Many microbes and cells are in deep sleep, waiting for the right moment to activate.

Harsh conditions like lack of food or cold weather can appear out of nowhere. In these dire straits, rather than keel over and die, many organisms have mastered the art of dormancy. They slow down their activity and metabolism. Then, w

Sitting around in a dormant state is actually the norm for the majority of life on Earth: By some estimates, 60% of all microbial cells are hibernating at any given time. Even in organisms whose entire bodies do not go dormant, like most mammals, some cellular populations within them rest and wait for the best time to activate.

“Life is mainly about being asleep.”

Because dormancy can be triggered by a variety of conditions, including starvation and drought, the scientists pursue this research with a practical goal in mind: “We can probably use this knowledge in order to engineer organisms that can tolerate warmer climates,” Melnikov said, “and therefore withstand climate change.”

Balon is notably absent from Escherichia coli and Staphylococcus aureus, the two most commonly studied bacteria and the most widely used models for cellular dormancy. By focusing on just a few lab organisms, scientists had missed a widespread hibernation tactic, Helena-Bueno said. “I tried to look into an under-studied corner of nature and happened to find something.”

“Most microbes are starving,” said Ashley Shade, a microbiologist at the University of Lyon who was not involved in the new study. “They’re existing in a state of want. They’re not doubling. They’re not living their best life.”

“This is not something that’s unique to bacteria or archaea,” Lennon said. “Every organism in the tree of life has a way of achieving this strategy. They can pause their metabolism.”

“Before the invention of hibernation, the only way to live was to keep growing without interruptions,” Melnikov said. “Putting life on pause is a luxury.”

It’s also a type of population-level insurance. Some cells pursue dormancy by detecting environmental changes and responding accordingly. However, many bacteria use a stochastic strategy. “In randomly fluctuating environments, if you don’t go into dormancy sometimes, there’s a chance that the whole population will go extinct” through random encounters with disaster, Lennon said. In even the healthiest, happiest, fastest-growing cultures of E. coli, between 5% and 10% of the cells will nevertheless be dormant. They are the designated survivors who will live should something happen to their more active, vulnerable cousins.

More fundamentally, Melnikov and Helena-Bueno hope that the discovery of Balon and its ubiquity will help people reframe what is important in life. We all frequently go dormant, and many of us quite enjoy it. “We spend one-third of our life asleep, but we don’t talk about it at all,” Melnikov said. Instead of complaining about what we’re missing when we’re asleep, maybe we can experience it as a process that connects us to all life on Earth, including microbes sleeping deep in the Arctic permafrost.

Valtonen’s goal is to put CPUs back in their rightful, ‘central’ role. In order to do that, he and his team are proposing a new paradigm. Instead of trying to speed up computation by putting 16 identical CPU cores into, say, a laptop, a manufacturer could put 4 standard CPU cores and 64 of Flow Computing’s so-called parallel processing unit (PPU) cores into the same footprint, and achieve up to 100 times better performance. Valtonen and his collaborators laid out their case at the IEEE Hot Chips conference in August.

Highlights

We may be close to rediscovering thousands of texts that had been lost for millennia. Their contents may reshape how we understand the Ancient World.

We don’t have original copies of anything, not of the Iliad, or the Aeneid, or Herodotus, or the Bible. Instead of originals, we find ourselves dealing with copies. These were first written on scrolls but later in books – the Romans called books codexes – starting in the first century AD. Did I say copies? That’s actually not correct either. We don’t have first copies of anything. What we do have is copies of copies, most of which date hundreds of years after the original was penned. Even many of our copies are not complete copies.

To most fully acclimate the reader to how tenuous this process is, this essay will focus on three different texts. The first will be a very well-known work that was never lost. Nevertheless, almost no one read it in earnest until the nineteenth century. I will then focus on a text that was lost to history, but that we were able to recover from the annals of time. Such examples are fortuitous. Our third example will be a text that we know existed, but of which we have no copies, and consider what important ramifications its discovery could hold. Finally, we’ll turn our attention again to the Villa of the Papyri and the gold mine of texts discovered there that new technologies are currently making available to classicists.

