# Understanding the programming language of DNA? **URL:** \ **Category:** Factual Questions\ **Created:** [February 12, 2014, 8:59pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188 "2014-02-12T20:59:49Z")\ **Posts on this page:** 20\ **Page:** 2
**Author:** ![dasmoocher](https://avatars.discourse-cdn.com/v4/letter/d/dbc845/32.png) [@dasmoocher](https://boards.straightdope.com/u/dasmoocher)\ **Post date:** [February 13, 2014, 1:25am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/21 "2014-02-13T01:25:02Z")
> [@kaltkalt](#): > > The Flying Spaghetti Monster (marinara be upon him) created all life on earth, DNA, etc. but that doesn’t mean we can’t understand his creation. Hallow be His Meatballs. ---
**Author:** ![watchwolf49](https://avatars.discourse-cdn.com/v4/letter/w/e9c0ed/32.png) [@watchwolf49](https://boards.straightdope.com/u/watchwolf49)\ **Post date:** [February 13, 2014, 1:31am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/22 "2014-02-13T01:31:26Z")
> [@dasmoocher](#): > > Hallow be His Meatballs. I need to smoke better pot I guess, ---
**Author:** ![dracoi](https://avatars.discourse-cdn.com/v4/letter/d/90db22/32.png) [@dracoi](https://boards.straightdope.com/u/dracoi)\ **Post date:** [February 13, 2014, 1:31am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/23 "2014-02-13T01:31:35Z")
> [@kaltkalt](#): > > There has to be some underlying organization and meaning to all those proteins and chemicals interacting. It’s the same for all life on earth. An elephant or a tube worm at the bottom of the ocean all rely on the same building blocks. > > How about this. My dream pet is a mini pygmy elephant. Like the size of a golden retriever, with a trunk about a foot long. How far away do you think we are from being able to engineer something like that? I’m not sure we could even estimate how far away we are. It could be that there’s already a gene in elephants that can produce extreme dwarfism and it’s merely inactive. In that case, a very small tweak - maybe even an epigenetic change that doesn’t affect DNA directly - could result in the elephant you want. We could probably pull it off within a year or two if knew this to be the case. (And it’d be that long mostly because we still have to gestate the embryo in an actual elephant.) On the other hand, if we have to build the right gene from scratch, make sure it’s executed at the right time, that it doesn’t adversely interact with other genes, etc. etc. then it could be quite a challenge. I would say it’s a challenge like computers using natural language, flying cars and nuclear fusion. If I say it’s fifty years away today, I’ll still be saying it’s fifty years away after fifty years have passed. ---
**Author:** ![dasmoocher](https://avatars.discourse-cdn.com/v4/letter/d/dbc845/32.png) [@dasmoocher](https://boards.straightdope.com/u/dasmoocher)\ **Post date:** [February 13, 2014, 1:34am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/24 "2014-02-13T01:34:36Z")
> [@watchwolf49](#): > > I need to smoke better pot I guess, Pastafari, sez I… ---
**Author:** ![watchwolf49](https://avatars.discourse-cdn.com/v4/letter/w/e9c0ed/32.png) [@watchwolf49](https://boards.straightdope.com/u/watchwolf49)\ **Post date:** [February 13, 2014, 1:44am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/25 "2014-02-13T01:44:11Z")
“And if you’re thirsty I will quench you With my pesta And if you’re hungry I will feed you With my tenticles And all I ask of you is that you slurp as I do” ---
**Author:** ![kaltkalt](https://avatars.discourse-cdn.com/v4/letter/k/bb73d2/32.png) [@kaltkalt](https://boards.straightdope.com/u/kaltkalt)\ **Post date:** [February 13, 2014, 1:49am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/26 "2014-02-13T01:49:51Z")
Could we ever look at a piece of DNA and read exactly what it creates? I don’t mean merely identifying it as human or fruit fly or whatever. I mean actually reading it and being able to determine that it makes something extremely specific. I want a mini pygmy elephant so bad. I’d rather have that than a flying car (people are too stupid to ever actually have that, teleportation would be more realistic IMO). If we DID create pygmy mini-elephants we should obviously design them to NOT grow ivory so asshole fucktards won’t be stealing our pets to kill for their small amount of ivory. Maybe we could design cattle that grows big ivory tusks - we’re gonna kill them for the beef anyway so I doubt anyone would have a problem with that. ---
**Author:** ![watchwolf49](https://avatars.discourse-cdn.com/v4/letter/w/e9c0ed/32.png) [@watchwolf49](https://boards.straightdope.com/u/watchwolf49)\ **Post date:** [February 13, 2014, 2:00am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/27 "2014-02-13T02:00:08Z")
> [@kaltkalt](#): > > I want a mini pygmy elephant so bad. FSM has provideth thee … “The Columbian mammoth (_Mammuthus columbii_) produced a separate, isolated population at the end of the Pleistocene. One of these isolated groups was formed on the Channel Islands of California, most likely about 40,000 years ago (although the time of isolation is not fully known). Selective forces on the Channel Islands [California] resulted in smaller animals, forming a new species, the Pygmy Mammoth _Mammuthus exilis_. Channel Islands mammoths ranged from 150–190 cm in shoulder height.” Just steal that DNA. ---
