the movie wasn't too bad. kind of slow, though.



now you're just splitting hairs   

but on the issue, it isn't just people dung... dead bodies, heck dead skin cells if they can be made useful -- all of it will likely need to be reused.

incidentally, i checked out C. S. Lewis' sci-fi triology - don't know if the trilogy has a name - but they're Out of the Slient Planet, Perelandra, and That Hideous Strength. i've been trying to check these out for a year!

I think the issue of brining livestock and agriculture to mars and the concept of teraforming are kinda hitting the same nail with two different hammers.

The be truely self sufficent, we need to implant an entire cyclic ecosystem on Mars. Everythign from Nitrogen fixing bacteria, to plants, to "wildlife". Whether on the surface, in domes, or underground, you must have 100% conservation of mass (specifically organic mass) for the ecosystem to survive or have to Import resources from Earth (like fertilizer). In addition, this would be for self sufficency only, Exporting food would remove nutrients (and thus, carbons) from the Mars ecosystem.

I think in terms of reasonableness, unless there is a significant carbon source that the colony can incorporate into its ecosystem, the colony will be dependant on Earth for organics. This isn't necesarrily bad though, as it opens up a trade lane. All of our previous discussion invlove A colony mining/making something and sending it home. Here, Mars would import, say organic waste (sewage) to use as fertilizer and export food to earth. Thus a more interesting (in terms of a book) dynamic relationship.



Our ecosystem that we would implant on mars would probably be enitely genetically modiifed to some extent. This way, we can ensure incompatibility of the different organisms, and use that to make the simplest ecosystem possible (reducing infastructure and loss of resources)

connivers and omnivores dung is good fertilizers.

however most herbivores dung has the bacteria needed to break down the dung into useful plant food.

Sory, couldn't edit my last post, but we could use genetic to alter the growth cycle of the plant, surplanting its circadian rythmn. Year round harvests anyone? That would destroy the soil, I know, but if the colony was receiveing fresh "fertilizer" every day, that wouldn't be a hug problem.

That largest problem you would have is the gradual salination of the soil (becomes to salty) We currently can make Salt resistant plants via genetic modification, but there is a limit to how effective this is. Since the soil is artifically contained, I would guess that we could simply shut down a farm unit (dome, cave, whatever) and totally remove all of the old, salty soil and replace with new soil. The old soil could be burned, maybe desalinatied to produce new soil (though still prety dead) and salt?

i don't think this would be that big of a problem to start with. depending on what kind of fertilizer you use

the majority of asteroids are mostly carbon. they'd solve that problem and not deplete the earth's resources.



i agree with your suggestion for the most part, however i'd add one caveat. i don't think we'll every be able to engineer an entirely new ecosystem. there is so much complexity, so many variables. i think we'd be much better off to introduce a huge variety of modified life forms into some sort of roughly suitable environment, and then let evolution run its course. yes, it'd take millenia. but terraforming Mars was going to take about that long anyway, at least in our discussion here.



this is why the "fertile crescent" is a dessert now. once upon a dawn of civilization, it was lush and covered with trees. ditto for Greece.

rotating crops is one of the better solutions, all things considered. the problem with genetic modification in general is that we can't always change certain things about planets. here's an example.

you should never eat wild almonds. they could poison you with cyanide. some almond trees, however, have a genetic variation in the gene that proscribes the production of cyanide. it was from these genetic mutants that all domestic almond trees of today are derived. it was "easy" to domesticate them because there is only one gene that proscribes the undesirable trait.

on the other hand, people have been trying to domesticate oak trees for their acorns for centuries, and even modern genetic science has had little success. the problem with acorns, as you probably know, is the nauseating level of alkaloids they contain. native americans of california used to leech the alkaline from acorn meal to make it eadible, but this also saps most of the flavor and a chunk of the nutrients. we've been trying to domesticate the tree, but it seems that there are several different genes proscribing the production of alkaloids. breeding one that lacks any of those genes on either side of its DNA has proven difficult, since we haven't even apperantly identified all of those genes.

