Daniel Lemire's blog

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Science and Technology links (November 11th, 2017)

Read the following quote from the New York Times:

Business is taking an interest in artificial intelligence, or A.I., and some professors, are forming or joining companies to capitalize on the expected boom. But the new move toward commercialization is disrupting the academic community and provoking fears that university research will be hurt.

Some researchers welcome the business interest. Others, however, complain that corporations are outbidding the campus for scarce personnel, and that work is being diverted from long-term research to short-term problems with immediate application.

It was written in 1982.

The Spectator has a piece arguing that moderate drinking is good for you and that this fact is being suppressed by health professionals. (My thoughts: I think it is far from certain that alcohol is good for you, but it is probably not what will kill you.)

We all know that human activity is wiping out some animal species. According to professor Chris Thomas… a different story can be told

The biological processes of evolutionary divergence and speciation have not been broken in the Anthropocene, they have gone into overdrive. Come back in a million years and we might be looking at several million new species whose existence can be attributed to humans. In the end, the Anthropocene biological revolution will almost certainly represent the sixth mass genesis of new biological diversity. It could be the fastest acceleration of evolutionary diversification in the last half-billion years.

In a short talk, the famous polymath Eric Weinstein argues that Physics is lost to theoretical nonesense… that it is stuck away from reality. He suggests that it might be time for outsiders to come in an disrupt the discipline.

You can spot cancer cells because they burn through sugar very fast, generating heat. Canadian researchers have designed a very low-cost device that cools the skin and then measure the temperature to reliably spot skin cancers. If not for regulations, this could be available cheaply at Amazon in a few years?

A boy was suffering from a terrible genetic skin disease. Doctors took skin samples, corrected the genetic anomaly, regrew the skin and put it back in place. It worked. The vast majority of his skin had to be replaced.

You may have heard that chocolate was a health food? According to a story in the Atlantic, there is some really bad research practices involved:

If you look at the most recent version of their clinical trials registry, it was published in January 2015, three months after they published their Nature Neuroscience article. So they went back after article was published in Nature and changed their clinical trial registry. There is no mention of this in the trial report, Drysdale added.


The bigger concern is that people are trying to do a better job of selling the research itself and not just telling what the straight out answer is, University of Toronto nutrition researcher Richard Bazinet said. This study only showed that over a period of three months, in a small group, according to a very narrow test that taps a very specific region of the brain, cocoa supplements enhanced cognition. That became chocolate fights Alzheimer’s, a message Mars surely appreciated.

As we grow older, we accumulate senescent cells. These are old cells that won’t replicate or function normally. It is strongly associated with several diseases of old age. Currently, there are a few initiatives to develop safe drugs that can kill senescent cells. Amazon’s Jeff Bezos is funding one such initiative. Unexpectedly, some researchers have done breakthrough work that shows we can possibly reverse the senescent state:

The researchers applied compounds called reversatrol analogues, chemicals based on a substance naturally found in red wine, dark chocolate, red grapes and blueberries, to cells in culture. The chemicals caused splicing factors, which are progressively switched off as we age to be switched back on. Within hours, the cells looked younger and started to rejuvenate, behaving like young cells and dividing.

The discovery has the potential to lead to therapies which could help people age better, without experiencing some of the degenerative effects of getting old. Most people by the age of 85 have experienced some kind of chronic illness, and as people get older they are more prone to stroke, heart disease, and cancer.

This week, I learned that molecules inside our cells move really, really fast:

You may wonder how things get around inside cells if they are so crowded. It turns out that molecules move unimaginably quickly due to thermal motion. (…) a molecule will collide with something billions of times a second and bounce off in a different direction. (…) As a result of all this random motion, a typical enzyme can collide with something to react with 500,000 times every second. (…) In addition, a typical protein is tumbling around, a million times per second. Imagine proteins crammed together, each rotating at 60 million RPM, with molecules slamming into them billions of times a second. (…) enzymes spin at up to 700 revolutions per second, which is faster than a jet engine.

Waymo, the Alphabet [i.e., Google] self-driving car company, now has cars driving on public roads in the Phoenix metropolitan area with no one in the driver’s seat.

