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Software Emulates Organism's Entire Lifespan

Soulskill posted more than 2 years ago | from the sit-on-couch-and-eat-potato-chips,-increment dept.

Software 86

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.'"

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Different viewpoints (3, Insightful)

SmlFreshwaterBuffalo (608664) | more than 2 years ago | (#40719135)

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 (-1)

Anonymous Coward | more than 2 years ago | (#40719211)

This video explains it really well. http://www.youtube.com/watch?v=2po8QX8F5T0

Re:Different viewpoints (2)

interkin3tic (1469267) | more than 2 years ago | (#40719679)

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 (2)

nashv (1479253) | more than 2 years ago | (#40723283)

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.

OOP (1, Funny)

Anonymous Coward | more than 2 years ago | (#40719139)

I always figured OOP had some usefulness when used properly :)

But it's not really OOP ... (1)

dltaylor (7510) | more than 2 years ago | (#40719767)

It's a distributed processing system with interprocess (regardless of the node on which the process resides) message passing.

While some, or even all, of he process modules MAY have been written in a object-oriented language AND style, this sort of processing predates all of the OOP languages and nearly all of the literature.

If I wanted to get there quickly and scalably, I'd use the distributed systems created for weather or nuclear simulations as a starting point, since intracellular activity has no small amount chaos (for example, due to Brownian Motion, the collisions and binding of various transmitters is not directed to a specific site on a specific RNA strand, but may attach to any compatible site along its trajectory).

Re:But it's not really OOP ... (1)

Anonymous Coward | more than 2 years ago | (#40721975)

There's no way this simulation was at an atomic or even molecular scale.

Re:But it's not really OOP ... (0)

Anonymous Coward | more than 2 years ago | (#40722623)

That's what she said.

Re:OOP (1)

LSDelirious (1569065) | more than 2 years ago | (#40721637)

Organism Oriented Programming?

Re:OOP (2)

chebucto (992517) | more than 2 years ago | (#40721887)

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

Re:OOP (2)

ultranova (717540) | more than 2 years ago | (#40722359)

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 (5, Funny)

Celarent Darii (1561999) | more than 2 years ago | (#40722411)

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.

This story sponsored by the Zik-Zak Corporation (1)

emurphy42 (631808) | more than 2 years ago | (#40719149)

So how much extra data do we need for a parrot?

Re:This story sponsored by the Zik-Zak Corporation (0)

Anonymous Coward | more than 2 years ago | (#40719261)

3 bits more:

  1. Is it Norwegian blue?
  2. Is it pining for the fjords?
  3. Does Polly want a cracker?

Re:This story sponsored by the Zik-Zak Corporation (1)

EdIII (1114411) | more than 2 years ago | (#40721585)

Does Polly want a cracker?

Don't be ridiculous. That's a constant, not a variable.

Re:This story sponsored by the Zik-Zak Corporation (1)

keeboo (724305) | more than 2 years ago | (#40720269)

I guess that depends on how long are the silly songs you wish to be part of the parrot's repertory.

Obligatory... (2)

Anonymous Coward | more than 2 years ago | (#40719157)

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

Re:Obligatory... (1)

cowtamer (311087) | more than 2 years ago | (#40719313)

Mod parent up! My first reaction was "F@#*( -- Charles Stross was right!" For the uninitiated, here's a summary [wikipedia.org] and here's the full text of the mind bending novel Accelerando [jus.uio.no] .

Re:Obligatory... (1)

HiThere (15173) | more than 2 years ago | (#40724605)

The interesting part is that at the time that he wrote it, someone at the University of California (in southern California, but I don't remember which campus) was doing a simulation of a lobster neural net. Don't know how detailed. And I don't know if he knew about it, but naturally one suspects that he did.

Great submission (0)

Anonymous Coward | more than 2 years ago | (#40719159)

Thank God this is slashdot, where submissions contain poor explanations about what OOP is, yet leave out interesting informations such as which bacterium.