genes, like ecosystems, are incredibly complex. while i think we can certainly make a great deal of headway for our own goals through genetic engineering, i don't think we'll ever be able to do better than evolution - except perhaps occasionally by virtue of dumb luck.

i still think single-celled organisms make the most sense, at least as a first step. because they reproduce so quickly, they can be modified to do what we want in an environment we want much more quickly than any given plant species, including moss (which are plants; blue-green algae might be a better canditate for the kind of things you've been mentioning with regard to moss, Danielost). we wouldn't even necessarily have to modify them by replacing genes through direct molecular engineering; it'd probably be cheaper and more stable to slowly introduce environmental factors more like those of Mars to various populations of simple, fast-reproducing life forms. it's also thought that though, i suspect a combination of the two methods would be used; if we have a tool to do something, we tend to use it.

speaking of both caves and bacteria, i'm now reminded of an episode of Nova i saw on PBS a while back: The Mysterious Life of Caves. during the show, several caves and ongoing research projects were presented that suggest many of our caves aren't formed by slow water trickle, but by bacteria that make use of sulfer in their metabolic cycle. the bi-product of this is sulfuric acid, which eats away at the limestone or dolomite that is the rock wall of most caves. we could use them to build our caves on Mars. or course, then we'd have to contend with our homes being full of sulfuric acid   

Yes, but we might run out of asteroids.



The best thing to do is generate a simple environment and then let creatures evolve into a new creature that can live on mars and still be edible.



Let me restate that... The best way to survive ANYWHERE is to use everything and waste nothing.

true. but then there are Jupiter's trojans and greeks, the centaurs, and the Neptunian trojans, plus all the moons all over the place. that's a lot of building material.

also, carbon has a special place in fusion physics. at least stellar fusion physics. everything that's atomically lighter than carbon can be fused to release energy, but fusing carbon requires energy input. in other words, carbon could be a natural bi-product of highly advanced fusion technology.

and if we need stuff to fuse, there's always the Kupier belt, the scattered disc objects, and the Oort cloud. from what we can tell so far, they're mostly water and methane ice (plus methane contains carbon). in general, they'd be a useful resource to exploit (given the time and economics to support it).



agreed. except perhaps instead of saying "a creature," i'd say "a biome."



agreed.

edit: the centaurs are actually also icy... and i couldn't find details on the Neptunian trojans.

Actually, iron is the last element that can be fused to release energy.

oops, my mistake. you're indeed correct. i think i was confused with the CNO cycle. though technically, iron is the product of the last energy-releasing fusion, no? (now i'm splitting hairs). but the point remains: carbon can be produced via fusion. and actually if we're willing to input energy, couldn't we produce just about any element through fusion?

Since every elemental atom is made of protons, electrons, & nuetrons, you could technically make any atom by rearanging the protons etc.

I don't know if fusion would do it alone....

i was reading up on the discoveries/creations of the superheavy elements last night, ununtrinium through ununoctium (atomic numbers 113-118). they're created in particle acceloraters. technically the process that creates them is fusion, because it's two atoms becoming one (well, actually, it was two atoms becomming two different atoms, in the method they employed). the reading i did made it seem that this wouldn't be anything close to a method to produce usable amounts of those elements (for example, IIRC only 3 atoms of Uuo have been created so far).

but at least if we can mimic solar fusion we can produce iron and everything lighter than it, and those are some of the most useful elements anyway (carbon and aluminum come to mind immediately)

True, we can make any type of element we wish. However, heavy elements must be made one at a time, in a massive, energy consuming particle accelerator, which just isn't practical. However, for light elements, just starting the fusion of one will release enough energy to fuse the next, and so on, so all we have to do is A/ ignite it, which could be done with a few particles of antimatter, and then B/ prevent it from blowing up the factory. This takes significantly less energy and time than making heavy elements, so it is only these elements that we could mass-produce and use in building other things.

