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.

This has been an eventful month in terms of politics but things have been calmer in the world of science. I do still have some cool stuff to share.

• I really love the stories about how the pandemic related lockdowns around the world result in inadvertent natural experiments so here’s another one to add to the file. This one is about how the sleep patterns of children has been affected by the extended closure of schools. They found that children on average shifted their sleeping schedule two hours later than usual with online schooling starting later as well. This apparently resulted in higher sleep quality and less daytime sleepiness, suggesting than forcing children to wake up at the break of dawn to go to school in order to accomodate the working schedules of adults may not be for the best.
• The most significant news this month in my opinion is the discovery that it is possible to effectively shape and manipulate magnetic fields from a distance. Normally in order to generate such a field, the source must lie within the field itself. This basic fact has not changed but one team found that by creating multiple fields and shaping them in a specific way, they were able to generate a combined virtual field which appears as if its collective source lies outside the field. It’s early days yet for this discovery and apparently the current experimental setup is very limited but if this pans out, the possible applications would be the stuff of science-fiction.
• Next is this paper which nicely illustrates what a big difference genetically modified foods can make. This one is about the impact of GM brinjal introduced into Bangladesh based on a randomized controlled trial with a control group given a conventional variety of brinjal to plant and another group given a variety that is identical in all respects except that it has an added gene that is meant to have extra protection against pests. The result is a 51% increase in yields per hectare compared to a control group and a 37% drop in pesticides costs. They also note that the very significant drop in pesticide use also resulted in noticeably better health outcomes for the farmers involved.
• I also like this article about a population of seals that live in Lake Baikal, effectively isolating them from other seals and they are the world’s only known species of freshwater seals. Scientists however wonder how they manage to find enough food to eat as there are so many of them within a closed ecosystem. It turns out that they eat amphipoda, tiny shell-less crustaceans, in addition to a more normal diet of fish. This is surprising because such creatures are far too small to be eaten by other seals and indeed it proves that this particular population of seals have evolved comb-like structures in their teeth that allow them to filter the amphipoda out of the water. This is of course very similar to how some whales collect and consume krill, inviting speculation that these may be whales in the making.
• Finally here is another paper that involves CRISPR because it’s the gift that keeps on giving. This one involves using the technology to treat metastatic cancers, using it to target the damaged DNA of cancer cells and cut out that DNA, thus preventing the cells from replicating. Preliminary trials on mice show promising results but the most important part of this approach is that in theory it should only target cancer cells and leave normal cells alone, hence the researchers insistence that this isn’t chemotherapy with its heavy collateral damage. Of course, this is early days yet and we have seen plenty of other results using CRISPR where the targeting isn’t truly precise but there is no doubt that there is a huge step forwards in curing cancer.

A real wealth of science stuff this month and that’s coming off of the slew of science writing related to the Nobel Prize announcements earlier. Hope you’re prepared to do a lot of reading.

• We’ll get the big headline-grabbing bit of news out of the way first though I’m personally not so sure that it makes much of a difference. This is of course the discovery of the world’s first superconductor that works at room temperature. This is of course a staple of science-fiction and a technology that would revolutionize everything if works reliably and cheaply enough to be widely deployed. However in this case, it relies on squeezing hydrogen, carbon and sulfur together at a pressure of about 2.6 million times that of Earth’s atmosphere. As such this discovery is interesting in that opens up new pathways to explore but it’s not in any way a practical technology.
• Next is an article that I actually find interesting because it reminds me even when we think we already know everything, there still may be things that we have missed. After all what can be more settled science than human anatomy and yet this team announced that they have found a heretofore unnoticed set of salivary glands in the human nasopharynx, the upper part of the throat behind the nose. The existence of these glands was suspected because radiotherapy for cancer patients in this region brings unexpected side effects and their presence was then confirmed with PET/CT scans. This is effectively a discovery of a new organ, albeit a very small one, of the human body.
• Still on the subject of humans, I like this neat little experiment about measuring how well we form a mental map of our environment. In a setup that resembles one we usually use for mice and the like, participants were tasked to navigate a path through a space in which different types of food were placed. They were then asked to recall the locations of each food and predictably they were much better at remembering the locations of high calorie foods like brownies and potato chips than low calorie ones like fruit, regardless of their individual personal diets. It’s an obvious result but it’s nice to have the confirmation.
• Next is my favorite science article this month. This isn’t a report of a single new discovery but rather a broad overview about how the the scientific understanding of hybrid species and their role in evolution has changed over time. Previously hybrids were mostly thought of as being evolutionary dead ends that are either sterile or less well adapted than their parents. Growing evidence however has emerged that some hybrids can inherit combined traits from their parents that leave them better off and that there are mechanisms which prevent them from being absorbed back into the parent species. Furthermore such hybridisation seems to be much more common than previously thought and can result in an explosive growth of new species in a short amount time, overturning the old understanding of evolution by mutation as a slow process. The result is that the old picture of evolution as a tree is hopelessly outdated and evolution looks more like a tangled web that keeps criss-crossing back and forth. It took a long time to convince biologists to change their thinking of evolution and it will take longer yet for this to filter down to the general public.
• Then we have this paper that purports to show the support given to Trump in the 2016 election stems not from those who were economically left behind but instead from groups who felt that their previously high status were being threatened by future developments, including those anxious over the perceived erosion of US dominance in the world. The claim here is that the difference between these two causes is established by a set of carefully crafted surveys but this is always tricky to prove. Still I include it here because it makes for interesting reading.
• Finally here is the last one which I can only classify into the I don’t know what to make of it category but it sure seems important. It’s about time crystals interacting with one another. This is a strange form of matter that has the ability to repeat motions through time, with no external force being applied, apparently indefinitely, in a way that doesn’t violate the laws of thermodynamics. The claim is that scientists have now observed two time crystals interacting with one another in a controlled fashion and this is an important step in using them for any practical purpose but I won’t pretend I actually understand what is going on here.