Re:Great submission (1)

Shikaku (1129753) | more than 2 years ago | (#40719251)

News for Nerds

http://google.com/ [google.com] Here is where you can start learning.

It causes an STD -- lives in the genital tract. (4, Funny)

bdwoolman (561635) | more than 2 years ago | (#40719365)

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

Re:It causes an STD -- lives in the genital tract. (1)

dalias (1978986) | more than 2 years ago | (#40719785)

So Slashdot users need not worry about it.

Sex on the brain (3, Funny)

DigiShaman (671371) | more than 2 years ago | (#40719227)

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

Re:Sex on the brain (0)

Anonymous Coward | more than 2 years ago | (#40719309)

What's an orgasim?

Re:Sex on the brain (1)

jelizondo (183861) | more than 2 years ago | (#40719439)

Obvious, an ORGAnic SIMulation, you anonymous moron!

What? A typo?

Sorry about that...

Re:Sex on the brain (3, Funny)

daremonai (859175) | more than 2 years ago | (#40720183)

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

Re:Sex on the brain (2)

biometrizilla (1999728) | more than 2 years ago | (#40722847)

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 (4, Interesting)

robi5 (1261542) | more than 2 years ago | (#40719299)

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 (0)

Anonymous Coward | more than 2 years ago | (#40719349)

Exactly. To simulate this accurately, an artificial neural network would have to essentially link many of the systems.

Re:OO vs real life (1)

phantomfive (622387) | more than 2 years ago | (#40719487)

My guess is they didn't completely emulate an organism, they simulated it roughly, but simulated it with enough detail to make it useful for testing drugs , theories, etc.

I don't understand biology well enough to verify this in this case, but I do know it has been true of recent high-profile brain simulations.

Re:OO vs real life (1)

HiThere (15173) | more than 2 years ago | (#40724665)

I certain you are correct ... for a given value of roughly. They certainly didn't specify the position of each atom. And I really doubt that the simulated the positions of water molecules, though they possibly simulated hydration levels by subdivision of the cell.

The thing is, you need to decide which details are significant, and simulate those. If you pick the right selection, then specifying more carefully doesn't buy you much. E.g., you might gain by having a thermostat in each room, and possibly by having both one at floor level and one at ceiling level. But as you increase the density of measurement, each additional measure is less significant, and the controls to use the new data become more expensive.

It *MIGHT* be interesting to know whether the model even specified spatial dimensions. And into how many "simulation cells" the cell was subdivided. But I would make a bet that all such sub-cells didn't hold the same volume.

Re:OO vs real life (2)

garaged (579941) | more than 2 years ago | (#40727573)

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

Re:OO vs real life (5, Informative)

macklin01 (760841) | more than 2 years ago | (#40719609)

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 (1)

robi5 (1261542) | more than 2 years ago | (#40721957)

Thank you for the answer! Not having access to the body of the article, it is informative.
I bumped into this cool video: http://www.youtube.com/watch?v=au4sl9CjKFU [youtube.com]

How useful OO is interesting, because it is possibly one of the first uses of OO as applied to modeling wetware behavior, and there must be some lessons learned.

Calling it OO may be something to do with a superficial aspect of the realization, but at its core, it looks like a giant filter [wikipedia.org] where the external signals to be processed are the time series of stimuli to the cell (chemical gradients near the cell etc.) and the results are probability distributions of the actions of the cell (both internal and external). The giant filter is itself composed of a large number of more elementary filters, or in other words, mathematical functions (probably stochastic differential equations) that take time series data and output time series data. So it's fundamentally a network of SDEs. Modeling it as such seems to be the way and I don't know what value OO adds, other than grouping SDEs, possibly in a hierarchical manner. Is there a reliance on polymorphism, inheritance, multiple inheritance, single method dispatch, multiple method dispatch [wikipedia.org] , and objects potentially changing their class in run-time? Was there a modeling challenge due to a large number of interactions between "objects" relative to an ordinary OO design, because of the wide range of interactions and cross-talk that characterizes cellular biology? How were these solved, and are there lessons learned as far as OO modeling is concerned? Are there limitations caused by using OO?

