Tag: science

Radioactivity & deep time

Radium forever transformed attitudes to time and where we may be within history – creating the first efflorescence of truly long-term thinking. Until that point, we knew the Earth was old, but hadn’t fully embraced how many more millions – or even billions – of years could lie ahead for humanity and the planet. In Europe, Christians assumed they were much closer to time’s end than its beginning. Judgement Day was anticipated soon. Then, the 1900s dawned, and radioactivity was discovered. This changed everything. From thinking they lived near history’s end, people now recognized they could be living during its very beginning. Humanity’s universe, no longer decrepit, now seemed positively youthful.

Astrocytes

The star-shaped cells usually help clear away toxic particles that build up in the brain naturally or after head trauma, and are supposed to nourish neurons. But laboratory tests on mice show astrocytes also release toxic fatty acids to kill off damaged neurons, confirming a suspicion many neurologists have had for years. “Our findings show the toxic fatty acids produced by astrocytes play a critical role in brain cell death. The results provide a promising new target for treating, and perhaps even preventing, many neurodegenerative diseases”.

Astrocytes regulate the response of the central nervous system to disease and injury and have been hypothesized to actively kill neurons in neurodegenerative disease. Here we report an approach to isolate one component of the long-sought astrocyte-derived toxic factor. Notably, instead of a protein, saturated lipids contained in APOE and APOJ lipoparticles mediate astrocyte-induced toxicity. Eliminating the formation of long-chain saturated lipids by astrocyte-specific knockout of the saturated lipid synthesis enzyme ELOVL1 mitigates astrocyte-mediated toxicity in vitro as well as in a model of acute axonal injury in vivo. These results suggest a mechanism by which astrocytes kill cells in the central nervous system.

Differences in differences

The Nobel Prize goes to David Card, Joshua Angrist and Guido Imbens. If you seek their monuments look around you. Almost all of the empirical work in economics that you read in the popular press is due to analyzing natural experiments using techniques such as difference in differences, instrumental variables and regression discontinuity. The obvious way to estimate the effect of the minimum wage is to look at the difference in employment in fast food restaurants before and after the law went into effect. But other things are changing through time so circa 1992 the standard approach was to “control for” other variables by also including in the statistical analysis factors such as the state of the economy. Include enough control variables, so the reasoning went, and you would uncover the true effect of the minimum wage. Card and Krueger did something different, they turned to a control group. Pennsylvania didn’t pass a minimum wage law in 1992 but it’s close to New Jersey so Card and Kruger reasoned that whatever other factors were affecting New Jersey fast food restaurants would very likely also influence Pennsylvania fast food restaurants. The state of the economy, for example, would likely have a similar effect on demand for fast food in NJ as in PA as would say the weather. In fact, the argument extends to just about any other factor that one might imagine including demographics, changes in tastes, changes in supply costs. The standard approach circa 1992 of “controlling for” other variables requires, at the very least, that we know what variables are important. But by using a control group, we don’t need to know what the other variables are only that whatever they are they are likely to influence NJ and PA fast food restaurants similarly. Put differently NJ and PA are similar so what happened in PA is a good estimate of what would have happened in NJ had NJ not passed the minimum wage. Thus what Card and Kruger estimated the effect of the minimum wage in New Jersey by calculating the difference in employment in NJ before and after the law and then subtracting the difference in employment in PA before and after the law. Hence the term difference in differences. By subtracting the PA difference (i.e. what would have happened in NJ if the law had not been passed) from the NJ difference (what actually happened) we are left with the effect of the minimum wage. Brilliant!

Multicellular Emergence

Environments favoring clumpy growth are all that’s needed to quickly transform single-celled yeast into complex multicellular organisms.

During the first 100 days, the clusters in all 15 of the tubes 2x in size. Then they mostly plateaued until the 250th day, when the sizes in 2 of the tubes that didn’t use oxygen started to creep upward again. Around day 350, Bozdağ noticed something in 1 of those tubes. There were clusters he could see with the naked eye. “As an evolutionary biologist … you think it’s a chance event. Somehow they got big, but they are going to lose out against the small ones in the long run — that is my thinking. I didn’t really talk about this with Will at the time.” But then clusters showed up in the 2nd tube. And around day 400, the 3 other tubes of mutants that couldn’t use oxygen kicked into gear, and soon all 5 tubes had massive structures in them, topping out at about 20000X their initial size. “I wasn’t honestly sure if this was a system that would saturate at 1000 cells. We have to continue evolving them and see what they can do. We need to see, if we push these guys as far as we can for decades, for 10000s of generations. If we don’t do that, I will always regret not having taken the opportunity. It’s a once-in-a-lifetime opportunity, to try to push a nascent multicellular critter to become more complex and see how far we can take them.”


2022-11-05: Multicellularity has metabolic benefits

the hollow spheres were Vibrio’s solution to the complicated challenge of eating at sea. An individual bacterium can produce only so much enzyme; breaking down alginate goes much more quickly when Vibrio can cluster together. It’s a winning strategy — up to a point. If there are too many Vibrio, the number of bacteria outstrips the available alginate.

The bacteria resolved the conundrum by developing a more complex life cycle. The bacteria live in 3 distinct phases. At first, an individual cell divides repeatedly and the daughter cells huddle in growing clumps. In the second phase, the clumped cells rearrange themselves into a hollow sphere. The outermost cells glue themselves together, forming something rather like a microscopic snow globe. The cells inside become more mobile, swimming about as they consume the trapped alginate. In the third phase, the brittle outer layer ruptures, releasing the well-fed inner cells to start the cycle anew.
By altering their life cycle to include a multicellular stage, the bacteria can digest the alginate efficiently: Their numbers increase, and the hollow shell helps to concentrate the enzymes. Meanwhile, the structure of the community prevents too many cells from being born. The cells in the shell lose the opportunity to reproduce, but their DNA lives on in the next generation anyway, since all the cells in the orb are clones.

