Line #69 Analysis/LegoGenetics


1	!!The RealLife comparison:
2	Despite what movies would have you think, the area of genetics is vastly more complicated than "Add a pinch of X" or "Swap Y with Z". The basis of such inaccuracies come from the simplified way genetics is taught in middle and high school: The double-helix is like a ladder, with the rungs being nucleobases Adenine, Cytosine, Thymine, and Guanine. Each rung fits together, A to T, and C to G. Mix each rung around and presto! You got a tail! This is also how it's portrayed in movies with CG effects showing the double helix spinning around, taking out one rung and putting another in, with the whole thing glowing to show how it's been affected.
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4	This trope gets even stranger when the genes in question come from somewhere besides Earth. DNA is not just "genetic material." It's a specific molecule that we humans, and almost every living thing on Earth, use. It's one of boundless possible candidates for the job. Viruses may use DNA or its sister RNA for their genome. There's no reason to think extraterrestrial genetic material should be the same as ours--although there's no reason that it ''wouldn't'' be the same, either, if it emerged in a biochemically similar environment.[[note]]That's a bit of a debate: Is the terrestrial method for complex life--cells consisting of water solution contained in lipid membranes with proteins for structure, with DNA to store genetic information--a product of random chance, or the "path of least resistance" for life that would most likely appear on most planets with carbon-based life?[[/note]] Additionally, DNA contains lots of special little sequences besides genes. These include viruses that simply hopped onto our DNA and get copied with it (endogenous retroviruses), sequences which are apparently just "junk" we can't get rid of, and sequences which tell cells how often to turn on each gene and when to shut it down. This also requires that almost all living cells on Earth interpret a gene the same way. That's the genetic code; almost all cells interpret a particular sequence of three "rungs" to mean the same amino acid when they turn the gene on and start making protein. Yet when the plot demands it, an alien has DNA and all the ancillary stuff to be compatible with our genetic heritage. That's so absurdly improbable that if an organism from another planet were to have DNA at all, rather than some other possible molecule, most scientists would immediately start wondering if we had a common origin (or scream "Hoax!") In fiction, aliens have DNA and interpret it just as things which evolved on Earth do. NoBiochemicalBarriers indeed! Just slap it into our cells and away we go making a HalfHumanHybrid and more.
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6	It should be noted that gene therapy, the alteration, addition or removal of existing genes in an adult organism, [[TruthInTelevision exists]]. Yes, we no longer need the more atrocious method of Eugenics to eradicate debilitating genetic diseases. However, it can be more problematic than presented in fiction, and can wear off after a little while. Additionally, it normally requires very complicated surgery (or the use of gutted viruses) to carry out; you can't simply inject some foreign DNA into your blood and wait for the mutations to take place. However, evidence for the plausibility of gene therapy lies in the existence of Endogenous retrovirus DNA. One of our ancestors got infected by a retrovirus, which made its way into the said ancestor's germ cells. Bingo! Now his/her children inherit the virus DNA with the parent DNA, until this day. Some of the endogenous retrovirus DNA has since mutated and became junk DNA, but some of those viruses are actually still active and facilitating mutations and evolution, for better or for worse (like helping the embryo implant in the womb, or playing a role in several diseases).
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8	Addition of genes via plasmids (segments of DNA or RNA transplanted between organisms) also exists; it is how viruses reproduce and how bacteria and small beings can adapt. In genetic transfer, plasmids are faster and more efficient in propagating beneficial genes between species than sexual reproduction (which was only useful due to multicellular organisms lacking plasmid capabilities), and this is why bacteria can share antibiotic-resistance genes so fast and easily. Human experimentation has reproduced this, but this is limited to adding new traits to ''cells''. So far, said cells may propagate, successfully integrate into an organism and produce a blood vessel network, but this can only happen in the embryonic stage, and in most cases are yet incapable of forming complicated structures typical of most organs by themselves. However, genetically altered cells may still be used to produce proteins and hormones an organism wouldn't be able to create naturally due to genetic illness, for example giving diabetics the capability to produce insulin and live normally.
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10	!!The Hox Genes
11	Genes generally break down into a few main categories: The first type is regulatory, which makes sure the right chemicals are in the right places and cells are doing the right things at the right time. The second type codes "recipes" for various proteins, enzymes, and other processes that the body carries out. The third type serves as blueprints for building various tissues and structures within a creature.
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13	The fourth type are the Hox genes, and they, plain and simple, are what make any multicellular life more complicated than a jellyfish possible.
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15	Research and experimentation into these genes and the [[JustThinkOfThePotential staggering potential they present]] is somewhat young, and warrants careful handling by potentially invoking 5, possibly 6, of the [[ScaleOfScientificSins Scientific Sins]] simultaneously. What ''has'' been learned so far is that hox genes are potentially the most important, and some of the oldest, genes in life as we know it.
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17	The Hox genes are an extraordinarily old chunk of DNA which seems to date back to the first organism with proto-limbs and a vague concept of bilateral symmetry. They are found virtually unaltered in all branches of complex life, and as best we understand them, they serve as the basic toolkit all complex organisms use for assembling various types of tissues, and generating, maintaining, and regenerating a body plan. These are the genes that tell the body things like how many limbs it should have, where they should be placed, how to assemble its scales, skin, feathers, and/or fur, and what colors these should be. They are the reason that you have ten fingers and ten toes, and none of them are on your head. If you ''have'' more than ten fingers and/or toes, and/or if any of them ''are'' on your head, you can probably thank the Hox genes for ''that'', too. These are, in essence, the bricks for playing Lego Genetics.
