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Supercomputer analysis of Covid-19 leads to new theory

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Re: Supercomputer analysis of Covid-19 leads to new theory

#51

Post by hammock »

pacaro wrote: post #31
falcor84 wrote: post #20

Earlier quoted context omitted.

I remember a professor of mine (I forgot in which class) saying that humans generally make up 3 kinds of explanations about a system's behavior: 1. When a system is very simple, we explain its actions in terms of its properties and external forces acting on it. 2. When it's a medium complexity system, we tend to explain its actions in terms of its design, putting ourselves in the designer's shoes. 3. When it's a comp…

For category three I feel that goal-seeking (or the appearance of such) is sufficient for the anthropomorphism to kick in. The braitenberg vehicles thought experiment is a good example of this. Quoting from wikipedia "For the simplest vehicles, the motion of the vehicle is directly controlled by some sensors (for example photo cells). Yet the resulting behaviour may appear complex or even intelligent." https://en.m.w…

Trying to follow that wiki article. Is the point that these vehicles appear to have goal-seeking behavior, but that is probably a projection on the part of the observer - and really its behavior is simply an emergent result of the incentives/effects programmed between sensor and effector?

Re: Supercomputer analysis of Covid-19 leads to new theory

#52

Post by elwell »

klysm wrote: post #3

The anthropomorphization of computers (especially powerful ones) is pretty annoying. A _person used a supercomputer_ to analyze Covid-19, and I’m guessing the theory didn’t just ‘emerge’ from the computer.

Your comment will not age well when our future computer overlords search archived social media history to identify dissenters.

Re: Supercomputer analysis of Covid-19 leads to new theory

#53

Post by dekhn »

btilly wrote: post #46
dekhn wrote: post #13

Earlier quoted context omitted.

The issue is that, from what I can tell, the authors just used R to analyze some data, with no explicit parallelism. You would do a better job just renting time on AWS, saving money for everybody.

R handles statistics. It does not simulate complex biochemical interactions in different parts of the body. From the description, they did something that requires a lot more horsepower.

I read the underlying article (https://elifesciences.org/articles/59177) and was unable to find any evidence of that. In fact the paper doesn't mention anything about SUmmit or details on the computations :(

There certainly wasn't any "heavy biochemical calculations"; this work is entirely comparative genomics, so just operating on DNA strings.

I see this fluff article https://www.ornl.gov/blog/genomics-code-exceeds-exaops-summi... and there may be more detail here: https://www.hpcuserforum.com/presentations/april2019/Joubert... which shows near-linear performance they ascribe to "Made possible by aggressive communication overlap and low-congestion Mellanox Infiniband fat tree network with adaptive routing"

So there may actually be an HPC/supercomputer story in there, but I'm having trouble figuring out what they did in this most recent work.

Re: Supercomputer analysis of Covid-19 leads to new theory

#54

Post by avmich »

traceroute66 wrote: post #8
klysm wrote: post #3

The anthropomorphization of computers (especially powerful ones) is pretty annoying. A _person used a supercomputer_ to analyze Covid-19, and I’m guessing the theory didn’t just ‘emerge’ from the computer.

"I'm sorry Dave. I'm afraid I can't do that."

Computers better be familiar with that story and with what happens next.

Re: Supercomputer analysis of Covid-19 leads to new theory

#55

Post by Orou »

R0b0t1 wrote: post #38
pacaro wrote: post #31

Earlier quoted context omitted.

For category three I feel that goal-seeking (or the appearance of such) is sufficient for the anthropomorphism to kick in. The braitenberg vehicles thought experiment is a good example of this. Quoting from wikipedia "For the simplest vehicles, the motion of the vehicle is directly controlled by some sensors (for example photo cells). Yet the resulting behaviour may appear complex or even intelligent." https://en.m.w…

But if you observe the behavior of a bacterium, operating under similar principles but seeking instead a salt or pH value, you would do well to describe it similarly. The bacterium is seeking a certain condition. It can not think, but it is a machine that acts with purpose and must be modeled accordingly.