**Author:** ![kaltkalt](https://avatars.discourse-cdn.com/v4/letter/k/bb73d2/32.png) [@kaltkalt](https://boards.straightdope.com/u/kaltkalt)\ **Post date:** [February 13, 2014, 2:07am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/28 "2014-02-13T02:07:49Z")
> [@watchwolf49](#): > > FSM has provideth thee … “The Columbian mammoth (_Mammuthus columbii_) produced a separate, isolated population at the end of the Pleistocene. One of these isolated groups was formed on the Channel Islands of California, most likely about 40,000 years ago (although the time of isolation is not fully known). Selective forces on the Channel Islands [California] resulted in smaller animals, forming a new species, the Pygmy Mammoth _Mammuthus exilis_. Channel Islands mammoths ranged from 150–190 cm in shoulder height.” > > Just steal that DNA. I’m actually aware of this, but as far as I know we don’t have any of their DNA. Also, we don’t know if mammoths (let alone these pgymy ones) were as smart, friendly, loving, caring, etc as contemporary elephants are. We’ve found frozen baby full-size mammoths but not one of these. Of course I’d settle for a baby mini pygmy mammoth. But I’d rather have an elephant because it would shed less. I’ll continue to pray to FSM (parmesan be upon him) to have this dream of mine realized. No animal would make a better pet than a little mini pgymy elephant. It’s the ultimate pet. I’d actually worry about dogs going extinct hehe ---
**Author:** ![lazybratsche](https://avatars.discourse-cdn.com/v4/letter/l/ba8739/32.png) [@lazybratsche](https://boards.straightdope.com/u/lazybratsche)\ **Post date:** [February 13, 2014, 2:09am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/29 "2014-02-13T02:09:35Z")
> [@kaltkalt](#): > > Could we ever look at a piece of DNA and read exactly what it creates? I don’t mean merely identifying it as human or fruit fly or whatever. I mean actually reading it and being able to determine that it makes something extremely specific. In principle, with completely infinite computing power, probably not. Organismal development never starts with a truly blank slate. With an egg and the first few stages of the embryo, the mother provides all of the initial “hardware” that an embryo uses to decode the “software” in its genome. For fruit fly embryonic development, this includes defining which end of the embryo is the front, and which side is up, using proteins deposited precisely in the egg. But that only happens because there is an ovary that has a structure that is defined by a sequence of developmental processes going all the way back to the embryo. If you had a complete DNA sequence and a complete description of the entire biochemistry in the embryo? The best I can say is it’s probably not impossible. You’d have to simulate the entire process of development: how each and every cell grows and divides, how every gene is regulated in every cell, how every cell interacts with the cells around it, etc. Someday we might know enough about those processed to have reasonable abstractions. But for now, we can’t really even understand the function and structure of a single protein just from its DNA sequence. Good old fashioned animal husbandry and selective breeding would get you a pygmy elephant much faster. ---
**Author:** ![dasmoocher](https://avatars.discourse-cdn.com/v4/letter/d/dbc845/32.png) [@dasmoocher](https://boards.straightdope.com/u/dasmoocher)\ **Post date:** [February 13, 2014, 2:10am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/30 "2014-02-13T02:10:48Z")
> [@kaltkalt](#): > > Could we ever look at a piece of DNA and read exactly what it creates? I don’t mean merely identifying it as human or fruit fly or whatever. I mean actually reading it and being able to determine that it makes something extremely specific. A common tool is called [BLAST](http://blast.ncbi.nlm.nih.gov/Blast.cgi). It can take a DNA sequence and see if it matches a known or predicted protein sequence (blastx). From there, you can can follow links to what the protein is and what it does (or is predicted to, or what it is similar to, etc.). There are a lot of bioinformatics tools available to look at this. A DNA sequence to translated protein sequence search is very basic. ETA:Mis-read question. I’m talking about short sequences of DNA, not whole genomes. ---
**Author:** ![watchwolf49](https://avatars.discourse-cdn.com/v4/letter/w/e9c0ed/32.png) [@watchwolf49](https://boards.straightdope.com/u/watchwolf49)\ **Post date:** [February 13, 2014, 2:17am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/31 "2014-02-13T02:17:08Z")
> [@kaltkalt](#): > > I’ll continue to pray to FSM (parmesan be upon him) to have this dream of mine realized. Don’t forget to send 15% of your after tax income to 350 North Orleans Street, Chicago, Illinois, 60654 … c/o Watchwolf49 … and Linguine will never vex you. ---
