Software Emulates Organism's Entire Lifespan

An anonymous reader "Scientists have developed a software simulation, running on 128 computers, of an entire organism, a step toward carrying out full experiments without traditional instruments (abstract). 'For their computer simulation, the researchers had the advantage of extensive scientific literature on the bacterium. They were able to use data taken from more than 900 scientific papers to validate the accuracy of their software model. Still, they said that the model of the simplest biological system was pushing the limits of their computers. "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Dr. Covert wrote. "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that." In designing their model, the scientists chose an approach that parallels the design of modern software systems, known as object-oriented programming. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth. Similarly, the simulated bacterium is a series of modules that mimic the different functions of the cell.'"

Comments

Different viewpoints

[SmlFreshwaterBuffalo]

We often think of the DNA as the storage medium...

You might, but I'm betting physicists think differently. It all depends on the information to which you're referring.

Re:Different viewpoints

[interkin3tic]

I think "we" meant "biologists" there, and "THE storage medium" as "that a cell uses."

And that would be true, most biologists tend to assume that the nucleus is where the vast majority of the data of the cell is. We're aware that DNA is not the end all be all of the cell, but we often don't think about the other inputs into a cell's behavior as being as important. For instance, we often study isolated human cells isolated in a petri dish, and what changes when we turn off or on different genes. There's a lot to be learned there that isn't wrong, but we do know that cells typically behave very differently in their native context.

I'm blanking on the details, but there were reports that neurons migrating required some gene, based on how they moved in a culture system. You delete that gene, they don't migrate right in the dish. However, when people looked at what happened when you deleted that gene from a whole organism, their brain cell migration was fine. Perhaps the body provides information that makes that bit of DNA redundant. Realizing that DNA isn't the only information a cell responds to moves that initial discovery from pretty important to fairly trivial. Of course, factoring in all the different things acting on a cell is probably well beyond any human comprehension without the aid of a computer.

Re:Different viewpoints

[nashv]

Biologists do not see DNA as merely a storage medium. This might be an issue of semantics, but when biologists say "DNA" , they mean the molecule. Just plain DNA.

For it's 'non-storage-only' functions, DNA needs a bunch of proteins and RNA molecules. This entire functional and dynamic assemblage is referred to as 'chromatin'. This is why a bunch of other terms exist - exon, intron, promoter, enhancer, gene, telomere, tandem repeats, restriction site, nucleosome etc. Clearly, these are made up of DNA, but encode functions that are referred to by different names.

Obligatory...

[Anonymous Coward]

Well I, for one, welcome our uploaded lobster simulations, and the following Vile Offspring overlords :)

Sex on the brain

[DigiShaman]

For a moment, I read that as Software Emulates Orgasim's Entire Lifespan.

Re:Sex on the brain

[daremonai]

There is no "I" in orgasim. Oh, wait, I guess there is!

Re:Sex on the brain

[biometrizilla]

If that were the case the emulation would have completed much more quickly for the male and would likely never finish running for the female.

OO vs real life

[robi5]

I wonder how naturally an object oriented design worked out, given that molecular pathways are extremely complex and there are causal links between almost any pairs of phenomena. While OO is OK for CAD and man-made things, nature was much less restrained about high cohesion, low coupling, encapsulation and other heuristics. So the details would be interesting about inheritance, state representation, graph complexity, time-varying behavior etc.

Re:OO vs real life

[macklin01]

Simplified answer:

These models tend to be object-oriented in the sense that a genetics "module" interacts with a protein signaling module, etc. In each module, you'd have the member data (say, a list of all proteins) and member functions (say, a model of the reaction network that discretizes the massive system of ODEs).

The objects then interact. You have well-defined interfaces between these modules to codify currently known (or hypothesized!) biology. For example, members of the proteins module activate certain genes in the genetics module to (eventually) drive synthesis of more proteins.

You write the rules based upon our current state-of-the-art in understanding cell biology, simulate, and see what happens. To the extent that it quantitatively matches experiments, we can assess the underlying hypotheses, refine them, or toss them out.

