First Digital Simulation of an Entire Life Form

An anonymous reader writes "LiveScience is reporting on what appears to be the first digital simulation of an entire life form. Researchers created more than a million digital atoms to reverse engineer the satellite tobacco mosaic virus, a relatively simple organism. But is it really a life form? From the article: 'Viruses are tiny bundles of protein and genetic material that straddle the line between life and non-life. Many scientists prefer to call them "particles" because even though they contain RNA or DNA like other lifeforms, they can only replicate inside other living cells.'"

Life is not a binary distinction

[wsherman]

But is it really a life form?

Language is digital (as opposed to analog) in the sense that you either use a word in a sentence or you don't. You can either use the word "life" in a sentence or not but you can't use a fraction of the word ("li" or "fe" don't mean fractional life - or anything at all for that matter). This creates (willful?) confusion in the minds of people who are very focused on a literal interprtation of language based laws and moral codes that "life" is a binary distinction.

The reality, however, is that the word "life" refers to a whole variety of concepts. There are all different ways of being alive and there are all different levels of being alive. Certainly we can find examples of things that are very "alive" just as we can find examples of colors that are very "blue" - but that doesn't mean every color is either pure blue not blue at all and it doesn't mean that something is either completely alive or not alive at all.

Going way off topic, the whole "life begins at conception" is what we in the sciences refer to as "not even wrong". After all, it's kind of hard for dead people to have children. If you really want to talk about when life began it would be at the big bang when matter developed the properties that cause it to form into complex self-replicating patterns over very long time scales.

Its awesome

[mnmn]

Simulating life is awesome. Now the next step is to simulate something like an Amoeba in water... let its DNA drive it to 'eat' a food particle, and see how accurate the digestion (and binary replication) is with the input being only the DNA and initial conditions. I wonder what kind of computers are required to simulate all that, in how much time? I'd more gladly donate cpu cycles to this than to SETI.

Next I wonder if the computer can be used to run regression tests to create the ideal bacteria or virii for a given situation. Virii can be built to repair human DNA in various ways... a particularly disadvantageous gene can be switched off throughout the body once infected with the virus.

Of course this only allows Cybernet to have more destroying power once it 'wakes up'.

You are not a life form, then?

[Roadkills-R-Us]

But is it really a life form? From the article: 'Viruses are tiny bundles of protein and genetic material that straddle the line between life and non-life. Many scientists prefer to call them "particles" because even though they contain RNA or DNA like other lifeforms, they can only replicate inside other living cells.'"

The same could be same for most species of animals; they ``contain RNA or DNA like other lifeforms, they can only replicate inside other living organisms''.

Re:Simulating intelligence?

[jackelfish]

The simple answer to your question is no. In the field of Molecular Modeling, we have a pretty good idea of how to simulate a system at the atomistic level. As the article states, we are pushing the limits of computational resources and time to complete the simulations at the level of about 1 million atoms (this is state of the art). The simulation discussed in this article is of a Satellite Virus (not even a true virus by strict definition, as it requires a cell to be previously infected by a virus) and as such is the smallest "living" organism on the planet (it has only 2 genes; 1 to synthesize its coat protein and another which we have no idea of its function). Now think of a bacteria like E.coli which has something on the order of 4500 genes, several of which are expresed in multiple copies. Don't forget all of the metabolites and water also. This takes the simulation from 1 million atoms up to at least say 5-10 orders of magnitude in size. So a simulation that took 12 days on a 256 CPU SGI cluster would now take 1.2 million to 1.2e11 days on the same cluster (you can also do the math to figure out how scaling the cluster would effect the time). So, long story short, we have no hope of doing an all atomistic model of even Ecoli any time soon. But, lets not forget that these simulations were only atomistic in the Newtonian sense of the word (we are only simulating atoms as point masses using Newtonian Physics, commonly referred to as Molecular Mechanics). If we want to simulate chemical reactions (an essential component of life), we require Quantum solutions for these simulations and we are looking at a limit of somewhere on the order of 400 to 4000 atoms for these types of simulations. So to really simulate E coli, lets add another 10 orders of magnitude to our estimates. The next order of business is to simulate a eukaryotic cell which may have 10,000 genes in it. Then lets go to multi-celled organisms...and so on. The long and the short of it is that there is no realistic hope, any time soon, of doing simulations on this order, until there is a significant leap made in either the way the simulations are done, or the power of the computers on which we do them. There may be ways of abstracting things by making assumptions that will reduce the accuracy of the models, but that is another story.

"life" is a lousy line to draw

[smellsofbikes]

I think we can agree that bacteria are alive. But there are types of bacteria, the ones that cause leprosy and chlamydia, frinstance, that cannot reproduce outside of a living cell. (They, unlike most bacteria, invade and live inside cells.) It's fairly difficult to draw a hard line between them and some viruses that have lipid bilayers full of receptors on their outsides. Even prions self-amplify, so where do you draw the lines on what's alive?

Re:Life vs. Non-life

[pomo monster]

Human beings do nothing outside a very specific environment tailored to their needs, where temperature, pressure, oxygen content of air, gravity, radiation, &c., all lie within specific bounds. How is this different from a virus needing an environment that includes cellular structures in order to replicate?

Me, I subscribe to structuralism.