It's actually easier to mutate the singled cell to do what we want rather than allow evolution to take place. Case in Point: I used to work in a lab (doing genetic modifications acutally, lol). I can give a bacteria antibiotic resitance and grow millions of them in aobut 2 days. It took almost 40-50 year for antibiotic resistant bacteria to really start showing up in hospitals. In addition genetic modification has multiple advantages over evolution. First pff, we can use markers to track and control the species and remove other contaminating species. A simple system like the Lac Z or anitbiotic resistance, etc would garuntee that Only our species is present (no competition for resources with that contaminating species that say, might not be edible ar harvestable). Secondly, you can use genetics to ensure domesticity. Whie this is against the grain of "Terraforming" we can hinder our crop species so that they remain reliant on us. Perhaps by making it so they cannot convert natural carbon/mineral resources present and rely entirely on fertilizer that be provide (that we can make in a factory using the natural carbon/mineral resource of the planet). This would keep our species from reproducing out of control or unbalancing our "ecosystem"

Evolution is random. There is no garuntee that what will happen is what we want to happen. And what if our species doesn't evolve right? Think how many species go extinct. Genetics work, especially on animals and some plants. Is very very tricky. But we can already do many amazing things with genetics and I think we'll be able to do a lot more in the near/far future.

I was never in fear of being infected by my antibiotic resistant bacteria. Never. And it was for those reasons above. It couldn't survive outside of the test tube cause its ability to process food was genetically limited so that it could only process food that I gave it (amp-LB). I don't have LB in my veins, although I did spill some on my pants once... But the point was that I was in control, not at teh whims of evolution

Well, we have a big fuel storage of hydrogen real close to us. The Moon. Free hydrogen is trapped in lunar soil and rock. If we had a base there...there would be plenty of fuel. First step... permanent settlement on the moon. Just my 2 cents

denyasis,
your last post interests me greatly. i wanted to respond earlier, but i didn't have time before leaving work, and i've had a busy evening. i will reply tomorrow. as a prelude, i don't disagree; truth be told, genetics and molecular biochemistry are the areas of biological science in which i have the weakest understanding. the point is, i'm very glad to have someone with first-hand experience in a genetics lab involved in this discussion. had i realized earlier, i may well have cut short my discussions of propulsion. at any rate, thank you very much for your reply. i look forward to my next post (and hope you'll see it and be interested in some of the questions and speculations i have).

I was in the Engine part and was read and i would choose Ion Engine for short distances..... An Ion Eninge used on the NSTAR goes 62,000 mph or about 17 mps and the SOL is about 180,000 mps and the faster u go the more hard it is to achive SOL since the vessel keeps getting heavier. Also u need to have something to protect against space partivles that can break through a bessels hull at higher speeds so u need to have shields or something like triple hull to protect the crew and the vessel as u go faster.... To achive SOL will be near impossible as of now and in the future for years if vessels get heavier as the faster they get... most of this is theories like SOL stuff but protection part is true that is y shuttles, probes, satallites have this one like armor which has layers to protect the equipment on board......

so i guess the broadest question i have about the point you made is this: how do you know what gene sequence to splice into the bacteria's DNA that will give it antibiotic resistance? was it recomined from existing super-bacteria, is it a matter of trial and error? can geneticists read a DNA sequence and have a sense of the proteins it proscribes?

i'm asking because it seems a lot easier to create super bacteria in a lab because we already have super bacteria in nature, and we alread know the trait the gene variations proscribe.

what if you wanted to take anartic blue-green algae, and engineer it so that it can survive in a much thinner atmosphere, with less sunlight, make sure it's tolerant to fairly large amounts of rust, but yet it also, given what it has to work with, has a super-charged photosynthesis cycle. tall order, no? i'm not so much asking you for the minutiae of the process, more just your opinion of how difficult something like that would be, and the general process that'd best achieve the goal.

the topic of genetic engineering interests me for more than the sake of terraforming. i also have this idea for later in this series: if human beings do indeed colonize relatively distant star systems, such that trade isn't really economically worthwhile, cultures would drift. perhaps some of those human cultures would engage in violitional evolution: i.e., genetically engineering their own offspring.

