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Science without Validation in a World without Meaning

americanaffairsjournal.org

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Re: Science without Validation in a World without Meaning

#111

Post by pdonis »

jbay808 wrote: post #63
pdonis wrote: post #46

Earlier quoted context omitted.

> I hope we can agree that is an ideal to aspire to. It's an ideal to aspire to, but only if the ideal includes a very strict standard on what level of knowledge justifies dictating a public policy at all.

snowwrestler has repeatedly made the point that you can't not have a public policy about something; you can only accept or change the status quo. England has a public policy that people drive on the left. America has a public policy that people drive on the right. In a society that had no codified rule about which side of the road to drive on, where people just weave back and forth, the choice to not enforce a partic…

> England has a public policy that people drive on the left. America has a public policy that people drive on the right.

Neither of these policies were imposed by government. They were conventions that naturally evolved without any top-level policy being dictated, because they are obvious ways of solving an obvious coordination problem about using roads, and only got codified in law after that natural process of evolution had taken place.

> in general you should only need the preponderance of evidence to suggest that a public policy change will do more good than harm in order to adopt it

Even this standard, while it is weaker than the one I have suggested for what is needed to dictate public policy to everyone, is still strong enough to exclude many public policies that are currently in force, or suggested.

Re: Science without Validation in a World without Meaning

#112

Post by Balgair »

memexy wrote: post #56
cgiles wrote: post #44

I work in molecular biology research, and I think this is a great article that strikes at the heart of many problems in the field. I can't comment on the climate change stuff, although I wish he hadn't included it because it was almost certain to distract people from the overall point. The problem is that there are no remotely comprehensive, predictive, and mathematical models of what goes on inside of cells. It is p…

What's missing from current mathematics to make predictive models for biology? I did a search for "neural network cell simulation" and got a few hits, e.g. https://ieeexplore.ieee.org/document/8805421 . So it seems that people are working on the problem of predictability (or at least augmenting the researcher's/experimenter's ability to do some analysis ahead of time based on simplified models).

Flops.

Cells balance right on the edge of Maxwell's Demon. Even a few thousand ions can change behavior radically. So, you are forced to track all the ions, proteins, lipids, etc. Which means you have to do a lot of atom-by-atom tracking. There are a few tricks here, but since the cell is not crystalline, you can't do a lot of fun physicsy math to get the problem to be easier.

Also, most of the time, since this is 'research' to begin with, you don't know what's in the cell. That's the point of looking. We've nearly no idea what all the proteins are in any given cell. DNA gives some guide, but a stochastic switch from coding to non-coding happens, constantly. So you don't know what all the proteins in a cell are, where they are, what they do, what they don't do, what the extracellular space is like, etc.

Cells are just really complicated. So you need a lot of flops.

Re: Science without Validation in a World without Meaning

#113

Post by Ma8ee »

Gatsky wrote: post #106
Ma8ee wrote: post #98

Earlier quoted context omitted.

> "The simplest complete model of an organism is the organism itself." But that is trivially true about everything, including golf balls. The interesting question isn't if the model is complete, but if it is sufficient (or complete enough) to make predictions. And in the case of golf balls we can make quite good predictions with a very simple model, mostly because we are only interested in if it ends up in the hole o…

It is definitely not trivially true about anything. A golf ball can be modelled easily. You are adding external complications to the system. An electron can be impossible to model if you inject it into a complex system. Anyway the point is a golf ball will not evolve into a sentient being who will then fly to mars and write poetry, which is what cells have done. This shows you can’t even put a meaningful bound on wha…

But that is not a complete model of a golf ball. A complete model will include the wave function of all the particles in golf ball. It won’t be simpler than the model an organism of the same size. And in this case I mean by simpler that the number of bits required would be lower.

How does the capacity of the thing you try to model affect the complexity of the model?

Re: Science without Validation in a World without Meaning

#114

Post by mturmon »

cgiles wrote: post #83
mturmon wrote: post #72

Earlier quoted context omitted.

