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Javier E

DeepMind uncovers structure of 200m proteins in scientific leap forward | DeepMind | Th... - 0 views

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  • Proteins are the building blocks of life. Formed of chains of amino acids, folded up into complex shapes, their 3D structure largely determines their function. Once you know how a protein folds up, you can start to understand how it works, and how to change its behaviour
  • Although DNA provides the instructions for making the chain of amino acids, predicting how they interact to form a 3D shape was more tricky and, until recently, scientists had only deciphered a fraction of the 200m or so proteins known to science
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  • In November 2020, the AI group DeepMind announced it had developed a program called AlphaFold that could rapidly predict this information using an algorithm. Since then, it has been crunching through the genetic codes of every organism that has had its genome sequenced, and predicting the structures of the hundreds of millions of proteins they collectively contain.
  • Last year, DeepMind published the protein structures for 20 species – including nearly all 20,000 proteins expressed by humans – on an open database. Now it has finished the job, and released predicted structures for more than 200m proteins.
  • “Essentially, you can think of it as covering the entire protein universe. It includes predictive structures for plants, bacteria, animals, and many other organisms, opening up huge new opportunities for AlphaFold to have an impact on important issues, such as sustainability, food insecurity, and neglected diseases,”
  • In May, researchers led by Prof Matthew Higgins at the University of Oxford announced they had used AlphaFold’s models to help determine the structure of a key malaria parasite protein, and work out where antibodies that could block transmission of the parasite were likely to bind.
  • “Previously, we’d been using a technique called protein crystallography to work out what this molecule looks like, but because it’s quite dynamic and moves around, we just couldn’t get to grips with it,” Higgins said. “When we took the AlphaFold models and combined them with this experimental evidence, suddenly it all made sense. This insight will now be used to design improved vaccines which induce the most potent transmission-blocking antibodies.”
  • AlphaFold’s models are also being used by scientists at the University of Portsmouth’s Centre for Enzyme Innovation, to identify enzymes from the natural world that could be tweaked to digest and recycle plastics. “It took us quite a long time to go through this massive database of structures, but opened this whole array of new three-dimensional shapes we’d never seen before that could actually break down plastics,” said Prof John McGeehan, who is leading the work. “There’s a complete paradigm shift. We can really accelerate where we go from here
  • “AlphaFold protein structure predictions are already being used in a myriad of ways. I expect that this latest update will trigger an avalanche of new and exciting discoveries in the months and years ahead, and this is all thanks to the fact that the data are available openly for all to use.”
Javier E

How Climate Change Is Changing Therapy - The New York Times - 0 views

  • Andrew Bryant can still remember when he thought of climate change as primarily a problem of the future. When he heard or read about troubling impacts, he found himself setting them in 2080, a year that, not so coincidentally, would be a century after his own birth. The changing climate, and all the challenges it would bring, were “scary and sad,” he said recently, “but so far in the future that I’d be safe.”
  • That was back when things were different, in the long-ago world of 2014 or so. The Pacific Northwest, where Bryant is a clinical social worker and psychotherapist treating patients in private practice in Seattle, is a largely affluent place that was once considered a potential refuge from climate disruption
  • “We’re lucky to be buffered by wealth and location,” Bryant said. “We are lucky to have the opportunity to look away.”
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  • starting in the mid-2010s, those beloved blue skies began to disappear. First, the smoke came in occasional bursts, from wildfires in Canada or California or Siberia, and blew away when the wind changed direction. Within a few summers, though, it was coming in thicker, from more directions at once, and lasting longer.
  • Sometimes there were weeks when you were advised not to open your windows or exercise outside. Sometimes there were long stretches where you weren’t supposed to breathe the outside air at all.
  • Now lots of Bryant’s clients wanted to talk about climate change. They wanted to talk about how strange and disorienting and scary this new reality felt, about what the future might be like and how they might face it, about how to deal with all the strong feelings — helplessness, rage, depression, guilt — being stirred up inside them.
  • As a therapist, Bryant found himself unsure how to respond
  • while his clinical education offered lots of training in, say, substance abuse or family therapy, there was nothing about environmental crisis, or how to treat patients whose mental health was affected by it
  • Bryant immersed himself in the subject, joining and founding associations of climate-concerned therapists
  • could now turn to resources like the list maintained by the Climate Psychology Alliance North America, which contains more than 100 psychotherapists around the country who are what the organization calls “climate aware.”
