vitamin of Vitamin A. The name derives from its golden color, provided by the beta carotene, the same thing that makes carrots orange. Carrots, by the way, were originally white and were modified through breeding to produce beta carotene, which was a very successful biofortified campaign in Europe that effectively combated vitamin A deficiency.

In response to my post from last week on biofortified GM crops, one commenter did a large “cut and paste” into the comments (generally considered a comment etiquette no-no, but I let it through because the topic is so important) with essentially the full anti-golden rice propaganda. The commenter seemed to think this constituted a “convincing” argument. Let’s see.

*GR IS STILL NOT READY

While there have been long delays in the development of GR since it was “invented” in 2000 (1), this has not been due to the activities of anti-GMO activists, but to basic R&D problems.

This is confirmed in a statement by the International Rice Research Institute, the main body working on the GR project (2). According to the Institute, the time frame for developing a new product is about 13 years, and GR is “still under development and evaluation”. In September 2013 the IRRI expected GR to take another two years before it was ready.

While this point is essentially correct, it is not an argument against the adoption of golden rice. Golden rice (GR) development began in the 1980s. By 2000 the first GR variety was ready, but it produced too little beta carotene to be effective. GR2, using different genes, was ready by 2005 and contained 23 times as much beta carotene as GR 1. This is enough to effectively combat vitamin A deficiency in cultures that consume rice as their primary staple.

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Jan 16 2015

Trans-Neptunian Objects

Published by under Astronomy
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My mental map of our solar system has evolved over the years, as I have learned more about astronomy and as astronomers have learned more about our solar system. When I was younger that mental map ended with Pluto, the ninth and outermost planet of our system. I then learned that Pluto’s orbit takes it within the orbit of Neptune, and from 1979 to 1999 Neptune was actually the furthest planet.

My mental map expanded greatly when I learned about the Kuiper belt and the Oort cloud (I can’t remember now which one I learned about first). The Kuiper belt is a doughnut shaped region of space beyond Neptune that contains many small icy worlds. The Oort cloud is a spherical shell farther out still that contains small chunks of dirty ice and is likely the source of many long period comets that sometimes fall into the inner solar system. Short period comets likely come from the Kuiper belt.

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Jan 15 2015

Marketing Biofortified GMOs

The first generation of genetically modified organisms (GMOs) to hit the market mainly possessed agronomic traits, such as insect resistance and herbicide tolerance. These traits mainly benefit farmers, and when consumers accept such produce they expect them to be cheaper because of the increased efficiency.

There is a second generation of GMOs waiting in the wings, however, that have biofortified traits that can directly benefit the consumer. A recent article in Nature Biotechnology reviews these GMOs and marketing research about their acceptability.

There are six GMO staple crops ready for the market but awaiting regulatory approval. These include golden rice fortified with vitamin A, which has been held up in regulation for 15 years. Other products include rice fortified with folate, and multi-fortified crops such as corn fortified with vitamin A, folate, and vitamin C.

It is also possible to increase mineral content, such as iron, zinc, and copper. This can be done by increasing uptake by the roots, transport to edible tissues, or bioavailability (ability to be absorbed once eaten).

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Jan 13 2015

Chimp and Human DNA

I was recently asked to respond to an apologist page that  challenged the scientific claim that human and chimpanzee DNA are very similar, which is evidence that we are descended from a recent common ancestor. You have probably heard the claim that human and chimp DNA are 96% the same. The apologist was referencing the work of Jeffrey Tomkins in his “peer reviewed” study showing that there is only 70% similarity. In fact, the the DNA of chimps and humans are so different, Tomkins claims, that there would not have been enough time for evolution to account for all the changes.

This is what I like to call, “sophisticated nonsense.” The very purpose of pseudoscience such as this is to confuse the public with complicated arguments that only scientists are likely to understand. We can turn such pseudoscience, however, into teachable moments.

For background, it is helpful to understand that there is no completely objective way to come up with one number that represents the percent similarity between the DNA of two species. There are just too many different choices to make in terms of how to count similarity. For example, how do you count chromosomal differences? Do you just compare the sequences of genes in common? What about insertions, gene duplications, and deletions? Do you line up sequences to their best match and just count point mutations? Do you count non-coding segments?

There is no one right way to do it to give a definitive answer of similarity. However, if you have a specific question in mind, then the method you choose should be designed to answer the question.

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Jan 12 2015

Another Salvo in the Mammoth Extinction Controversy

There are many enduring controversies within science, and they are fun to follow. There are raging debates about the so-called Hobbit or Homo floresiensis, is it a new species or a diseased human? You may be surprised to hear that there is still a controversy over whether or not the dinosaur extinction was due to a meteor impact or other terrestrial factors (although I think this one is heavily tilting toward the impact theory).

One controversy I have been following, here and on the SGU, concerns the Young Dryas and whether or not the cooling characteristic of that period was due to melting glaciers or a local comet impact.

Such controversies always raise a few general issues for me. The first is how the mainstream media covers them, which I always find disappointing. Properly covering genuine scientific controversies is challenging, but that is what science journalists are supposed to do. What I find is that they tend to present each new study in the debate as if it is definitive and has ended the debate, rather than putting it into the proper context of the ongoing controversy.

Another common mistake is to rely on one expert rather than getting a reasonable sample. They tend to weight the story toward the side of the expert on which they relied, and maybe provide only token coverage of other views. There is also, of course, the issue of proper balance. Reporting should reflect the balance of opinion in the scientific community. It’s OK to present minority opinions but they should be presented as such.

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