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.
Some very important discoveries this month including a big one that may well be the most important finding for decades, if it doesn’t turn out to be a fluke.
The big news is that an experiment conducted at Fermilab observed muons behaving in a manner not consistent with the Standard Model of physics. After checking the math, the conclusion is that the model is wrong and there well may be a fifth, heretofore unknown, fundamental force in nature that would be needed to account for the behavior. For now, even though it is statistically unlikely to be a fluke, the Standard Model is so well established that no one is going to throw it out based on just this one result and certainly no one knows what is going to come next. But we can be sure that theoretical physicists are up all night trying to make sense of this.
Another important announcement, if it eventually proves to work on humans, is the discovery of a method of regrowing lost teeth. It uses an antibody to suppress one particular gene, USAG-1, and that was enough to stimulate tooth growth in mice and ferrets. There’s a long way to go before it would be even considered for testing on humans but if it works this certainly counts as a discovery that would make a big impact on everyone’s lives.
Next is a review of collected research to suggest that a strategy of promoting bilingualism, even if that means teaching a second language to the elderly or strengthening long unused language skills, is useful to delay the onset of dementia. It seems that even Cantonese and Mandarin spoken bilingualism is sufficient to have measurable effects on the onset of dementia. Since has no effect on Malaysians as we speak multiple languages already but it is interesting to see language learning being promoted as a healthcare measure.
Everyone knows how amazing it is that the world has been able to develop multiple effective COVID-19 vaccines in so short a time to address the ongoing pandemic. This paper argues that this has been possible partly because of the many lessons learned about vaccines across the decades spent trying to develop one for HIV. That effort was met with failure after failure but the argument is that it built up the necessary vaccine expertise to quickly develop one for COVID-19 and so research funds for vaccine development are never wasted.
Finally here’s some fascinating reading material about a particular species of ant known as the Indian jumping ant. As we all know, each ant colony only has a single queen. So what happens when the queen dies? In the case of this type of ant in particular, the surviving females compete to become the new queen and to do this their bodies transform into an intermediate form known as a gamergate to fight each one another with shrunken brains. Eventually a winner will emerge to become the queen but then the losers who survive the fight will transform back into normal ants, which involves their brains growing back again. And yes, queen ants don’t need big brains because all they do is pump out babies.
Trying something a bit different for this month’s edition of serving up cool science news and a couple of pieces really benefit from a visual presentation of the discoveries.
The first of these is a new paper that for the first time lays out a complete model of the workings of the famous Antikythera Mechanism. This is effectively a mechanical calculator or computer from ancient Greece, the fragments of which were recovered in 1901. A complete understanding of how the device worked was difficult to achieve given that only about a third of the mechanism survives. This paper explains how x-ray CT techniques were used to infer the parts that are missing and uses investigative work to fill in the blanks to prove that the entire device was used to calculate the positions of the Sun, the Moon and the five planets known at the time, according to a geocentric model of the cosmos. This excellent video was made to accompany the paper to explain what the device does and how the team arrived at the conclusions they did.
It’s a short month and slow in terms of interesting science news, so I don’t have much.
First we have a long feature about the earliest known domesticated dogs. Based on studies of both human and dog DNA as well as the observation that the genetic lines of dogs and humans tend to merge or spit together in the same places because humans bring their dogs along with them as they move, the current hypothesis is that dogs were first domesticated somewhere in northern Siberia roughly 23,000 years ago. Unfortunately just as more successful human settlers killed off natives as they invade, so do the dogs they bring displace the dog lineages of the natives, all of which can be noted in the mitochondrial DNA evidence.
Here is an amusing story about how pigs can seemingly be trained to play simple video games. They used a ruggedized version of a familiar joystick and had a dispenser for food rewards when the pigs won. Yet some of the pigs still played even after the dispenser mechanism broke down. This isn’t too surprising a result as we already know that pigs are quite intelligent and yes, I would agree that there is a moral imperative to move towards synthetic meat.
Finally this is potentially a huge thing once it can be proven to work on humans. Despite decades of effort, there is currently no contraceptive pill that can be taken by men. This paper talks about triptonide, a natural compound extracted and purified from a herb used in traditional Chinese medicine. Studies involving mice and monkeys show that it induces deformed sperm, greatly reducing its movement ability and hence causes infertility. Moreover it is fully reversible several weeks after cessation of the drug and seems to have no toxic side effects. Needless to say once it becomes available for humans, it will help shift the burden of preventing unwanted pregnancies from being borne entirely by women.
First month of the year and there is already plenty of cool science stuff.