Sodom Air Burst

people may have passed down accounts of the spectacular disaster as oral history over generations, providing the basis for the biblical story of Sodom and Gomorrah—which, like Tall el-Hammam, were supposedly located near the Dead Sea.

The proposed airburst was larger than the 1908 explosion over Tunguska, Russia, where a ~ 50-m-wide bolide detonated with ~ 1000× more energy than the Hiroshima atomic bomb. A city-wide ~ 1.5-m-thick carbon-and-ash-rich destruction layer contains peak concentrations of shocked quartz (~ 5–10 GPa); melted pottery and mudbricks; diamond-like carbon; soot; Fe- and Si-rich spherules; CaCO3 spherules from melted plaster; and melted platinum, iridium, nickel, gold, silver, zircon, chromite, and quartz. Heating experiments indicate temperatures exceeded 2000 °C. Amid city-side devastation, the airburst demolished 12+ m of the 4-to-5-story palace complex and the massive 4-m-thick mudbrick rampart, while causing extreme disarticulation and skeletal fragmentation in nearby humans. An airburst-related influx of salt (~ 4 wt.%) produced hypersalinity, inhibited agriculture, and caused a ~ 300–600-year-long abandonment of ~ 120 regional settlements within a > 25-km radius. Tall el-Hammam may be the second oldest city/town destroyed by a cosmic airburst/impact, after Abu Hureyra, Syria, and possibly the earliest site with an oral tradition that was written down (Genesis). Tunguska-scale airbursts can devastate entire cities/regions and thus, pose a severe modern-day hazard.

2022-02-01: while the Sodom Air burst has been debunked, there’s other interesting meteorites in history:

Combinatorial Cell Signaling

In particular, in systems where ligands bind uniquely to receptors, the number of types of ligands limits how many different cell types or targets can be uniquely addressed. In a combinatorial system, different pairings between a small number of ligands and receptors can specify a much larger number of targets. The differences between the pairings also permit graded effects rather than an all-or-nothing response.

Thermodynamic Clocks

an ideal clock — one that ticks with perfect periodicity — would burn an infinite amount of energy and produce infinite entropy, which isn’t possible. Thus, the accuracy of clocks is fundamentally limited. “What we’ve done is to show that even if time is a perfect, classical and smooth parameter governing time evolution of quantum systems, we would only be able to track its passage” imperfectly, through stochastic, irreversible processes. “Could it be that time is an illusion and smooth time is an emergent consequence of us trying to put events into a smooth order? It is certainly an intriguing possibility that is not easily dismissed.”

Hycean Worlds

Hycean worlds are hot mini-Neptunes with hydrogen-rich atmospheres and vast oceans on their surfaces. The heat and the pressure wouldn’t be very inviting to us humans, but it’s possible that some forms of life might find it idyllic. these worlds can be up to 2.6x the width of Earth, up to 10 Earth masses, and temperatures in their atmospheres could reach 200 °C. However, conditions in their oceans might be more comfortable. They’re likely to be common too, nestled in between the smaller, rockier Super-Earths and the gaseous, larger mini-Neptunes. Hycean planets could be one of the most promising places to look for signs of life. Not only because they’re common, but biomarkers of life, such as methyl chloride and dimethyl sulphide, could be readily spotted in their atmospheres

Roman Food Dimorphism

By measuring the isotopes of carbon and nitrogen in the bone amino acids, researchers were able to reconstruct the diets of people who lived contemporaneously in much more detail than was previously thought possible. “We found significant differences in the proportions of marine and terrestrial foods consumed between males and females, implying that access to food was differentiated according to gender.” Males were more likely to be directly engaged in fishing and maritime activities, they generally occupied more privileged positions in society, and were freed from slavery at an earlier age providing greater access to expensive commodities, such as fresh fish.

Hypergraphs

The higher-order analogue of a graph is called a hypergraph, and instead of edges, it has “hyperedges.” Purvine and her colleagues analyzed a database of biological responses to viral infections, using hypergraphs to identify the most critical genes involved. They also showed how those interactions would have been missed by the usual pairwise analysis afforded by graph theory. However, generalizing from graphs to hypergraphs quickly gets complicated. There are lots of ways of generalizing this notion of a cut to a hypergraph. But there’s no one clear solution, because a hyperedge could be severed various ways, creating new groups of nodes.

2023-04-13: Another powerful concept only very vaguely related are Hypervectors (though this Github project seems to allow you to play with both)

Hyperdimensional computing promises a new world in which computing is efficient and robust, and machine-made decisions are entirely transparent.
Hyperdimensional computing tolerates errors better, because even if a hypervector suffers significant numbers of random bit flips, it is still close to the original vector. Another advantage of hyperdimensional computing is transparency: The algebra clearly tells you why the system chose the answer it did. The same is not true for traditional neural networks. It’s also compatible with “in-memory computing systems,” which perform the computing on the same hardware that stores data (unlike existing von Neumann computers that inefficiently shuttle data between memory and the central processing unit). Some of these new devices can be analog, operating at very low voltages, making them energy-efficient but also prone to random noise. For von Neumann computing, this randomness is “the wall that you can’t go beyond”. But with hyperdimensional computing, “you can just punch through it.”