**Author:** ![Obnoxious\_Hood\_Ornament](https://avatars.discourse-cdn.com/v4/letter/o/3be4f8/32.png) [@Obnoxious\_Hood\_Ornament](https://boards.straightdope.com/u/Obnoxious_Hood_Ornament)\ **Post date:** [February 13, 2014, 4:32am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/32 "2014-02-13T04:32:01Z")
> [@watchwolf49](#): > > Do you mean [Covergent Evolution](http://en.wikipedia.org/wiki/Covergent_evolution)? Lotus and water lilies are something of a real world example. Well, not really… although that was an interesting read. I guess what I’m asking, if I wanted to put it better, is if it’s possible to have two unique sets of DNA that have identical results. In computer programming, there are nearly limitless ways of expressing sets of code to generate an exact result, and I wondered if the principle applied to DNA as well. ---
**Author:** ![Danja](https://avatars.discourse-cdn.com/v4/letter/d/48db29/32.png) [@Danja](https://boards.straightdope.com/u/Danja)\ **Post date:** [February 13, 2014, 5:47am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/33 "2014-02-13T05:47:52Z")
> [@spazurek](#): > > You’re basically looking for a course in developmental biology. Before that you will need courses in cell & molecular biology and genetics. The short version: The system is extremely complex and there are still many unanswered questions. But it’s not the case that DNA can make any cell/organism do anything you can imagine. > > **To take one example, programming a cell’s DNA to make acetaminophen would require that you create a whole suite of new proteins inside a cell that can do something completely new to the cell without otherwise destroying it. Even if we knew how to do such a thing (we don’t), the process involved would be a staggering technical challenge.** > > While it seems like life has accomplished a nearly infinite range of engineering feats, each one is only possible when all the ingredients are just right. Spider silk requires the whole spider, not just its DNA. And overall, the many things cells can do are done with a fairly small tool chest. You’ve mostly got carbon, hydrogen, oxygen, nitrogen, phosphorus to work with. Temperature and pH have to be maintained in a fairly narrow range (except for a few extremophiles). And you’re stuck with a lot of historical baggage and inefficiency. > > Basically, you can do a lot in theory with biology, but in practice it’s a real headache. I disagree with the bolded above. I’m a bioengineer (grad student) so this is an interest of mine. I think that unless we have different understandings of the magnitude of “staggering”, this is not a staggering challenge. It would take a team of researchers and a well-equipped laboratory many years, but I think it’s possible with current technology. Acetaminophen is a fairly simple molecule; looking at the structure, you could probably use tyrosine as a precursor, maybe use a (modified) P450 to oxidize the aryl C-C bond (C-C bond cleavage has been shown before, but I’m not sure if it can occur when one of the participating carbons is aromatic), and then build the amide functional group off that intermediate. I of course can’t prove it, but I suspect it could be done. Now changing the spatial structure of an organism via DNA modification (adjusting various body proportions, etc)… that is a task for research labs 50 - 100 years from now, if not later. We’re just now understanding the simplest of concentration gradient-driven processes, as described beautifully by **Smeghead** above. ---
**Author:** ![JWT\_Kottekoe](https://avatars.discourse-cdn.com/v4/letter/j/3ec8ea/32.png) [@JWT\_Kottekoe](https://boards.straightdope.com/u/JWT_Kottekoe)\ **Post date:** [February 13, 2014, 5:51am UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/34 "2014-02-13T05:51:01Z")
> [@RaftPeople](#): > > There is most likely no 3-D coordinate system that the DNA explicitly references during development regarding placement/positioning, instead I believe chemical gradients guide a lot of development - but someone else more knowledgeable will need to go into detail. Well, in fact, there are 3-D coordinate systems established in the development of higher organisms. Actually, there are many overlapping coordinate systems that are maintained by the chemical gradients that you mentioned and controlled by the Hox genes that were also mentioned. For example, a 3-D coordinate system is established by chemical gradients that establish front/back, up/down, and left/right. In arthropods and vertebrates there are multiple, highly similar coordinate systems in segments that give rise, for example, to all the segments of a millipede or a spine. Within each segment additional coordinate systems are created which control the develop of legs, antennae, wings, etc. There is a wonderful book that describes these amazing facts in some detail. It is “Endless Forms, Most Beautiful,” by Sean Carroll. I highly recommend it. The title is taken from the end of “The Origin of Species.” ---
