Biological Engineering on a large scale

[Max.Planck]

Main Question or Discussion Point

Why aren't we still able to create/alter organisms for energy and food production,
since we can easily sequence and cut and paste DNA?

 

[Biosyn]

Because PETA is watching. lol.

 

[Pythagorean]

Because IACUC is regulating. lol.

fixed!

 

[Biosyn]

fixed!

Oh right right!



Just the link from PETA I was reading..
http://www.peta.org/issues/animals-used-for-experimentation/alternatives-testing-without-torture.aspx[/SIZE] [Broken]

 

[SW VandeCarr]

Why aren't we still able to create/alter organisms for energy and food production,
since we can easily sequence and cut and paste DNA?

Because biologists are too proud to ask the physicists to come in and show them how the Einstein Stress-Energy Tensor or QFT can describe the proteome.

 

[thorium1010]

in the news recently - Growing meat in a petridish

http://www.bbc.co.uk/news/technology-15402552

 

[PVastro]

Well we do alter DNA all the time with things like plants for food. Some plants even have insect and bacteria DNA put into their genetic sequence.

 

[penta-d]

I am not sure I understand the question. We are able to alter organisms for energy and food production, and it is done on a large scale all the time. If you are asking why biotechnology has not led to an end to hunger or to independence from fossil and other fuel sources, that is a complex question which probably depends as much upon politics, economics and social factors as on science.

Regarding QFT description of the proteome, have at it. Why would physiscists wait for an invitation if they believe it could be productive?

 

[SW VandeCarr]

I am not sure I understand the question. We are able to alter organisms for energy and food production, and it is done on a large scale all the time. If you are asking why biotechnology has not led to an end to hunger or to independence from fossil and other fuel sources, that is a complex question which probably depends as much upon politics, economics and social factors as on science.

Regarding QFT description of the proteome, have at it. Why would physiscists wait for an invitation if they believe it could be productive?

I was not being serious. Going by the OP's username. I thought he/she might have some association with or interest in physics. However, I seriously doubt understanding the proteome is going to occur at the level of QFT (or whatever replaces it) anytime soon. Certainly, the stress energy tensor is not going to be of use afaik, but it sounds impressive.

While the genome is better understood, understanding how genes exert their effect via coding of proteins is going to take a while. Of course, anyone who wants to try can apply for funding, but don't mention QFT in your application.

 

[penta-d]

They do sound very impressive!

And I agree that understanding how genes exert their effects is going to take quite some time.

 

[Ryan_m_b]

Why aren't we still able to create/alter organisms for energy and food production,
since we can easily sequence and cut and paste DNA?

We do alter organisms all the time for both food and scientific research and are starting for fuel. Problems with both of them being public/political/economical opposition (some of which is legitimate) and that genetic modification is totally non-trivial. Sure you can cut and paste DNA but that's little more effective than taking a passage from one book that you really like and slapping it randomly in another and hoping the new story will take on the attributes of the older.

The problem with thinking about genetic engineering in this way is that it works on the assumption that analogies about genes being codes and genomes blueprints being correct. In actual fact this is not the case. Genes code for RNA that (most of the time) is converted to protein. These molecules interact with each other and others from the environment to create a metabolism that determines cell (and by extension organism) behaviour. So for the most part genes do not really map to defined traits, you can't just take the gene from one organism, put it in and expect it to work the same way. Whilst our knowledge and capability of genetic modification continues to grow and will continue to be useful (especially in the emerging field of synthetic biology) it wont be until we've started cracking the proteome, the transcriptome, the glycome and the metabolome that we could really begin radical engineering/creation of organisms for specific purposes. In fact once we have all those we may be able to seriously attempt to crack the phenome though I'm sceptical.

 

[Max.Planck]

The problem with thinking about genetic engineering in this way is that it works on the assumption that analogies about genes being codes and genomes blueprints being correct. In actual fact this is not the case. Genes code for RNA that (most of the time) is converted to protein. These molecules interact with each other and others from the environment to create a metabolism that determines cell (and by extension organism) behaviour. So for the most part genes do not really map to defined traits, you can't just take the gene from one organism, put it in and expect it to work the same way. Whilst our knowledge and capability of genetic modification continues to grow and will continue to be useful (especially in the emerging field of synthetic biology) it wont be until we've started cracking the proteome, the transcriptome, the glycome and the metabolome that we could really begin radical engineering/creation of organisms for specific purposes. In fact once we have all those we may be able to seriously attempt to crack the phenome though I'm sceptical.

Thanks for the post. Isn't it possible to simulate metabolism using computer simulation, or are the models incomplete?

 

[Ryan_m_b]

Thanks for the post. Isn't it possible to simulate metabolism using computer simulation, or are the models incomplete?

I'm afraid not. We can't even accurately simulate protein folding which is a very routine part of basic biochemistry (though there are interesting novel approaches to that problem). In addition there are a few other problems:

• We haven't identified all the biochemical components of any organism and its environment.
• There are far too many variables to compute with current computational power.
• We don't understand/can't build models of all the physical laws governing biochemical interactions.
• If this was ever done for a conscious animal we would run into ethical issues.