Re:OO vs real life (0)

Anonymous Coward | more than 2 years ago | (#40722797)

Can you explain what the the input and output of the program are? Is the input the DNA, and the output the set of fabricated proteins over time? It is still not clear to me. What do you mean by "simulate genes"? Thanks.

Re:OO vs real life (1)

interkin3tic (1469267) | more than 2 years ago | (#40719693)

I wonder how naturally an object oriented design worked out

I don't know the details, but if they really did replicate the results from a diverse range of 900 or so studies, then that to me says their simulation is pretty good.

Re:OO vs real life (0)

rmstar (114746) | more than 2 years ago | (#40722213)

I don't know the details either. But if they as much as claim that they could replicate the results of 900 or so studies, then I would start from the assumption that they are full of it.

Perhaps I should read the paper. But as someone who knows how how the information in "studies" gets there (you choose the nicest picture), and how much it is worth (the result will be mostly OK, but the data will have, ah, simmered a little bit in hot water), I can tell you that replicating the results of 900 or so studies is like having a simulation of middle earth. Impressive, sure, but fantasy nonetheless.

At least, this is the first thought I have after reading the headline and the blurb.

Re:OO vs real life (1)

Eponymous Hero (2090636) | more than 2 years ago | (#40719835)

"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.

life's too short for java. http://farm4.staticflickr.com/3245/2652438835_4f0f3b366b.jpg [staticflickr.com]

Re:OO vs real life (0)

Anonymous Coward | more than 2 years ago | (#40720209)

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.

There's an inheritence joke or fifty in there somewhere.

Re:OO vs real life (1)

tbird81 (946205) | more than 2 years ago | (#40721069)

I understand because it was OO, it was difficult (but not impossible) to write in C.

I misread the title (1)

Andrio (2580551) | more than 2 years ago | (#40719315)

Software Emulates Orgasms in Japan

Re:I misread the title (1)

Farmer Tim (530755) | more than 2 years ago | (#40719811)

Software Emulates Orgasms in Japan

We all know how much the Japanese love their gadgets, I doubt anyone considers a reciprocating function news (or surprising, anyway).

Re:I misread the title (1)

shutdown -p now (807394) | more than 2 years ago | (#40722065)

In Japan of all places, I'm pretty certain that software doesn't emulate orgasms, but rather actually experiences them.

Data Requirements (0)

Anonymous Coward | more than 2 years ago | (#40719329)

I think the important thing to remember is that DNA is destroyed and replaced constantly whereas the experimental model is likely being documented at every possible point. There is no realistic comparison to the memory usage in a computer-generated model vs. biology. I can honestly say nobody remembers what that skin cell on my pinkie toe was doing yesterday. Somewhere in there the neighboring cells recognized it died and the dna got copied into a new cell.

Stupid question (1)

Anonymous Coward | more than 2 years ago | (#40719343)

How are they calculating protien conformations? I can't believe this is being calculated in realtime on only 128 processors.

Re:Stupid question (0)

Anonymous Coward | more than 2 years ago | (#40719381)

Just read the summary, but it actually says it's not real time unless it really takes a single cell 10 hours to divide.

Re:Stupid question (1)

WaffleMonster (969671) | more than 2 years ago | (#40719527)

Just read the summary, but it actually says it's not real time unless it really takes a single cell 10 hours to divide

NYT article says so...

"Currently it takes about 9 to 10 hours of computer time to simulate a single division of the smallest cell â" about the same time the cell takes to divide in its natural environment."

Re:Stupid question (1)

fisted (2295862) | more than 2 years ago | (#40719643)

yeah... one.

Re:Stupid question (0)

Anonymous Coward | more than 2 years ago | (#40720185)

Guess that's why I should read the article and not just the summary. Biologies not my subject, but it's surprising that cell division really is 10 hours.

