How Base 3 Computing Beats Binary

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• Author: Stephen Ornes
• Category: rss
• URL: https://www.quantamagazine.org/how-base-3-computing-beats-binary-20240809/

Highlights

Three, as Schoolhouse Rock! told children of the 1970s, is a magic number. Three little pigs; three beds, bowls and bears for Goldilocks; three Star Wars trilogies. You need at least three legs for a stool to stand on its own, and at least three points to define a triangle.

If a three-state system is so efficient, you might imagine that a four-state or five-state system would be even more so. But the more digits you require, the more space you’ll need. It turns out that ternary is the most economical of all possible integer bases for representing big numbers.

Surprisingly, if you allow a base to be any real number, and not just an integer, then the most efficient computational base is the irrational number e.

Despite its natural advantages, base 3 computing never took off, even though many mathematicians marveled at its efficiency. In 1840, an English printer, inventor, banker and self-taught mathematician named Thomas Fowler invented a ternary computing machine to calculate weighted values of taxes and interest. “After that, very little was done for years,” said Bertrand Cambou, an applied physicist at Northern Arizona University.

Why didn’t ternary computing catch on? The primary reason was convention. Even though Soviet scientists were building ternary devices, the rest of the world focused on developing hardware and software based on switching circuits — the foundation of binary computing. Binary was easier to implement.

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.

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.

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.

Securing bolts properly is about the lowest-hanging fruit of high-reliability engineering.

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