However, many of the scrolls from the Villa of the Papyri remain not only unread, but also unopened. This is because the eruption of Vesuvius left the scrolls carbonized, making it nearly impossible to open them. Despite this obstacle, Dr. Brent Seales pioneered a new technology in 2015 that allowed him and his team to read a scroll without opening it. The technique, using X-ray tomography and computer vision, is known as virtual unwrapping, and it was first used on one of the famous Dead Sea Scrolls, specifically the En-Gedi scroll, the earliest known copy of the Book of Leviticus (likely 210–390 CE). The X-rays allow scholars to create a virtual copy of the text that can then be read like any other ancient document by those with the proper language and paleography skills. Using Dr. Seales’s technique, scholars have been able to upload many of the texts online. A group of donors led by Nat Friedman and Daniel Gross have offered cash prizes to teams of classicists who can decipher the writings. The race to read the virtually unwrapped scrolls is known as the Vesuvius Challenge.

Highlights

When seawater gets cold, it gets viscous. This fact could explain how single-celled ocean creatures became multicellular when the planet was frozen during “Snowball Earth,” according to experiments.

A series of papers from the lab of Carl Simpson proposes an answer linked to a fundamental physical fact: As seawater gets colder, it gets more viscous, and therefore more difficult for very small organisms to navigate. Imagine swimming through honey rather than water. If microscopic organisms struggled to get enough food to survive under these conditions, as Simpson’s modeling work has implied, they would be placed under pressure to change — perhaps by developing ways to hang on to each other, form larger groups, and move through the water with greater force. Maybe some of these changes contributed to the beginning of multicellular animal life.

The experiment comes with a few caveats, and the paper has yet to be peer-reviewed; Simpson posted a preprint on biorxiv.org earlier this year. But it suggests that if Snowball Earth did act as a trigger for the evolution of complex life, it might be due to the physics of cold water.

It is difficult to precisely date when animals arose, but an estimate from molecular clocks — which use mutation rates to estimate the passage of time — suggests that the last common ancestor of multicellular animals emerged during the era known as the Sturtian Snowball Earth, sometime between 717 million and 660 million years ago. Large, unmistakably multicellular animals appear in the fossil record tens of millions of years after the Earth melted following another, shorter Snowball Earth period around 635 million years ago.

The paradox — a planet seemingly hostile to life giving evolution a major push — continued to perplex Simpson throughout his schooling and into his professional life. In 2018, as an assistant professor, he had an insight: As seawater gets colder, it grows thicker. It’s basic physics — the density and viscosity of water molecules rises as the temperature drops. Under the conditions of Snowball Earth, the ocean would have been twice or even four times as viscous as it was before the planet froze over.

As large creatures, we don’t think much about the thickness of the fluids around us. It’s not a part of our daily lived experience, and we are so big that viscosity doesn’t impinge on us very much. The ability to move easily — relatively speaking — is something we take for granted. From the time Simpson first realized that such limits on movement could be a monumental obstacle to microscopic life, he hasn’t been able to stop thinking about it. Viscosity may have mattered quite a lot in the origins of complex life, whenever that was.

“Putting this into our repertoire of thinking about why these things evolved — that is the value of the entire thing,” he said. “It doesn’t matter if it was Snowball Earth. It doesn’t matter if it happened before or after. Just the idea that it can happen, and happen quickly.”

Highlights

Amanda Randles wants to copy your body. If the computer scientist had her way, she’d have enough data — and processing power — to effectively clone you on her computer, run the clock forward, and see what your coronary arteries or red blood cells might do in a week. Fully personalized medical simulations, or “digital twins,” are still beyond our abilities, but Randles has pioneered computer models of blood flow over long durations that are already helping doctors noninvasively diagnose and treat diseases.

Her latest system takes 3D images of a patient’s blood vessels, then simulates and forecasts their expected fluid dynamics. Doctors who use the system can not only measure the usual stuff, like pulse and blood pressure, but also spy on the blood’s behavior inside the vessel. This lets them observe swirls in the bloodstream called vortices and the stresses felt by vessel walls — both of which are linked to heart disease. A decade ago, Randles’ team could simulate blood flow for only about 30 heartbeats, but today they can foresee over 700,000 heartbeats (about a week’s worth). And because their models are interactive, doctors can also predict what will happen if they take measures such as prescribing medicine or implanting a stent.

It’s a lot of data. We’re running simulations with up to 580 million red blood cells. There’s interactions with the fluid and red blood cells, the cells with each other, the cells with the walls — you’re trying to capture all of that. For each model, one time point might be half a terabyte, and there are millions of time steps in each heartbeat. It’s really computationally intense.

Fascinating, I like this kind of Magick.

This is interesting and potentially useful for anyone, who works in the corp which does not allow Linux laptops, but you can get your hands on Macs.

