Biotech

AI Used To Design a Multi-Step Enzyme That Can Digest Some Plastics 33

Leveraging AI tools like RFDiffusion and PLACER, researchers were able to design a novel enzyme capable of breaking down plastic by targeting ester bonds, a key component in polyester. Ars Technica reports: The researchers started out by using the standard tools they developed to handle protein design, including an AI tool named RFDiffusion, which uses a random seed to generate a variety of protein backgrounds. In this case, the researchers asked RFDiffusion to match the average positions of the amino acids in a family of ester-breaking enzymes. The results were fed to another neural network, which chose the amino acids such that they'd form a pocket that would hold an ester that breaks down into a fluorescent molecule so they could follow the enzyme's activity using its glow.

Of the 129 proteins designed by this software, only two of them resulted in any fluorescence. So the team decided they needed yet another AI. Called PLACER, the software was trained by taking all the known structures of proteins latched on to small molecules and randomizing some of their structure, forcing the AI to learn how to shift things back into a functional state (making it a generative AI). The hope was that PLACER would be trained to capture some of the structural details that allow enzymes to adopt more than one specific configuration over the course of the reaction they were catalyzing. And it worked. Repeating the same process with an added PLACER screening step boosted the number of enzymes with catalytic activity by over three-fold.

Unfortunately, all of these enzymes stalled after a single reaction. It turns out they were much better at cleaving the ester, but they left one part of it chemically bonded to the enzyme. In other words, the enzymes acted like part of the reaction, not a catalyst. So the researchers started using PLACER to screen for structures that could adopt a key intermediate state of the reaction. This produced a much higher rate of reactive enzymes (18 percent of them cleaved the ester bond), and two -- named "super" and "win" -- could actually cycle through multiple rounds of reactions. The team had finally made an enzyme.

By adding additional rounds alternating between structure suggestions using RFDiffusion and screening using PLACER, the team saw the frequency of functional enzymes increase and eventually designed one that had an activity similar to some produced by actual living things. They also showed they could use the same process to design an esterase capable of digesting the bonds in PET, a common plastic.
The research has been published in the journal Science.
China

China To Develop Gene-Editing Tools, New Crop Varieties (reuters.com) 21

China issued guidelines on Friday to promote biotech cultivation, focusing on gene-editing tools and developing new wheat, corn, and soybean varieties, as part of efforts to ensure food security and boost agriculture technology. From a report: The 2024-2028 plan aims to achieve "independent and controllable" seed sources for key crops, with a focus to cultivate high-yield, multi-resistant wheat, corn and high-oil, high-yield soybean and rapeseed varieties. The move comes as China intensifies efforts to boost domestic yields of key crops like soybeans to reduce reliance on imports from countries such as the United States amid a looming trade war.
Biotech

Brain Implant That Could Boost Mood By Using Ultrasound To Go Under NHS Trial (theguardian.com) 48

An anonymous reader quotes a report from The Guardian: A groundbreaking NHS trial will attempt to boost patients' mood using a brain-computer-interface that directly alters brain activity using ultrasound. The device, which is designed to be implanted beneath the skull but outside the brain, maps activity and delivers targeted pulses of ultrasound to "switch on" clusters of neurons. Its safety and tolerability will be tested on about 30 patient in the 6.5 million-pound trial, funded by the UK's Advanced Research and Invention Agency (Aria).

[...] The latest trial will test a device developed by the US-based non-profit Forest Neurotech. In contrast to invasive implants, in which electrodes are inserted into a specific location in the brain, Forest 1 uses ultrasound to read-out and modify activity. Aria describes the device as "the most advanced BCI in the world" due to its ability to modify activity across multiple regions simultaneously. This widens potential future applications to a huge patient population affected by conditions such as depression, anxiety and epilepsy, which are all "circuit level" conditions rather than being localized in a specific brain region.

The NHS trial will recruit patients who, due to brain injury, have had part of their skull temporarily removed to relieve a critical buildup of pressure in the brain. This means the device can be tested without having to perform surgery. When placed beneath the skull, or in individuals with a skull defect, ultrasound can detect tiny changes in blood flow to produce 3D maps of brain activity with a spatial resolution of about 100 times that of a typical fMRI scan. The same implant can deliver focused ultrasound to mechanically nudge neurons towards firing, providing a way to remotely dial activity up at precise locations. Participants will wear the device on their scalp at the site of the skull defect for two hours. Their brain activity will be measured and researchers will test whether patients' mood and feelings of motivation can be reliably altered.

