20 replies to this topic

[JLL]

If one wanted to simulate what happens in the human body in different scenarios (for example when consuming something or exercising) on a computer model, how much of it could be done currently?

What I mean in practice is that you would feed the model with a banana and it would give you a report with all the parameters of the body that changed: a rise in blood glucose, an increase in potassium levels etc.

I'm sure if we were able to incorporate all the data we currently have about the human body we would be able to build some kind of a rough model, but how just how rough would it be? Do you think simulating each cell separately would be needed, or would it be sufficient to use more general algorithms (like X amount of glucose in blood --> Y amount of insulin) based on empirical data? We do have quite a bit of knowledge of different pathways, for example.

This is far-fetched, sure, but if we had this kind of a model we could do all sorts of interesting experiments on it (like looking for Sirtuin activators). If the model produced a desirable result, we could then test it on real humans.

Do you think pursuing something like this is even desirable, or is it better just to put resources into in vitro and in vivo experiments?

[JLL]

If you're in any way familiar with this stuff, feel free to say if the idea is a) impossible to implement or b) just plain silly. I just like to toy around with ideas like this.

[modelcadet]

If one wanted to simulate what happens in the human body in different scenarios (for example when consuming something or exercising) on a computer model, how much of it could be done currently?

What I mean in practice is that you would feed the model with a banana and it would give you a report with all the parameters of the body that changed: a rise in blood glucose, an increase in potassium levels etc.

I'm sure if we were able to incorporate all the data we currently have about the human body we would be able to build some kind of a rough model, but how just how rough would it be? Do you think simulating each cell separately would be needed, or would it be sufficient to use more general algorithms (like X amount of glucose in blood --> Y amount of insulin) based on empirical data? We do have quite a bit of knowledge of different pathways, for example.

This is far-fetched, sure, but if we had this kind of a model we could do all sorts of interesting experiments on it (like looking for Sirtuin activators). If the model produced a desirable result, we could then test it on real humans.

Do you think pursuing something like this is even desirable, or is it better just to put resources into in vitro and in vivo experiments?

A full simulation of the human body would be great for research, but I must point out that a full simulation requires a brain simulation, which in and of itself is much more useful for advancing science. I don't see heuristic simulations as particularly useful, though in theory it could be done (although again, with an accurate heuristic model for the whole body, we'd be able to create much better tools than body simulation).

That being said, medical testing is about to become incredibly exciting due to the loosening of stem cell research restrictions...

[niner]

Simulation of various aspects of humans has been going on for years. There's even a NASDAQ-listed company that does it. The simulations look at things like oral absorption and pharmacokinetics of compounds, as well as metabolism of such compounds, and other things. These are all things that are of interest to the pharmaceutical industry.

[JLL]

Simulation of various aspects of humans has been going on for years. There's even a NASDAQ-listed company that does it. The simulations look at things like oral absorption and pharmacokinetics of compounds, as well as metabolism of such compounds, and other things. These are all things that are of interest to the pharmaceutical industry.

Nice. GastroPLUS is just about exactly what I was talking about. I'm thinking that building a similar open source application is not impossible. You could make it extendable so that anyone who knows about how a specific thing works can add knowledge to the database. Additions could be peer-reviewed etc.

[Infinitytimes2]

Ive been thinking about this a lot lately, reaching the petaflop opens up new possibilities. Has anyone seen Tim Berners lee's presentation at TED about linked data? does anyone know if any of todays super computers are currently running linked together?, that sounds like massive computational power.
Also, I'm not sure if many of you are big on Craig Venter but his presentation at TED was pretty fascinating.


http://www.youtube.c...re=channel_page < Tim Berners-Lee: The next Web of open, linked data

< Craig Venter: On the verge of creating synthetic life

[Putz]

Folding@home uses millions of personal computer power today to simulate single proteins at a time in a few select reactions, "folding". If in a few decades if computers and software is powerful enough to simulate the entire human body at the molecular level, then technically you can create a computer simulated clone of someone just by entering their DNA into the computer program and you can watch them grow up, interact with such creations in virtual reality, and if nanotech manufacturing is advanced enough, "copy" its entire body into the real world. Merely extrapolating here.

[cyborgdreamer]

Folding@home uses millions of personal computer power today to simulate single proteins at a time in a few select reactions, "folding". If in a few decades if computers and software is powerful enough to simulate the entire human body at the molecular level, then technically you can create a computer simulated clone of someone just by entering their DNA into the computer program and you can watch them grow up, interact with such creations in virtual reality, and if nanotech manufacturing is advanced enough, "copy" its entire body into the real world. Merely extrapolating here.

