Comment by nojvek | Hacker News Reader

Comment by nojvek | Hacker News Reader

Someone who is a molecular biologist, please correct my understanding.

DNA is a molecule, made out of 4 amino acids. ACTG. There are 18 different kinds of amino acids. Amino acids are made out of carbon, nitrogen, hydrogen, oxygen. Amino acids make proteins. Proteins are the structural bricks (like LEGO) that are combined in various sequences by enzymes to build more complex machinery.

The proteins make up cell organelles, which make up cells.

How much of how DNA turns into proteins and different proteins build different structures is understood? Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures?

How close are we for computer science folks to actually start writing compilers, debuggers, frameworks and simulation tools for DNA and man made cell machinery ?

How far away are we from making custom DNA + cells that act like 3D printers taking collagen and building nanometer precision complex structures?

It seems our cells already do nano manufacturing and computation, how do I tap into that ?

DNA is made of nucleic acids (deoxyribonucleic acids), not amino acids. DNA is translated to amino acids, except when it encodes long-noncoding RNAs, or miRNAs, or piRNAs, or untranslated regions, or intergenic regions, or transposons, or psuedogenes.

And the protein coding sequences are coded into proteins, except when there are alternative splicing sites, or anti-sense RNAs.

And then the protein sequence folds into their minimum free energy state, except when they are assisted by other proteins, or when they exist as disordered proteins.

And it's not always DNA -> protein. Sometimes proteins make other proteins, for example circular proteins can only be made from other proteins.

Then there are post-translational modifications, which change the RNA sequence between DNA to RNA and RNA to protein. And then there's RNA interference, where miRNAs interfere with RNA to protein translation.

And then there's epigenetics such as DNA methlyation or histone modifications (histones are protein which compress DNA) which change what genes can be expressed when.

Really, for every rule that you've been taught, there is an exception. Biology is so much more complicated than we understand. And understanding how to make a biological computer (different from the biological computing of Adelman, yes the same Adelman as RSA) would involve understanding how all the pieces fit together.

As an outsider, microbiology is hopelessly complex.

> Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures?

Determining the physical structure of a protein from the amino acid sequence is NP-Hard : https://ieeexplore.ieee.org/document/6965037

Without a very significant breakthrough either in computation or some biological discovery that gives a shortcut I don't think a "DNA compiler" will be available anytime soon.

DNA is made out of nucleic acids. Each sequence of 3 DNA nucleotides codes for an amino acid. There are 21 amino acids.

How DNA -> proteins is well understood. Protein folding though is incredibly complex to model.

It is easy to know the amino acid sequence, but hard to know how the protein will end up folding.

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