We'll be doing things like this in vitro rather than in silico for a long time yet.

 

[Pythagorean]

but you can help figure it out with this fun protein folding game!

http://fold.it/portal/

 

[Ryan_m_b]

but you can help figure it out with this fun protein folding game!

http://fold.it/portal/

Beat you to it

...though there are interesting novel approaches to that problem...

I haven't played the game yet but it's an excellent idea. I'd be really interested to see what other types of problem could be solved with gamified software outsourced to the crowed.

 

[Pythagorean]

doh!

I played around with it for a while; it's not as exciting as Skyrim, but it's neat to see how proteins work. The basic premise is that a computer can't perform the solving algorithm but human visual system/mind can.

 

[Ryan_m_b]

doh!

I played around with it for a while; it's not as exciting as Skyrim, but it's neat to see how proteins work. The basic premise is that a computer can't perform the solving algorithm but human visual system/mind can.

Cool, I might give it a go at some point. Is it that computers aren't powerful enough to solve the problem or that an algorithm hasn't been produced that can solve it do you know?

 

[Ryan_m_b]

but you can help figure it out with this fun protein folding game!

http://fold.it/portal/Beat you to it

...though there are interesting novel approaches to that problem...

I just remembered of another project which works by members of the public downloading some software (IIRC a screensaver) that then links together with all the other computers and works to compute folding:

http://folding.stanford.edu/

 

[Pythagorean]

Cool, I might give it a go at some point. Is it that computers aren't powerful enough to solve the problem or that an algorithm hasn't been produced that can solve it do you know?

Well... that's kind of a catch 22. You can always use a brute-force method and just randomly try different solutions of some sort to fit some empirical data. So in that sense, we don't have the power.

But I think here, we have an algorithm based on some basic rules that humans can follow and adhere to, but it can't be translated to computer. The aglorithm as written for humans probably uses fuzzier language and involved more spatial intuition (like translating "fill the area" to a computer in 3D space would require a lot of literal assumption-making if you don't want to the computer to try a bunch ridiculous solutions that a spatially-aware human brain would already immediately reject).

We also, playing this game, have a much more intense feedback relationship with the proteins. You get to swing molecules around and try different positions while watching how it affects things

http://www.genengnews.com/keywordsandtools/print/4/24357/

 

[Ygggdrasil]

A few thoughts:

1) There are two parts of the protein folding problem: a) predicting the correct final 3D structure of a protein from its amino acid sequence, and b) figuring out the mechanism by which an unfolded polypeptide chain coming off of the ribosome folds into its final 3D structure. I will refer to these problems as the structure prediction problem and the folding mechanism problem.

2) Obviously the folding mechanism problem is more complex and solving this would automatically solve the structure prediction problem. FoldIt is designed primarily to investigate the structure prediction problem. Efforts such as the Folding@Home project are geared more towards the folding mechanism problem.

3) The structure prediction problem is essentially a global optimization problem: given a long polypeptide chain, find the lowest energy conformation of that chain. Searching for the lowest energy conformation is difficult because the search space is large and contains many local minima.

4) The state-of-the-art structure prediction programs are able to generate a decent starting model for the protein structure by comparing the amino acid sequence with the sequences of proteins of known structure. The programs then play around with the structure (rotating bond angles, moving various pieces of the protein around). The program will compare the energy of the structure prior to the change with the energy after and if the change has lowered the energy of the structure, it will accept the change.

5) Often, the search gets caught in a local minima, where small changes to the structure all raise the energy, even though the overall structure is not correct. Often, visually inspecting these "trapped" structures can reveal more drastic changes to the structure that may move the structure out of the local minima and closer to the correct structure. It is this part of the algorithm, recognition of local minima and identification of the large changes to allow escape of these minima, that benefit most from human intervention.

6) With regard to the original question (why isn't biological engineering used more in fuel production), Hartmut Michel, who won the Nobel Prize for his work studying photosynthesis, has an interesting editorial in Angewandte Chemie (a major chemistry journal) titled, "The Nonsense of Biofuels." In it, he argues that electric cars run from solar energy makes much more sense than using biofuels because of the inherent inefficiency of biological photosynthesis:

Commercially available photovoltaic cells already possess a conversion efficiency for sunlight of more than 15%, the electric energy produced can be stored in electric batteries without major losses. This is about 150 times better than the storage of the energy from sunlight in biofuels. In addition, 80% of the energy stored in the battery is used for the propulsion of a car by an electric engine, whereas a combustion engine uses only around 20% of the energy of the gasoline for driving the wheels. Both facts together lead to the conclusion that the combination photovoltaic cells/electric battery/electric engine uses the available land 600 times better than the combination biomass/biofuels/combustion engine.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201200218/pdf

His article is a bit too dismissive of some biofuel technologies and doesn't really address some of the issues with solar power, but he does make some very good points. Although biologists often marvel at how well nature is able to perform some tasks, it is good to sometimes admit when we have built devices that surpass nature's abilities.