Thanks for this generous comment. The author of TFA has articulated a genuine problem that is central to many large-scale investigations these days, across many domains. We rely a lot on complex computer simulations, or complex physics-based models, that have a lot of fiddly details that are understood by only a limited set of people. Yet, we want to learn from these models, and we want to reach conclusions from them…

> Mere Monte Carlo state exploration is wasteful and doesn't provide much insight. Often we don't have error bars on model outputs to even know if an "improvement" in a metric is significant. The funny thing is, I didn't check the author's name until just now. Ed Dougherty, who people below have derided as a "mere engineer", has been working on these problems forever. I'm honestly surprised he's still active or even…

I also didn't care for the coarse characterizations nearby.

I take your point about the distinction between models that reproduce behavior ("simply predictive") vs. models of underlying components, and what you can learn from both.

This comes up in fields I work on with machine learning models vs. physics-based models. E.g., ML models that take a field of wind vectors at time t, and predict the wind at time t+1, vs. physical models that implement the flow equations. You can fit parameters of both flavors of models to match observations, but we certainly have more confidence in the robustness of the physics-based models.

About mathematically-challenged biologists - here's a hypothesis. I'll bet that if you started scanning conference abstracts in your domain for "uncertainty quantification," then some more carefully-posed modeling activities would crop up. (As you suggest, probably in the domains where more quantitative work is done.)

Re: Science without Validation in a World without Meaning

#115

Post by memexy »

Balgair wrote: post #112
memexy wrote: post #56

Earlier quoted context omitted.

What's missing from current mathematics to make predictive models for biology? I did a search for "neural network cell simulation" and got a few hits, e.g. https://ieeexplore.ieee.org/document/8805421 . So it seems that people are working on the problem of predictability (or at least augmenting the researcher's/experimenter's ability to do some analysis ahead of time based on simplified models).

Flops. Cells balance right on the edge of Maxwell's Demon. Even a few thousand ions can change behavior radically. So, you are forced to track all the ions, proteins, lipids, etc. Which means you have to do a lot of atom-by-atom tracking. There are a few tricks here, but since the cell is not crystalline, you can't do a lot of fun physicsy math to get the problem to be easier. Also, most of the time, since this is 'r…

How is "edge of Maxwell's Demon" related to "edge of chaos"?

Re: flops. I understand brute force is a good way to simulate dynamics but we constantly solve hard problems by approximation and have gotten pretty far with that approach. So what approximations have been tried and why have they been considered failures?

Also https://mobile.twitter.com/SteveStuWill/status/1268111230020...: > "Scientists created fully functional mini-livers out of human skin cells, then successfully transplanted them into rats. The research is a proof-of-concept for potentially revolutionary technology and provides a glimpse of an organ donor-free future." Wow!

That's unrelated to the original points but I see plenty of innovative approaches to problems in biology. Simulating cells is just one way to figure them out and we don't need to figure them out completely through computational means to put them to good uses. Biology is already computronium and if we can understand how to "program" then we don't need to simulate everything.

Re: Science without Validation in a World without Meaning

#116

Post by bobbydroptables »

pdonis wrote: post #108
bobbydroptables wrote: post #64

Earlier quoted context omitted.

>But public policy decisions affect everybody, so the criterion needs to be a lot stricter for how complete the information needs to be and how confident we need to be in our knowledge before we impose a public policy on everybody. Again, your own logic destroys your argument. We have made public policy decisions that heavily subsidize oil, cars, lowered air quality, etc. These decisions affect everyone not just car…

> We have made public policy decisions that heavily subsidize oil, cars, lowered air quality, etc. Yes, and I have already said that I oppose those decisions. The government should not be playing favorites. > why should Cletus who like to roll coal on Tesla drivers be able to take uncalculated risks that affect everybody? Cletus' behavior doesn't affect everybody; it only affects the few people who are within range o…

>Yes, and I have already said that I oppose those decisions. The government should not be playing favorites.

So you agree that government should stop subsidizing roads and suburbs?

>Cletus' behavior doesn't affect everybody; it only affects the few people who are within range of his coal rolling.

Actually air doesn't work this way. Pollution can and does carry for hundreds of miles.

But we can proceed with your fictional conception of aerodynamics.

How are the people that Cletus rolled coal on supposed to get compensated for their loss?