Highlights

European beech trees more than 1,500 kilometers apart all drop their fruit at the same time in a grand synchronization event now linked to the summer solstice.

From England to Sweden to Italy — across multiple seas, time zones and climates — somehow these trees “know” when to reproduce. But how?

Their analysis of over 60 years’ worth of seeding data suggests that European beech trees time their masting to the summer solstice and peak daylight.

The discovery of the genetic mechanism that governs this solstice-monitoring behavior could bring researchers closer to understanding many other mysteries of tree physiology.

So it’s easy to see why masting trees synchronize their seed production. Understanding how they do it, however, is more complicated. Plants usually synchronize their reproduction by timing it to the same weather signals.

Then the team stumbled across a clue by accident. One summer evening, Bogdziewicz was sitting on his balcony reading a study which found that the timing of leaf senescence — the natural aging process leaves go through each autumn — depends on when the local weather warms relative to the summer solstice. Inspired by this finding, he sent the paper to his research group and called a brainstorming session.

It’s the first time that researchers have identified day length as a cue for masting. While Koenig cautioned that the result is only correlational, he added that “there’s very little out there speculating on how the trees are doing what they’re doing.”

If the solstice is shown to activate a genetic mechanism, it would be a major breakthrough for the field. Currently, there’s little data to explain how trees behave as they do. No one even knows whether trees naturally grow old and die, Vacchiano said. Ecologists struggle just to study trees: From branches to root systems, the parts of a tree say very little about the physiology of the tree as a whole. What experts do know is that discovering how trees sense their environment will help them answer the questions that have been stumping them for decades.

OG

How We Built the Internet

Metadata

• Author: Anna-Sofia Lesiv
• Category: article
• URL: https://every.to/p/how-we-built-the-internet

Highlights

The internet is a universe of its own.

The infrastructure that makes this scale possible is similarly astounding—a massive, global web of physical hardware, consisting of more than 5 billion kilometers of fiber-optic cable, more than 574 active and planned submarine cables that span a over 1 million kilometers in length, and a constellation of more than 5,400 satellites offering connectivity from low earth orbit (LEO).

“The Internet is no longer tracking the population of humans and the level of human use. The growth of the Internet is no longer bounded by human population growth, nor the number of hours in the day when humans are awake,” writes Geoff Huston, chief scientist at the nonprofit Asia Pacific Network Information Center.

As Shannon studied the structures of messages and language systems, he realized that there was a mathematical structure that underlied information. This meant that information could, in fact, be quantified.

Shannon noted that all information traveling from a sender to a recipient must pass through a channel, whether that channel be a wire or the atmosphere.

Shannon’s transformative insight was that every channel has a threshold—a maximum amount of information that can be delivered reliably to a sender.

Kleinrock approached AT&T and asked if the company would be interested in implementing such a system. AT&T rejected his proposal—most demand was still in analog communications. Instead, they told him to use the regular phone lines to send his digital communications—but that made no economic sense.

What was exceedingly clever about this suite of protocols was its generality. TCP and IP did not care which carrier technology transmitted its packets, whether it be copper wire, fiber-optic cable, or radio. And they imposed no constraints on what the bits could be formatted into—video text, simple messages, or even web pages formatted in a browser.

David Clark, one of the architects of the original internet, wrote in 1978 that “we should … prepare for the day when there are more than 256 networks in the Internet.”

Fiber was initially laid down by telecom companies offering high-quality cable television service to homes. The same lines would be used to provide internet access to these households. However, these service speeds were so fast that a whole new category of behavior became possible online. Information moved fast enough to make applications like video calling or video streaming a reality.

And while it may have been the government and small research groups that kickstarted the birth of the internet, its evolution henceforth was dictated by market forces, including service providers that offered cheaper-than-ever communication channels and users that primarily wanted to use those channels for entertainment.

In 2022, video streaming comprised nearly 58 percent of all Internet traffic. Netflix and YouTube alone accounted for 15 and 11 percent, respectively.

At the time, Facebook users in Asia or Africa had a completely different experience to their counterparts in the U.S. Their connection to a Facebook server had to travel halfway around the world, while users in the U.S. or Canada could enjoy nearly instantaneous service. To combat this, larger companies like Google, Facebook, Netflix, and others began storing their content physically closer to users through CDNs, or “content delivery networks.”

Instead of simply owning the CDNs that host your data, why not own the literal fiber cable that connects servers from the United States to the rest of the world?

