Posts Tagged ‘biochemistry’
“The earth is bountiful, and where her bounty fails, nitrogen drawn from the air will refertilize her womb.”*…
As the Iran War continues to unfold, there is understandably a great deal of concern about energy prices (and the prices of things that depend on energy). We might forget that the Middle East is also crucial to the world’s fertilizer supply– though not for long, as farmers (along with everyone else in the food chain, all the way down to all of us eaters) are beginning to feel the pain.
But, as Diana Kruzman reports, even as fertilizer trade concerns are growing, a revolutionary sourcing alternative has emerged– one that could make a huge positive difference if it proves out at scale…
The world has an almost insatiable demand for nitrogen. Crops need it to grow, but although it makes up 78 percent of our atmosphere, plants can’t just pull it in from the air the way they do with oxygen. Instead, they rely on bacteria in the soil to convert it into nitrate, a form they can use; in the case of agriculture, think of fertilizer spread by humans. Leaving aside organic options like cow manure, most farmers use ammonia produced mainly from natural gas using a technique called the Haber-Bosch process, which was invented in 1909. [See also here.]
Haber-Bosch is expensive and energy-intensive, responsible for up to two percent of the world’s annual greenhouse gas emissions. It’s also spurred a global nitrogen pollution crisis; as much as two-thirds of nitrogen fertilizer applied to crops is never used, and the excess escapes into the soil, air, and water, raising the cancer risk in nearby communities and contributing to climate change.
Researchers have been trying to find an alternative way to get nitrogen to plants for decades — turning to everything from microbes to human urine. But so far, these scientific advancements haven’t translated into much practical change for farmers, who for the most part still rely on ammonia (which, granted, is getting greener, but is increasingly vulnerable to global price shocks).
That could soon change with the growth in popularity of a new technology known as plasma activated water, or PAW. Around the U.S., scientists and startups are experimenting with this high-tech solution, which uses electricity to pull nitrogen from the air, mix it with water, and create fertilizer straight on the farm. The concept, on the surface, seems suspiciously rosy — on-demand nitrogen, in a form plants can use, at just the cost of electricity (and the initial price of the machine used to make it). But early adopters have told Offrange that it genuinely works…
… PAW uses electricity to transform air into plasma — the fourth state of matter (besides gases, solids, and liquids), which typically forms at high temperatures. When the plasma comes into contact with water, it encourages chemical reactions that form nitrates — the type of nitrogen that plants need. Though this process was actually invented in 1903, even before Haber-Bosch, it required so much energy that it never achieved widespread use.
But in recent years, those energy needs have gone down thanks to the development of “cold plasma” technology, which operates at less than 60 degrees Fahrenheit. It’s also used for medical sterilization and food safety, and over the last decade researchers have worked to develop new ways to apply it for agricultural production…
More at: “Pulling Nitrogen From the Air” from @dkruzman.bsky.social.
* Nikola Tesla (who, around 1900, imagined and experimented with something like the Birkeland–Eyde-based plasma process described above)
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As we count on creativity, we might send healthy birthday greetings to a man who explained one of the central ways in which we depend on the food that we eat, William Cumming Rose; he was born on this date in 1887. A biochemist, he researched amino acids, discovered threonine, and established the importance of the nine essential amino acids in human nutrition (that’s to say, the amino acids that our bodies cannot synthesize and that we must consume in our food). He received the National Medal of Science in 1966.
“Advances are made by answering questions. Discoveries are made by questioning answers.”*…
Three years ago, Google’s AlphaFold pulled off the biggest artificial intelligence breakthrough in science to date [see here]. Yasemin Saplakoglu explains how this has accelerated molecular research and kindled deep questions about why we do science….
In December 2020, when pandemic lockdowns made in-person meetings impossible, hundreds of computational scientists gathered in front of their screens to watch a new era of science unfold.
They were assembled for a conference, a friendly competition some of them had attended in person for almost three decades where they could all get together and obsess over the same question. Known as the protein folding problem, it was simple to state: Could they accurately predict the three-dimensional shape of a protein molecule from the barest of information — its one-dimensional molecular code? Proteins keep our cells and bodies alive and running. Because the shape of a protein determines its behavior, successfully solving this problem would have profound implications for our understanding of diseases, production of new medicines and insight into how life works.
At the conference, held every other year, the scientists put their latest protein-folding tools to the test. But a solution always loomed beyond reach. Some of them had spent their entire careers trying to get just incrementally better at such predictions. These competitions were marked by baby steps, and the researchers had little reason to think that 2020 would be any different.