I'm curious at what point an organism is considered to be capable of thought. From a mechanistic standpoint, it seems like the goal-seeking behavior of a simple organism could be modeled as a gradient ascent toward a local optima. But even complex organisms are still seeking certain conditions to maximize their ability to survive and reproduce. Is the existence of a brain enough for a creature to be considered capable of thought? How complex does an organism have to be before we no longer think of it as being a biological "machine"?

Or do we simply fall into the trap the GP described, where once something is complex enough that we don't understand what is going on from a purely mechanical perspective we consider it close enough to human to empathize with it?

Re: Supercomputer analysis of Covid-19 leads to new theory

#56

Post by tzs »

searine wrote: post #11
dekhn wrote: post #2

I can't really see why you would need a supercomputer to do the analysis they did (it shows SC centers are getting desperate for users; I wouldn't even have been allowed to run this code on a supercomputer when I was an academic, because it didn't need interconnect for strong scaling.

>I can't really see why you would need a supercomputer to do the analysis they did The article is fluff. 98% of all bioinformatics is done on "supercomputers" or 'high performance computing environments" saying the researchers used supercomputers to analyze the expression data is like saying someone used a shovel to dig a hole.

The article doesn't simply say they used a supercomputer. It says they used Oak Ridge's Summit supercomputer, the second fastest in the world. Unless 98% of all bioinformatics done on a top 2 supercomputer, your point fails.

Re: Supercomputer analysis of Covid-19 leads to new theory

#57

Post by jmvoodoo »

kovek wrote: post #37
shubhamjain wrote: post #27

Earlier quoted context omitted.

This Medium article was written on March 10 [1]. "Put simply, medics found that severely ill flu patients nursed outdoors recovered better than those treated indoors. A combination of fresh air and sunlight seems to have prevented deaths among patients; and infections among medical staff.[1] There is scientific support for this. Research shows that outdoor air is a natural disinfectant. Fresh air can kill the flu vir…

That air is a natural disinfectant is super interesting. I read that vitamin D and observed benefits for those who have vitamin D is a correlation. Meaning that taking vitamin D supplements might not be as helpful as getting sunlight (a natural way to get vitamin D)

What I found interesting about this article is that it isn't based on a correlation of outcomes and vitamin D like most other results are. It's actually looking at potential mechanisms and vitamin D is coming up as a candidate.

Re: Supercomputer analysis of Covid-19 leads to new theory

#58

Post by gh02t »

Enginerrrd wrote: post #42
raverbashing wrote: post #34

Earlier quoted context omitted.

Yes but can it kill viruses and bacteria in vivo?

If it produces better outcomes in vivo, does it matter whether or not the proposed mechanism is correct?

Ideally you'd like to understand the mechanism so that you can isolate and optimize the the effect, as well as predict possible interactions/side effects.

Re: Supercomputer analysis of Covid-19 leads to new theory

#59

Post by woeirua »

DoofusOfDeath wrote: post #36
woeirua wrote: post #29

Seems like it should be really straightforward to determine if this hypothesis is right by measuring bradykinin levels in Covid patients versus non-Covid patients. One thing that I think strongly suggests that this hypothesis is wrong is that there is no strong relation between ACE-inhibitors and Covid mortality. Indeed, most of the studies that I've seen suggest that ACE-inhibitors have a somewhat protective effect…

> One thing that I think strongly suggests that this hypothesis is wrong is that there is no strong relation between ACE-inhibitors and Covid mortality. Perhaps you can clear up something for me. We've all heard how obesity and hypertension are risk factors for covid morbidity. But I could never get a clarification regarding treated vs. untreated hypertension. AFAIK, many obese people take ACE inhibitors to treat hyp…

The answer to treated vs untreated hypertension right now is that we simply do not know. What we do know is that treated hypertensive patients don't appear to have significantly worse outcomes.

This article does a great job outlining the current state of the knowledge on the subject of Covid/hypertension as well as some clinical trials that should be posting results early next year [1].

I haven't seen any studies that try and tease apart all of the complex relationships amongst various comorbidities, but I think we have seen pretty conclusively that obesity is a very significant risk factor.

[1]https://www.acc.org/latest-in-cardiology/articles/2020/07/06...

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