**Author:** ![watchwolf49](https://avatars.discourse-cdn.com/v4/letter/w/e9c0ed/32.png) [@watchwolf49](https://boards.straightdope.com/u/watchwolf49)\ **Post date:** [February 13, 2014, 2:27pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/35 "2014-02-13T14:27:31Z")
> [@Obnoxious\_Hood\_Ornament](#): > > Well, not really… although that was an interesting read. I guess what I’m asking, if I wanted to put it better, is if it’s possible to have two unique sets of DNA that have identical results. In computer programming, there are nearly limitless ways of expressing sets of code to generate an exact result, and I wondered if the principle applied to DNA as well. I’m troubled by the idea of two unique sets of code. Sure, code in PHP and another in C++ would give the same result, but wouldn’t both programs call up the same operating system code, say for example both languages would use the same “Arithmetic Logic Unit” or ALU. I believe the same is true for DNA, some very basic cell processes use the same DNA in most all cellular organism. I’ve heard humans and banana trees share 50% of their DNA, and I heard that on NPR, so it _has_ to be true. I’d say it is possible, if economy wasn’t a consideration, perhaps using a different set of amino acids. Perhaps we could even skip using DNA/RNA, some other organic molecule to carry the genetic information. I do think we’re stuck using carbon, I don’t know of any other element that readily bonds with itself. May I have 4.7 billions years to work on it? I’m curious, just how obnoxious is your hood ornament? ---
**Author:** ![Smeghead](https://avatars.discourse-cdn.com/v4/letter/s/f1d935/32.png) [@Smeghead](https://boards.straightdope.com/u/Smeghead)\ **Post date:** [February 13, 2014, 3:32pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/36 "2014-02-13T15:32:23Z")
> [@kaltkalt](#): > > There has to be some underlying organization and meaning to all those proteins and chemicals interacting. Again, we kinda sorta have some basic understanding of this. We know the forces involved in how molecules interact. It all boils down to electromagnetism - positive charges attract negative charges…hydrophobic interactions…van der Waals forces…it’s all basic electromagnetism. So we understand _how_ all these interactions happen. It’s just that it’s so incredibly complex that we can’t (easily) do the math to predict even a relatively simple interaction. So we look for larger-scale patterns. One example is protein motifs. It turns out that many proteins are modular, and if we understand what a specific module does, that tells us something about all proteins containing that module. For example, if we know that a specific string of amino acids makes a shape that binds to DNA, then we can reasonably assume that other proteins with that string probably have the ability to bind to DNA. > [@Obnoxious\_Hood\_Ornament](#): > > I guess what I’m asking, if I wanted to put it better, is if it’s possible to have two unique sets of DNA that have identical results. In computer programming, there are nearly limitless ways of expressing sets of code to generate an exact result, and I wondered if the principle applied to DNA as well. There is a trivial example of this. For most amino acids, there are multiple codons in the DNA and RNA that code for that amino acid. So, if in molecule A, all of the leucine codons are TTG, then you could go through and change them all to, say, CTA, and you’d still get the same protein molecule out. You could do the same with the other amino acids. The end result is a fairly different DNA molecule that makes the exact same protein. You could go further and start swapping out amino acids for similar amino acids - replace leucines with isoleucines, for instance. Proteins often can tolerate a surprising amount of change without strongly affecting their function. But I realize that’s not exactly what you’re asking about. ---
**Author:** ![njtt](https://avatars.discourse-cdn.com/v4/letter/n/ecd19e/32.png) [@njtt](https://boards.straightdope.com/u/njtt)\ **Post date:** [February 13, 2014, 3:37pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/37 "2014-02-13T15:37:30Z")
> [@kaltkalt](#): > > There has to be some underlying organization and meaning to all those proteins and chemicals interacting. This would only really be true if there were an Intelligent Designer. Developmental biology does not make rational engineering sense. It is not how anyone would design a system from getting from an instruction set (DNA) to a morphology. Morphologies arose by the trial and error of evolution: make a small change in the DNA and keep the outcome if it works. No account was taken of the causal chain , which might be incredibly long and complex, and different in each case, between any particular DNA change and the survival or reproduction-relevant outcome. > [@kaltkalt](#): > > How about this. My dream pet is a mini pygmy elephant. Like the size of a golden retriever, with a trunk about a foot long. How far away do you think we are from being able to engineer something like that? Someone might discover a gene controlling how big elephants grow next week. More likely they will not, and maybe hundreds of interacting genes are involved. Given that elephant size is not a particularly significant scientific problem in itself, we might never find out all the details, even if we come to understand the general principles much better than we do now. Of course, there is a method that has a good chance of being able to create a pigmy elephant for you. Find the smallest male and the smallest female elephants that you can, and breed them together. Select their smallest male and female offspring and breed them together. Repeat, over the generations, until your desired size it attained. Darwin discovered natural selection after studying artificial selection of this sort. In neither case do you have to understand what is going on inside the organisms for the process to work. ---
