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Scientists Creating Life From Scratch
Rubberbando writes "MSNBC is running a story about bioengineering organisms to do specific tasks such as produce hydrogen or ethenol. It also goes into the risks and ethical issues of playing with this sort of science. Some of the scientists involved are saying it's more of an art instead of a science due to its 'biohacking' style of experimentation."
FYI, the title is incorrect. There is no "from scratch" component to the life. What they're doing is building custom DNA, then injecting it into a living cell.
Javascript + Nintendo DSi = DSiCade
If you actually want to read about the project on creating life "from scratch", that would be here
http://en.wikipedia.org/wiki/Miller-Urey_experimen t
Assume I was drunk when I posted this.
Making stuff is the big deal. Most chemicals are made from petrol nowadays and the chemical companies are searching for a way out of this dependency on petrol. One way is plants (as raw material) + bacteria(for their enzymatic reactions). Quite a few microbiology labs are now working in discovery, selection and bio-engeneering of bacteria for this very purpose. Personally, I think the discovery part is very important since we know close to nothing about the biodiversity of bacteria. A number I heard recently is that 70% of the biomass of this planet is made of bacteria, and most of them live in the ground and are very difficult to isolate and study and thus mostly unknown. Look up metagenomic in google for more info.
I'll do it for cheesy poofs.
Molecular biologists have been cloning genes in prokaryotes and eukaryotes for tens of years. It's not a new idea to clone a series of genes that work cooperatively to change biochemical behaviour of an organism.
Something I find more note-worthy, as a biological chemist, is a new trend to expand the amino-acid table (past 20). Many of the codons (DNA or RNA triplets) are degenerate or they are stop codons. The idea is to add synthetic amino-acids to specific tRNAs. Chemically modified amino-acids are incorporated at the desire of the molecular biologist. This technology has already been developed, and the scientists in this field (not myself) are discussing using directed evolution with organisms with an expanded codon base. Very interesting.
This is extremely unlikely to happen. Different plant species have different proteins and biochemicals, and an organism tailored to deal with the product of one plant is not going to be effective at dealing with those of others. This is why parasitic organisms and infective bacteria, viruses and fungi are so specific to particular species.
No, that's not true. For example, we find Leishmania using canines (dogs) as a reservoir for infection, and then infecting humans.
Cross-species parasitic organisms are fairly common, as a recent work by some European scientists in France and the UK said, with a publication date of 2005, and unpredicatable results can happen even by removing quail from a parasitic ecosystem, as many parasites have multiple hosts in their life cycles, including backup or reserve (temporary/seasonal) hosts.
So, I disagree. It only needs to utilize the other plants and metabolize enough to survive until it gets to its desired or sufficiently optimal source, but that won't stop it's behavior, especially if it's a primitive organism.
Now, virii or bacteria, those tend to be more specific, but the literature shows that they are much more adaptable than you may think on surface inspection, especially with mutations due to unexpected cross-breeding (including the original non-bioengineered organism).
-- Tigger warning: This post may contain tiggers! --
Ab initio calculations are limited to ~200 atoms.
:)
;)
/etc.
Less even. Largest our group has done is about 120.
The current solution to that problem is to use a hybrid Quantum Mechanic / Molecular Mechanic (QM/MM) method that only uses ab initio calculations for the atoms located near the catalytic site and use regular molecular dynamic simulations for all other atoms.
Right. But MM is not ab-initio, and DFT QM isn't either if you're a purist. And you still need a reliable structure
So, you're right when you say "you cannot make an ab-initio model", but if the end goal is to _predict_ the dynamics of a whole cell then one doesn't need to perform quantum calculations _on everything_. And the calculations don't need to be performed at the same time.
Absolutely. But that's pretty much in line with my original point: That even though we do not know exactly what is going on at every given moment, we don't really need that information either. And it doesn't mean we don't have a 'deeper understanding' of what's going on.
Now, of course, there's experimental data out there so we don't need to in silico predict _everything_.
That's not quite true though. For instance, say you want to predict how a certain foreign substance interacts in the cell environment. Which is a rather important scenario to drug companies, to say the least. Then you'd have to go off and do a huge number of experiments to get parameters for that substance. In the end, you're better off just feeding it to a rat and waiting to see what happens.
For non-empirical models of chemical reaction kinetics, look up 'transition path sampling'. It's a way to sample the possible reaction mechanisms of a reaction and calculate kinetics. You need to perform a lot of sampling so it's currently limited to quickly occurring reactions (but it has recently worked on calculating the kinetics of small protein folding). The method does require that the reaction mechanism is known (ie. what the reaction coordinates are).
It requires a full potential energy surface to work with. And that would be either empirical (MM, which is incapable of breaking/forming bonds) or non-empirical (QM, which is way too expensive to do any kind of PES scanning).
Nobody I know of using QM or QM/MM for reaction mechanisms uses an automated procedure.
For the hybrid QM/MM stuff, look up 'Darrin York'.
Well, my own research group does this already.
That stuff still needs some sort of reaction coordinate defined, but the simulations don't assume anything about the catalysis process itself.
Well saying that you need the reaction coordinate (of the transition-state, presumably) means that you already know (or assume) what the reaction mechanism is, as you said yourself. And either you automate that search (too expensive), or you use your chemistry skills to make some qualified guesses and do the calculation to see if they're viable.
But we do not have a 'black box' where you can put in the arbitrary substances A and B, choose a temperature and solvent and find out what they will do to eachother.
When you're working with thousands of atoms, it's hard to determine at which point did the substrate turn into product
That's wrong though. The transition-state is easily defined: The highest-energy point on the substrate-to-product pathway. This can be verified even for a single coordinate, just as for any function: Zero derivative of energy W.R.T coordinates, and a negative second-derivative. The numbers will also tell you which atoms are the ones actually reacting.
(Now the transition-state isn't always the limiting factor in the kinetics. It could be a very fast reaction limited by diffusion for instance, but that's a different story)