A Silk Road stopover might have been the epicentre of one of humanity’s most destructive pandemics.

People who died in a fourteenth-century outbreak in what is now Kyrgyzstan were killed by strains of the plague-causing bacterium Yersinia pestis that gave rise to the pathogens responsible several years later for the Black Death, shows a study of ancient genomes.

“It is like finding the place where all the strains come together, like with coronavirus where we have Alpha, Delta, Omicron all coming from this strain in Wuhan,” says Johannes Krause, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who co-led the study, published on 15 June in Nature.

Fascinating read on new research on the origins of Black Death. As you can imagine, it’s not an easy task to find genomic data from the plague bacteria, several centuries after the pandemic. Then, like now, how the pandemic spread mattered quite a lot of how and where a lot of humans came together and then dispersed, carrying the deadly disease with them.

Today, a startling new discovery: prodding the brain with light, a group of scientists got an unexpected surprise – they were able to turn back on a part of the brain that had been shut down by Alzheimer’s disease. This new science is not a cure, and is far from a treatment, but it’s a finding so … simple, you won’t be able to shake it. Come join us for a lab visit, where we’ll meet some mice, stare at some light, and come face-to-face with the mystery of memory. We can promise you: by the end, you’ll never think the same way about Christmas lights again.

I’ve been meaning to post about this particular episode ever since I listened to it. This is the Nature paper about this study. They found that simply flashing light of a certain frequency at a certain interval helps with some of the brain waves that are diminished in mice with Alzheimer’s. It’s absolutely fascinating.

(I’m not going into too much technical jargon here; go listen to the episode!)

If you don’t listen to Radiolab in general, you definitely should; it’s one of the best podcasts there are.

In this study, we continuously monitored Egyptian fruit bats for months, recording audio and video around-the-clock. We analyzed almost 15,000 vocalizations, which accompanied the everyday interactions of the bats, and were all directed toward specific individuals, rather than broadcast. We found that bat vocalizations carry ample information about the identity of the emitter, the context of the call, the behavioral response to the call, and even the call’s addressee. Our results underline the importance of studying the mundane, pairwise, directed, vocal interactions of animals.

This is brilliant. They were able to correlate their data analysis of the bats’ vocalizations with the behavior and responses that they observed… so now we know more about how bats communicate! Simply by listening to the vocalization, the context, addressee, and even “the outcome of the interaction can be predicted above chance level”. Fascinating.

From the discussion:

It is important to note that we used one set of acoustic features for classification. However, many other multi-dimensional spectro-temporal representations can be tested. The bat’s brain could thus be using some other representation that encapsulates much more information regarding different social aspects. The bat may be able to classify the context of an interaction with higher confidence, based on some acoustic feature which it evolved to use and is yet to be determined. Our analysis is thus probably only a lower bound on what a bat is capable of extracting from aggressive social vocalizations. For example, we did not include any temporal information in our analysis.

In any acoustic signal, and especially where communication is involved, the time parameter is usually crucial and will add rich layers of information. For example, just imagine taking a piece of human speech, and (a) only looking at the overal speech parameters, versus (b) observing how the speech parameters change during the speech. Case (b) will provide far more information than case (a). I think we will discover over time that bats have a pretty well-evolved communication scheme.

This is fascinating stuff.

I’ve written about the naked mole rat before, about how it seems to be immune to acid.

Well, it turns out it has more tricks up its genetic sleeve.

To compare how the naked mole rat made their proteins, they inserted an engineered gene in the naked mole rat as well as in mice, which allowed them to compare the rate of errors in making proteins. And here’s what they found:

[The naked mole rat] built the engineered protein far more accurately, in other words. Naked mole rats, the scientists found, made anywhere from four to ten times fewer mistakes. Yet the naked mole rats can make their proteins as quickly as the sloppier mice.

This seems to be a fascinating creature the more we study it!

I wonder, though, why other species did not pick up this brilliant piece of evolution. Are there side effects to this that are detrimental, overall, to other species but which don’t affect the naked mole rat? As I said in my earlier post, intriguing.

(Original source, quoted by National Geographic: Jorge Azpurua et al.“Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage.” PNAS 2013

I wrote a small piece on fair use of our biotechnology on my Tumblr, but since I’m planning to write longer pieces on this blog, I wanted to cross-post it here as well.

Joe Hanson, of It’s Okay To Be Smart, wrote:

Can Biotechnology and Genetic Engineering Save an American Icon?

What I find so interesting is that the techniques being used to save this tree, and one day reintroduce it to the wild, are not that different from those that are used to create genetically modified crops. How does saving a dying species by inserting a gene differ from creating an herbicide-resistant soybean, or rice that produces extra vitamins? I have my opinions, but I want to know: What do you think?

My thoughts are below.

The two are different in only the following way—in one case, we’re using our technology to help another being survive better; in another case we’re using technology to extract more from a being we intend to use as a ‘resource’, in this case food.

I think they’re both fine uses of our technology.

As humans, we have always wanted to modify our surroundings to suit us better. That’s who we are; that’s what defines us as a species and helps us move unflinchingly deeper into the unknown.

It was the same when we invented agriculture; it was the same when we domesticated animals; it was the same when we forced natural selection to go in a certain direction to create “man’s best friend”.

The only difference today is that instead of indirect approaches, we’re learning to make pin-point, particular modifications exactly as we require.

Yes, this is a sensitive topic, and rightfully so. With great power does come great responsibility, and we’re only now learning to harness the power of genetic engineering. I feel we should find it easy to stay on the straight and narrow as long as we remember one rule—no interference for the fun of it. I’ll explain more.

Only organisms capable of photosynthesis are able to produce their own energy. Every other living being must depend on other living beings for energy and sustenance, and we are no different. As long as our genetic engineering endeavours are focussed towards areas that we must harvest for our nutrition, we should be okay. Genetically modified crops are okay—as long as we understand the effects of what we are doing. Edit*: There is a lot of ambivalence towards genetically modified food crops, but the problem isn’t the technology itself, but that we don’t yet understand* the technology well enough to implement it perfectly. Let’s keep at it; we’ll get there.

In addition, being the sole species on this planet with advanced technology, we owe it to our planet-mates to share. Just as in this example of chestnut trees dying from a fungus, when we see an organism dying from infection, and we realize we can help—by all means, we should! We already try to help species that we are afraid will become extinct (often, unfortunately, to our own greedy exploits)–why should that help not include our latest and greatest knowledge?

Let’s just not play with our planet-mates simply because we can. That would be abuse of power, no?