Re:Stupid question (0)

Anonymous Coward | more than 2 years ago | (#40719769)

They're not doing protein folding calculations. Even now, that's still a prohibitively slow process. What they're looking at is the synthesis rates, interaction constants and average lifetimes of different proteins and modelling that.

Welcome to the Matrix (0)

Anonymous Coward | more than 2 years ago | (#40719357)

And so it begins.

I thought they killed these off... (0)

Anonymous Coward | more than 2 years ago | (#40719375)

Giga Pets were awful things. Can you imagine the facebook tie in to growing and nurturing your new organism. Organismville.

actually not an emulation so much as a model (1)

brillow (917507) | more than 2 years ago | (#40719393)

It's just a model of gene-expression and metabolism. Not exactly what I would call emulation. They haven't generated any hypotheses with it which have been found to be true, so of course, there is no reason to think it has anything to do with anything.

Some colleagues of mine did just this thing on a smaller scale in a different system last year, it didn't go too well and generated absurd predictions which were so assumption heavy as to be interesting only as a theoretical exercise.

It's not like they can tell you what will happen if you treated the bacteria with a drug by running a simulation.

Really so complex? (3, Funny)

chrism238 (657741) | more than 2 years ago | (#40719455)

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

Re:Really so complex? (1)

dargaud (518470) | more than 2 years ago | (#40721941)

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

That's only the top API...

More seriously I wonder why simulations are not used more commonly in biology/medicine. One example is endocrinology. If you go to an endocrinologist for hormonal balance (for instance because you have a missing thyroid), over time (s)he adjusts the dosage of your medicine 'out of thin air' (and a lot of experience, Okay), but there are so many retro-actions that I'm sure they'd do it much faster if they just punched in the numbers (your past and current analyses and your current hormonal intakes) into a numerical model. It would also be easier to explain it to the patient.

Re:Really so complex? (2)

FailedTheTuringTest (937776) | more than 2 years ago | (#40723059)

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!

You communicate by passing data? (0)

Anonymous Coward | more than 2 years ago | (#40719459)

Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth.

You communicate by passing data? Really? I thought it communicates using the magic tooth fairy.

We Know Everything? (0)

Anonymous Coward | more than 2 years ago | (#40719475)

I thought we didn't know exactly how a cell divides. Something about thousands of little strands inside a cell that help guide things to where they need to be. How do those strands get there and how do they know where they belong? I'm really fuzzy on it. Does anyone know what I'm talking about?

Wrong paradigm (1)

wbr1 (2538558) | more than 2 years ago | (#40719497)

"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.

Wrong paradigm.. I can create a 100k program that generates that much data. DNA is storage and instructions, but it creates more than it holds from that small data set.

At What Level? (1)

Kozar_The_Malignant (738483) | more than 2 years ago | (#40719599)

At what level are they simulating the organism? Is it at a gross molecular level, or are they simulating each individual electron transport path through the Krebs Cycle, or somewhere in between?

OOP (0)

ericloewe (2129490) | more than 2 years ago | (#40719611)

Is this some ploy by the united front of Object-Oriented Programmers to convince the world that multiple inheritance isn't as bad as everyone thinks it is? I'm sure the global union of Object-Oriented Programmers is already planning a seminar on how Interfaces are appropriate subsitutes for multiple inheritance.

*THIS* is the future (0)

Anonymous Coward | more than 2 years ago | (#40719637)

Not 3D printing, not space colonies. LIFE and how it works!

Re:*THIS* is the future (0)

Anonymous Coward | more than 2 years ago | (#40719909)

"Not 3D printing, not space colonies. LIFE and how it works!"

You obviously haven't tried to get a job in the life sciences lately.