There are safety considerations, as ultrasound can cause tissue to heat up. Prof Elsa Fouragnan, a neuroscientist at the University of Plymouth, which is collaborating on the project, said: "What we're trying to minimize is heat. There's a safety and efficacy trade-off." She added that it would also be important to ensure that personality or decision-making were not altered in unintended ways -- for instance, making someone more impulsive. The study will run for three and a half years starting from March, with the first eight months focused on securing regulatory approval. If successful, Forest hopes to move into a full clinical trial for a condition such as depression.
Aimun Jamjoom, a consultant neurosurgeon at the Barking, Havering and Redbridge university hospitals NHS trust, who is leading the project, said: "[T]he ability to offer a safer form of surgery is very exciting. If you look at conditions like depression or epilepsy, [up to] a third of these patients just don't get better. It's those groups where a technology like this could be a life-changing solution."
Crime

Elizabeth Holmes Breaks Her Silence In First Interview From Prison (people.com) 138

Convicted Theranos founder, Elizabeth Holmes, had her first interview since being reported to prison in 2023, telling People magazine that she is still working on "research and inventions" in the healthcare space. Here's an excerpt from the article: Scheduled for release on April 3, 2032, Holmes says she hopes to travel with her family and to fight for reform of criminal justice system. She recently drafted an American Freedom Act bill -- a seven-page handwritten document -- to bolster the presumption of innocence and change criminal procedure. "This will be my life's work," says Holmes, adding that she is speaking out now as part of her mission to advocate on behalf of incarcerated persons and those ripped away from their children.

And, despite her global reputation as a biotech con artist who put lives at risk, she says she's continuing to write patents for new inventions and plans to resume her career in healthcare technology after her release. "There is not a day I have not continued to work on my research and inventions," she says. "I remain completely committed to my dream of making affordable healthcare solutions available to everyone."

For now, however, she is sustained by weekend visits from her family, when she can cuddle Invicta, watch William gather acorns in the prison yard and hold Evans's hand and briefly hug and kiss. (Conjugal visits are not allowed.) "It kills me to put my family through pain the way I do," she says. "But when I look back on my life, and these angels that have come into it, I can get through anything. It makes me want to fight for all of it."

Biotech

Technology For Lab-Grown Eggs Or Sperm On Brink of Viability, UK Watchdog Finds (theguardian.com) 99

An anonymous reader quotes a report from The Guardian: Bolstered by Silicon Valley investment, scientists are making such rapid progress that lab-grown human eggs and sperm could be a reality within a decade, a meeting of the Human Fertilization and Embryology Authority board heard last week (PDF). In-vitro gametes (IVGs), eggs or sperm that are created in the lab from genetically reprogrammed skin or stem cells, are viewed as the holy grail of fertility research. The technology promises to remove age barriers to conception and could pave the way for same-sex couples to have biological children together. It also poses unprecedented medical and ethical risks, which the HFEA now believes need to be considered in a proposed overhaul of fertility laws.

Peter Thompson, chief executive of the HFEA, said: "In-vitro gametes have the potential to vastly increase the availability of human sperm and eggs for research and, if proved safe, effective, and publicly acceptable, to provide new fertility treatment options for men with low sperm counts and women with low ovarian reserve." The technology also heralds more radical possibilities including "solo parenting" and "multiplex parenting." Julia Chain, chair of HFEA, said: "It feels like we ought to have Steven Spielberg on this committee," in a brief moment of levity in the discussion of how technology should be regulated. Lab-grown eggs have already been used produce healthy babies in mice -- including ones with two biological fathers. The equivalent feat is yet to be achieved using human cells, but US startups such as Conception and Gameto claim to be closing in on this prize.

The HFEA meeting noted that estimated timeframes ranged from two to three years -- deemed to be optimistic -- to a decade, with several clinicians at the meeting sharing the view that IVGs appeared destined to become "a routine part of clinical practice." The clinical use of IVGs would be prohibited under current law and there would be significant hurdles to proving that IVGs are safe, given that any unintended genetic changes to the cells would be passed down to all future generations. The technology also opens up myriad ethical issues.
Thompson said: "Research on IVGs is progressing quickly but it is not yet clear when they might be a viable option in treatment. IVGs raise important questions and that is why the HFEA has recommended that they should be subject to statutory regulation in time, and that biologically dangerous use of IVGs in treatment should never be permitted."