They were wrong about that.
That week, a relative newcomer to the protein science community named John Jumper had presented a new artificial intelligence tool, AlphaFold2, which had emerged from the offices of Google DeepMind, the tech company’s artificial intelligence arm in London. Over Zoom, he presented data showing that AlphaFold2’s predictive models of 3D protein structures were over 90% accurate — five times better than those of its closest competitor.
In an instant, the protein folding problem had gone from impossible to painless. The success of artificial intelligence where the human mind had floundered rocked the community of biologists. “I was in shock,” said Mohammed AlQuraishi, a systems biologist at Columbia University’s Program for Mathematical Genomics, who attended the meeting. “A lot of people were in denial.”
But in the conference’s concluding remarks, its organizer John Moult left little room for doubt: AlphaFold2 had “largely solved” the protein folding problem — and shifted protein science forever. Sitting in front of a bookshelf in his home office in a black turtleneck, clicking through his slides on Zoom, Moult spoke in tones that were excited but also ominous. “This is not an end but a beginning,” he said…
[Saplakoglu tells the story of AlphaFold and of subsequent developments…]
… Seventy years ago, proteins were thought to be a gelatinous substance, Porter said. “Now look at what we can see”: structure after structure of a vast world of proteins, whether they exist in nature or were designed.
The field of protein biology is “more exciting right now than it was before AlphaFold,” Perrakis said. The excitement comes from the promise of reviving structure-based drug discovery, the acceleration in creating hypotheses and the hope of understanding complex interactions happening within cells.
“It [feels] like the genomics revolution,” AlQuraishi said. There is so much data, and biologists, whether in their wet labs or in front of their computers, are just starting to figure out what to do with it all.
But like other artificial intelligence breakthroughs sparking across the world, this one might have a ceiling.
AlphaFold2’s success was founded on the availability of training data — hundreds of thousands of protein structures meticulously determined by the hands of patient experimentalists. While AlphaFold3 and related algorithms have shown some success in determining the structures of molecular compounds, their accuracy lags behind that of their single-protein predecessors. That’s in part because there is significantly less training data available.
The protein folding problem was “almost a perfect example for an AI solution,” Thornton said, because the algorithm could train on hundreds of thousands of protein structures collected in a uniform way. However, the Protein Data Bank may be an unusual example of organized data sharing in biology. Without high-quality data to train algorithms, they won’t make accurate predictions.
“We got lucky,” Jumper said. “We met the problem at the time it was ready to be solved.”
No one knows if deep learning’s success at addressing the protein folding problem will carry over to other fields of science, or even other areas of biology. But some, like AlQuraishi, are optimistic. “Protein folding is really just the tip of the iceberg,” he said. Chemists, for example, need to perform computationally expensive calculations. With deep learning, these calculations are already being computed up to a million times faster than before, AlQuraishi said.
Artificial intelligence can clearly advance specific kinds of scientific questions. But it may get scientists only so far in advancing knowledge. “Historically, science has been about understanding nature,” AlQuraishi said — the processes that underlie life and the universe. If science moves forward with deep learning tools that reveal solutions and no process, is it really science?
“If you can cure cancer, do you care about how it really works?” AlQuraishi said. “It is a question that we’re going to wrestle with for years to come.”
If many researchers decide to give up on understanding nature’s processes, then artificial intelligence will not just have changed science — it will have changed the scientists too.
Meanwhile, the CASP organizers are wrestling with a different question: how to continue their competition and conference. AlphaFold2 is a product of CASP, and it solved the main problem the conference was organized to address. “It was a big shock for us in terms of: Just what is CASP anymore?” Moult said.
In 2022, the CASP meeting was held in Antalya, Turkey. Google DeepMind didn’t enter, but the team’s presence was felt. “It was more or less just people using AlphaFold,” Jones said. In that sense, he said, Google won anyway.
Some researchers are now less keen on attending. “Once I saw that result, I switched my research,” Xu said. Others continue to hone their algorithms. Jones still dabbles in structure prediction, but it’s more of a hobby for him now. Others, like AlQuraishi and Baker, continue on by developing new algorithms for structure prediction and design, undaunted by the prospect of competing against a multibillion-dollar company.
