Decent mix of stuff though all in the life sciences.

• Easily the most exciting of the lot is the discovery of a new class of programmable DNA modifying systems. In this blog, I have talked many times about CRISPR and how it is a game-changer in enabling easy DNA editing but it is always better to have more than one tool in your toolbox. The acronym for this one is OMEGA, standing for Obligate Mobile Element Guided Activity. This is an RNA-guided DNA-cutting enzyme that originated in bacteria is only about one third the size of the Cas9 protein, which should help make it even more useful. Needless to say this is early days yet and we have no way of knowing if this will eventually be deployed but it is exciting news.
• One bit of news that has been all over the net this month is this paper about how quickly some elephants in Mozambique have evolved to lose their tusks as a response to poaching. The elephant population declined by 90% at the height of poaching activity but as the population recovered, more elephants are born tuskless. All of them however are female as the gene responsible for the change is lethal when expressed in male elephants but females can survive the mutation if they receive a non-mutated version of the gene in one of their two X chromosomes. Of interest is how quickly tusklessness increased during the Civil War that enabled widespread poaching and also now that the situation has stabilized female elephants are regaining their tusks as they are after all a useful tool.
• The next bit of news shouldn’t be much of a surprise but I think it makes for an interesting wake up call. It’s about a survey of wildlife, specifically wild boars and rat snakes, in the Fukushima Exclusion Zone which found no significant adverse health effects in the wildlife despite the exposure of varying levels of relatively low-dose radiation exposure. The team suggests that perhaps people shouldn’t be too fearful of moving back into the area but it goes without saying that health standards for humans and wildlife are very different, and rightly so. To me, this shows as in Chernobyl, that the wildlife is able to bounce back quite well following environmental disasters as the benefits from the simple absence of humans outweigh the adverse effects of the pollution.
• Finally, and I think this bit will resonate with quite a few people as we have all had to sit through the sales pitch at opticians’ shops, we have a paper about a randomized controlled trial that aims to determine how helpful blue-blocking lenses really are. This is a straightforward and simple experiment involving participants wearing glasses who were all led to believe that they were using such lenses and assigned to various computer tasks. Afterwards they tried to measure the eye strain experienced by the participants and found no significant difference between those actually using the blue-blocking lenses and those who weren’t. One possible objection is that the period of time under study, two hours of computer use, is relatively short but this isn’t the first time that objections have been raised that these lenses are an expensive add-on of doubtful benefit.

It’s Nobel Prize month and once again I like to highlight the science prizes because of how little mainstream news coverage they get. I don’t think there’s anything too surprising this year except that some people wondered why there’s been no acknowledgment of the mRNA technology that has powered many of the vaccines used to fight the ongoing pandemic. That’s silly of course given the time scales of how the Nobel Prize committee works such that it takes a while for a discovery to be deemed important enough to merit an award.

I suppose the most headline grabbing prize this year is the one for physics because it’s being described as being an award for climate change research. It’s more complicated than that of course as it is really about methods to describe and predict the behavior of large, complex systems with a lot of chaos and the planet’s climate is the best possible use case for such methods. This story begins in the 1960s with Syukuro Manabe for linking increased levels of carbon dioxide in the atmosphere with higher temperatures and developed the first models of the Earth’s climate.

Some ten years later Klaus Hasselmann showed that local weather despite being chaotic and unpredictable could lead to reliable long-term predictions of the climate as a whole. Then in the 1980s Giorgio Parisi, studying complex materials such as spin glass such as a matrix of copper atoms that also contain scatted iron atoms and hence have complicated magnetic orientations, devised mathematical ideas to understand this complexity. Naturally these are also applicable to other fields including climate science.

Hopefully most people still reading this already know what catalysts are and why they are essential in chemical reactions to turn one type of molecule into another. It was thought however that catalysts fall into two types: enzymes, which are large, complicated protein molecules, and transition metals, the elements in the middle of the periodic table. Benjamin List and David MacMillan, working independently but towards the same ends, discovered an entirely new type of catalysts now called organocatalysts, for which they have been awarded the prize for chemistry.