...this part is becomming tangental, so anyone plese feel free to chime in. the idea i had in mind specifically related to a mutation of ear physiology. what if some of the 'hair' cells in the inner ear, which are genetically programmed to detect sound vibrations, were suddenly laden with magnetite (the most magnetically reactive mineral known, Fe3O4), and part of the brain were wired to "hear" magnetic fields? that seems far fetched, of course - sort of a "where the heck do you start" question with relation to genetic science, and a "what's the point". sensation really interests me; that's the point (for me at least).

what about something on a much smaller scale, like giving us the ability to smell a greater number of chemicals and in smaller concentrations than we can now?

of course, the problem with making the senses more accute is that it (is believed to require) a corresponding increasing in brain size. but many neuropysiologists believe our brains can't get any bigger. if our crainia got bigger, we couldn't pass through the birth canal safely. if the birth canal got bigger, women would have problems moving and standing. and our brains already seem to be at maximum density. about all we can do, given known physiology, is use our brain mass differently. though, i can point out that in a science fiction world, we could increase brain size without worry of the birth canal if all deliveries were via caesarean section.

so, this is a change in topic, but i hope no one takes that as a cue that previous topics of discussion are 'closed' or anything.

Dystopic

I'd be glad to answer your questions. Keep in mind though, I haven't worked in a lab for over a year (I'm doing the police thing now, lol). I went to school for forensic Chemistry (half chemistry, half genetics+micro). I also did Lab work mutating E coli and Yeast for about a year (part of a larger project studying specific proteins), So I hope I can answer all your questions.



Both. Right now with current science, we can make DNA sequences from sctarch. Its expensive. The ones I orderd from a catalogue were 20 Bp long and cost $200+. For reference, a simple bacteria or yest gene can be 1500 Bp long and much longer. Animals and plants are plain huge (thousands). As you can see, Currently custom builing our own gene isn't practical. So when we insert a new gene into a different organism, that gene had to have existed in another differnt organism. It essentially is trial and error and basically works like this:

Find Bacteria with the trait we wish to study (in this case Antibiotic reisistance to AMPicillin)
Code its genome - get the DNA sequecence for the bacteria.
Find genes - ID all the different genes. This doesn't mean we know what the gene codes for, just that there is a gene there.
Elinimate obvoious genes - Most genes are very similar between related or similar species. Our genes for hemoglobin are not much different than hemoglibn genes for other mammals. So we can immediately eliminate the genes that essentially look like genes in other bacteria that aren't AMP resistant. This gives us only a few "unknown" genes left.

Now we can take these genes ( We'll call them A, B, C) and put them into different bacteria that are not AMP resistant. 1 gene per bacteria. We then grow the newly mutated bacteria in AMP-LB (bacteria food with AMP mixted in). If after 2 days, The A colony has grown, but the B and C colonies have not, you've ID'd which gene has the anitboitic resitance!

That's a really really simple version, and there are alot of other ways to ID genes. I Know there is a lot you can do on the protein side, like Identifiying the proteins that casues Amp resistance and then looking at the protein to decipher part of its genetic code, thus giving you something to look for when searching for genes, but my protein experience is very thin, and I'm not to sure of the limits of that ability.



Yes and that's the second part. We can't do it realy well, as the gene describes a 3 dimentional protein, and some proteins are made of multiple parts that are interlinked. Most of the research into finding out what a gene does, come from destroying it. We break it and see what the organism no longer makes or can no longer do.