**Author:** ![Chronos](https://sea3.discourse-cdn.com/straightdope/user_avatar/boards.straightdope.com/chronos/32/134_2.png) [@Chronos](https://boards.straightdope.com/u/Chronos)\ **Post date:** [February 13, 2014, 4:16pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/38 "2014-02-13T16:16:12Z")
> [@](#): > > Quoth **Smeghead** : > > There is a trivial example of this. For most amino acids, there are multiple codons in the DNA and RNA that code for that amino acid. So, if in molecule A, all of the leucine codons are TTG, then you could go through and change them all to, say, CTA, and you’d still get the same protein molecule out. You could do the same with the other amino acids. The end result is a fairly different DNA molecule that makes the exact same protein. I was going to say that, too, but you might still have issues with the epigenetics. For a simple example, the organism might have evolved some restriction enzymes that don’t attack any sequences in the organism’s own DNA, but which defend against viral intrusions. Change which codons you’re using for the amino acids, though, and you might end up with some of those sequences after all. ---
**Author:** ![Lemur866](https://sea3.discourse-cdn.com/straightdope/user_avatar/boards.straightdope.com/lemur866/32/434_2.png) [@Lemur866](https://boards.straightdope.com/u/Lemur866)\ **Post date:** [February 13, 2014, 5:19pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/39 "2014-02-13T17:19:30Z")
For dwarf elephants it seems pretty likely that we would be able to do this. Dwarfism is just the result of various growth factors getting deactivated somehow. So to create a dwarf elephant, we just find the genes that create Elephant Growth Hormone, and break one of them, creating an elephant with pituitary dwarfism. [Growth hormone deficiency - Wikipedia](http://en.wikipedia.org/wiki/Growth_hormone_deficiency). It is very likely that the various dozens of species of island dwarf proboscideans evolved in exactly this way–a baby was born with a mutation that gave it pituitary dwarfism, and then a famine happened and most of the larger elephants starved while the dwarf elephant survived. But the interesting thing is that if you could breed two dwarf elephants from different populations together, you might get a full sized elephant, if the mechanisms that caused dwarfism on the two islands were different, the offspring might be heterozygous for both genes and develop “normally” into a large elephant. This is assuming the dwarf elephant populations haven’t been isolated for so long that they were incapable of interbreeding. Often mutations like this can be the result of a single nucleotide change that results in a single amino acid substitution in a critical enzyme, and the enzyme no longer functions properly. So there are probably dozens of simple ways to easily create dwarf elephants, with varying side effects. The problem of course is that elephants are large animals, with long gestation periods, slow growth, are incredibly expensive to care for, and are an endangered species. If you want to breed dwarf animals humans have already created dozens of examples, although not usually via genetic engineering but rather waiting for a trait that causes dwarfism to arise through natural mutation and then breeding those dwarfed animals. This is how you turn a wolf into a chihuahua. ---
**Author:** ![Obnoxious\_Hood\_Ornament](https://avatars.discourse-cdn.com/v4/letter/o/3be4f8/32.png) [@Obnoxious\_Hood\_Ornament](https://boards.straightdope.com/u/Obnoxious_Hood_Ornament)\ **Post date:** [February 13, 2014, 5:34pm UTC](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188/40 "2014-02-13T17:34:54Z")
> [@](#): > > There is a trivial example of this. For most amino acids, there are multiple codons in the DNA and RNA that code for that amino acid. So, if in molecule A, all of the leucine codons are TTG, then you could go through and change them all to, say, CTA, and you’d still get the same protein molecule out. You could do the same with the other amino acids. The end result is a fairly different DNA molecule that makes the exact same protein. > > You could go further and start swapping out amino acids for similar amino acids - replace leucines with isoleucines, for instance. Proteins often can tolerate a surprising amount of change without strongly affecting their function. Thank you. That’s what I wanted to know. I still need to do my homework! As a programmer I feel like this is all relevant to my interests. 🙂 [Previous page](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188.md?page=1) [Next page](https://boards.straightdope.com/t/understanding-the-programming-language-of-dna/681188.md?page=3)