There are huge ethical issues with that, seeing as a deep enough simulation of the brain might become conscious. On a more practical level, even if you had enough computing power to model the person, you would still have to model the environment in significant detail. You'd need to model the chemicals in the womb; the protiens, fats, carbs, vitamins, minerals and fiber the person eats; foreign microbes that affect the body; and the experiances necessary for brain developement (including social interaction which would require at least partially modelling many other people).

Edited by cyborgdreamer, 21 April 2009 - 10:36 PM.

[AgeVivo]

If in a few decades if computers and software is powerful enough to simulate the entire human body at the molecular level

you mean, in a few centenaries perhaps? just to store the information of someone (without any simulation) you'd typically need a memory that has the size of that person. And even with the most straightforward algorithm ever, the cpu (or equivalent) should be several/many times the size of the person.
I wonder *today* how to simulate the human body on a computer with a sufficient model (model=simplification) to fight aging. Personnally i have no clue at this moment.

Edited by AgeVivo, 22 April 2009 - 10:26 AM.

[maestro949]

I wonder *today* how to simulate the human body on a computer with a sufficient model (model=simplification) to fight aging. Personnally i have no clue at this moment.

It'd be nice but I'm fairly certain that full atomic simulations are not necessary to combat aging. Much of biology is redundant thus simulating 75 trillion cells of 200 or so types is pretty much a waste of CPU cycles. I spend a lot of time trying to answer the question of `what can we do with informatics in the next 20 years` and I think we can instead build dynamic simulations that are specific to gene regulatory processes that are quite illustrative of how cells lose their fidelity with age. Simulations at this level could open many therapeutic doors such as stem cell, (epi)genetic therapies and even significant improvements to the development of traditional pharmaceuticals. There are quite a few challenges with building these simulations but the data emerging from the early systems biology work being done on dynamic gene expression data is hinting that this may not be as intractable a problem as once thought.

[JLL]

Folding@home uses millions of personal computer power today to simulate single proteins at a time in a few select reactions, "folding". If in a few decades if computers and software is powerful enough to simulate the entire human body at the molecular level, then technically you can create a computer simulated clone of someone just by entering their DNA into the computer program and you can watch them grow up, interact with such creations in virtual reality, and if nanotech manufacturing is advanced enough, "copy" its entire body into the real world. Merely extrapolating here.

There are huge ethical issues with that, seeing as a deep enough simulation of the brain might become conscious.

What ethical issues are there besides the same ones that apply to humans? We already have the power to create humans from seemingly nothing. The number one moral rule for all humans is the non-aggression principle. If we apply that same principle to computer programs that express the capability for abstract reasoning and independent thought (which I think is a requirement for being classified as a human), I don't see a problem.

It's strange to me how people are always looking for problems instead of solutions. Throwing words like "ethical issues" is a convenient way to attempt to stop progress. Consider stem cells research, for example. Instead of actually thinking about what the ethical issues involved might be and how to solve them, the reserach pretty much stopped for years because somebody yelled "but what about the ethical issues!".

Btw, this was not meant to be directed at you, but as a general rant.

[cyborgdreamer]

Folding@home uses millions of personal computer power today to simulate single proteins at a time in a few select reactions, "folding". If in a few decades if computers and software is powerful enough to simulate the entire human body at the molecular level, then technically you can create a computer simulated clone of someone just by entering their DNA into the computer program and you can watch them grow up, interact with such creations in virtual reality, and if nanotech manufacturing is advanced enough, "copy" its entire body into the real world. Merely extrapolating here.

There are huge ethical issues with that, seeing as a deep enough simulation of the brain might become conscious.

What ethical issues are there besides the same ones that apply to humans? We already have the power to create humans from seemingly nothing. The number one moral rule for all humans is the non-aggression principle. If we apply that same principle to computer programs that express the capability for abstract reasoning and independent thought (which I think is a requirement for being classified as a human), I don't see a problem.

It's strange to me how people are always looking for problems instead of solutions. Throwing words like "ethical issues" is a convenient way to attempt to stop progress. Consider stem cells research, for example. Instead of actually thinking about what the ethical issues involved might be and how to solve them, the reserach pretty much stopped for years because somebody yelled "but what about the ethical issues!".

Btw, this was not meant to be directed at you, but as a general rant.

I guess I should've gone into more detail instead of just saying 'ethical issues'. What I meant was that it would be unethical to keep a person trapped in a computer against his or her will, especially if s/he were the only conscious mind in the simulation. And it would be even worse to decieve that person into thinking the simulation was reality (whatever reality is). I'm not saying there aren't solutions, though. We could engineer the person's brain so that it wouldn't care that it was a simulation. Or we could simplify the model of the brain so that the simulation wouldn't be conscious at all.