In this work, it looks like they pulled information from 900 papers on this species of bacterium to simulate 525 genes, God knows how many proteins (genes can encode multiple proteins), and 28 processes.

Notably, there is no spatial component (e.g., transport of proteins, RNAs, cell volume changes, cell mechanics, etc.), but it's an incredible set of work. And to be able to predict phenotype solely based upon the emergent behavior of this network is pretty incredible.

Re:OO vs real life

[garaged]

And neglecting atomic level interactions invalidates the method for most phamaceutic studies.

It causes an STD -- lives in the genital tract.

[bdwoolman]

Mycoplasma genitalium. No jokes, please. This is Science.

Really so complex?

[chrism238]

What? You mean the dividing cell doesn't just call fork() ?

Re:Really so complex?

[FailedTheTuringTest]

For most of biology, we haven't yet been able to create numerical models. There are a huge number of variables, interactions, and feedback loops, and frankly we don't even fully understand how many biological processes work, so creating mathematical models is very difficult. But this is sure to be a productive area of research so any young computer geeks with an appetite for the squishy science should take note!

organism emulation

[danielpauldavis]

"I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds." To posit that information came from ignorance (vacuum, nothing) is astonishing. To posit that it arose with a mere 13,700,000,000 years boggles the mind at the imagination of some people.

Re:OOP

[chebucto]

IMHO they should have used C; after all, it is the language of God and Root.

Re:OOP

[ultranova]

IMHO they should have used C; after all, it is the language of God and Root.

But Melkor sought to improve it and add themes of his own making, and thus the cacophonous abomination known as C++ was born.

I knew it!

Re:OOP

[Celarent Darii]

No, no, no. Everyone knows God wrote the universe in LISP. He only had six days after all !

For those too young to remember the song by Julia Eklar

http://www.songworm.com/lyrics/songworm-parody/EternalFlame.html

I was taught assembler in my second year of school.
It's kinda like construction work -- with a toothpick for a tool.
So when I made my senior year, I threw my code away,
And learned the way to program that I still prefer today.

Now, some folks on the Internet put their faith in C++.
They swear that it's so powerful, it's what God used for us.
And maybe it lets mortals dredge their objects from the C.
But I think that explains why only God can make a tree.

For God wrote in Lisp code
When he filled the leaves with green.
The fractal flowers and recursive roots:
The most lovely hack I've seen.
And when I ponder snowflakes, never finding two the same,
I know God likes a language with its own four-letter name.

Now, I've used a SUN under Unix, so I've seen what C can hold.
I've surfed for Perls, found what Fortran's for,
Got that Java stuff down cold.
Though the chance that I'd write COBOL code
is a SNOBOL's chance in Hell.
And I basically hate hieroglyphs, so I won't use APL.

Now, God must know all these languages, and a few I haven't named.
But the Lord made sure, when each sparrow falls,
that its flesh will be reclaimed.
And the Lord could not count grains of sand with a 32-bit word.
Who knows where we would go to if Lisp weren't what he preferred?

And God wrote in Lisp code
Every creature great and small.
Don't search the disk drive for man.c,
When the listing's on the wall.
And when I watch the lightning
Burn unbelievers to a crisp,
I know God had six days to work,
So he wrote it all in Lisp.

Yes, God had a deadline.
So he wrote it all in Lisp.

Re:still a long way to go

[TheLink]

From what I see at least some amoebas aren't that stupid:
https://www.youtube.com/watch?v=kGJvZotBHzc
https://www.youtube.com/watch?v=02_94cGye1E
(the above amoebas build shells to protect themselves!)

Even some of the stuff amoeba eat don't seem that stupid either:
https://www.youtube.com/watch?v=YsLoFHKJjiM
Look at them moving about - its not that random. Not too different from some stupid fish.

White blood cells too:
https://www.youtube.com/watch?v=I_xh-bkiv_c
https://www.youtube.com/watch?v=I9zSe0qmXGw#t=0m16s

To me it seems as if many multicellular organisms are like vehicles/"mecha" which single cell organisms working together build and use in order to sense and explore the world in a different scale.