Wouldn't building a virus lifespan been easier? (0)

Anonymous Coward | more than 2 years ago | (#40719661)

It would have been a lot easier to created a virus lifespan analogue with OO technique, especially if their dev platform was windows.
But I guess these guys are most likely stuck on doing things the old fashioned way on an xterm ;->

Log files... (0)

Anonymous Coward | more than 2 years ago | (#40719669)

> "generates half a gigabyte of data"

> "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds."

Someone should tell them to set the log level to FATAL.

Was already done.... (1, Insightful)

ArcadeNut (85398) | more than 2 years ago | (#40719805)

Long time ago :)

http://www.bitstorm.org/gameoflife/ [bitstorm.org]

Ok, so maybe it's not as sophisticated as this version...

It happened at Wildfire (0)

Anonymous Coward | more than 2 years ago | (#40720025)

601.

still a long way to go (1)

keeboo (724305) | more than 2 years ago | (#40720323)

Don't get me wrong (I think that's really cool and stuff)...

But I wonder what will take to simulate a few amoebas in a petri dish, what is not exactly the apex of biological complexity.
Obviously multicellular organisms are out of question for some time still.

Re:still a long way to go (2)

TheLink (130905) | more than 2 years ago | (#40722647)

From what I see at least some amoebas aren't that stupid:
https://www.youtube.com/watch?v=kGJvZotBHzc [youtube.com]
https://www.youtube.com/watch?v=02_94cGye1E [youtube.com]
(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 [youtube.com]
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 [youtube.com]
https://www.youtube.com/watch?v=I9zSe0qmXGw#t=0m16s [youtube.com]

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.

Re:still a long way to go (1)

TheLink (130905) | more than 2 years ago | (#40722685)

If you watch the second video ( https://www.youtube.com/watch?v=02_94cGye1E [youtube.com] ) at 4x or higher speed it does resemble a snail moving about and eating stuff.

See also:
http://throughthesandglass.typepad.com/through_the_sandglass/2010/06/life-and-art-sand-and-glass-the-wonders-of-difflugia.html [typepad.com]

When it grows to a certain size, the cell then reproduces by dividing its body equally into two. One of these inherits the ancestral home; the other is left the bundle of building material. These stones, we know not how, are then moved to the body surface and arranged to create the distinctive architecture of this species. Just enough particles of the right sizes, big and small, have been picked up to accomplish this.

(I understand the above to mean that the amoeba collects enough suitable particles to make a new second home before splitting - in my opinion this requires a fair bit of intelligence).

And: http://www.brianjford.com/a-ISR_Ford.pdf [brianjford.com]

Object-oriented programming (1)

Art3x (973401) | more than 2 years ago | (#40720355)

From the summary:

In designing their model, the scientists chose an approach that parallels the design of modern software systems, known as object-oriented programming.

No wonder the program is enormous!

I thought it said "orgasm's lifespan" (1)

abarrow (117740) | more than 2 years ago | (#40720411)

and I thought "Damn, that must be a pretty short program.

Ummm... (0)

Anonymous Coward | more than 2 years ago | (#40720605)

while(1)
{ fork(); }

Done.

organism emulation (2)

danielpauldavis (1142767) | more than 2 years ago | (#40720679)

"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.

Problem is, there's no data integrity (1)

sam_handelman (519767) | more than 2 years ago | (#40721285)

This is cool, but as I read it here (and someone correct me if I'm wrong), it's no substitute for doing a real experiment. I'm going to launch into a long explanatory diatribe - models like this one can be VERY useful for hypothesis generation, or to try and understand seemingly disconnected results that (very often) arise in a biological experiment. They are especially useful when you have some hypothesis/theory of how a complex system is governed and you need to generate some prediction which you can experimentally test based on your theory.

  But not a substitute for the real experiment, no way no how. Why? Because living things aren't designed, and they don't respect your modularity, abstract data typing, etc. etc.

  For example, suppose your bacterium starts making some huge amount of a membrane protein (a common thing you do in the lab, for reasons outside the scope of this example). What's going to happen?