[niner]

We could engineer the person's brain so that it wouldn't care that it was a simulation. Or we could simplify the model of the brain so that the simulation wouldn't be conscious at all.

Or we could send in a simulated thug with a simulated 9mm to pop a cap in the simulation's head.

[kismet]

 We could engineer the person's brain so that it wouldn't care that it was a simulation.

Yeah, so much more ethical! I concur! Give 'em soma, or what other drugs you have, maybe a slight lobotomy if it makes them care less about the situation. 

There are no ethical implications which should stop us from proceeding now. If we somehow manage to succeed in creating conscious intelligence (very utopical in the near term) we will deal with the issue; obviously, if AI existed it would be granted the necessary rights. However, I don't think simulating consciousness is the same as keeping someone 'trapped' in a simulation. Perhaps it depends on the way we simulate.

[maestro949]

I don't think simulating consciousness is the same as keeping someone 'trapped' in a simulation.

Does it matter where consciousness resides? Silicon wafers versus biologically goo? One can be trapped in the latter via brain stem damage. If we develop synthetic consciousness we should give it senses such that it can interact with the universe.

[AgeVivo]

I wonder *today* how to simulate the human body on a computer with a sufficient model (model=simplification) to fight aging. Personnally i have no clue at this moment.

It'd be nice but I'm fairly certain that full atomic simulations are not necessary to combat aging.

Appearently I wasn't clear because that's exactly my first point ;-)
My 2nd point was how to use computers against aging, and you give an answer:

build dynamic simulations that are specific to gene regulatory processes that are quite illustrative of how cells lose their fidelity with age. Simulations at this level could open many therapeutic doors such as stem cell, (epi)genetic therapies and even significant improvements to the development of traditional pharmaceuticals. There are quite a few challenges with building these simulations but the data emerging from the early systems biology work being done on dynamic gene expression data is hinting that this may not be as intractable a problem as once thought.

Although we have pretty much free access to the required data via genbank and the like (http://www.ncbi.nlm.nih.gov/) I personnally doubt i could really get useful results against aging out of it. Is anyone here familiar with the subject?

Edited by AgeVivo, 24 April 2009 - 01:48 PM.

[cyborgdreamer]

 We could engineer the person's brain so that it wouldn't care that it was a simulation.

Yeah, so much more ethical! I concur! Give 'em soma, or what other drugs you have, maybe a slight lobotomy if it makes them care less about the situation. 

Engineering a simulated person so that they're 'born' happy is not the same a forcibly altering someone. For example, it would be horrible to damage someone's brain so that they'd have the mind of a dog, but that doesn't mean it's unethical to breed dogs.

[maestro949]

I wonder *today* how to simulate the human body on a computer with a sufficient model (model=simplification) to fight aging. Personnally i have no clue at this moment.

It'd be nice but I'm fairly certain that full atomic simulations are not necessary to combat aging.

Appearently I wasn't clear because that's exactly my first point ;-)

I was simply trying to provide a more clear and concise answer to the larger question as to whether we even need to do full organism simulations. I had the same questions several years ago but have answered most of them through due diligence.

My 2nd point was how to use computers against aging, and you give an answer:

build dynamic simulations that are specific to gene regulatory processes that are quite illustrative of how cells lose their fidelity with age. Simulations at this level could open many therapeutic doors such as stem cell, (epi)genetic therapies and even significant improvements to the development of traditional pharmaceuticals. There are quite a few challenges with building these simulations but the data emerging from the early systems biology work being done on dynamic gene expression data is hinting that this may not be as intractable a problem as once thought.

Although we have pretty much free access to the required data via genbank and the like (http://www.ncbi.nlm.nih.gov/) I personnally doubt i could really get useful results against aging out of it. Is anyone here familiar with the subject?

It's very unlikely that by observing the informatics data alone you are going to devise any significant aging therapies or full-scale aging simulations at this point in time. The -omics datasets and the tools built atop them are primarily used in conjunction with wetlab research that is already targeting a disease / pathology. Within the field of aging, this is usually a specific sub-disease that happens to have an aging component to it as up until recently, most biogerontology work has been quite general and only trying to identify broad mechanisms of aging in model organisms. Only recently have researchers turned their attention to more specific subcellular/molecular/pathway specific/genetic aspects of aging and that's due to the technology coming online (e.g. the genome project, microarrays, etc) . The systems biology approach I describe above is in reference to the (hopefully nearterm) potential to build more sophisticated models of aging that can elucidate therapeutics that have much more precision and effectiveness than current solutions.

[kismet]

I don't think simulating consciousness is the same as keeping someone 'trapped' in a simulation.