Many of the major events this year has been cancelled but the Nobel Prizes have been awarded even if fewer people than usual are still paying attention.

The prize for Physiology or Medicine this year is probably the easiest to understand. It goes to Harvey J. Alter, Michael Houghton and Charles M. Rice for their work in isolating and identifying the virus that causes Hepatitis C. Alter was a colleague of Baruch Blumberg who was awarded the Nobel Prize in 1976 for the discovery of the Hepatitis B virus. The team realized that blood transfusions were still causing hepatitis even after screening for Hepatitis A and Hepatitis B.

Alter proved this by showing that chimpanzees developed hepatitis after being given blood free of Hepatitis A and B but attempts to isolate the new virus proved futile. In was only until 1989 that Houghton managed it by amplifying genetic material drawn from infected chimpanzees and using human antibodies to identify which portions of the genetic sequence they attached themselves to. However this cloned, purified version of the virus still could not infect chimpanzees and it was Rice who in 1997 noticed a mutable portion of the new virus and realized that it might be hindering replication. After he used genetic engineering to stabilize the virus, he proved that it was indeed the cause of Hepatitis C and which is why we are now able to reliably screen for it.

The prize for Physics will probably get the most mainstream attention because it is for the discovery of black holes, awarded to Roger Penrose, Reinhard Genzel and Andrea Ghez. Penrose is practically a household name for fans of science-fiction so it’s a little funny that he is only now gaining mainstream fame. Black holes were always a theoretical possibility ever since Einstein published his general theory of relativity but Einstein himself never believed they really existed in the real universe. It was Penrose who worked out the detailed mathematical proof that real stars and dust clouds can indeed collapse to form black holes.

Black holes are by definition invisible to direct detection but their presence can be inferred from the effect of their gravity on visible stars. Genzel and Ghez each lead separate teams. They used the world’s largest telescopes to track for decades the movements of the brightest stars at the center of our galaxy to show that they are all orbiting a massive, invisible object at the center of the Milky Way galaxy, what we now call the Sagittarius A* supermassive black hole that has 4 million times the mass of our sun.

The subject of the prize for Chemistry will be a familiar one to those few who regularly read this blog, the CRISPR/Cas9 gene editing technique. As it goes to Emmanuelle Charpentier and Jennifer A. Doudna, this has been lauded for going to an all women team but I think it’s also significant for how recent the discovery is and yet how obvious this award is given that everyone now uses the technique.

This story begins in 2011 when Charpentier noticed that the immune system of the Streptococcus pyogenes bacteria possess a mechanism that cleaves the DNA of viruses in two. She then collaborated with Doudna to recreate this pair of genetic scissors in a test tube and simplified it. They also proved that it could be reprogrammed to target any DNA molecule instead of just viral DNA, turning it into a powerful, general purpose tool.