  • Over and over, he read the same story, of potential patients who’d gone looking for someone to talk to about climate change and other environmental crises, only to be told that they were overreacting — that their concern, and not the climate, was what was out of whack and in need of treatment.
  • “You come in and talk about how anxious you are that fossil-fuel companies continue to pump CO2 into the air, and your therapist says, ‘So, tell me about your mother.’”
  • In many of the messages, people asked Bryant for referrals to climate-focused therapists in Houston or Canada or Taiwan, wherever it was the writer lived.
  • his practice had shifted to reflect a new reality of climate psychology. His clients didn’t just bring up the changing climate incidentally, or during disconcerting local reminders; rather, many were activists or scientists or people who specifically sought out Bryant because of their concerns about the climate crisis.
  • Climate change, in other words, surrounds us with constant reminders of “ethical dilemmas and deep social criticism of modern society. In its essence, climate crisis questions the relationship of humans with nature and the meaning of being human in the Anthropocene.”
  • It had been a challenging few years, Bryant told me when I first called to talk about his work. There were some ways in which climate fears were a natural fit in the therapy room, and he believed the field had coalesced around some answers that felt clear and useful
  • But treating those fears also stirred up lots of complicated questions that no one was quite sure how to answer. The traditional focus of his field, Bryant said, could be oversimplified as “fixing the individual”: treating patients as separate entities working on their personal growth
  • Climate change, by contrast, was a species-wide problem, a profound and constant reminder of how deeply intertwined we all are in complex systems — atmospheric, biospheric, economic — that are much bigger than us. It sometimes felt like a direct challenge to old therapeutic paradigms — and perhaps a chance to replace them with something better.
  • In one of climate psychology’s founding papers, published in 2011, Susan Clayton and Thomas J. Doherty posited that climate change would have “significant negative effects on mental health and well-being.” They described three broad types of possible impacts: the acute trauma of living through climate disasters; the corroding fear of a collapsing future; and the psychosocial decay that could damage the fabric of communities dealing with disruptive changes
  • All of these, they wrote, would make the climate crisis “as much a psychological and social phenomenon as a matter of biodiversity and geophysics.”
  • Many of these predictions have since been borne out
  • Studies have found rates of PTSD spiking in the wake of disasters, and in 2017 the American Psychological Association defined “ecoanxiety” as “a chronic fear of environmental doom.”
  • Climate-driven migration is on the rise, and so are stories of xenophobia and community mistrust.
  • eventually started a website, Climate & Mind, to serve as a sort of clearing house for other therapists searching for resources. Instead, the site became an unexpected window into the experience of would-be patients: Bryant found himself receiving messages from people around the world who stumbled across it while looking for help.
  • Many say it has led to symptoms of depression or anxiety; more than a quarter make an active effort not to think about it.
  • A poll by the American Psychiatric Association in the same year found that nearly half of Americans think climate change is already harming the nation’s mental health.
  • In June, the Yale Journal of Biology and Medicine published a paper cautioning that the world at large was facing “a psychological condition of ‘systemic uncertainty,’” in which “difficult emotions arise not only from experiencing the ecological loss itself,” but also from the fact that our lives are inescapably embedded in systems that keep on making those losses worse.
  • According to a 2022 survey by Yale and George Mason University, a majority of Americans report that they spend time worrying about climate change.
  • This is not an easy way to live.
  • Living within a context that is obviously unhealthful, he wrote, is painful: “a dimly intuited ‘fall’ from which we spend our lives trying to recover, a guilt we can never quite grasp or expiate” — a feeling of loss or dislocation whose true origins we look for, but often fail to see. This confusion leaves us feeling even worse.
  • When Barbara Easterlin first started studying environmental psychology 30 years ago, she told me, the focus of study was on ways in which cultivating a relationship with nature can be good for mental health
  • There was little or no attention to the fact that living through, or helping to cause, a collapse of nature can also be mentally harmful.
  • the field is still so new that it does not yet have evidence-tested treatments or standards of practice. Therapists sometimes feel as if they are finding the path as they go.
  • Rebecca Weston, a licensed clinical social worker practicing in New York and a co-president of the CPA-NA, told me that when she treats anxiety disorders, her goal is often to help the patient understand how much of their fear is internally produced — out of proportion to the reality they’re facing
  • climate anxiety is a different challenge, because people worried about climate change and environmental breakdown are often having the opposite experience: Their worries are rational and evidence-based, but they feel isolated and frustrated because they’re living in a society that tends to dismiss them.