  Well, that protein is going to try and fold up in the membrane, but as you make more and more of it, the protein is going to fail to get there. Other proteins destined for the membrane are going to experience the same problem. Are you going to update every single module that contains something membrane bound, to reflect this? As they accumulate in the membrane, the membrane curvature is going to change, and this in turn is going to change the relative concentrations of various lipids on each leaf of the membrane, which alters the chemistry of everything that interacts with the membrane in any way (a whole bunch more modules.)

  Even if you have those effects covered, they're going to have indirect (and non-linear) effects on the concentration of various ions in the cytosol (all of which, just for starters, interact with the inner membrane with different affinities), the excess protein is going to start accumulating in inclusion bodies which are going to start taking up physical space inside the cell. These two changes alter the likelihood of interaction and the energy of interaction of every single other thing going on in the cell (!). So good luck with that.

  That's just one example. The same thing would happen if you sheared the DNA, or heat shocked the cell, or put the cell in an environment of rapidly changing nutrient concentrations. To put all that in CS terms - the actual cell isn't object oriented, there's all sorts of cross-talk between the different components (because they're physical objects in a little tiny soap bubble, they're bumping into each other) and no abstraction layer or anything of that kind.

  To be quite honest, I am of the opinion that a living cell is an irreducible system, and the only way you'd get a real substitute for experiments on actual cells would be JUST MAYBE if you ran a molecular dynamics simulation on all 10^14 or so atoms; and if you did so with a much better physics engine than we have now.

Re:Problem is, there's no data integrity (1)

Rich0 (548339) | more than 2 years ago | (#40722113)

I don't think anybody is suggesting that this is a substitute for in-vivo studies.

However, I suspect we could learn quite a bit through simulations and modelling just the same, as you basically start out.

I think some challenges are going to be spacial partitioning and kinetics. If you just model your cell as a uniform box that makes the math a lot easier, but it completely ignores the fact that cells actively manage their micro-environment (especially as you scale up to eukaryotes). The concentration of some protein isn't going to be the same in two different regions of the cell, and even for small molecules when some membrane protein produces something it won't instantly be binding to some DNA regulator.

For simple cells maybe some of these effects are easier to ignore (no ER, nuclear membrane, etc). Even so, the fact that bacteria can react to chemical gradients clearly demonstrates that there are all kinds of spacial kinetics/etc going on.

I think the best these kinds of simulations will be able to do is modeling the cell in conditions close to the natural ones. Expecting something like this to model what happens when some virus comes in and takes over 90% of the ribosomes in the bacteria just isn't realistic. That would be like taking a really good weather model and then asking what happens if a supervolcano raises the temperature in Wyoming by 500 degrees for 10 years. Only ab-initio models can do this sort of thing accurately, and even those fail of you try to model the big bang or other situations where the physics are unknown.

fraud (1)

Anonymous Coward | more than 2 years ago | (#40721419)

These so-called constraint flux based analysis (FBA) models are a big fraud. Perhaps most people in this field do not even realize this, but I think such models are of little direct biological value.

Some time ago, I switched from experimental physiology/mol biology to computational biology. As part of my job, I was overseeing two students starting on such FBA models. What these models generally do is ask a genome or expression database for a list of all expressed genes. Then filter out things that have a biochemical annotation (from www.genome.jp/kegg for example) to make a network of the biochemistry.

Because kinetic info on the enzymes is usually sparse, it is ignored. Instead, steady state is assumed and input/output fluxes+maximum fluxes on every reaction are guestimated. This creates a linear problem that is contraint by the network topology and the max/min rates for every reaction (which are mostly guessed). The solution space is a couple of million (depending on the nr of reactions) options.

Although methods exist to analyse the solution space, it obviously does not tell you that much (most of the solutions are bullshit and for example thermodynamically impossible). A great innovation was the definition of an "objective funtion" which assumes that the organism is perfectly optimized in something. Usually growth rate. Thus, you optimize your system of reactions to yield the maximum biomass. This gives only 1 solution.