"This is the latest of a range of detailed recommendations on scientific developments that we are looking at to future-proof the HFE Act, but any decisions around UK modernizing fertility law are a matter for parliament."
Biotech

OpenAI Has Created an AI Model For Longevity Science (technologyreview.com) 33

OpenAI has developed a language model designed for engineering proteins, capable of converting regular cells into stem cells. It marks the company's first venture into biological data and demonstrates AI's potential for unexpected scientific discoveries. An anonymous reader quotes a report from MIT Technology Review: Last week, OpenAI CEO Sam Altman said he was "confident" his company knows how to build an AGI, adding that "superintelligent tools could massively accelerate scientific discovery and innovation well beyond what we are capable of doing on our own." The protein engineering project started a year ago when Retro Biosciences, a longevity research company based in San Francisco, approached OpenAI about working together. That link-up did not happen by chance. Sam Altman, the CEO of OpenAI, personally funded Retro with $180 million, as MIT Technology Review first reported in 2023. Retro has the goal of extending the normal human lifespan by 10 years. For that, it studies what are called Yamanaka factors. Those are a set of proteins that, when added to a human skin cell, will cause it to morph into a young-seeming stem cell, a type that can produce any other tissue in the body. [...]

OpenAI's new model, called GPT-4b micro, was trained to suggest ways to re-engineer the protein factors to increase their function. According to OpenAI, researchers used the model's suggestions to change two of the Yamanaka factors to be more than 50 times as effective -- at least according to some preliminary measures. [...] The model does not work the same way as Google's AlphaFold, which predicts what shape proteins will take. Since the Yamanaka factors are unusually floppy and unstructured proteins, OpenAI said, they called for a different approach, which its large language models were suited to. The model was trained on examples of protein sequences from many species, as well as information on which proteins tend to interact with one another. While that's a lot of data, it's just a fraction of what OpenAI's flagship chatbots were trained on, making GPT-4b an example of a "small language model" that works with a focused data set.

Once Retro scientists were given the model, they tried to steer it to suggest possible redesigns of the Yamanaka proteins. The prompting tactic used is similar to the "few-shot" method, in which a user queries a chatbot by providing a series of examples with answers, followed by an example for the bot to respond to. Although genetic engineers have ways to direct evolution of molecules in the lab, they can usually test only so many possibilities. And even a protein of typical length can be changed in nearly infinite ways (since they're built from hundreds of amino acids, and each acid comes in 20 possible varieties). OpenAI's model, however, often spits out suggestions in which a third of the amino acids in the proteins were changed. "We threw this model into the lab immediately and we got real-world results," says Retro's CEO, Joe Betts-Lacroix. He says the model's ideas were unusually good, leading to improvements over the original Yamanaka factors in a substantial fraction of cases.

Biotech

Startup Raises $200 Million To 'De-Extinct' the Woolly Mammoth, Thylacine and Dodo (venturebeat.com) 123

An anonymous reader quotes a report from VentureBeat: Colossal BioSciences has raised $200 million in a new round of funding to bring back extinct species like the woolly mammoth. Dallas- and Boston-based Colossal is making strides in the scientific breakthroughs toward "de-extinction," or bringing back extinct species like the woolly mammoth, thylacine and the dodo. [...] Since launching in September 2021, Colossal has raised $435 million in total funding. This latest round of capital places the company at a $10.2 billion valuation. Colossal will leverage this latest infusion of capital to continue to advance its genetic engineering technologies while pioneering new revolutionary software, wetware and hardware solutions, which have applications beyond de-extinction including species preservation and human healthcare.

"Our recent successes in creating the technologies necessary for our end-to-end de-extinction toolkit have been met with enthusiasm by the investor community. TWG Global and our other partners have been bullish in their desire to help us scale as quickly and efficiently as possible," said CEO Colossal Ben Lamm, in a statement. "This funding will grow our team, support new technology development, expand our de-extinction species list, while continuing to allow us to carry forth our mission to make extinction a thing of the past."
Here's a summary of the startup's progress on its efforts to bring back the woolly mammoth, thylacine and the dodo:

Woolly Mammoth De-extinction Progress
- Generated chromosome-scale reference genomes for elephants and the first de novo assembled mammoth genome
- Acquired and aligned 60+ ancient mammoth genomes and 30+ genomes of extant elephant species, improving mammoth-specific variant accuracy
- Derived pluripotent stem cells for Asian elephants, advancing reproductive technologies essential for de-extinction

Thylacine De-extinction Progress
- Created a 99.9% complete ancient genome for the thylacine using long-read and RNA sequencing
- Assembled telomere-to-telomere genomes of dasyurid species to understand evolutionary relationships and support conservation of marsupials
- Progress in genomics and reproductive technologies positions Colossal ahead of schedule on critical de-extinction steps

Dodo De-extinction Progress
- Completed high-coverage genomes for the dodo, its relatives, and the critically endangered manumea
- Developed tools for avian genome engineering, including techniques for craniofacial gene-editing and primordial germ cell cultivation
- Significant advances in avian-specific genetic techniques are driving progress toward dodo restoration and bird conservation
Biotech

Neuralink Implants Third Brain Chip. Plans '20 or 30' This Year, Eventually 'Blindsight' Devices (yahoo.com) 111

"Neuralink Corp.'s brain-computer device has been implanted in a third patient," reports Bloomberg, "and the company has plans for about 20 to 30 more implants in 2025, founder Elon Musk said."

