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biomcgary

2,554 karma · joined August 29, 2012

Computational biologist. Modeling individual human health using multi-omic approaches and machine learning. Searching for islands of causality in seas of correlation. Cross-species translation of biological systems: Of mice and men (and zebrafish, worms and yeast).
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biomcgary··on Big Bang theory is wrong, claim scientists
I heard about big bounce/crunch models before, but thought they were discounted due to the acceleration of expansion, which suggests that gravity will not lead to a contraction. Does anyone understand how this new bounce model deals with that problem?

If inflation is naturally fast early, this model is already better than the previous bounce/crunch versions.

biomcgary··on Cysteine depletion triggers adipose tissue thermogenesis and weight loss
Cysteine plays a key role in redox metabolism and removing reactive oxygen species (ROS). During brown fat burning, high flux of electrons increases the NADH/NAD⁺ and FADH₂/FAD ratios — shifting redox state toward a more reduced environment, which is exactly what you would need if deprived of cysteine.
biomcgary··on Can I stop drone delivery companies flying over my property?
Sometimes (often?) technical legal definitions considered without context lead to absurd conclusions that don't manifest in practice.

Does the FAA have jurisdiction over paper planes? What about the airspace in my house and does it matter if the doors are open?

On the other hand, I don't think government agencies have much incentive to preemptively limit the scope of their authority, but would be happy to hear of counter-examples.

biomcgary··on DNA is maybe 60-750MB of data
Your genome only needs to store the information necessary for the lineage leading to you to survive and compete in the range of environmental variation that actually happened.

Consequently, your DNA has less information about how to survive on Jupiter or in the absence of oxygen.

However, your genome contains a fair amount of data on how to identify a mate that will maximize your reproductive success in an environment similar to the one your lineage experienced, e.g., a preference for symmetrical faces.

Until we can measure the environment of humans accurately, all the algorithmic complexity measures applied to the genome are going to be missing the relevant context.

biomcgary··on I should have loved biology too
I was paid to get a PhD in Biology, albeit just enough to live on. Most people in PhD programs are, either through being a TA (teacher's assistant) or RA (research assistant). The real financial cost is the opportunity cost of 5-6 years of your life.

Whether or not broad support for training scientists holds up during and after the current administration remains to be seen.

biomcgary··on High time to tackle drug-resistant fungal infections
Everything that reproduces is in an evolutionary arms race (https://en.wikipedia.org/wiki/Evolutionary_arms_race), so the "kicking the can" objection doesn't really make sense in this context.

There is no alternative to inventing new weapons continuously. We are simply used to winning without much effort since Fleming found penicillin, a naturally occurring fungal compound. Previous successes have limited the economics of continuing to develop new solutions, which is contributes to the uptick in resistance.

This doesn't mean we shouldn't be judicious in the tradeoffs that we choose and try to avoid a purely chemical solution to the arms race. For example, as robotics get better, we should move away from mono-cropping toward combinations of plants that naturally ward off pests. There are better ways to stay ahead than blunt tools.

biomcgary··on An experiment that turned back biological time
An excellent description of a recent fundamental discovery. The post might have a bit more jargon than a non-biologist would immediately recognize, but it does convey the complexity and logic of both discovery and validation.

As a computational biologist, I enjoy the parallels between the logic of hypothesis generation and testing in biology and algorithm-development on the CS side. In both areas, asking the right big questions is important. But in other cases, recognizing the importance and application of an otherwise obscure discovery is important, e.g., CRISPR and penicillin or discovery of transformers at Google vs their application at OpenAI.

biomcgary··on Microsoft researchers developed a hyper-efficient AI model that can run on CPUs
Should be 1-trit.
biomcgary··on Scientists: Protein IL-17 fights infection, acts on the brain, inducing anxiety
Yes, one would expect kin / group selection to play a role.
biomcgary··on The Church FAQ
In the end, I suspect most cults want all your organs.
biomcgary··on Stoicism's appeal to the rich and powerful (2019)
Marcus Aurelius was the last of the Five Good Emperors because he did not adopt a competent, non-biological son to take his place like the previous four. Instead, he set up Commodus as Caesar and his heir, despite his mental instability. That decision alone calls into question his Stoic resolve.
biomcgary··on Zelensky leaves White House after angry meeting
Washington's opinion might well have changed and, as noted in other comments, an armada of nuclear ICBMs does negate the distance that he referenced.

Regardless of the hypothetical, isn't it clear that Trump IS meddling and not following Washington's injunction? (Also applies to Israel/Gaza.)

In family and community (and internet) dynamics, meddling in other people's quarrels often leads to blowback. (Yes, I'm aware of the irony of making this comment on HN.) Is it really any different on the global stage?

My genuine question: What are the best criteria for deciding when getting involved is better than remaining on the sidelines? Do those criteria apply at both hyper-local and global scales, or this there a phase transition in applicability?

biomcgary··on Zelensky leaves White House after angry meeting
George Washington's farewell address (1796) - on Europe: The great rule of conduct for us in regard to foreign nations is in extending our commercial relations, to have with them as little political connection as possible. So far as we have already formed engagements, let them be fulfilled with perfect good faith. Here let us stop. Europe has a set of primary interests which to us have none; or a very remote relation. Hence she must be engaged in frequent controversies, the causes of which are essentially foreign to our concerns. Hence, therefore, it must be unwise in us to implicate ourselves by artificial ties in the ordinary vicissitudes of her politics, or the ordinary combinations and collisions of her friendships or enmities.