Also keep in mind that when we do do mutations, its not always a simple transplant. We can splice genes together to make fusion proteins, or chop genes down to make simpler proteins. For example I can smash the gene I wish to study together with a bioluminesence genes (Its really trippy cool - but essentially its the ability to glow in UV light). After I insert the gene into my target organism, I can tell if the organism has A) accepted the gene and is producing the protein that the gene codes for when I shine the UV light on it.



hmmmm, let me think. I'm gonna tell you, that right now its probably out of the realm of our science. Genetically engineering Eukaryotes is very tricky due to the more complex organization of the DNA (Junk DNA, Silencers, enhancers). Essentially, if you can find an organism with the trait you want , its should be possible to insert the genes for that trait into your aglea. We've taken genes from bacteria, fungi, etc and placed them into common plants like tobacco and corn with a lot of sucess.

There are limits though. Our Vectors (the Plasmids [DNA rings] we use to insert genes) have limits to how much they can hold in terms of genetic info. If they get to big, they won't be stable. So there is a size limit to how much DNA you can stuff into an organism. Also, some organisms don't take to Plasmids very well (like us!). You can try to insert a gene directly into the genome, (like the Ti binary Plasmid system or virus), but there is a chance you'd damage the host genome, but that's ok, as if you do it en masse, the damaged organisms will live and reproduce, elimiating that problem.

You can pretty much only do one mutation at a time (to difficult to track problems and ensure sucess). The only way I can see us accomplishing this would be like this:

Take our Algea
Add in Gene 1 via Virus directly to the genome
Grow a few generations - test to make sure the gene is there and works (via immunoassay)
Add Gene 2 via Virus direct tot he genome
Grow a few generations - test to make sure the gene is there and works (via immunoassay)
And on and on



I remember reading there there are organisms that can detect the magnetic feild of earth. I believe it was same birds. Something about an Iron type deposit in their brain. Sorry, Zoology isn't my strong point. But like I said, if the trait exists, with some work, there is a chance we can move it to another organism. I doubt moving a trait from a higher organism to a lower organism would work though, so you have to be careful about that. Ex. Giving a bacterium the genes for our nose won't result in teh bacteria growing a nose. So, with the bird, you could only really move it arounf the higher animals. Also remember a trait doesn't not necesarily mean 1 gene. The ability for a bird to detect magnetic feilds could be the result of 10's or more genes. Moving this many genes and making them Work in another organism, probably wouldn't be possible.



Hehe, its a catch22. Simply add genes that code for new receptors (the things that let us smell) and some how get them to express themselves in the nose (tricky part). Here's the evil catch, with complex organisms like us, our cells differentiate. A liver cell doesn't use DNA that intended for a nerve. With single celled organisms, adding a trait is easy, give it the gene and tell it to make the product. With higher organisms its much more difficult. Not only do you have to get the gene to integrated into the genome, you have to get the (we'll say human) human body to express that gene at the proper place and time. We're still looking at differentiaion and how it works, but from what I know, you could pretty much set the new gene up to look just like a normal nose recptor gene (same Silencer, enhancers, promotors, GC content) and hope it works. Unfortunately we don't have control of where a gene goes when its shot straight into the Host genome so it could be shot in to a regoin of DNA that isn't used much (atleast by the nose).

Its not impossible, I know we've inserted genes into higher animals, but its not easy. And generally, they are generic Genes, for biolumenesce or something that is not specific to a system or tissue type. There are many many more variables compared to a single celled organism (everything from Size, to DNA organization, to immune systems).

I hope that answered your questions. If you want specifcs or anything, Id be glad to help. There's a lot about genetics that we do know, and we can manipulate genes very well in that regard. However, there is even more about genetics that we are still tryig to figure out, and thus we are pretty limited with what we can do. In addition organisms are so different, that what works in yeast, won't in bacteria, or in a plant, or human. There are a lot of catches.

Peace!