In an interview streamed on X.com, Musk says "We've got now three humans with Neuralinks implanted and they're all working well," according to The Times of India: "We upgraded the devices, they'll have more electrodes, basically higher bandwidth, longer battery life and everything. So, expect 20 or 30 patients this year with the upgraded Neuralink devices...."

"[O]ur next part will be Blindsight devices where even if somebody has lost both eyes or has lost the optic nerve, we can interface directly with the visual cortex in the brain and enable them to see. We already have that working in monkeys," Musk added.

Science

Scientists Explore Longevity Drugs For Dogs That Could Also 'Extend Human Life' (theguardian.com) 80

U.S. biotech startup Loyal plans to launch a lifespan-extending drug for dogs in early 2025, potentially offering insights into human longevity. The San Francisco-based company has secured $125 million in funding for LOY-002, a beef-flavored daily pill designed to extend canine lifespans by at least one year. The drug works by targeting age-related metabolic changes and insulin regulation, according to Loyal CEO Celine Halioua.

Simultaneously, the Dog Aging Project is studying rapamycin, an immunosuppressant drug, which preliminary research suggests could add three years to dogs' lives. Researchers believe these canine studies could accelerate human longevity research, though experts note the lack of standardized aging biomarkers remains a significant hurdle for human trials.
Biotech

Scientists Have Finally Found the Gene That Gives Cats Orange Fur (science.org) 57

Slashdot reader sciencehabit writes: Most orange cats are boys, a quirk of feline genetics that also explains why almost all calicos and tortoiseshells are girls. Scientists curious about those sex differences—or perhaps just cat lovers—have spent more than 60 years unsuccessfully seeking the gene that causes orange fur and the striking patchwork of colors in calicos and tortoiseshells. Now, two teams have independently found the long-awaited mutation and discovered a protein that influences hair color in a way never seen before in any animal... Using skin samples collected from various cats, the researchers were able to hone in a mutation on the X chromosome that impacts how much of a protein a gene called Arhgap36 produces. Increasing the amount of the Arhgap36 in pigment producing cells called melanocytes activates a molecular pathway that produces a light red pigment.
"Scanning a database of 188 cat genomes, Barsh's team found every single orange, calico, and tortoiseshell cat had the exact same mutation," writes Science magazine. "The group reports the discovery this month on the preprint server bioRxiv. A separate study, also posted to bioRxiv this month, confirms these findings... They also found that skin from calico cats had more Arghap36 RNA in orange regions than in brown or black regions." Arhgap36's inactivation pattern in calicos and tortoiseshells is typical of a gene on the X chromosome, says Carolyn Brown [a University of British Columbia geneticist who was not involved in either study], but it's unusual that a deletion mutation would make a gene more active, not less. "There is probably something special about cats." Experts are thrilled by the two studies. "It's a long-awaited gene," says Leslie Lyons, a feline geneticist at the University of Missouri. The discovery of a new molecular pathway for hair color was unexpected, she says, but she's not surprised how complex the interactions seem to be. "No gene ever stands by itself."

Lyons would like to know where and when the mutation first appeared: There is some evidence, she says, that certain mummified Egyptian cats were orange. Research into cat color has revealed all kinds of phenomena, she says, including how the environment influences gene expression. "Everything you need to know about genetics you can learn from your cat."

Science

Scientists Announce Progress Toward Ambitious Atlas of Human Cells (reuters.com) 5

Scientists unveiled on Wednesday the first blueprint of human skeletal development as they make progress toward the goal of completing a biological atlas of every cell type in the body to better understand human health and diagnose and treat disease. From a report: The work is part of the ongoing Human Cell Atlas project that was begun in 2016 and involves researchers around the world. The human body comprises roughly 37 trillion cells, with each cell type having a unique function. The researchers aim to have a first draft of the atlas done in the next year or two.

Aviv Regev, founding co-chair of the project and currently executive vice president and head of research and early development at U.S. biotech company Genentech, said the work is important on two levels. "First of all, it's our basic human curiosity. We want to know what we're made of. I think humans have always wanted to know what they're made of. And, in fact, biologists have been mapping cells since the 1600s for that reason," Regev said. "The second and very pragmatic reason is that this is essential for us in order to understand and treat disease. Cells are the basic unit of life, and when things go wrong, they go wrong with our cells, first and foremost," Regev said.