In a timid study, a small amount of blood plasma from young people was transfused into people suffering from Alzheimer’s. The study failed to show massive benefits:

Nine patients with mild to moderate Alzheimer’s got four once-weekly infusions of either saline (as a placebo) or plasma from 18- to 30-year-old male donors. After a 6-week break, the infusions were switched so that the patients who had gotten plasma got saline, and the patients who had gotten saline received plasma. Another nine patients received young plasma only, and no placebo. (…) The remaining patients who completed the young plasma treatment performed no better overall on objective cognitive tests given by medical staff. However, on average their scores improved slightly 4.5 points on a 30-point scale on a caregiver survey about whether they needed help with daily activities such as making a meal or traveling. The patients’ average scores also improved modestly on another survey that asks caregivers how well patients can perform simple tasks like getting dressed and shopping. (…) Wyss-Coray agrees that not much can be concluded from the small trial, but says, It’s tempting to feel hopeful about the improvement in functional scores. Because the treatment seemed safe, Alkahest now wants to launch another trial that will use just the fraction of the blood plasma that contains growth factors, but not coagulation factors and other components that may do more harm than good. In animals, this plasma fraction was more effective at improving cognition in the mice with an Alzheimer’s-like condition than whole plasma, Wyss-Coray says. Alkahest also wants to test a range of doses and include patients with more severe Alzheimer’s.

Recall that we do know that parabiosis, the transfer of blood between two animals, can age or rejuvenate, but the best evidence suggests that we simply acquire aging factors as we age: there are no magical youthful factors. So it might be a total waste of time to add a bit of young plasma in the blood of older individuals. Instead, we need to find a way to normalize the composition of the blood of older people. This problem may prove very hard with our current technology. Or not.

It is usually assumed that peer review, as practiced by science journal, improves research articles. It may not be so simple:

Peer reviewers fail to detect important deficiencies in reporting of the methods and results of randomised trials. The number of changes requested by peer reviewers was relatively small. Although most had a positive impact, some were inappropriate and could have a negative impact on reporting in the final publication.

Alzheimer’s disease may not start in the brain. Without kidding: there is some evidence that unhealthy teeth and gums could lead to Alzheimer’s.

A young girl that was doomed as a baby due to a spinal muscular atrophy was rescued due to gene therapy.

I always assumed that prestigious journals had better peer review. That might not be so:

If you take all journals and rank them according to prestige,the most prestigious journals publish the least reliable science (at least when you look at the available evidence from experimental fields).


In the field of genetics, it appears that errors in gene names (and accession numbers) introduced are more common in higher ranking journals


statistical power has been declining since the 1960s and that statistical power is negatively correlated with journal rank (i.e., a reproduction of the work above, with an even worse outcome). Moreover, the fraction of errors in calculating p-values is positively correlated with journal rank, both in terms of records and articles

What might explain this effect? Maybe high prestige attracts certain types of people with goals the differ from that of science.

A breast cancer drug appears to cure arteriosclerosis (a condition responsible for heart diseases) in mice.

Systematic reviews of the state-of-the-art are often produced in medical research to summarize the research. I always expected this work to be top-notch. It may not be so, as these studies fail to provide the necessary information to make their analysis reproducible:

the data needed to recreate all meta-analytic effect estimates (…) in only 65% of SRs. Only 30% of SRs mentioned access to datasets and statistical code used to perform analyses.

It is just not possible to check whether a review paper has done its work properly. You cannot double check the computations.

According to the New York Times, the best college majors according to wages are engineering, economics, computer science and nursing. These worst are education, social work, humanities, philosophy, liberal arts, psychology, English, and biology. Business and accounting are somewhere in the middle.

The hole is the ozone layer is shrinking.

Amazon’s Jeff Bezos has funded a company that is buidling a gigantic indoor farm in Seattle.

Lifting weights twice a week is the best routine to keep your muscles as you age. Lifting weights is better than cardio to stay fit as you age.

Sleep deprivation messes with your neurons in a bad way, according to Nature.