Can someone simplify what Denyasis just said?

If I read that whole post, my head would explode!

P.S.=Holy cow that's one huge post!

denyasis, thanks for the thorogh explanation! i think i understood it for the most part.



i'll take a stab at it.

very short version:
genetic engineering is very possible with our current science, however achieving many of the fanciful ideas of super-human power that we encounter in science fiction would very complicated and very expensive.

longer version:
producing new traits through genetic engineering is done by mixing a number of methods. this makes sense; most scientists employ every appropriate method at their disposal. sometimes they take pieces of one organism's DNA and put them into other organisms, which may or may not be closely related to the donor organism. we can take genes that make certain animals glow, such as jellyfish, and put them into other animals' genes to make them glow. take for example, Alba, the glowing bunny.

however, genes for "new" traits are typically taken from organisms that already have them, so something like titanium bones (which has no known genes to cause it in an organism) probably wouldn't be possible. also, engineering any new trait into a multicellular organism is a lot more tricky than bacteria and other single-celled life forms. our original cells, as the slowly devide while we're en utero, start behaving differently, and eventually turn variously into heart, brain and prison cells. no, wait, prison cells come later.

the reasons this happens are still not completely understood. part of the thing about genes is that they interact with the environment, so that in one set of conditions, they might be active, but in different conditions they won't be. one of my science teachers once said that you can view multicellular life forms as colonies of highly specialized single-celled life forms that happen to share the same gene sequence. it's just that some of those cells receive enviornmental cues to turn them into brain cells, while others, muscle cells or liver cells or what have you.

denyasis, i do have one more question, as well as a slightly more substantive response. i had a different idea of 'trial and error' in mind when i originally wrote the words, though your use of the term made perfect sense. i guess i had more the idea of, "well, this gene is for a nose; i wonder what'd happen if i replaced it with a random sequence of nucleotides." but from your response, it sounds like that isn't even really possible.

the comment i had was in response to this:



are you familiar at all with current nanotechnology research, or scientifically grounded speculation about where it could go? i specifically have in mind medical nanorobots. though 'robot' is a bit of a misnomer for what i have in mind.

i'm imagining engineering a molecule that'd sort of act like a virus, but it'd be chemically structured such that it could only act on a very specific sequence of DNA. so let's say you want to change a realtively small sequence of nucleopeptides, we'll say they spell GATACCA for the sake of discussion and amusement (the movie's title was intentionally spelled only with letters that stand for nucleotide base pairs). but being so short, the GATACCA sequence can be found on many points in the whole genome. what you'd need to do, then, is start looking at the base pairs on either or both sides of the particular GATACCA occurance you want to affect. a computer could determine the smallest sequence of non-repeating base pairs (i.e., a sequence of base pairs that includes the GATACCA you're targeting, but isn't found anywhere else on the DNA strand). a supramolecule could then be engineered that'd only react to that particular sequence, swap out the GATACCA for what you want, and then either break down or become totally inert.

i'm not envisioning this as a viable gene therapy for an even partially grown organism, but it seems like it'd solve the no control issue of where a spliced gene ends up. what do you think?

(and as for treating genetic diseases, i think the most likely form that will take is protein replacement and supression therapy; if we supress the maladaptive proteins that defective genes proscribe, we supress the disease, AND we give the medical industry a new crop of drugs they can charge people for throughout their lives).

I was going to do some of my own explaining, but denyasis seems to be much more familiar than I.

Though I wouldn't recommend placing magnetite in the ear. All that would result was an ear-splitting headache, until the hairs became totally defunct. Besides, don't creatures that use magnetic sensitivity do so in order to navigate? They would have to be able to extrapolate the direction of a magnetic field, not merely the presence of one.

Just implant a compass in everyone's head.