  • One of the emerging tenets of climate psychology is that counselors should validate their clients’ climate-related emotions as reasonable, not pathological
  • it does mean validating that feelings like grief and fear and shame aren’t a form of sickness, but, as Weston put it, “are actually rational responses to a world that’s very scary and very uncertain and very dangerous for people
  • In the words of a handbook on climate psychology, “Paying heed to what is happening in our communities and across the globe is a healthier response than turning away in denial or disavowal.”
  • But this, too, raises difficult questions. “How much do we normalize people to the system we’re in?” Weston asked. “And is that the definition of health?
  • Or is the definition of health resisting the things that are making us so unhappy? That’s the profound tension within our field.”
  • “It seems to shift all the time, the sort of content and material that people are bringing in,” Alexandra Woollacott, a psychotherapist in Seattle, told the group. Sometimes it was a pervasive anxiety about the future, or trauma responses to fires or smoke or heat; other times, clients, especially young ones, wanted to vent their “sort of righteous anger and sense of betrayal” at the various powers that had built and maintained a society that was so destructive.
  • “I’m so glad that we have each other to process this,” she said, “because we’re humans living through this, too. I have my own trauma responses to it, I have my own grief process around it, I have my own fury at government and oil companies, and I think I don’t want to burden my clients with my own emotional response to it.”
  • In a field that has long emphasized boundaries, discouraging therapists from bringing their own issues or experiences into the therapy room, climate therapy offers a particular challenge: Separation can be harder when the problems at hand affect therapist and client alike
  • Some therapists I spoke to were worried about navigating the breakdown of barriers, while others had embraced it. “There is no place on the planet that won’t eventually be impacted, where client and therapist won’t be in it together,” a family therapist wrote in a CPA-NA newsletter. “Most therapists I know have become more vulnerable and self-disclosing in their practice.”
  • “If you look at or consider typical theoretical framings of something like post-traumatic growth, which is the understanding of this idea that people can sort of grow and become stronger and better after a traumatic event,” she said, then the climate crisis poses a dilemma because “there is no afterwards, right? There is no resolution anytime in our lifetimes to this crisis that we nonetheless have to build the capacities to face and to endure and to hopefully engage.”
  • “How,” she asked, “do you think about resilience apart from resolution?”
  • many of her patients are also disconnected from the natural world, which means that they struggle to process or even recognize the grief and alienation that comes from living in a society that treats nature as other, a resource to be used and discarded.
  • “I’m so excited by what you’re bringing in,” Woollacott replied. “I’m doing psychoanalytic training at the moment, and we study attachment theory” — how the stability of early emotional bonds affects future relationships and feelings of well-being. “But nowhere in the literature does it talk about our attachment to the land.”
  • Torres said that she sometimes takes her therapy sessions outside or asks patients to remember their earliest and deepest connections with animals or plants or places. She believes it will help if they learn to think of themselves “as rooted beings that aren’t just simply living in the human overlay on the environment.” It was valuable to recognize, she said, that “we are part of the land” and suffer when it suffers.
  • Torres described introducing her clients to methods — mindfulness, distress tolerance, emotion regulation — to help them manage acute feelings of stress or panic and to avoid the brittleness of burnout.
  • She also encourages them to narrativize the problem, including themselves as agents of change inside stories about how they came to be in this situation, and how they might make it different.
  • then she encourages them to find a community of other people who care about the same problems, with whom they could connect outside the therapy room. As Woollacott said earlier: “People who share your values. People who are committed to not looking away.”
  • Dwyer told the group that she had been thinking more about psychological adaptation as a form of climate mitigation
  • Therapy, she said, could be a way to steward human energy and creative capacities at a time when they’re most needed.
  • It was hard, Bryant told me when we first spoke, to do this sort of work without finding yourself asking bigger questions — namely, what was therapy actually about?
  • Many of the therapists I talked to spoke of their role not as “fixing” a patient’s problem or responding to a pathology, but simply giving their patients the tools to name and explore their most difficult emotions, to sit with painful feelings without instantly running away from them
  • many of the methods in their traditional tool kits continue to be useful in climate psychology. Anxiety and hopelessness and anger are all familiar territory, after all, with long histories of well-studied treatments.
  • They focused on trying to help patients develop coping skills and find meaning amid destabilization, to still see themselves as having agency and choice.