Re: Science without Validation in a World without Meaning

#117

Post by N1H1L »

I read the full article. And it feels like much ado about nothing.

One, the author for some reason is uncomfortable with a purely mathematical description of the world - without giving reasons beyond that humans cannot physically comprehend what the equations represent.

Two, the whole piece disregards the advances in emergent phenomena, complex systems and statistics. Yes, we do not understand how individual electrons look like in copper, but statistical descriptions of copper dimensions, purity and grain size are enough to get an exceptionally accurate idea of the electrical behavior of a copper wire. This extends for exceptionally complex systems like lungs (smoking will significantly increase your cancer/emphysema risk), or planetary systems (increasing CO2 concentrations will increase surface temperatures).

Three, There is also a weird bias against modeling. I am an experimental scientist, but I work closely with modellers, as all experimentalists do nowadays. Personally, I believe, that this bias against modeling often has a political component due to anthropogenic global warming. But in reality, there is a very vibrant dialogue between modellers and experimentalists, and hybrid scientists, people who are trained in both fields are the rage right now for hiring committees. Models have also improved dramatically - density functional theory is exceptionally accurate for smaller systems, while ReaxFF for dynamic systems and molecular dynamics simulations for more complex systems become better every year. The whole point about complex systems, applies to modelling too. I do not need to know the location of every molecule in the north Atlantic to predict the path of the hurricane - high pressure ridges and sea surface temperatures will give me really good results.

Re: Science without Validation in a World without Meaning

#118

Post by jbay808 »

pdonis wrote: post #111
jbay808 wrote: post #63

Earlier quoted context omitted.

snowwrestler has repeatedly made the point that you can't not have a public policy about something; you can only accept or change the status quo. England has a public policy that people drive on the left. America has a public policy that people drive on the right. In a society that had no codified rule about which side of the road to drive on, where people just weave back and forth, the choice to not enforce a partic…

> England has a public policy that people drive on the left. America has a public policy that people drive on the right. Neither of these policies were imposed by government. They were conventions that naturally evolved without any top-level policy being dictated, because they are obvious ways of solving an obvious coordination problem about using roads, and only got codified in law after that natural process of evol…

If I start putting some stuff into your tapwater, or into the air around your house, and you feel convinced it's going to cause you harm, but I insist that it's perfectly safe, what standard of proof do you think you should have to put together to stop me from doing that? And what would need to constitute harm?

If it didn't hurt humans but just insects that you're fond of, or just the ozone layer that protects you from radiation, or just the climate that you've come to enjoy, what standard of proof is needed?

Re: Science without Validation in a World without Meaning

#119

Post by mensetmanusman »

This is a great article, but I wish it would have really dealt with the idea of complexity.

Nature is not ‘unintelligible’ it is ‘complicated’ because of the large number of discrete interactive constitutive units.

In fact, if you plot # of constitutive quarks/atoms being worked with versus uncertainty, you see an interesting layout of the sciences. e.g. take this plot by xkcd ( https://xkcd.com/435/ ) and think about how much matter is under observation (i.e. increasing complexity to the left). Somewhere on the left would be climate in this example (as in the article).

Re: Science without Validation in a World without Meaning

#120

Post by mensetmanusman »

cgiles wrote: post #83
mturmon wrote: post #72

Earlier quoted context omitted.

Thanks for this generous comment. The author of TFA has articulated a genuine problem that is central to many large-scale investigations these days, across many domains. We rely a lot on complex computer simulations, or complex physics-based models, that have a lot of fiddly details that are understood by only a limited set of people. Yet, we want to learn from these models, and we want to reach conclusions from them…

> Mere Monte Carlo state exploration is wasteful and doesn't provide much insight. Often we don't have error bars on model outputs to even know if an "improvement" in a metric is significant. The funny thing is, I didn't check the author's name until just now. Ed Dougherty, who people below have derided as a "mere engineer", has been working on these problems forever. I'm honestly surprised he's still active or even…

Thanks for the info on the author, he has great articles!

https://asiatimes.com/2018/12/the-american-crisis-in-science...

He is a canary in the coal mine that our society ignores, kind of like how we ignored the warnings about a corona virus over the last decade.

Sigh

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