Tag: science

Gauge CNN

going beyond the Euclidean plane would require them to reimagine one of the basic computational procedures that made neural networks so effective at 2D image recognition in the first place. This procedure, called “convolution,” lets a layer of the neural network perform a mathematical operation on small patches of the input data and then pass the results to the next layer in the network. Gauge CNNs can detect patterns not only in 2D arrays of pixels, but also on spheres and asymmetrically curved objects. “This framework is a fairly definitive answer to this problem of deep learning on curved surfaces”

this has been applied to proteins:

Correia’s system, called MaSIF (short for molecular surface interaction fingerprinting), avoids the inherent complexity of a protein’s 3D shape by ignoring the molecules’ internal structure. Instead, the system scans the protein’s 2D surface for what the researchers call interaction fingerprints: features learned by a neural network that indicate that another protein could bind there. “The idea is that when any 2 molecules come together, what they’re essentially presenting to 1 another is that surface. So that’s all you need,. It’s very, very innovative.”

Intellectual Progress

the single most important thing I discovered this decade (due to a random comment in the SSC subreddit!) was the predictive coding theory of the brain. I started groping towards it (without knowing what I was looking for) in Mysticism And Pattern-Matching, reported the exact moment when I found it in It’s Bayes All The Way Up, and finally got a decent understanding of it after reading Surfing Uncertainty. At the same time, thanks to some other helpful tips from other rationalists, I discovered Behavior: The Control Of Perception, and with some help from Vaniver and a few other people was able to realize how these 2 overarching theories were basically the same. Discovering this area of research may be the best thing that happened to me the second half of this decade (sorry, everyone I dated, you were pretty good too).

Psychedelics are clearly interesting, and everyone else had already covered all the interesting pro-psychedelic arguments, so I wrote about some of my misgivings in my 2016 Why Were Early Psychedelicists So Weird?. The next step was trying to fit in an understanding of HPPD, which started with near-total bafflement. Predictive processing proved helpful here too, and my biggest update of the decade on psychedelics came with Friston and Carhart-Harris’ Relaxed Beliefs Under Psychedelics And The Anarchic Brain, which I tried to process further here. This didn’t directly improve my understanding of HPPD specifically, but just by talking about it a lot I got a subtler picture where lots of people have odd visual artifacts and psychedelics can cause slightly more (very rarely, significantly more) visual artifacts. I started the decade thinking that “psychedelic insight” was probably fake, and ended it believing that it is probably real, but I still don’t feel like I have a good sense of the potential risks.

In mental health, the field I am supposed to be an expert on, I spent a long time throwing out all kinds of random ideas and seeing what stuck – Boorsboom et al’s idea of Mental Disorders As Networks, The Synapse Hypothesis of depression, etc. Although I still think we can learn something from models like those, right now my best model is the one in Symptom, Condition, Cause, which kind of sidesteps some of those problems. Again, learning about predictive processing helped here, and by the end of the decade I was able to say actually useful things that explained some features of psychiatric conditions, like in Treat The Prodrome. Friston On Computational Mood might also be in this category, I’m still waiting for more evidence one way or the other.

Underworld Continents

Giant blobs nestled deep in the Earth may influence everything from the structure of island chains to mass-extinction events. If buoyed to the surface, they would be hot enough to cause gigantic, sustained eruptions. In turn, that volcanism could have changed the climate and even led to mass extinctions. Such a sequence, if verified, would be the ultimate antediluvian time bomb — apocalyptic extinctions triggered by subterranean structures buried since the birth of the world.

Physics & Biology

13 tips for engaging with physicists, as told by a biologist this is a great, and unfortunately rare, example of interdisciplinary work:

Understand what ‘I do not understand’ means When physicists do not understand something that you have said about biology, it’s possible that you do not understand that topic either. 2. Seek common ground When a physicist does not understand an aspect of biology, they are not requesting a ‘biology 101’ explanation. In my experience, when physicists ask a biology question, they want to apply the thinking of physics to biology; specifically, they are searching for universal, mathematical explanations. 4. Keep in mind the maths shortfall in biology For most biological phenomena, we don’t have precise equations — unlike in physics. This is not to say that we don’t have maths, but our field needs a lot more detailed quantification. This lack is the Achilles heel of biology, and affects even the concepts we use every day.

there’s also a view from the other side: 12 tips for engaging with biologists, as told by a physicist

Get comfortable being uncomfortable I went from being one of the most knowledgeable people in my research field at the end of my PhD to knowing less than most of the first-year PhD students in my new lab. For me, that meant I was doing something right, but you do have to be OK with taking that hit and spending time building a new skill set Do not blindly accept dogma Challenging prevailing ideas in biology using your perspective can bring about revolutions. I greatly admire colleagues who have upturned decades of accepted dogma using quantitative methods that were not even considered by the biological community.

Biodiversity Evolution

Biodiversity alters strategies of bacterial evolution

a paper published in Nature found that when a bacterial species resides in even a very simple ecological community — one that includes just a few other kinds of microbes — it evolves very different defense strategies against a predatory bacteriophage virus than it does when it’s left alone with the phage. The research is expanding these ideas into the context of the microbiome, where bacteria exist alongside loads of other species. The finding not only elevates the value of biodiversity as an evolutionary factor in its own right, but suggests that some earlier conclusions about the behaviors and capabilities of microorganisms, drawn from laboratory studies of species in isolation, may be seriously incomplete. It also sounds a note of caution about some contemplated strategies for beating drug resistance in bacteria.

Salvator Mundi decoded

The world’s costliest painting depicts a glass sphere with curious optical properties. Computer scientists figured out what the artist was getting at.

After comparing their renderings with the original, they have concluded that the orb is not solid at all. Instead, they show that the painting is a realistic physical representation of a hollow sphere with a radius of 6.8 centimeters but a thickness of just 1.3 millimeters.

Multiplex editing

Enhancing Organs for Cryonics, Space and Transplants

They are able to multiplex edit on the repeating gene sequences. The repeating gene sequences are key to many aspects of antiaging and cancer and other diseases. They are working to multiplex editing for enhancing organs. The can make the organs more resistant to cryopreservation and disease immunity. They can make people better able to travel in space and be more radiation resistant

A Causal Sequence

Here is how I currently understand the relationship between correlation and causality, and the collective findings of meta-scientific research: a shockingly large fraction of psychological research and other fields is simple random noise which cannot be replicated ‘everything is correlated’—even things which seem to have no causal relationship whatsoever most efforts to change human behavior and sociology and economics and education fail in randomized evaluation in every field from medicine to economics, when we directly ask how well correlations predict subsequent randomized experiments, we find that the predictive power is poor all variables are part of enormous dense causal graphs ‘folk causality’ often performs badly, especially in extremely complex fields with ambiguous long-term outcomes