Moult and the conference organizers are trying to evolve. The next round of CASP opened for entries in May. He is hoping that deep learning will conquer more areas of structural biology, like RNA or biomolecular complexes. “This method worked on this one problem,” Moult said. “There are lots of other related problems in structural biology.”
The next meeting will be held in December 2024 by the aqua waters of the Caribbean Sea. The winds are cordial, as the conversation will probably be. The stamping has long since died down — at least out loud. What this year’s competition will look like is anyone’s guess. But if the past few CASPs are any indication, Moult knows to expect only one thing: “surprises.”…
When one door closes, another opens: “How AI Revolutionized Protein Science, but Didn’t End It,” from @yasemin_sap in @QuantaMagazine.
See also: “How Colorful Ribbon Diagrams Became the Face of Proteins” from the same author.
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As we ponder progress, we might spare a thought for Edmond H. Fischer; he died on this date in 2021. A biochemist, he and his collaborator, Edwin G. Krebs were awarded the Nobel Prize in Physiology or Medicine in 1992 for describing how reversible phosphorylation works as a switch to activate proteins and regulate a number of cellular processes. Their discovery was a key to unlocking how glycogen in the body breaks down into glucose. It fostered techniques that prevent the body from rejecting transplanted organs and opened new doors for research into cancer, blood pressure, inflammatory reactions, and brain signals.
“There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy”*…
And some of them were recently found in the woods near Boston…
Researchers have unearthed a trove of wonders in the soil of a Massachusetts forest: an assortment of giant viruses unlike anything scientists had ever seen. The find suggests this group of relatively massive parasites has an even greater ecological diversity and evolutionary importance than researchers knew.
Giant viruses can exceed 2 micrometers in diameter, on par with some bacteria. They can also harbor immense genomes, which reach 2.5 megabases—larger than the genomes of far more complex organisms. Between the discovery of these impressively sized viruses in algae and the culturing of amoeba-infecting Mimiviruses, most of the research on the group has focused on viruses that inhabit freshwater environments. But DNA sequencing has long indicated that giant viruses are diverse and abundant elsewhere, too—especially in sediments and soils, which are estimated to host some 97% of all the viral particles on Earth. Indeed, genomic sequencing of the soils of Harvard Forest—a roughly 16-square-kilometer area west of Boston—indicated the presence of numerous, novel giant viruses.
Now, electron microscopy has allowed scientists to see what others had only sequenced. The diversity of forms was astounding, they report in a bioRxiv preprint. Not only did the researchers see the 20-sided icosahedral shapes they expected, they spotted ones with myriad modifications—tails, altered points, and multilayered or channeled structures abounded. There were even viruses with long tubular appendages, which the team dubbed “Gorgon” morphology [photo above]. Furthermore, many of these putative viral particles were coated with almost hairlike projections, which varied in length, thickness, density, and shape.
The findings suggest virologists have much to discover about how giant viruses interact with their host cells. That likely means the ecological roles these viruses play in soils—and elsewhere they’re found—are woefully underappreciated…
Microbes come in a variety of shapes, hinting at undiscovered ecological diversity: “Alien-looking viruses discovered in Massachusetts forest,” in @ScienceMagazine.
* Shakespeare, Hamlet
As we marvel at multifariousness (and note that viruses, while generally considered to be non-living and thus not considered microorganisms, are colloquially lumped in with microbes), we might spare a thought for Sidney Walter Fox; he died on this date in 1998. A biochemist, he was responsible for a series of discoveries about the origin of life. Fox believed in the process of abiogenesis, by which life spontaneously organized itself from the colloquially known “primordial soup,” poolings of various simple organic molecules that existed during the time before life on Earth. In his experiments (which possessed, he believed, conditions like those of primordial Earth), he demonstrated that it is possible to create protein-like structures from inorganic molecules and thermal energy. Dr. Fox went on to create microspheres that he said closely resembled bacterial cells and concluded that they could be similar to the earliest forms of life or protocells.
“Nature is full for us of seeming inconsistencies and glad surprises”*…
George Musser talks with biologist Michael Levin about his practice of uncovering the incredible, latent abilities of living things…
Michael Levin, a developmental biologist at Tufts University, has a knack for taking an unassuming organism and showing it’s capable of the darnedest things. He and his team once extracted skin cells from a frog embryo and cultivated them on their own. With no other cell types around, they were not “bullied,” as he put it, into forming skin tissue. Instead, they reassembled into a new organism of sorts, a “xenobot,” a coinage based on the Latin name of the frog species, Xenopus laevis. It zipped around like a paramecium in pond water. Sometimes it swept up loose skin cells and piled them until they formed their own xenobot—a type of self-replication. For Levin, it demonstrated how all living things have latent abilities. Having evolved to do one thing, they might do something completely different under the right circumstances.
