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Progress in Biology Is Slow – Here's How We Can Speed It Up

adamashwal.com

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Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#11
The notion that computational reducibility is the key principle underpinning difficulty in life (and probably social) sciences is extremely insightful, and had me optimistic for the second half.

But the author's suggestion to address this problem is just... to chase the combinatorial explosion harder? That's a pretty underwhelming solution. And impossible cost scaling aside, another key part of the problem is that we don't even know how to enumerate what the relevant parameters are. What about the effects of a mouse's environment on natural immune response and drug efficacy, for example? Such a highly roboticized environment would be highly unpleasant for a mouse, presumably, and adverse effects seem well within the realm of possibility.

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#12
post #3

> If we care about blood pressure, for example, why have we not given every drug, at every dosage, every regiment, and in every combination to a mouse and actually seen what happens? One of the answers is hidden behind this question: Ethics. We could make a ton of progress if we started growing humans for lab testing. Then we could run massively parallel tests and get data much quicker. I mean, think about how much w…

[deleted]

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#13
post #11

The notion that computational reducibility is the key principle underpinning difficulty in life (and probably social) sciences is extremely insightful, and had me optimistic for the second half. But the author's suggestion to address this problem is just... to chase the combinatorial explosion harder? That's a pretty underwhelming solution. And impossible cost scaling aside, another key part of the problem is that we…

I would think that we have to consider the entire parameter space or model space of a reductionist view of biology as a space of models, then search for the smaller subspace of models with fewer, stiffer parameters. http://www.lassp.cornell.edu/sethna/Sloppy/WhatAreSloppyMode...

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#14
No, no, no.

This is just an argument for putting more effort into a failed strategy. The reason why we haven't made much progress towards extending healthy human life isn't because the disease state is complex, it is because the primary strategy adopted by the research community is to reverse engineer the disease state, and then work backwards towards its cause.

Typical project: pick away at a small chunk of the altered metabolism of [age-related disease of choice]. Find a proximate cause of pathology that has some small contribution to the whole - an altered gene expression level, say, something really, really far removed from root causes. Find a small molecule that adjusts expression. Publish. Patent. Tech transfer finds someone willing to tinker with that family of small molecules to have a short at achieving a small alteration in the disease state. Goes into trials, fails at phase II or phase III.

This happens constantly. It is the bulk of all medical research for age-related disease. It is pointless. May as well not happen. Applying computational prowess to this process won't make it any better. You'll just have a lot more low yield approaches that still do nothing more than tinker with proximate causes in late stage disease, and will do next to nothing for patients. (With the occasional success like statins, which produce the amazing-for-this-strategy result of a 22% reduction in mortality. You still die, just slightly less often).

The only practical way forward for age-related disease is to entirely reject this approach to medicine in favor of a much, much better one.

1) Infer the root causes of aging and best points of intervention (already done, several times over).

2) Fix one of those causes, in isolation.

3) Observe the results.

Steps 1-3 have been achieved for removal of senescent cells. The results in animal studies are absolutely amazing, robust, night and day better than anything else anyone has done for the treatment of aging and age-related disease. Reversal of scores of diseases and measures of aging, every lab can do it, replicated many, many times via numerous different approaches.

Everyone is now backfilling their models of age-related disease, their understanding of disease etiology, to add senescent cells. Because they are clearly an important cause.

Once Unity Biotechnology has stopped being silly about their subpar approach to senescent cell clearance, and the rest of the dozen or so companies have started their trials, we should expect those human trials to follow the same sort of pattern.

This is the way to make progress. Infer root causes, target root causes, figure out which work by trying them. Backfill your understanding of age-related disease based on new data.

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#15
I'm a layperson, but there seem to be a few problems with this:

1. Mouse models are not perfect simulations of human biology

2. Cost as has been mentioned multiple times

3. Patient response to treatments depend not just on drug formulation, but also disease state and progression

4. Even mice likely have population dependent responses to drugs

Given the above, a "combinatorial explosion" of drug cocktails tested on mice would likely only tell you what's safe for a given strain of mice, not what's safe for humans, much less what's effective. Factor in disease state, dosage, mouse model impedance, and the numerous other little things that go into using drugs to treat illnesses, and the "grad student brute force" approach begins to seem a lot more intelligent in comparison. Especially since some of those grad students are already using AI to reduce the search space of interesting drugs.

EDIT - my wife (PharmD) adds that if you're targeting diseases with this approach and not just general safety, then a lot of diseases have no known cause, but they do have treatments. That means there's no good way to simulate this in mice because the cause is unknown. Diseases are being discovered every day for which there are no known causes. Furthermore mouse models require manual labor. No way to scale that up.

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#16

I'm a layperson, but there seem to be a few problems with this: 1. Mouse models are not perfect simulations of human biology 2. Cost as has been mentioned multiple times 3. Patient response to treatments depend not just on drug formulation, but also disease state and progression 4. Even mice likely have population dependent responses to drugs Given the above, a "combinatorial explosion" of drug cocktails tested on mi…

Not to mention that one of the biggest bottlenecks in drug development is the preclinical (e.g. mice) to clinical (humans) transition.