  • Weston, the therapist in New York, has had patients who struggle to be in a world that surrounds them with waste and trash, who experience panic because they can never find a place free of reminders of their society’s destruction
  • eston said, that she has trouble with the repeated refrain that therapist and patient experiencing the same losses and dreads at the same time constituted a major departure from traditional therapeutic practice
  • she believed this framing reflected and reinforced a bias inherent in a field that has long been most accessible to, and practiced by, the privileged. It was hardly new in the world, after all, to face the collapse of your entire way of life and still find ways to keep going.
  • Lately, Bryant told me, he’s been most excited about the work that happens outside the therapy room: places where groups of people gather to talk about their feelings and the future they’re facing
  • It was at such a meeting — a community event where people were brainstorming ways to adapt to climate chaos — that Weston, realizing she had concrete skills to offer, was inspired to rework her practice to focus on the challenge. She remembers finding the gathering empowering and energizing in a way she hadn’t experienced before. In such settings, it was automatic that people would feel embraced instead of isolated, natural that the conversation would start moving away from the individual and toward collective experiences and ideas.
  • There was no fully separate space, to be mended on its own. There was only a shared and broken world, and a community united in loving it.
Javier E

Functional medicine: Is it the future of healthcare or just another wellness trend? - I... - 0 views

  • Functional Medicine is the alternative medicine Bill Clinton credits with giving him his life back after his 2004 quadruple heart by-pass surgery. Its ideology is embraced by Oprah and regularly features on Gwyneth Paltrow's Goop.
  • Developed in 1990 by Dr Jeffrey Bland, who in 1991 set up the Institute of Functional Medicine with his wife Susan, today the field is spearheaded by US best-selling author Dr Mark Hyman, adviser to the Clintons and co-director of the controversial Cleveland Clinic for Functional Medicine.
  • "Functional Medicine is not about a test or a supplement or a particular protocol," he adds. "It's really a new paradigm of disease and how it arises and how to restore health. Within it there are many approaches that are effective, it's not exclusive, it doesn't exclude traditional medications, it includes all modalities depending on what's right for that patient."
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  • Functional Medicine isn't a protected title and a medical qualification isn't a prerequisite to practice. The result is an unregulated and disparate field, with medical doctors, nutritionists, naturopaths and homeopaths among the many practitioners.
  • Some other chronic illnesses the field claims to treat include heart disease, type 2 diabetes, irritable bowel syndrome, ulcerative colitis, depression, anxiety and arthritis
  • ll kinds of different reasons, some might have gluten issues, gut issues, others might have a deficiency causing neurological issues, MS is a symptom."
  • "There are components of Functional Medicine that absolutely lack an evidence base and there are practitioners of what they call Functional Medicine, they charge people for intravenous nutritional injections, they exaggerate claims, and that is professionally inappropriate, unethical and it lacks evidence.
  • On Dr Mark Hyman's view of MS he says, "there are a lot of terms put together there, all of which individually make a lot of sense, but put together in that way they do not.
  • "What does FM actually mean? It means nothing. It's a gift-gallop of words thrown together. It's criticised by advocates of evidence-based medicine because it's giving a veneer of scientific legitimacy to ideas that are considered pseudoscientific. For example, it'll take alternative medicine modalities like homeopathy and then call them 'bio-infusions' or something similar, rebranding it as something that works.
  • "It's a redundant name, real medicine is functional."
  • Next month the third annual Lifestyle and Functional Medical conference will take place in Salthill, Galway on November 3. Last year's event was attended by more than 500 people and featured a keynote address by honorary consultant cardiologist Dr Aseem Malhotra, author of bestselling The Pioppi Diet (which was named one of the top five worst celebrity diets to avoid in 2018 by the British Dietetic Foundation).
  • Dr David Robert Grimes is physicist and visiting fellow of Oxford and QUB. His research into cancer focuses on modelling tumour metabolism and radiation interactions. For Dr Grimes, the lack of definition, or "double-speak" as he puts it, in FM is troubling.
  • As well as the cost of appointments, FM practitioners commonly charge extra for tests. An omega finger prick test is around €100. A vitamin D test can cost upwards of €60, full thyroid panel more than €150 and a gut function test €400. Prices vary between practitioners.
  • "If I, as a GP, engaged in some of these behaviours I would be struck off." Specifically? "If I was recommending treatments that lacked an evidence base, or if I was promoting diagnostic tests which are expensive and lack an evidence base.