Actually, we already have part of what you propose. DNA profiling used in criminal investigations works by (gel electrophoresis?) using a few enzymes to cut specific short sequences in the DNA, resulting in chunks of different sizes. Then an electrical current is generated, and the smaller pieces are able to flow more easily through the gel substance, while larger pieces have more drag, so the result is the little bars where the pieces have settled. What you seem to be proposing is an enzyme which not only cuts a certain segment, but replaces it with a new one, right? This wouldn't be too far a stretch, I think.


Not related to genetics, but related to sci-fi: what were you envisioning being used a fuel sources in the future, particularly on other worlds?

fair enough; cybernetics could just as easily be "the" major science as could genetic engineering. and actually, my university does some very interesting projects along those lines.

for example, UCSD's cognitive science dept. is working on developing a much more advanced method of brain imaging that could in principal lead to the ability to 'read thoughts' once properly calibrated.

i've also heard that the bioengineering dept. has several ongoing projects to develop neural interfaces for prosthetic limbs, though i couldn't find any links for that very easily.



well... i'm not so sure. it sounds like the gel electrophoresis sounds sort of random, though i think it at least helps provide some of the theoretical insights. the tougher challenge to what i described would be engineering those custom molecules to perform very specific gene splicing (or engineering highly complex molecules in general). i suppose it might be just as easy (difficult) to engineer a molecule that could reassemble and chopped up DNA strand, so who's to say?



do you mean fuel for propulsion, or fuel for power? well, it's basically the same question, just a matter of energy conversion.

i think in general we'll probably try to gather as much power as we can. so any natural, renewable source on another planet would eventually be exploited: wind, solar, geothermal and tidal power, where applicable. planetary travel would, i imagine, be carried our on battery power. but i think i the end, fusion will be our most reliable energy source; i mean, it's already the universes main source of energy, right? i also think it'll be the best means of propulsion, gathering interstellar hydrogen, comprssing it, and using small amounts of antimatter to fuse it. sort of like detonating a small hydrogen bomb every few seconds (or minutes, or whatever). and yea, throwing a particle accelorater onto a space ship would make it huge and expensive, but i never imagined colonizing other star systems would be cheap.

I'm very very familliar with the latter. And you kinda answere you own question here:



There are known genes in many organims (including ours - ALU is the most famous, I beleive) that are called Jumping Genes. These genes have the ability to phyically move their location in the genome.

Taking a step back, enzymes that interact with DNA do so in a very very specific way. The enzymes that millertime335 mentioned are called Restriction enzymes. In nature they are bacterial defensive enzymes. Bacteria make these enzymes to breakdown foreign DNA (like from a virus). These enzymes are highly (like 99.9%) specific under the right conditions. What they do is they will find a peaice of DNA and move along it until they find a certian code (usually 3-7 bp long). When they find this code they will cleave the DNA stand. Now denpending on the enzyme, they will always cut the Stand in a certian way (a clean break - blunt ends, Sticky ends 3'-5', or sticky ends 5'-3'), thus destroying an infecting virus. How does tha bacteria keep from destroyinh its own DNA? Simple, the bacteria's DNA doesn't have that Code pattern anywhere in its genome!

Inscision systems like ALU and other methods that would insert DNA into a host genome (like the way a virus does it) are very very specific. However, the specific sight they will insert them selves into, like, GATTACA (Have that movie, I like it!) may be numerous, and thus there are multiple possible insertion sites. It would be even more problematic, if the Gene inserted itsself into the DNA coding for a functionally important gene! This is why its pretty tricky.



Actually the opposite. Gel and Capilary electrphoresis are THE analytical tools for genetics. We can tell the difference in size down to 1 bp (one nucleotide). millertime335 Pretty much explained it to a T. By using Multple Restriction enzyme digestions, we can make a restriction map of a Gene or Genome using electrophoresis (ie, find every restriction site physically in a gene or genome). This is how projects like the Human genome Project get started. Their end project was essentially a set of gels that separated chunks of DNA base pair by base pair and by nucleotide. Thus starting at the bottom of the gel, they could read the code.