Biotech

23andMe To Lay Off 40% of Its Workforce, Discontinue All Therapy Programs (bbc.com) 72

The genetic testing company 23andMe announced it will cut 40% of its workforce, or 200 jobs, and halt the work on therapies it was developing. As the BBC notes, the company is fighting for survival after hackers gained access to personal information of millions of its users, causing the stock to crater by more than 70%. All seven of its independent directors also resigned in September, following a protracted negotiation with founder and Chief Executive Anne Wojcicki over her plan to take the company private. The BBC reports: On Tuesday, the company warned investors of "substantial doubt" about its ability to continue operating, as it reported that revenue had fallen to $44 million between July and September compared to $50 million in the same period last year. Losses fell to $59 million from $75 million. The job cuts are expected to lead to one-off costs of $12 million, including severance pay, for the plan that will result in savings of $35 million. "We are taking these difficult but necessary actions as we restructure 23andMe and focus on the long-term success of our core consumer business and research partnerships," Ms Wojcicki said.

The company also said it is considering what to do with the therapies it had in development, including licensing or selling them. 23andMe is a giant of the growing ancestor-tracing industry. It offers genetic testing from DNA, with ancestry breakdown and personalised health insights. Its customers include famous names, from rapper Snoop Dogg to multi-billionaire investor Warren Buffett. The company was valued at roughly $3.5 billion when it listed on the Nasdaq stock exchange in 2021 and its share price peaked at $17.65. But they have since tumbled and are currently trading at less than $5.

Biotech

Researchers Develop New Method That Tricks Cancer Cells Into Killing Themselves (stanford.edu) 21

Our bodies divest themselves of 60 billion cells every day through a natural process called "apoptosis". So Stanford medicine researchers are developing a new approach to cancer therapy that could "trick cancer cells into disposing of themselves," according to announcement from Stanford's medical school: Their method accomplishes this by artificially bringing together two proteins in such a way that the new compound switches on a set of cell death genes... One of these proteins, BCL6, when mutated, drives the blood cancer known as diffuse large cell B-cell lymphoma... [It] sits on DNA near apoptosis-promoting genes and keeps them switched off, helping the cancer cells retain their signature immortality.

The researchers developed a molecule that tethers BCL6 to a protein known as CDK9, which acts as an enzyme that catalyzes gene activation, in this case, switching on the set of apoptosis genes that BCL6 normally keeps off. "The idea is, Can you turn a cancer dependency into a cancer-killing signal?" asked Nathanael Gray, PhD, co-senior author with Crabtree, the Krishnan-Shah Family Professor and a chemical and systems biology professor. "You take something that the cancer is addicted to for its survival and you flip the script and make that be the very thing that kills it...."

When the team tested the molecule in diffuse large cell B-cell lymphoma cells in the lab, they found that it indeed killed the cancer cells with high potency. They also tested the molecule in healthy mice and found no obvious toxic side effects, even though the molecule killed off a specific category of of the animals' healthy B cells, a kind of immune cell, which also depend on BCL6. They're now testing the compound in mice with diffuse large B-cell lymphoma to gauge its ability to kill cancer in a living animal. Because the technique relies on the cells' natural supply of BCL6 and CDK9 proteins, it seems to be very specific for the lymphoma cells — the BCL6 protein is found only in this kind of lymphoma cell and in one specific kind of B cell. The researchers tested the molecule in 859 different kinds of cancer cells in the lab; the chimeric compound killed only diffuse large cell B-cell lymphoma cells.

Scientists have been trying to shut down cancer-driving proteins, one of the researchers says, but instead, "we're trying to use them to turn signaling on that, we hope, will prove beneficial for treatment."

The two researchers have co-founded the biotech startup Shenandoah Therapeutics, which "aims to further test this molecule and a similar, previously developed molecule," according to the article, "in hopes of gathering enough pre-clinical data to support launching clinical trials of the compounds.

"They also plan to build similar molecules that could target other cancer-driving proteins..."
Science

Eating Less Can Lead To a Longer Life: Massive Study in Mice Shows Why (nature.com) 58

Cutting calorie intake can lead to a leaner body -- and a longer life, an effect often chalked up to the weight loss and metabolic changes caused by consuming less food. Now, one of the biggest studies of dietary restrictions ever conducted in laboratory animals challenges the conventional wisdom about how dietary restriction boosts longevity. From a report: The study, involving nearly 1,000 mice fed low-calorie diets or subjected to regular bouts of fasting, found that such regimens do indeed cause weight loss and related metabolic changes. But other factors -- including immune health, genetics and physiological indicators of resiliency -- seem to better explain the link between cutting calories and increased lifespan. "The metabolic changes are important," says Gary Churchill, a mouse geneticist at the Jackson Laboratory in Bar Harbor, Maine, who co-led the study. "But they don't lead to lifespan extension."