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19	A good way to understand why the Hox genes are so important is thinking of DNA as exactly what it is: a wetware operating system with all of the convoluted strangeness you would expect of an open source project a few billion years old. In this analogy, the Hox genes are the DOS- the part of DNA that makes DNA able to read, organize, and execute particular sections of DNA based on the cell's position in the body, and functions ''very'' similarly to "syntax calls" in computer code, The most fundamental purpose of the Hox genes is to form the Homeobox; the genetic equivalent of an ".init file" for both an organism, and the individual cell. This is a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting the organism's actual structure from head to tail, each chunk of which triggers a particular "programmed" set of genes flagged by a matching ~6 nucleotide long sequence[[note]]Think of it like a search of a digital photo album displaying all pictures tagged "beach"[[/note]].
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21	Translating this into pseudo-code, a fruitfly would read roughly something like this:
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23	!!!the homeobox:
24	--> do(LAB,PB,DFD,SCR,ANTP,UBX,ABD-A,ABD-B)
25	->returns: fruitfly body
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27	!!!What the genes link to:
28	->''define LAB:''
29	--> all of the following structures belong in the center front section of the area to be designated as "head"
30	--> build(top_of_head),build(limbs(short)[[note]]limb.type defaults to "antennae"[[/note]]),build(brain_eye)
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32	->''define PB''
33	--> These structures belong below and behind section designated by LAB
34	--> build(mouth),build(larynx)
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36	->''define DFD:''
37	-->everything before this is "head"
38	--> do(REAPER)[[note]]Acutal name of a gene that creates pinched neck of fly in larva by killing off tissue cells behind head en-masse.[[/note]]
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40	->''define SCR:''
41	-->everything after this is "thorax"
42	--> build(limbs)
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44	->''define ANTP''
45	-->set limb.type for previous and all following pairs of limbs to "legs"
46	--> build(limbs(long))
47	-->set can_have_wings_? = yes
48	-->@thorax build(wing)
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50	->''define UBX''
51	-->set can_have_wings_? = no
52	-->build(wing)[[note]]Normally this makes a pair of halteres, a tiny wing modified into a balance/airflow sensor- if the gene turning off wings here is damaged, the fly will have ''four'' wings, the reverse is true for the wing-promoting gene in ANTB[[/note]]
53	-->build(limbs)
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55	->''define ABD-A''
56	-->build(abdomen_a)
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58	->''define ABD-B''
59	-->build(abdomen_b)
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62	What is interesting about these genes is that they are ''exactly'' as modular as this would make it seem. The Hox genes do not code for the structures they build; they only tell the body that the "genetic pathway"[[note]]the genetic equivalent of an .exe file, basically[[/note]] with this particular flag should be executed at this particular place, with these particular settings. This system is quite flexible: like a really good or really bad contractor, when the blueprints ask the body to build something odd and the measurements its told to use don't quite add up, [[MacGyvering it just makes it work as best it can]].
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64	The ramifications of this "eh, close enough" method of body assembly might be obvious at this point to anyone who has played with a Mr. Potato Head: one common mutation in fruit flies creates a SequenceBreaking error by moving ANTP to run before SCR. This sets the normal call for the previous and all following limbs to be legs, when the last set of limbs declared are ''supposed'' to be antenna. [[BodyHorror The result is a fruit fly with perfectly formed legs on its head instead of antenna.]] Another duplicates the ABD-A call: this gives you a fly with an extra body segment. Essentially, when the Hox genes are altered randomly, BodyHorror ensues because a developing embryo or creature undergoing {{Metamorphosis}} will build whatever the Hox genes and the gene pathways they point to tell it to build. The vast majority of five legged chickens and one eyed cows are caused by errors in the execution of the Hox genes; essentially the biological equivalent of a GameBreakingBug or KillScreen.
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66	The JustThinkOfThePotential sets in with this: All organisms use this same basic template, and tweaks in what the Hox genes activate are what leads to whether a creature has feathers or scales, hands or fins. In many cases ancestral traits are still found buried in DNA- it is simply that the organism's Hox genes are no longer linked to those now useless chunks of DNA, and they are essentially junk, never to be expressed. For just one example of the real-world implications of the Hox genes on the TwentyMinutesIntoTheFuture future front, numerous scientists have suggested that a pseudo-dinosaur could be reverse engineered out of a bird by tweaking its Hox genes. Birds retain the genes for saurian jaws and teeth and clawed hands, and experiments have shown that is a fairly simple matter of artificially activating these sequences and deactivating the bird sequences at the right time in embryo development to create a creature that bears a startling resemblance to an embryonic dinosaur.[[note]]None of these have been allowed to develop past the early embryonic stage due to ethical concerns, for the record.[[/note]]
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68	In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embryo and creating a butterfrog]]. Where the trouble comes in is tweaking the Hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be slightly complicated. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solving the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then figuring out how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And how to make swarms of butterfrogs NOT hunger for human flesh.]]
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70	Further than that, once the Hox genes are fully decoded and well understood, the only thing really preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombardier beetle]] DNA, and the ethics of CreatingLife knowing that it might take dozens, or perhaps hundreds of [[FlawedPrototype beta attempts doomed to live a short and unpleasant life]] to work out the kinks in your bad coding.
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74	In essence, the potential [[ForScience for scientific advancement]] is there; the bigger issue is finding ethical ways to go about it, and being certain that we aren't just PlayingWithSyringes.
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76	For more information, try UsefulNotes.{{Genetics}}.

Context Analysis / LegoGenetics