Does it matter where consciousness resides? Silicon wafers versus biologically goo? One can be trapped in the latter via brain stem damage. If we develop synthetic consciousness we should give it senses such that it can interact with the universe.

I'm not sure, I should have formulated it more like a question. But did you think it through the other way around? You are trapped in *this* life and can't enter the simulation (at least for now and for the sake of the argument), but apparently you're not worried at all. So depending on the type of simulation there's a million of interesting questions and it would depend on the type of simulation in the first place. Does the simulated brain get any sensory input or input representing a real world? (I was assuming yes) I'm not sure about the implications of a consciousness being trapped somewhere without any sensory input at all... if it was similar to a human consciousness it would not feel trapped anyway: an infant does not understand what's going on at first.

Neither of those facts should stop us from doing to necessary research, though.

[AgeVivo]

It's very unlikely that by observing the informatics data alone you are going to devise any significant aging therapies or full-scale aging simulations at this point in time.

I guess so, unless someone here could be strong enough to lead us do such a thing???

The -omics datasets and the tools built atop them are primarily used in conjunction with wetlab research that is already targeting a disease / pathology. Within the field of aging, this is usually a specific sub-disease that happens to have an aging component to it as up until recently, most biogerontology work has been quite general and only trying to identify broad mechanisms of aging in model organisms.

Like sequence comparison programs, etc. Like Folding @ Home doesn't directly fight aging, but some researchers in wetlabs can combine it to obtain specific findings in Alzheimer research. Very indirect...

Only recently have researchers turned their attention to more specific subcellular/molecular/pathway specific/genetic aspects of aging and that's due to the technology coming online (e.g. the genome project, microarrays, etc) . The systems biology approach I describe above is in reference to the (hopefully nearterm) potential to build more sophisticated models of aging that can elucidate therapeutics that have much more precision and effectiveness than current solutions.

TEME (an imminst related association) is working on a project, where they analyze gene expression from aging CR mice. This sort of stuff? IMO the available data isn't sufficient(ly centralized) at this stage to obtain great results, but it might get better. Quite more direct already...

Any idea of other computer programs/analysis quite directed against aging?

Edited by AgeVivo, 24 April 2009 - 05:42 PM.

[maestro949]

It's very unlikely that by observing the informatics data alone you are going to devise any significant aging therapies or full-scale aging simulations at this point in time.

I guess so, unless someone here could be strong enough to lead us do such a thing???

It's premature IMO. Enough gene expression data hasn't been extracted. That which has is too noisy. We're inching closer though. In regards to simulations though, there are still mindboggling challenges of integrating the various types of data.

The -omics datasets and the tools built atop them are primarily used in conjunction with wetlab research that is already targeting a disease / pathology. Within the field of aging, this is usually a specific sub-disease that happens to have an aging component to it as up until recently, most biogerontology work has been quite general and only trying to identify broad mechanisms of aging in model organisms.

Like sequence comparison programs, etc. Like Folding @ Home doesn't directly fight aging, but some researchers in wetlabs can combine it to obtain specific findings in Alzheimer research. Very indirect...

Precisely. Indirect but gaining value daily with more and higher quality data combined with the improving tools.

Only recently have researchers turned their attention to more specific subcellular/molecular/pathway specific/genetic aspects of aging and that's due to the technology coming online (e.g. the genome project, microarrays, etc) . The systems biology approach I describe above is in reference to the (hopefully nearterm) potential to build more sophisticated models of aging that can elucidate therapeutics that have much more precision and effectiveness than current solutions.

TEME (an imminst related association) is working on a project, where they analyze gene expression from aging CR mice. This sort of stuff? IMO the available data isn't sufficient(ly centralized) at this stage to obtain great results, but it might get better. Quite more direct already...

CR mimetics is getting lots of attention from a systems approach. Some groups have already chased the sirtuins down to their epigenetic roots. The AGEMAP database would be a good model for comparing CR'ed expression changes to.

Any idea of other computer programs/analysis quite directed against aging?

Meta analysis such as this will start to provide the first glimpses into the aging of regulatory, expression and epigenetic machinery. It's not clear whether any immediate gains could be gleaned from this type of work. I'm guessing that it's still going to take a couple of decades or so to translate this into human data sets and ultimatley pharma, stem cell and gene therapies.

One idea I have is to shadow the epigenetics research being done in cancer for the next decade. If the tentacles of aging's damage reaches down to these levels of transcription regulation and effective cancer treatments are found, then the histone deacetylase enzymes and (hypo)methylating agents used to treat cancer could also be tested as anti-aging therapies in model organisms. Many $Billions are being poured into cancer. Virtually nothing into the molecular roots of aging. Let's pirate their informatics booty