To outside investigators, the results drive home the intricate and individualized nature of the body's reaction to caloric restriction. "It's revelatory about the complexity of this intervention," says James Nelson, a biogerontologist at the University of Texas Health Science Center in San Antonio. The study was published today in Nature by Churchill and his co-authors, including scientists at Calico Life Sciences in South San Francisco, California, the anti-ageing focused biotech company that funded the study. Scientists have long known that caloric restriction, a regimen of long-term limits on food intake, lengthens lifespan in laboratory animals. Some studies have shown that intermittent fasting, which involves short bouts of food deprivation, can also increase longevity.

Earth

Plastic-Eating Bacteria Could Combat Pollution Problems, Scientists Hope (msn.com) 68

The Washington Post on scientists who "discovered that bacteria commonly found in wastewater can break down plastic to turn it into a food source, a finding that researchers hope could be a promising answer to combat one of Earth's major pollution problems." In a study published Thursday in Environmental Science and Technology, scientists laid out their examination of Comamonas testosteroni, a bacteria that grows on polyethylene terephthalate, or PET, a plastic commonly found in single-use food packaging and water bottles. PET makes up about 12 percent of global solid waste and 90 million tons of the plastic produced each year... Unlike most other bacteria, which thrive on sugar, C. testosteroni has a more refined palate, including chemically complex materials from plants and plastics that take longer to decompose.

The researchers are the first to demonstrate not only that this bacteria can break down plastic, but they also illuminate exactly how they do it. Through six meticulous steps, involving complex imaging and gene editing techniques, the authors found that the bacteria first physically break down plastic by chewing it into smaller pieces. Then, they release enzymes — components of a cell that speed up chemical reactions — to chemically break down the plastic into a carbon-rich food source known as terephthalate...

The bacteria take a few months to break down chunks of plastic, according to Rebecca Wilkes [a lead author on the study and postdoctoral researcher at the National Renewable Energy Laboratory]. As a result, if the bacteria are going to be efficient tools, a lot of optimization needs to take place to speed up the rate at which they decompose pollutants. One approach is to promote bacterial growth by providing them with an additional food source, such as a chemical known as acetate.

A senior author on the study (and associate professor of civil and environmental engineering at Northwestern University) tells the Washington Post that "The machinery in environmental microbes is still a largely untapped potential for uncovering sustainable solutions we can exploit."
Biotech

23andMe Is On the Brink. What Happens To All Its DNA Data? (npr.org) 60

The one-and-done nature of 23andMe is "indicative of a core business problem with the once high-flying biotech company that is now teetering on the brink of collapse," reports NPR. As 23andMe struggles for survival, many of its 15 million customers are left wondering what the company plans to do with all the data it has collected since it was founded in 2006. An anonymous reader shares an excerpt from the report: Andy Kill, a spokesperson for 23andMe, would not comment on what the company might do with its trove of genetic data beyond general pronouncements about its commitment to privacy. "For our customers, our focus continues to be on transparency and choice over how they want their data to be managed," he said. When signing up for the service, about 80% of 23andMe's customers have opted in to having their genetic data analyzed for medical research. "This rate has held steady for many years," Kill added. The company has an agreement with pharmaceutical giant GlaxoSmithKline, or GSK, that allows the drugmaker to tap the tech company's customer data to develop new treatments for disease. Anya Prince, a law professor at the University of Iowa's College of Law who focuses on genetic privacy, said those worried about their sensitive DNA information may not realize just how few federal protections exist. For instance, the Health Insurance Portability and Accountability Act, also known as HIPAA, does not apply to 23andMe since it is a company outside of the health care realm. "HIPAA does not protect data that's held by direct-to-consumer companies like 23andMe," she said.

Although DNA data has no federal safeguards, some states, like California and Florida, do give consumers rights over their genetic information. "If customers are really worried, they could ask for their samples to be withdrawn from these databases under those laws," said Prince. According to the company, all of its genetic data is anonymized, meaning there is no way for GSK, or any other third party, to connect the sample to a real person. That, however, could make it nearly impossible for a customer to renege on their decision to allow researchers to access their DNA data. "I couldn't go to GSK and say, 'Hey, my sample was given to you -- I want that taken out -- if it was anonymized, right? Because they're not going to re-identify it just to pull it out of the database," Prince said.