These are relatively small organic molecules that don’t include metal. The latter is a desirable trait because metal compounds are frequently toxic and metal-based catalysts don’t distinguish between different mirror-image versions of molecules and as these have different effects, drugmakers usually want only one specific version. Since about 2000 when these discoveries were made, organocatalysts have become widely used in many industrial processes.

The prize for medicine may not seem so exciting but it is a natural extension of the realization that our senses work through incredibly specialized organs and channels and we still don’t know all of them, including elementary ones like how we sense temperature. David Julius beginning in the 1990s studied capsaicin, the active ingredient that makes chili peppers hot, and worked out which protein in heat-receptor cells are sensitive to capsaicin. In doing so, he discovered the ion channel protein now called TRV1 and worked out it is triggered when heat rises to painful levels. This led to other discoveries of other temperature sensing receptors including work by both Julius and Ardem Patapoutian to use menthol to identify cold sensitive receptors.

Patapoutian also found touch sensitive receptors, beginning with Piezo1 which is actually found in organs like the bladder. This sensitivity to mechanical pressure is what causes people to feel the need to urinate. Through its similarity to Piezo1, he also found Piezo2 which is responsible for our more familiar sense of touch and proprioception, which lets us know the position and movement of our body.

Unlike the physical sciences, it is extremely difficult to perform experiments in the social sciences or economics. David Card however realized that one could identify natural experiments such as when the state of New Jersey passed a minimum wage law in 1992 but nearby Pennsylvania didn’t. Reasoning that the two states are similar enough, Pennsylvania could serve as the control group to work out the effects of the minimum wage law. This seems obvious today but apparently it was quite novel back then.

Often however such differences between two groups aren’t so neat as that, and it may be necessary to tease them out in clever ways. Joshua Angrist was one of those who realized that the date of birth of each school student makes a small but measurable difference in how much schooling that student gets in the US. Effectively those were born earlier in the year gets slightly less schooling than one born late in the year. This makes it possible to work how the length of schooling a person receives impacts lifetime earnings. Guido Imbens is also included as one of the winners for working out the theoretical framework to analyze the causal relationships in these empirical phenomena.

Another light month in terms of new discoveries, so how about a long, review-type feature article for your reading pleasure and edification. We’ll start off with a couple of articles about the ongoing pandemic and the technologies that have emerged around it however.

• First we have this one about an antibody treatment for the SARS-CoV-2 virus. Far less attention has been paid to them than vaccines, but such treatments are another important tool to manage the pandemic. This one seems particularly important it seems capable of neutralizing not only all known strains of SARS-CoV-2 but also all known serbecoviruses, which means it covers all viruses of the same genus. It achieves this by binding to a particular site on the coronavirus spike protein that is thought to be unlikely to vary by much from mutation.
• Meanwhile the same technology that enabled mRNA vaccines is making its way to cancer therapies with human trials starting in Europe. BioNTech actually has several different mRNA cancer therapies in the works, targeting different types of cancers but all work on the same principle of programming the immune system to target tumor cells. Needless to say if the human trials work out, this would make a huge difference in the health outcomes of cancer patients.
• Next here’s an announcement about a team succeeding at synthesizing starch out of carbon dioxide. They claim that their process is more efficient than conventional agriculture but I’m not sure what that means as it applies to energy-use or economics. Nevertheless this is clearly a major discovery especially as carbon dioxide is now seen as a major pollutant. Converting it to food seems incredible. Incidentally I’ve read recently that companies trying to grow meat without animals aren’t having much success at making it economical and it may well be impossible to achieve at scale.
• Finally here’s a broad review of the current state of physics. Essentially the field is in upheaval because the Large Hadron Collider has failed to find so-called sparticles, the heavier supersymmetric partners of the known fundamental particles. This throws the entire principle of supersymmetry into doubt and along with it string theory as the leading theory of everything. This is a real problem for physics as theoreticians have bet on it being true and have done a lot of theoretical work ahead of finding empirical evidence. Now the doors are thrown wide open again to alternative theories of everything with one favorite, among many others, being entropic gravity.