  • GPs engage every year in ongoing continuous professional development, I spend my evenings and my weekends outside of working hours attending educational events, small-group learning, large-group learning, engaging in research. This is an accusation that was levelled at the profession 30 years ago and then it was correct, but the profession has caught up…
  • "Obviously promoting wellness and healthy diet is very welcome but going beyond that and stating that certain aspects of 'functional medicine' can lead to reduced inflammation or prevent cancer, we have to be very careful about those claims.
  • Often the outcome of such tests are seemingly 'benign' prescriptions of vitamins or cleanses. However, dietitian Orla Walsh stresses that even these can have potentially harmful effects, especially on "vulnerable" patients, if not prescribed judiciously.
  • FM has five basic principles. 1. We are all genetically and biochemically unique so it treats the individual, not the disease. 2. It's science-based. 3. The body is intelligent and has the capacity for self-regulation. 4. The body has the ability to heal and prevent nearly all the diseases of ageing. 5. Health is not just the absence of disease, but a state of immense vitality.
  • She began her Functional Medicine career while training as a medical doctor and now travels the world working with high-profile clients. Dr McHale charges €425 for an initial consultation and €175 for follow-up appointments. Straightforward lab tests are €250 to €750, for complex cases testing fees can be up to €2,000.
  • "The term [Functional Medicine] tends to be bandied around quite a bit. Other things people say, such as 'functional nutritionist', can be misleading as a term. Many people are Functional Medicine practitioners but don't have any real medical background at all... I think regulation is always probably the best way forward."
  • "There's an awful lot to it in terms of biochemistry and physiology," she says. "You do need to have a very solid and well ingrained bio-chemistry background. A solely clinical background doesn't equip you with the knowledge to read a test.
  • "Evidence-base is the cornerstone of medicine and that has to be maintained. It becomes problematic in this area because you are looking at personalised medicine and that can be very difficult to evidence-base."
  • GP Christine Ritter travelled from England to attend the Galway conference last year with a view to integrating Functional Medicine into her practice.
  • "It was very motivating," she says. "Where it wasn't perhaps as strong was to find the evidence. The Functional Medicine people would say, 'we've done this study and this trial and we've used this supplement that was successful', but they can't show massive research data which might make it difficult to bring it into the mainstream.
  • "I also know the rigorous standard of trials we have in medicine they're not usually that great either, it's often driven by who's behind the trial and who's paying for it.
  • "Every approach that empowers patient to work on their destiny [is beneficial], but you'd have to be mindful that you're not missing any serious conditions."
  • Dr Hyman is working to grow the evidence-base for Functional Medicine worldwide. "The future is looking very bright," he says. "At the Cleveland Centre we're establishing a research base, building educational platforms, fellowships, residency programmes, rotations. We're advancing the field that's spreading across the world. We're seeing in China the development of a programme of Functional Medicine, South Africa, the UK, in London the Cleveland Clinic will hopefully have a Functional Medicine centre."
  • For Dr Mark Murphy regulation is a moot point as it can only apply once the field meets the standards of evidence-based medicine.
  • "Despite well intentioned calls for regulation, complementary and alternative medical therapies cannot be regulated," he says. "Only therapies that possess an evidence-base can enter our standard regulatory processes, including the Irish Medical Council, the Health Products Regulatory Authority and Irish advertising standards. In situations where complementary and alternative therapies develop an evidence base, they are no longer 'complementary and alternative', but in effect they become part of mainstream 'Medicine'.
  • l What are the principles?
  • "There's a huge variation between therapists, some are brilliant and some are okay, and some are ludicrous snake oil salesmen."
  • He is so concerned that patients' health and wealth are being put at risk by alternative therapies that earlier this year he joined Fine Gael TD Kate O'Connell and the Irish Cancer Society in introducing draft legislation earlier this year making it illegal to sell unproven treatments to cancer patients. Violators face jail and heavy fines.
  • Dr Grimes says criticism of variations in the standards of traditional medical research can be fair, however due to the weight of research it is ultimately self-correcting. He adds, "The reality is that good trials are transparent, independent and pre-registered.
  • "My involvement in shaping the Bill came from seeing first-hand the exploitation of patients and their families. Most patients undergoing treatment will take some alternative modalities in conjunction but a significant portion are talked out of their conventional medicine and seduced by false promises
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