Vera Eidelman, a staff attorney with the American Civil Liberties Union who specializes in privacy and technology policy, said the patchwork of state laws governing DNA data makes the generic data of millions potentially vulnerable to being sold off, or even mined by law enforcement. "Having to rely on a private company's terms of service or bottom line to protect that kind of information is troubling -- particularly given the level of interest we've seen from government actors in accessing such information during criminal investigations," Eidelman said. She points to how investigators used a genealogy website to identify the man known as the Golden State Killer, and how police homed in on an Idaho murder suspect by turning to similar databases of genetic profiles. "This has happened without people's knowledge, much less their express consent," Eidelman said.

Neither case relied on 23andMe, and spokesperson Kill said the company does not allow law enforcement to search its database. The company has, however, received subpoenas to access its genetic information. According to 23andMe's transparency report, authorities have sought genetic data on 15 individuals since 2015, but the company has resisted the requests and never produced data for investigators. "We treat law enforcement inquiries, such as a valid subpoena or court order, with the utmost seriousness. We use all legal measures to resist any and all requests in order to protect our customers' privacy," Kill said. [...] In a September filing to financial regulators, [23andMe CEO Anne Wojcicki] wrote: "I remain committed to our customers' privacy and pledge," meaning the company's rules requiring consent for DNA to be used for research would remain in place, as well as allowing customers to delete their data. Wojcicki added that she is no longer considering offers to buy the company after previously saying she was.

Open Source

New Flexible RISC-V Semiconductor Has Great Potential (ieee.org) 20

"For the first time, scientists have created a flexible programmable chip that is not made of silicon..." reports IEEE Spectrum — opening new possibilities for implantable devices, on-skin computers, brain-machine interfaces, and soft robotics.

U.K.-based Pragmatic Semiconductor produced an "ultralow-power" 32-bit microprocessor, according to the article, and "The microchip's open-source RISC-V architecture suggests it might cost less than a dollar..." This shows potential for inexpensive applications like wearable healthcare electronics and smart package labels, according to the chip's inventors: For example, "we can develop an ECG patch that has flexible electrodes attached to the chest and a flexible microprocessor connected to flexible electrodes to classify arrhythmia conditions by processing the ECG data from a patient," says Emre Ozer, senior director of processor development at Pragmatic, a flexible chip manufacturer in Cambridge, England. Detecting normal heart rhythms versus an arrhythmia "is a machine learning task that can run in software in the flexible microprocessor," he says...

Pragmatic sought to create a flexible microchip that cost significantly less to make than a silicon processor. The new device, named Flex-RV, is a 32-bit microprocessor based on the metal-oxide semiconductor indium gallium zinc oxide (IGZO). Attempts to create flexible devices from silicon require special packaging for the brittle microchips to protect them from the mechanical stresses of bending and stretching. In contrast, pliable thin-film transistors made from IGZO can be made directly at low temperatures onto flexible plastics, leading to lower costs...

"Our end goal is to democratize computing by developing a license-free microprocessor," Ozer says... Other processors have been built using flexible semiconductors, such as Pragmatic's 32-bit PlasticARM and an ultracheap microcontroller designed by engineers in Illinois. Unlike these earlier devices, Flex-RV is programmable and can run compiled programs written in high-level languages such as C. In addition, the open-source nature of RISC-V also let the researchers equip Flex-RV with a programmable machine learning hardware accelerator, enabling artificial intelligence applications.

Each Flex-RV microprocessor has a 17.5 square millimeter core and roughly 12,600 logic gates. The research team found Flex-RV could run as fast as 60 kilohertz while consuming less than 6 milliwatts of power... The Pragmatic team found that Flex-RV could still execute programs correctly when bent to a curve with a radius of 3 millimeters. Performance varied between a 4.3 percent slowdown to a 2.3 percent speedup depending on the way it was bent.

Biotech

A California Boy Was Kidnapped from a Park in 1951. He's Just Been Found Alive (sfgate.com) 132

An anonymous reader shared this story from SFGate: A boy who was kidnapped from an Oakland playground in 1951 has been found alive on the East Coast, a remarkable resolution to a mystery that has haunted his family for over half a century.

On February 21, 1951, 6-year-old Luis Armando Albino was playing with his older brother Roger at Jefferson Square Park. The boys had recently immigrated with their mother and four other siblings from Puerto Rico... That afternoon, Luis and 10-year-old Roger walked down the block from their home at 730 Brush Street to play in the park. They were approached by a woman in her 30s, wearing a green bandana over her hair, who began chatting with Luis in Spanish. She promised she would buy him candy if he came along with her, and little Luis agreed to join her. Wary, Roger trailed the pair for a while before returning home to alert an adult to the strange encounter. Oakland police were called by frantic family members and a search was immediately launched...