A mix of soft science stuff this month, not that much going on it seems.

• We start not with a new paper but a retraction of a particularly famous one. The original 2012 paper about how people who were made to sign an honesty declaration were subsequently less likely to commit fraud was widely publicized and actually put into practice by various governments. Subsequent attempts to replicate this effect however failed and the researchers involved now acknowledge that the data it was based on seems to have been faked. The most famous of the scientists involved is Dan Ariely who claims the data came from an insurance company but refuses to name the company. This is still an ongoing case which threatens to completely destroy Ariely’s reputation and body of work.
• Next we have an economics paper that questions the effectiveness of television advertising. Based on a study of 288 brands, the authors conclude that such advertising has a negative rate of return for more than 80% of those brands. That’s a lot more than the more commonly cited figure of around 50% of advertising spending being wasted but I can’t speak for the quality of this paper.
• This next article seems highly speculative to me, but it’s worth knowing about it. It claims that as people interact and cooperate with each other, the oscillations of their neural activities appear to synchronize. The call is for a wider understanding of the phenomenon of consciousness and to acknowledge that the boundaries of the self are subject to negotiation with the environment as well as other people. This isn’t completely kooky science. We already know that the mind is what the entire body does, not just the brain, but this way of looking at things does cast the net even wider.
• Finally, here’s is a longer read released by DeepMind which is now owned by Google about their efforts to create an AI capable of open-ended learning. We’ve all heard by now about AI being able to beat humans at kinds of game from chess to Starcraft II but these are single-purpose AIs trained on a specific set of data to handle a specific challenge. This article talks about having general purpose AI inhabit a 3D virtual world and learning to navigate and accomplish tasks within that world. There are plenty of pictures too, covering all kinds of thing that the AIs need to figure out without being specifically programmed to do so. It makes for a fascinating read especially as each agent in the virtual world learns to interact with other agents.

Light on anything noteworthy that I’ve seen this month. Perhaps I’ve just missed things.

• One thing that did grab my attention is this paper is this one that tries to test what is well known as Bergman’s rule: the hypothesis that animals in colder regions adapt by becoming larger in size while those in warmer place become smaller. This paper examines human fossils to determine if this holds in humans and determines that it is indeed broadly true. They were however unable to find correlations between temperature and brain sizes.
• Next is a paper giving us even more reason to care about clean air, as if it weren’t enough that we all need clean air to breathe. It argues that cleaner air has contributed to improved yield gains of maize and soybean in the US. This is based on measurements of four different pollutants, ozone, particulate matter, sulfur dioxide and nitrogen dioxide.
• Then we have a paper that combines economics with biology. It’s about the nematode worm which biologists love to study because of how simple it is, with a nervous system of just 302 neurons. Yet that is enough complexity for it to seek out food, and the researchers have found that it does so according to the Generalized Axiom of Revealed Preference, a classical measure of utility maximization in economics.
• Finally the last paper is hardly a surprising result but it doesn’t bode well either. Basically they had groups of people put together to solve some tasks represented by a game and then later interviewed them to ask who they would consider the leaders of the group. The result was those who spent the most time talking were considered the leaders. Even the person designated by the organizers to be the one to operate the user interface of the game were not more likely to be considered the leaders, nor those who have more experience from prior sessions of the game, nor those who scored more highly at cognitive tasks. The factor that matters most of all is simply being eager and willing to speak up the most.

Pretty much all biology this month. The ongoing pandemic is really giving a big boost to all kinds of biomedical research.