We start with the bit of science news that has been shared the most this month. Many tourists who have visited Bali would know about how the long-tailed macaques there are notorious about stealing items from tourists. A new paper however asserts that the monkeys have even learned how valuable different objects are to humans. Not only are they able to steal objects that have no inherent value to them such as wallets and hats in order to exchange them with things that they do want such as food, but they have learned the relative value of different objects and will only exchange objects of higher value with food that is more desirable. Furthermore they have determined that this is a learned behavior as adult monkeys are the best able to make such valuation judgments while juvenile ones make no such distinctions.
By now everyone will have heard of mRNA vaccines, an approach to making vaccines that is completely different from inactivated vaccines. But this technique is being used to treat more than just covid-19 as this paper talks about a promising vaccine for experimental autoimmune encephalomyelitis. This is an extremely scary condition in which the immune system acts up and starts attacking your own nervous system and for which no treatment currently exists. The news about this jumped out at me immediately because my wife and I actually know someone who has this condition.
Next is an article about how even the simplest of organisms, in this case, non-photosynthetic bacteria have internal clocks that align with the Earth’s 24-hour cycle. Scientists already knew that photosynthetic bacteria have such clocks, because they rely on the light of sun to make energy, This time they have found similar cycles of gene activity in a soil bacterium that does not use photosynthesis and that such cycles even in an environment that is always dark. This suggests that this is an essential feature of all life on Earth even if we don’t why or how it is achieved.
Finally for fun, here is an article about how the complete genome of the platypus has just been released. Just as you might expect from this weird hybrid animal, its genes are part bird, part mammal and part reptile. This gives intriguing information about its evolutionary history. For example, the platypus lays eggs like birds but produces milk for its young like mammals. Accordingly while birds and reptiles have three genes that encodes for egg proteins, the platypus have only one and humans are zero. Yet the platypus does have most of the milk genes possessed by other mammals. Meanwhile it has also lost all four genes that encode for tooth development in mammals and as such grinds up its food with horn-like plates.
For this last month of a tumultuous year, the theme is probably that of China’s ascendancy in the domain of the sciences as Chinese researchers churn out groundbreaking discoveries one after another. I don’t even have to include China’s moon mission for this as that has yet to yield any novel science.
We might as well start with those first so here’s the story of it switching on its tokamak for real. This a fusion reactor that has plasma as hot as the temperature as the sun swirling around inside, held in place only the magnetic fields created by supercooled electromagnets. The promise of fusion power forever being just beyond the horizon is an old one and it’s still likelier than not that China’s effort to chase viable fusion energy will amount to nothing. But there’s no denying that they are in the race for real now.
The other one is about China’s photon-based quantum computer it has named Jiuzang. Like Google’s Sycamore, this has been built to perform a single type of computation, the one here being known as boson sampling. This involves sending parallel streams of photons as inputs through a series of beam splitters to obtain a result. Apparently trying to simulate this calculation through conventional means takes so long as to be effectively, thus making this a second clear case of quantum supremacy. I have no idea however if this has any practical use.
Still neither of these can match the significance of the next bit of science news: the announcement that Google’s DeepMind AI has effectively solved the protein folding problem. They proved this at an annual competition that involves predicting what shapes given strings of amino acids will fold into. While DeepMind’s solutions were not perfect, they are still so accurate as to essential invalidate every other approach. Despite the fact this means the careers of many scientists in the field have been upended, pretty much everyone is in agreement that this is a truly revolutionary advance that will change the entire biotech industry.
Next is a paper about restoring sight by inducing the retinal ganglion cells in the eyes to regenerate. Techniques to restore youth to cells and turn back the epigenetic clock have long been the stuff of science-fiction so this is a case of it in reality. They achieved it engineering a virus to induce expression of transcription factors that can trigger mature cells that it infects to revert to an immature state. Tested in mice, this approach succeeded in repairing damage to the RGC axon and restoring sight. Naturally they are very interested to learn if this technique also works on neurons elsewhere in the brain and the spinal cord.
Finally there is this bit of news about progress in developing so-called C4 rice. To cover some basics, different plants have different photosynthetic pathways and rice uses the less efficient C3 pathway. Maize on the other hand uses the more efficient C4 pathway. So C4 rice has been a sort of dream project for some time as the C4 pathway is theoretically up to 50% more efficient, so C4 rice would require less nitrogen and less water. This announcement is just about the early stage of assembling a functioning C4 biochemical pathway for rice and the real thing is still many years off but apparently this is still a pretty major advance.