Finally the prize for Economics goes to Paul Milgrom and Robert Wilson, both of whom advanced the understanding of auctions. This takes into account the format of auctions, differing levels of information available to the participants and how participants expect other participants to behave. In particular the novel auction formats they devised were used by countries to sell off radio frequencies to telecoms operators.

Our usual monthly feature cannot help but include one of the most hyped up announcements in years. Unfortunately I think they hyped it up too much especially with all of the intrigue behind a press embargo and when the official announcement came out, it didn’t actually make much of a splash with the general public.

• This refers of course to the detection of phosphine gas in the atmosphere of Venus. This matters because phosphorus in gas form would be highly reactive and would be expected to exist primarily in oxidized forms. This means that some process on the planet must be continuously producing the gas and yet there are no known production routes that do not involve biological processes. So the upshot is that this is being as a very tentative sign of life on the planet. Still, it’s so speculative that it’s no wonder the general public isn’t very excited and there’s still a decent chance that the gas is produced by some abiotic process that is as yet unknown to us.
• Our next article is also in the realm of astrophysics and again, it’s more about the excitement of a huge event than any new science being discovered. This is the detection of a merger between two massive black holes some seven billion years ago using laser interferometer instruments to listen to vibrations in space-time. It’s somewhat interesting to get evidence that such intermediate black holes massing between 65 and 120 solar masses can exist and that fuels the theory that black holes can become bigger by merging with one another. But it’s probably more exciting to think that we can, today, observe an event that occurred so far back in the past.
• Moving on the biological sciences, here is a paper studying how mothers who rear their own offspring can confer lasting advantages. To me, it is especially convincing in that the subject of the study are actually Rhesus monkeys which I am guessing would result in cleaner, less controversial data. The result is that monkeys who are reared by their own mothers exclusively compared to those who are reared by humans for the first 40 days of their lives and then assigned to other adult monkeys have significantly better health and social rank outcomes. This might seem like an obvious finding but it’s an important one to make and we can derive lessons from it also for the bringing up of human children.
• The last article is about the study of dreams in a scientific manner. The problem with this is that you need to collect a lot of data and the only way to do this is from the dreamer’s own recollection. But then the written reports need to be assessed by someone and that adds another layer of subjectivity. So this project instead uses a language processing algorithm to assess the dreams and from there draw conclusions. The actual results are almost less interesting than the methodology but broadly confirm that the content of dreams do match the quotidien experiences of the dreamers.

A very eclectic mix of articles this month. I love how weird and unexpected many of these findings are.

• Last month we had an article about how the lockdowns around the world yielded some unexpected dividends for researchers in the field of quantum computing. Not too surprisingly this applies to many other fields as well as the phenomenon has since been noted as the longest and most significant reduction in seismic noise caused by humans on record. This paper talks about how this quiet period can be used to establish a baseline and how the intensity of human activity on Earth can now be estimated based on detected seismic noise from here on out.
• Here is one loosely related paper about how scientists can glean so much from just a little data. It talks about a technique to listen to the noise that a physical key makes when opening a lock and using that data to recreate that key.
• This next one is a little suspect in its conclusions but I love the attempt. With the goal of trying to learn what bats are communicating when they make their high-pitched squeals, the researchers recorded the sounds, used a machine learning algorithm to break them down into common sounds, and tried to match these to activities that they were observed as engaging in on video. They found that most of calls were related to arguing about food, complaining about their position in a sleeping cluster or when other bats get too close, or females fending off unwanted advances from males. I say it’s suspect because it’s trying to draw very broad conclusions with very little data but it’s a good attempt and as all philosophers of the mind know, learning how a bat thinks has special significance.
• Then we have this presentation that purportedly proves that cats are lazy. This begins with the observation that many animals exhibit contrafreeloading behavior, that is when offered both free food or an opportunity to do some task in exchange for food, the animal will often to choose to actually work. The researchers tried this with cats, with the work taking the form of a puzzle that the cats must solve to get the food, and could find no evidence of contrafreeloading behavior in cats, meaning they are perfectly happy to freeload if you let them.
• The last article is about the legendary lost colony of Roanoke, so well known that it has been the subject of innumerable television shows, books, comics and so on. This article talks about a new book which asserts that the colony was never lost at all when contact was lost but that they befriended the friendly Croatoans and eventually fully integrated into them. It claims that there is plenty of evidence for that in the form of artefacts such parts of guns and swords that exist in the same layer of soil as Indian pottery and arrowheads and stories of natives with blue eyes and who could read books. This actually isn’t a new theory but it is good to have all of the evidence laid one in one place.