• Perhaps the most predictable outcome of our extensive measures to contain the Covid-19 pandemic is that it has also reduced the genetic diversity of known subtypes of influenza. Prior to the pandemic, there were worries that clades of the virus family that causes influenza were drifting apart genetically, making it more difficult to formulate a vaccine that covers all of the strains. During the pandemic it seems that one of the clades has disappeared, though it’s likely that it’s present somewhere but transmission rates have dropped enough that it isn’t seen in circulation. This means that it becomes easier to make a vaccine for influenza again, at least for a while.
• The really big news this month is the announcement that scientists from a consortium of labs all around the world have finally sequenced the entire human genome. This is some 20 years since the first drafts of the human genome were first published. The long delay is because the final 8% of the missing genome has been particularly difficult to sequence, such as the centromeres, the points where the arms of the two chromosomes intersect. New techniques had to be devised to deal with these challenging sections but now that the entire genome is complete it will constitute a complete reference with no gaps and that could be very useful to all types of research.
• Next is the news that old-fashioned laughing gas, or nitrous oxide, seems to be a viable treatment for a particularly serious form of depression that is resistant to other forms of medication. Most people are likely familiar with the gas as a mild sedative sometimes used by dentists. The treatment here uses a much lower concentration of the gas and seems successful at reducing the symptoms of depression for months at a time. I honestly cannot understand why it wasn’t known earlier as it seems like an obvious thing to try.
• Most people should know that long period of physical activity very quickly leads to muscle loss and a drop in bone density in humans. At the same time, we also know that bears hibernate for months at a time yet they don’t seem to suffer from osteoporosis. A new paper describes the mechanisms that make this possible. In particular, the genes that code for bone resorption and apoptosis are turned down during hibernation but then so are the genes that code for the formation of new bone. It seems that all biological processes that changes the structure of the bone are turned off during hibernation. Needless to say, the ability to regulate bone activity in this way is worth investigating to develop a treatment for osteoporosis in humans.
• Finally here’s a paper about banded mongooses in Africa are able to maintain a more equal community by having all mothers give birth to pups on the same night. Thereafter they are seemingly unable to differentiate which pups belong to which mothers and so the community cares for the pups as a whole. It makes for an uplifting story but it’s too close to a just-so to ward off my skepticism.

Decently strong mix of articles this month from various disciplines, with an emphasis on discoveries that have a good chance of being very practically useful in the near future.

• Personally the most exciting bit of news to me is that it may soon be possible to make diagnosis of depression more reliable through a blood test. The test works by looking at 13 RNA markers that indicate how active the underlying genes have been, genes that are particularly correlated with the incidence of mood disorders or have been identified in previous work to be associated with depression. The test should also be capable to predicting who will go on to develop bipolar disorder and how serious the condition will be. This test, if it passes the testing stage, will likely only be used to accompany more traditional ways to diagnose rather than be used by itself, but it should be obvious to everyone how significant this will be if it is widely deployed.
• But I suspect that most people are excited about is TMSC’s announcement that it has invented a semiconductor that is smaller than 1 nanometer. I don’t know much about the details except that semi-metal bismuth as electrodes. TMSC also cautions that the technology may very well not not make it to commercial production at all. But it signals that we haven’t yet seen the end of incremental improvements to chip technology.
• Another piece of technology that I suspect will be deployed rather quickly is vertical wind turbines. The sight of windmill-shaped wind turbines are now a familiar sight in many landscapes but it seems that vertically oriented ones are more efficient and perform even better in a grid formation with some turbines behind others. In the traditional arrangement, this would result in turbulence in the rows of turbines behind those in front.
• This paper, though it has yet to be peer reviewed, could have major ramifications as well. As we all know, plants need nitrogen and a lot of what fertilizer does is give nitrogen to plants. This paper describes how a plant that is self-sufficient in nitrogen, by being able to use the nitrogen present in the atmosphere, could be made through synthetic biology.
• Finally a paper in economics that I believe adds more nuance to our understanding of wealth inequality. It describes how career earnings growth in the US more than doubled between 1960 and 2017 and this was because of the growing importance of jobs that requires decision-making skills. Accordingly while workers used to hit peak earnings in their 30s, they now hit it in their 50s. This reflects the importance of critical thinking skills in jobs and how learning skills and knowledge over a lifetime adds a great deal of value. I believe this helps explain some of the frustrations of the young in the present day and the disparity in earning potential.