(Solved) where can I learn synthetic biology?

cipher0

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10 years ago

Hello everyone. I'm a programmer who has recently learned about synthetic biology and the similarities between cells and computers, DNA and computer code, etc. have gotten me extremely interested in this field. Sadly I didn't know about this field few years earlier and I'm 21 now, a little old to learn from university and not enough free time or money to go that route.
I thought I can at least study this field like I did programming from the first time many years ago: via internet. I have only basic biology knowledge from high school courses. I understand there's *a lot* to learn, but I'm ready to spend years to learn something, the same way I was when I learned about what you could do with programming when I was a kid.

I'm not sure where to start learning synth bio. With programming you just type it in Wikipedia, learn its history and usage, available programming languages and then search for ebooks, join and post in forums/Q&A style sites and subscribe to few newsletters for news in the field.

With synth bio, I've only been able to find books that talk about particular subject (no introduction), or books about the history and potential of the field.
I've found this site called "OpenWetWare" which seems to allow to join a course in some university in some town by registering in the site.
I've also heard about diy bio groups around the world.
There are sadly no groups where I live.

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padre

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10 years ago

HI

I can't see how computer programming is related to synthetic biology, unless you're using a program to code an animation digitally. What did you have in mind?

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cipher0 Author

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10 years ago

Hi.
Here are some links I have.

http://ds9a.nl/amazing-dna/
http://www.wired.co.uk/news/archive/2013-03/06/tom-knight-biobricks
http://www.wired.co.uk/news/archive/2013-02/14/cell-circuits

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497497427624

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10 years ago

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padre

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padre

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10 years ago

Thanks

I can see how computers can be used to model proteins based on their amino acids, but programs like these have already been developed I think.

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cipher0 Author

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10 years ago Edited: 10 years ago, cipher0

Thanks 497497427624.

padre, if you were replying to me, then I think you've misunderstood what I want.
Firstly, I didn't say programming and synthetic biology are similar which wouldn't make sense. I said there are similarities between computers and cells, DNA and machine code, etc.
So as a programmer who has knowledge on how computers works and how code works, seeing this similarities makes me very interested in synthetic biology and makes me want to learn more.
This doesn't mean I'm thinking of using computer programming here. Maybe programming in DNA, or some abstract language which will be developed in the future. Face with Stuck-out Tongue

http://www.genomecompiler.com/

"...my lab is using Genome Compiler to design and debug DNA in order to build radically new genomes with useful properities like resistance to all viruses and enabling new amino acids..."
-George Church

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padre

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10 years ago

Quote from: cipher0 (10 years ago)

I said there are similarities between computers and cells, DNA and machine code, etc.

See, I disagree with this, given that I did a few years of programming before science. Algorithms and math go hand in hand, but all biological creatures have been inspired by nature (natural selection), and unlike math, nature tends to change every n amount of years. If DNA was as linear as computer programming, we would have figured out how the genome works by now, but we're not even close.

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cipher0 Author

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10 years ago

Then you are disagreeing with some influential people in this field I guess.
I don't know what you mean by programming being "linear".

I don't know how much you've studied programming, but I can think of many reasons why we haven't figured out how the "genome works". First, the "code" is extremely long. Finally, DNA is not your C++ or Java code. It's more like machine code, which is just 0's and 1's. All the abstraction modern programming languages provide are lost when it is converted to 0's and 1's (process called "compilation"). You can't convert the machine code back to C++, or some human-readable code. And reverse-engineered machine code is very-very long and difficult. All that people (hackers) are able to do with this machine code is make assumptions, remove or replace some parts and see what happens, kind of what biohackers are doing right now.

Maybe you meant unlike computers cells can change and make copies of themselves. True. But because modern computers can't do that doesn't mean they won't be able at some point and it doesn't change the fact that there are so many similarities either.

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padre

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10 years ago

Quote from: cipher0 (10 years ago)

First, the "code" is extremely long. Finally, DNA is not your C++ or Java code. It's more like machine code, which is just 0's and 1's.

That's where we don't see eye to eye. If that were the case, we would have understood by now which genes code which proteins, but because of alternative splicing, that's not possible. We've also discovered that different transcription factors for the same gene will produce a whole different outcome (protein) - now factor that into programming.

Quote from: cipher0 (10 years ago)

And reverse-engineered machine code is very-very long and difficult. All that people (hackers) are able to do with this machine code is make assumptions, remove or replace some parts and see what happens, kind of what biohackers are doing right now.

We have made assumptions with the DNA code. A lot of genes start with the same upstream code (promoter and enchancer regions). So what we've done as scientists is take those commonalities and super impose them on the DNA code to see which other regions have the same promoter region DNA codes. IF DNA was linear, we would have solved the code by now, but due to alternative splicing, it's not the case. Now, one gene can code for ten different proteins because of this.

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cipher0 Author

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10 years ago

padre, I don't know what alternative splicing or transcription factor is.
Can you please explain what you mean by programming being "linear" in simpler terms? I only used terms like "reverse engineering" and "machine code" because you said you had some programming knowledge and these are pretty basic stuff.

I'd like to say that I'm not aware of any hacker who has been able to reverse engineer any large program so far. It takes extremely long time to reverse engineer a computer program, seeing how much longer even the shortest sequenced genomes are, how little we know about the code as well as the "computer which executes that code" I'm not surprised any DNA hasn't been completely reverse engineered till now.

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padre

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10 years ago

Quote from: cipher0 (10 years ago)

I'd like to say that I'm not aware of any hacker who has been able to reverse engineer any large program so far.

Biologists do a lot of reverse engineering to figure out protein shape and composition (90% of all studies are done this way). DNA code - a gene - is useless to us if we don't know anything about the protein that it encodes. I could give you a gene, you implement it into a bacterial DNA, the bacterium produces the protein from that gene, but what do we do with that protein once it's produced? It's an in vitro study, done in a lab. That protein is not functional on its own and so we don't know where it belongs in the grand scheme of it all from the organism we derived the gene from.

To understand transcription factors and activation of genes, review this thread: https://biology-forums.com/index.php?topic=3644.0 (must see)

You do know what transcription is right?

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cipher0 Author

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#11

10 years ago

Sorry but I don't really understand what your point is. I still don't understand what you mean by programming being "linear". And yes, I did read the topic you linked to and watched the video.

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padre

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#12

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10 years ago

The link would have provided you an idea what a promoter region is and how transcription factors work, because you asked.

Computer programming is linear in the sense that most real-world bread-and-butter programming tasks are don’t require a parallel approach, i.e

if(variable is 0)
display x
elseif(variale is bigger than 0)
display y
else
display z

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cipher0 Author

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#13

10 years ago

And what do you mean parallel approach?

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