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#17
Well-written post, but the suggested solution of HTS on mice is nonsensical. First of all, we’ve cured cancer in mice many times but it’s obviously still unsolved in humans. Secondly, you’re constraining yourself to synthesized chemical space, which as others have mentioned is a grain of sand (charitably 10^10 in human history) compared to a planet’s worth (10^60 by some estimates) of possible druglike molecules.

Target ID is hard, but we also have known biologically valid targets that are simply undruggable so far (KRAS is the most obvious example). Solving computational chemistry problems is a much more tractable, high-leverage endeavor. And we can in fact use that progress to accelerate biological research itself — for example, quickly developing bioavailable tool compounds via virtual screen to test biological hypotheses in mice, a rational “pharmacological knockout” approach.

We can reduce the biological space in a smart way, we don’t have to brute force this.

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#18
post #3

> If we care about blood pressure, for example, why have we not given every drug, at every dosage, every regiment, and in every combination to a mouse and actually seen what happens? One of the answers is hidden behind this question: Ethics. We could make a ton of progress if we started growing humans for lab testing. Then we could run massively parallel tests and get data much quicker. I mean, think about how much w…

> If we're talking about biology in general, though, I think we have made enormous progress in the last 10-20 years.

And, funnily enough, this corresponds with PCR becoming commonplace.

I would argue that the lack of progress in biology was almost solely due to the fact that before PCR biology was effectively "alchemy" and that after PCR biology became "science". PCR and sequencing blew away entire subfields of biology as being testably untrue.

I still remember high school biology and feeling that whole tranches of it were complete bullshit. It wasn't until I had a molecular biology course (fairly new in 1986!) that I went "Oh, okay, biology can have a solid scientific basis and actually make sense."

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#19
post #18
post #3

> If we care about blood pressure, for example, why have we not given every drug, at every dosage, every regiment, and in every combination to a mouse and actually seen what happens? One of the answers is hidden behind this question: Ethics. We could make a ton of progress if we started growing humans for lab testing. Then we could run massively parallel tests and get data much quicker. I mean, think about how much w…

> If we're talking about biology in general, though, I think we have made enormous progress in the last 10-20 years. And, funnily enough, this corresponds with PCR becoming commonplace. I would argue that the lack of progress in biology was almost solely due to the fact that before PCR biology was effectively "alchemy" and that after PCR biology became "science". PCR and sequencing blew away entire subfields of biolo…

> PCR and sequencing blew away entire subfields of biology as being testably untrue.

As a non-biologist I would love to hear of some examples of this

Re: Progress in Biology Is Slow – Here's How We Can Speed It Up

#20
post #3

> If we care about blood pressure, for example, why have we not given every drug, at every dosage, every regiment, and in every combination to a mouse and actually seen what happens? One of the answers is hidden behind this question: Ethics. We could make a ton of progress if we started growing humans for lab testing. Then we could run massively parallel tests and get data much quicker. I mean, think about how much w…

A lot of this doesn't actually seem true though and the parts that resemble the truth only do so because they're so handwavingly broad.

>We could make a ton of progress if we started growing humans for lab testing.Maybe in some areas like wound treatment but certainly not overall. The point of using animals like mice and fish is also that they breed much faster than humans and certain parts of their biochemistry react the same as ours to certain compounds (use of fish in the development of psychiatric drugs comes to mind). Sure, eventually you need human testing, but that doesn't explain why we're not engaging in much more robust animal testing right now nor does it explain why such an expansion would be unethical.

>Once gene synthesis can be done in a garage, anyone could engineer anything they wanted (anthrax, ebola, whatever). Progress in biology is accelerating.None of this actually relates to discovering new things or otherwise advancing the field though, it just acknowlwdges that the ability to tread old ground has become more accessible and therefore weaponizable by terrorist groups (nations avoid biological weapons because of the collateral damage risks). We could already make and modify those scary things (and frequently do) in controlled labs.

>We've found other ways to get what we want from nature (shininess, gold color, conductivity, etc.) without using gold. The "living forever" argument also runs very quickly into philosophy (ship of Theseus) and away from biologyBut it doesn't! Biology has already been dealing with the ship of Theseus problem for decades and the conclusion has always been "Who cares, let the liberal arts majors squack about it". How many cells and mineral deposits do you think stay with you for the entirety of your life? How many of those cells do you think are brain cells? You don't need to be immortal to be uncertain if you're still you.

>I think it's much more interesting to consider the biological factories that we're building. Directed evolution, CRISPR, BIL Gates, gene drives, etc. We're making real headway into playing god.How is any of that more immediately interesting than evaluating where we could be improving research output in the present? We're already passed the point of ”should it exist” and well into "what's the least harmful way to discover if it exists". Whether any one country abstains from a topic doesn't matter in a globally connected world. If there's money on the table then refusing to play just means someone else gets more of the pot. At least if we're the first ones to discover something then we can set the pace of progress for as long as we're able to maintain the research lead.

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