Antonia [the boy's mother] was convinced her son was alive. "She came once a week, then once a month, then at least once a year, to see the shake of the head, to have the answer 'no' translated for her although she could read it in the officers' faces," the Oakland Tribune wrote in 1966...

Decades passed.

In 2020, Luis' niece, Alida Alequin, took a DNA test on a whim, the Mercury News reported. The service returned several possible family members to the Oakland woman. One of them was a man who Alequin had never met. After some internet sleuthing, she began to suspect this man might be the missing uncle she'd heard so much about. She reached out to the man but didn't hear back.

Earlier this year, Alequin tried again. Armed with photos, she took her evidence to the Oakland Police Department's missing persons unit. In short order, the FBI and California Department of Justice were also investigating Alequin's lead. They discovered the man was living on the East Coast, had worked as a firefighter and served two tours in Vietnam with the Marine Corps. This week, the Mercury News first reported that a DNA test confirmed what Alequin suspected: This was Luis Albino.

In June, Luis flew to California to reunite with his family, among them his devoted brother Roger... For over 70 years, he lived on the East Coast believing he was the son of another couple....

When Luis met Alequin for the first time this summer, he held her in an embrace. "Thank you," he said, "for finding me."

China

China's Startup Ecosystem Collapses as New Venture Formations Plunge 98% 63

China's once-booming venture capital industry is experiencing a severe downturn, with the number of new startups plummeting from 51,302 in 2018 to just 1,202 in 2023, according to data provider IT Juzi. This decline is starkly evident in science parks and innovation hubs across the country, where vacant offices and abandoned equipment have become commonplace, according to a stunning FT story.

Industry insiders attribute the crisis to a combination of factors, including China's economic slowdown, heightened US-China tensions, and President Xi Jinping's policies targeting the tech sector. The government's anti-corruption drive and increased scrutiny of successful entrepreneurs have further dampened the private sector's enthusiasm. The funding landscape has shifted dramatically, with state-backed funds now dominating the market. This has led to more conservative investment strategies, favoring lower-risk sectors like advanced manufacturing over traditionally popular areas such as biotech and consumer technology. Founders face increasingly stringent terms, including personal liability for investments and asset checks. Many established VC firms are downsizing operations and exploring overseas opportunities.
Government

Is the Tech World Now 'Central' to Foreign Policy? (wired.com) 41

Wired interviews America's foreign policy chief, Secretary of State Antony Blinken, about U.S. digital polices, starting with a new "cybersecurity bureau" created in 2022 (which Wired previously reported includes "a crash course in cybersecurity, telecommunications, privacy, surveillance, and other digital issues.") Look, what I've seen since coming back to the State Department three and a half years ago is that everything happening in the technological world and in cyberspace is increasingly central to our foreign policy. There's almost a perfect storm that's come together over the last few years, several major developments that have really brought this to the forefront of what we're doing and what we need to do. First, we have a new generation of foundational technologies that are literally changing the world all at the same time — whether it's AI, quantum, microelectronics, biotech, telecommunications. They're having a profound impact, and increasingly they're converging and feeding off of each other.

Second, we're seeing that the line between the digital and physical worlds is evaporating, erasing. We have cars, ports, hospitals that are, in effect, huge data centers. They're big vulnerabilities. At the same time, we have increasingly rare materials that are critical to technology and fragile supply chains. In each of these areas, the State Department is taking action. We have to look at everything in terms of "stacks" — the hardware, the software, the talent, and the norms, the rules, the standards by which this technology is used.

Besides setting up an entire new Bureau of Cyberspace and Digital Policy — and the bureaus are really the building blocks in our department — we've now trained more than 200 cybersecurity and digital officers, people who are genuinely expert. Every one of our embassies around the world will have at least one person who is truly fluent in tech and digital policy. My goal is to make sure that across the entire department we have basic literacy — ideally fluency — and even, eventually, mastery. All of this to make sure that, as I said, this department is fit for purpose across the entire information and digital space.

Wired notes it was Blinken's Department that discovered China's 2023 breach of Microsoft systems. And on the emerging issue of AI, Blinken cites "incredible work done by the White House to develop basic principles with the foundational companies." The voluntary commitments that they made, the State Department has worked to internationalize those commitments. We have a G7 code of conduct — the leading democratic economies in the world — all agreeing to basic principles with a focus on safety. We managed to get the very first resolution ever on artificial intelligence through the United Nations General Assembly — 192 countries also signing up to basic principles on safety and a focus on using AI to advance sustainable development goals on things like health, education, climate. We also have more than 50 countries that have signed on to basic principles on the responsible military use of AI. The goal here is not to have a world that is bifurcated in any way. It's to try to bring everyone together.

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