Our detached and distant situation invites and enables us to pursue a different course. If we remain one people under an efficient government, the period is not far off when we may defy material injury from external annoyance; when we may take such an attitude as will cause the neutrality we may at any time resolve upon to be scrupulously respected; when belligerent nations, under the impossibility of making acquisitions upon us, will not lightly hazard the giving us provocation; when we may choose peace or war, as our interest, guided by justice, shall counsel.

Why forego the advantages of so peculiar a situation? Why quit our own to stand upon foreign ground? Why, by interweaving our destiny with that of any part of Europe, entangle our peace and prosperity in the toils of European ambition, rivalship, interest, humor or caprice?

biomcgary··on Thermoelectric Solar Panel
My house has a super-insulated, passive solar design. I heat it with wood pellet stove, which requires electric power to run the fans and pellet feed system. I've often wanted to add a Stirling engine and a small battery to make it truly grid independent. However, the house design means I only burned about $20 worth of pellets this winter, so the ROI isn't remotely justifiable.
biomcgary··on Framework's first desktop is a strange–but unique–mini ITX gaming PC
Currently, I'm using generative AI of various kinds on my M1 Air (llm, image gen, TTS, STT), but am frustrated by the limitations - primarily memory and secondarily availability of an MLX adaptation.

Just an AI hobbyist, so I don't have time or inclination to tweak everything. Given the non-NVIDIA GPU, how painful will it be to play around with new AI models on this system?

biomcgary··on Periodic Cooking of Eggs
The 8 cycles between boiling and room temp would be tedious without automation. I wonder if a similar outcome would be achieved by sous vide followed by boiling briefly to set the white, much like sous vide steak followed by searing.
biomcgary··on Should we use AI and LLMs for Christian apologetics? (2024)
A Christian recommending a serpent-named language to get closer to God is pretty entertaining. What about Go "and make disciples"?
biomcgary··on I've acquired a new superpower
Is diverging harder? I find it easier. Maybe it is from long ago practice on stereograms, but I'm curious if it could be due to neurological/physiological differences.
biomcgary··on Relax while watching bouncing particles making connections when they get closer
Agglomerative clustering
biomcgary··on Short-term rentals are hollowing out communities with loose restrictions
I think owner-operated mother-in-law suites and similar allow neighborhoods to strike a nice balance between long-term community commitment and supporting reasonable amounts of of tourism.

My wife and I host an Airbnb just outside the city limits of Flagstaff. We have two houses on the property and live in one. Our listing makes it clear that we live on the property. Our neighbors never complain. There is an Airbnb two doors down that regularly generates complaints due to a remote owner.

biomcgary··on Magnetic swarm intelligence of mass-produced, programmable microrobot assemblies
Evidently someone is a fan of Big Hero 6.
biomcgary··on A Gentle Introduction to Graph Neural Networks
I've followed GNNs in biology and applied them in a couple domains, but have been disappointed by the results so far. I'm a bit surprised because I have successfully used other graph-based approaches in biology.
biomcgary··on The higher fertility of TSMC semiconductor workers
https://en.wikipedia.org/wiki/Tacit_knowledge
biomcgary··on Show HN: A Marble Madness-inspired WebGL game we built for Netlify
On the last level I ran into one of the raised blocks and tunneled into the cubes. I could still roll around inside, lol, but there was no way out.
biomcgary··on All Life on Earth Today Descended from a Single Cell. Meet LUCA
So many assumptions are necessary for this type of research, particularly for the timing. Inferring such an early age depends on a "clock" that varies based on the stringency of purifying selection. I.e., it is only clock-like to the degree that competition and the level of biological systems integration were essentially static through time.
biomcgary··on Personality Basins
Natural selection encodes adaptive responses to the environment in DNA (and other molecules), so memories can be encoded to the extent that they are adaptive and can be encoded (i.e., mechanisms may not exist to encode everything using only standing natural variation).
biomcgary··on Terence Tao: "It can become more rational to think and act more boldly"
Am I correct to assume people are upvoting this as a possible explanation for the outcome of the US Presidential election?

I.e., if people think that they are in economic doldrums or decline, taking a risk seems better than the status quo?

Voting out the incumbent party seems popular during economic downturns (real or perceived) unless the party clearly inherited the economic crisis AND seems to be addressing the problem energetically (e.g., post-1929 FDR).

biomcgary··on MomBoard: E-ink display for a parent with amnesia
Glad she recovered!
biomcgary··on MomBoard: E-ink display for a parent with amnesia
We know there are lots of biological mechanisms that retain state at the cellular level to put it in CS-ish terms. A fraction of these mechanisms could plausibly be transmitted outside the cell (e.g., miRNA).

These mechanisms may or may not encode memories as we typically understand them, i.e., the ability to remember an event or fact, but could very plausibly shift personality, preferences, etc.

biomcgary··on A new dental scam is to pull healthy teeth to sell you expensive fake ones
About 15 years ago my wife needed a fair amount of dental work due to a dentist screwing up her mouth in childhood. We traveled to Brazil and got the work done by a dentist that my family knew and spent a week hanging out with my family there. The cost including travel and the dentist, etc. was far less that what the US dentist quoted and my wife hasn't had a dental problem since. The procedures were far less invasive than what was recommended by the US.

Too many people uncritically accept the highly motivated claims of experts. Fortunately, if you get a second opinion from another dentist, they are unlikely to imagine the exact same set of fake problems as the first dentist.

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