Not long ago I met Levin at a workshop on science, technology, and Buddhism in Kathmandu. He hates flying but said this event was worth it. Even without the backdrop of the Himalayas, his scientific talk was one of the most captivating I’ve ever heard. Every slide introduced some bizarre new experiment. Butterflies retain memories from when they were caterpillars, even though their brains turned to mush in the chrysalis. Cut off the head and tail of a planarian, or flatworm, and it can grow two new heads; if you amputate again, the worm will regrow both heads. Levin argues the worm stores the new shape in its body as an electrical pattern. In fact, he thinks electrical signaling is pervasive in nature; it is not limited to neurons. Recently, Levin and colleagues found that some diseases might be cured by retraining the gene and protein networks as one might train a neural network. But when I sat down to talk to the audacious biologist on the hotel patio, I mostly wanted to hear about slime mold…
Read on for a fascinating conversation: “The Biologist Blowing Our Minds,” @drmichaellevin and @gmusser in @NautilusMag.
* Margaret E. Barber
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As we’re amazed, we might send tidy birthday greetings to Irwin Rose; he was born on this date in 1926. A biologist and biochemist, he shared the 2004 Nobel Prize in Chemistry for the discovery of ubiquitin-mediated protein degradation.
Ubiquitin is a small protein molecule that attaches to other proteins, tagging them for removal, which are thus recognized by the cell’s proteasomes. These structures are the cell’s waste-disposal units, allowing the proteins to be broken down into tiny pieces for reuse; this ubiquitin-mediated process cleans up unwanted proteins resulting during cell division, and performs quality control on newly synthesized proteins… which matters, as faulty protein-breakdown processes lead to such conditions as cystic fibrosis, several neurodegenerative diseases, and certain types of cancer.
“Real generosity towards the future lies in giving all to the present”*…
Iwan Rhys Morus suggests that we’re enthralled to a Victorian paradigm that haunts us still: the idea that inventors and entrepreneurs hold the keys to the utopian future…
Tech titans like Elon Musk and Jeff Bezos present themselves as men who could single-handedly shape the future. For their supporters, their ruthless drive toward success is their key virtue. And their showmanship — Musk sending a Tesla Roadster into space on a Falcon Heavy rocket, or Bezos sending Captain Kirk into orbit with Blue Origin — is a way of demonstrating that virtue and asserting they are in control.
We owe to the Victorians the idea that there is a firm link between virtue and technological agency. They established a powerful paradigm that continues to haunt us: that the future is (or can be) a utopia, and inventors and entrepreneurs are the ones who know how to get there.
While our notions of virtue have shifted today, we still assume that future-making is the prerogative of very specific sorts of innovators — even as their imagined identities have fractured and transformed. The assumption that innovation is the property of charismatic individuals still underlies the way we think about technology.
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The seductive power of Victorian thinking about the relationship between character, technology, and the future remains pervasive, even if views about just what the proper character of the inventor should be have shifted….
With its focus on individual virtue, the Victorian vision of the future is an exclusive one. When we subscribe to this paradigm about how — and by whom — the future is made, we’re also relinquishing control over that future. We’re acknowledging that tomorrow belongs to them, not to us.
“Back To The Victorian Future,” by @irmorus1 in @NoemaMag. Eminently worth reading in full.
* Albert Camus
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As we ponder power and its purpose, we might send inclusive birthday greetings to Jacques Lucien Monod; he was born on this date in 1910. A biochemist, he shared (with with François Jacob and André Lwoff) the Nobel Prize in Physiology or Medicine in 1965, “for their discoveries concerning genetic control of enzyme and virus synthesis.”
But Monod, who became the director of the Pasteur Institute, also made significant contributions to the philosophy of science– in particular via his 1971 book (based on a series of his lectures) Chance and Necessity, in which he examined the philosophical implications of modern biology. The importance of Monod’s work as a bridge between the chance and necessity of evolution and biochemistry on the one hand, and the human realm of choice and ethics on the other, can be seen in his influence on philosophers, biologists, and computer scientists including Daniel Dennett, Douglas Hofstadter, Marvin Minsky, and Richard Dawkins.
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