Most of the world’s submarine cable capacity is now either partially or entirely owned by a FAANG company—meaning Facebook (Meta), Amazon, Apple, Netflix, or Google (Alphabet).

Google, which owns a number of sub-sea cables across the Atlantic and Pacific, can deliver hundreds of terabits per second through its infrastructure.

In other words, these applications have become so popular that they have had to leave traditional internet infrastructure and operate their services within their own private networks. These networks not only handle the physical layer, but also create new transfer protocols —totally disconnected from IP or TCP. Data is transferred on their own private protocols, essentially creating digital fiefdoms.

SpaceX’s Starlink is already unlocking a completely new way of providing service to millions. Its data packets, which travel to users via radio waves from low earth orbit, may soon be one of the fastest and most economical ways of delivering internet access to a majority of users on Earth. After all, the distance from LEO to the surface of the Earth is just a fraction of the length of subsea cables across the Atlantic and Pacific oceans.

What is next?

Incantations

Metadata

• Author: Jos Visser
• Category: rss
• URL: https://josvisser.substack.com/p/incantations

Highlights

The problem with incantations is that you don’t understand in what exact circumstances they work. Change the circumstances, and your incantations might work, might not work anymore, might do something else, or maybe worse, might do lots of damage. It is not safe to rely on incantations, you need to move to understanding.

We can best view the method of science as the use of our sophisticated methodological toolbox

Metadata

• Author: OUP Academic
• Category: article
• URL: https://academic.oup.com/pnasnexus/article/3/4/pgae112/7626940?login=false

Highlights

Scientific, medical, and technological knowledge has transformed our world, but we still poorly understand the nature of scientific methodology.

scientific methodology has not been systematically analyzed using large-scale data and scientific methods themselves as it is viewed as not easily amenable to scientific study.

This study reveals that 25% of all discoveries since 1900 did not apply the common scientific method (all three features)—with 6% of discoveries using no observation, 23% using no experimentation, and 17% not testing a hypothesis.

Empirical evidence thus challenges the common view of the scientific method.

This provides a new perspective to the scientific method—embedded in our sophisticated methods and instruments—and suggests that we need to reform and extend the way we view the scientific method and discovery process.

In fact, hundreds of major scientific discoveries did not use “the scientific method”, as defined in science dictionaries as the combined process of “the collection of data through observation and experiment, and the formulation and testing of hypotheses” (1). In other words, it is “The process of observing, asking questions, and seeking answers through tests and experiments” (2, cf. 3).

In general, this universal method is commonly viewed as a unifying method of science and can be traced back at least to Francis Bacon's theory of scientific methodology in 1620 which popularized the concept

Science thus does not always fit the textbook definition.

Comparison across fields provides evidence that the common scientific method was not applied in making about half of all Nobel Prize discoveries in astronomy, economics and social sciences, and a quarter of such discoveries in physics, as highlighted in Fig. 2b. Some discoveries are thus non-experimental and more theoretical in nature, while others are made in an exploratory way, without explicitly formulating and testing a preestablished hypothesis.

We find that one general feature of scientific methodology is applied in making science's major discoveries: the use of sophisticated methods or instruments. These are defined here as scientific methods and instruments that extend our cognitive and sensory abilities—such as statistical methods, lasers, and chromatography methods. They are external resources (material artifacts) that can be shared and used by others—whereas observing, hypothesizing, and experimenting are, in contrast, largely internal (cognitive) abilities that are not material (Fig. 2).

Just as science has evolved, so should the classic scientific method—which is construed in such general terms that it would be better described as a basic method of reasoning used for human activities (non-scientific and scientific).

An experimental research design was not carried out when Einstein developed the law of the photoelectric effect in 1905 or when Franklin, Crick, and Watson discovered the double helix structure of DNA in 1953 using observational images developed by Franklin.

Direct observation was not made when for example Penrose developed the mathematical proof for black holes in 1965 or when Prigogine developed the theory of dissipative structures in thermodynamics in 1969. A hypothesis was not directly tested when Jerne developed the natural-selection theory of antibody formation in 1955 or when Peebles developed the theoretical framework of physical cosmology in 1965.

Sophisticated methods make research more accurate and reliable and enable us to evaluate the quality of research.

Applying observation and a complex method or instrument, together, is decisive in producing nearly all major discoveries at 94%, illustrating the central importance of empirical sciences in driving discovery and science.