My students analyzed a couple of papers published. In one of them (a photosynthetic organism), the optimization caused the respiratory cycle to run backwords (effectively fixing carbon) because of this optimization. It is perfectly valid from a model perspective, but it is completely contradictory our current biological understanding, and shows how silly this "objective function" is. However, the authors of such papers only look at individual pathways or reactions when it is correct, they do not highlight problems. It is impossible to talk about every reaction in a paper anyway, so nobody notices (unless you go over the model yourself for a couple of weeks). Other problems I noticed in incorrect annotations, incorrect reaction stoichiometry. There are many many errors in a lot of the published works.

There are more problems. Regulated exchange between compartments in eukaryotic organisms (from cytosol to mitochondria and such), is often ignored. In multicellular organism the method does not even make sense because only a single cell type is modelled (and assumed to aim for max growth).

I tried to contact the authors of such obviously erroneous works. Without much luck. Most of them are CS graduates. They have little understanding of the biology, and do not care. The models work and they publish in high IF journals. So why bother that a proton is missing from a reaction?

Saying that, as in the FA, this models the complete organism is wrong. It makes many assumptions, mostly focusses on the biochemistry (although some regulation can be included) and is generally steady-state. It is not predictive (the models are usually tweaked to whatever experiments are shown in the same papers). For bacteria, it might work to some extend, but although it has been claimed that it has lead to some discoveries, I think this has been mostly retrospective prediction....

Just download the DNA compiler (1)

viking80 (697716) | more than 2 years ago | (#40721825)

So far it is more of an assembler, but it includes all the "header files" for basic life functions like cell_wall.h, DNA_replication.h, ribosome.h, etc. Each of the header files describes the DNA code for all the needed proteins with all the switches needed.

It is called YADA.jar (Yet Another DNA Assembler)

Right now, the "printer" to get a real organism is cumbersome, but you can run the whole life form as a simulation. If you are Google, you may even grow real humans, and give them all kinds of fun functionality.

That is... (0)

Anonymous Coward | more than 2 years ago | (#40721877)

...the most complicated and pricy Tamagochi I've ever heard of.

Been There, Done That (1)

allo (1728082) | more than 2 years ago | (#40722209)

Maxis SimLife

How complex the model has to be? (1)

ArthurPaulBlack (2689491) | more than 2 years ago | (#40722389)

The idea of imitating a simple bacterial organism as a piece of software came through my mind a couple of times in the past. Although, it's really interesting, I think there is a fundamental problem with it. How deep the simulation has to go? To properly simulate a living organism, you would have to simulate more fundamental ideas laying inside, like chemistry behind substances involved or physics on a molecular level. As far as I know, there are still parts of these matters that have not been explored / discovered yet. It's pretty impossible to simulate something that you don't really know about everything.

Also, regarding the data contained in a cell. It's pretty obvious there is much more than just DNA. One example may be millions of different states that the cell can be at any particular time throughout its lifespan.

Re:How complex the model has to be? (1)

Hentes (2461350) | more than 2 years ago | (#40723249)

Yes, emulation is a huge overstatement, this project basically simulated only the DNA and the metabolism of the cell.

And yet some foolish people... (-1)

Anonymous Coward | more than 2 years ago | (#40722603)

... think living organisms arose by random interactions of nonliving matter. A laughable idea.

Oblig. xkcd (0)

Anonymous Coward | more than 2 years ago | (#40723739)

xkcd [xkcd.com]

This was my third year project (0)

Anonymous Coward | more than 2 years ago | (#40725151)

Artificial Intelligence bachelors at Sussex on a genetic algorithms module. I did almost exactly this only using one machine, a Sun Ray. I wasn't the only one either, it was a fairly popular project. Mine was a cow called PolyCow... it and its virtual offspring were represented as polygons. This is over a decade ago now... give me a break.

This is not new, it's just a bit bigger.

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