So when will we get a CLR JIT to DNA? | The Coffeehouse

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http://www.timesonline.co.uk/tol/news/uk/science/article6804599.ece

"Artificial life will be created within four months, a controversial scientist has predicted. Craig Venter, who led a private project to sequence the human genome, told The Times that his team had cleared a critical hurdle to creating man-made organisms in a laboratory.

“Assuming we don’t make any errors, I think it should work and we should have the first synthetic species by the end of the year,” he said.

Last January the team built a bacterium’s entire genetic code from scratch. The next step was to transfer this synthetic genome into a host cell, using the 2007 transplant technique, to “reboot” it with genetic instructions written by humans. This has failed so far because the synthetic genome will not work when it is transplanted into host cells."

Tongue Out

Seriously, if we're going to be building genetic codes, at some point we'll need high-level languages to build them, right? Anyone know about research in this area?

RoyalSchrubber
One. How many time travellers does it take to change a lightbulb?

This article is like those about new materials that could produce processors in teraherz range. In 20-40 years and event then only 'maybe'. It's best to stop paying attention to this kind of news really.

blowdart
Peek-a-boo

You'll see Linq To DNA first Smiley

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In reply to RoyalSchrubber

#Aug 24th @ 11:35 AM

Well yeah, it usually takes decades for new research to make its way into common industry and society, as we've often seen in software and programming languages and tools etc as well, but I don't see why that means we shouldn't be interested.

Bass
www.spreadfirefox.com/5years/

Yeah I did a research in bioinformatics in college, but not directly at this. DNA is unfortunately not as straight forward is a regular assembly language, the quantum mechanical interaction of the proteins within a cell leads to macroscopic emergent behavior that can not be readily predicted from the DNA sequence alone.

Ion Todirel
buuu

it's always nice to see those so called "scientists" making statements out of their leagues, why would they say x or y when that’s not their area of expertise?

RoyalSchrubber
One. How many time travellers does it take to change a lightbulb?

In reply to contextfree

#Aug 24th @ 11:45 AM

I stopped caring for any research that might yield results in distant future after I discovered digg. It's easy do be excited 24/7 - scientists discover new transistor material, scientist want to transmit data with light inside chips, they want to do 3d processors, quantum computers, use superconductivity and trasmit energy wirelessly. Most of these ideas were presented as news on such sites, but they don't tell you there is some catch and it's likely this technology will not be available in decates and somebody is doing PR to get more research money.

Now on this new artificial life.. I didn't bother to read article but I'm sure the experiment will be performed similarly to how they make geneticially improved crops.. they will take dna from few species and remix it somehow. Maybe in a novel way, but it will still be plain old lame remix. It's not like they've produced machine that could successfully produce molecules of dna that contain megabytes or even gigabytes of information much less produce their own dna sequences/data.

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In reply to RoyalSchrubber

#Aug 24th @ 12:35 PM

Yeah, you're probably right re this particular research. I just find it fun to think about the prospect of programming to DNA. Apparently Luca Cardelli of "A Theory of Objects" fame and currently of MSR is doing work in this area (PDF of "Strand Algebras for DNA Computing" paper)

"DNA technology is reaching the point where one can envision automatically compiling high-level formalisms to
DNA computational structures [18]. Examples so far include the ‘manual compilation’ of automata and Boolean
networks, where some impressive demonstrations have been carried out [1][8][15][16]. Typically one considers
sequential or functional computations, realized by massive numbers of molecules; we should strive, however, to
take more direct advantage of massive concurrency at the molecular level. To that end it should be useful to
consider concurrent high-level formalism, in addition to sequential ones. In this paper we describe three compilation
processes for concurrent languages. First, we compile a low-level combinatorial algebra to a certain class
of composable DNA structures [17]: this is intended to be a direct (but not quite trivial) mapping, which provides
an algebraic notation for writing concurrent molecular programs. Second, we compile a higher-level expression-
based algebra to the low-level combinatorial algebra, as a paradigm for compiling expressions of arbitrary
complexity to ‘assembly language’ DNA combinators. ..."

I think I'll try reading some of his papers. This is all pretty far removed from practical development of synthetic life forms of course, but it's interesting all the same.

Bass
www.spreadfirefox.com/5years/

In reply to contextfree

#Aug 24th @ 12:44 PM

I think it's within the realm of possibility. I might have said it all fancy before but the idea is that DNA maps to genes, which maps to amino acid strands which fold into proteins. But there is all these ions and crap that roam around in the cell that influences how things form in uncertain ways, as well as complex interactions between the proteins itself. Life is basically not a very clean, modular OO application, where DNA sequence (the source code) directly maps to the organism's "functionality". Everything seems to effect everything else in usual and often unpredictable ways. It's organized chaos.

You might be interested in "The Game of Life". It's a cellular automata which shows how seemingly simple rules and building blocks can lead to complex emergent behavior.

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In reply to Bass

#Aug 24th @ 1:21 PM

Oh yeah, I hope nobody thought I was being serious with the thread title. You probably need a very different programming/modeling ... model than current languages and environments provide. But I think the general idea of an HLL is still worth pursuing.

Bass
www.spreadfirefox.com/5years/

In reply to contextfree

#Aug 24th @ 1:39 PM

It is, definitely. Bioinformatics is in general a field with a lot of potential. The general idea is more then worth pursuing. Bioinformatics might possess be the hidden piece of the puzzle to finally cure cancer, for instance.

I don't think it gets enough attention from computer/software engineers. Same with general AI research.

In this day in age, I really wish that software engineers would stop writing the same stupid business apps over and over and focus on AI and bioinformatics.

There needs to be the Manhattan project of Computer Science. Like imagine if hundred thousand software developers just focused on general AI. I think we'd have it in a few years.

section31
OutOfCoffeeException

In reply to Bass

#Aug 24th @ 1:21 PM

I'm working for years as a programmer for molecular biologists. I saw a lot of data and a lot of algorithm. But the best thing to describe the whole thing is this cit. :

"There is a theory: That if ever anyone discovers exactly what the Universe is or and why it is here, it will instantly disappearand be replaced by something even more bizarre and inexplicable. There is another theory: this has already happened."

And i guess Life is part of the Universe.