Not quite. We no longer using restriction digestion for criminal DNA typing (we used to With VnTr's). My traing and education was actually spefically geared toward DNA Typing, and the modern method is via PCR (using STR's). Most people think that DNA typing is people in a crime lab reading the actual coding of your genes. This is myth courtesy of CSI and the like. First, we don't look at genes, essentially, from a practical standpoint, everyone's genes are the same (my hemoglobin gene is the same as yours, same with my seritonin gene, etc). We look at the Junk DNA. Secondly we don't actually decode the genome. We arealdy know what it says. We are actually looking the the Size of specific sections of junk in your DNA. These are more variable between people. Thus things like electrophoresis are really helpful since we separate people by essentially how "big" sections of thier DNA is. Genetics work is weird in that some of the major techniques and tools are a lot simpler than many people would think (separate by size, woa!)

Essentially we take a part of your DNA and make about 1 or 2 billion copies of it (artifically - in a test tube)using a process called PCR. After we've made that many copies we run it through the gel along with some standards, and other coparison samples (like DNA from blood left at a crime scene). The sections of DNA that we made a billion copies of will separate by size (along with all the other samples). We then compare the location of the bands of DNA to each other (that's why we made a billion copies, so its visible under UV light when treated with, crap, I think it was ethidium Bromide) to see if your DNA matched the DNA of the "evidence". Here's a little more info about it, along with apicture so you can see what it looks like.

Again electrophoresis, is well the number one Tool used in Genetics for looking at DNA. Everything from Sequencing DNA (finding the actual code), to typing, to making sure my mutations I did in lab are present in the new organism, is done using electrophoresis



We can do that with DNA Ligase (its a natural DNA repair protein). Its how we do mutations on single celled organims. We insert our gene into a plasmid (a ring of DNA that usally contains multiple genes) using the ligase and then transform the bacteria by inserting the plasmid into the bacteria. An inseresting thing about genetics is that most (probably almost all) of our tools are natrually occuring. When we make or copy or smash DNA together, the enzymes we use are naturally occuring proteins. There's no way we could do what we do with normal chemistry, nor can we artifically create our own protein from scratch (too complicated). All of our enzymes and proteins we use for genetics are harvested from nature (well, grown in a factory, but you get the idea).



I remember leanring about differentiation in a Class, so I went back to my books. We have a pretty good idea of the basics from doing Studies on Insect developlemet.
Essentially pre-birth developement is controlled by the Genes of the Mother. We found that when the Mother created an egg (remember Insects!), the chemicals in the egg are not homogeneous. Instead there are concentration gradient of various proteins throughout the egg (essentially, "pockets" of proteins in a spevific spot in the egg) As the embryo develops and grows it comes into contact with these "pockets". These proteins then activate specifc genes in the Embryo, causing the cells to differentiate. ie, Grow a head here, grow a tail here, etc etc. You've all seen pictures of larva with two head or two tails. That's because we've altered the Mother's DNA to put "Head protein" in the front and back of the egg (or "Tail protein" for that matter). Again a major part of genetic research is accomplished by breaking genes and seeing what happens (also pretty weird huh?). It's beleived that a similar, but more complicated process, works for other complex organisms like us.



That could be in teh realm of possiblity in teh near future. I don't know much about nanotech, but there are a lot of natural proteins that interact with DNA. Especially with higher organisms, like us. We have Tons of proteins that do everythign from "activating" genes to supressing, to repair, to diagnotstics. I'm by no means an expert on proteins, but I beleive the basic chemistry of these how a protein interacts with a DNA (like how it Physically attaches) is partially understood. I know its not perfectly understood mechanically, but if we can figure out which region of a protein interacts with a DNA strand (which we can do and we do know for the most part, depending on the protein), we could artfically created that region and say attach it to your nanorobot.

Right now we do it in reverse, we still have to study the protein to figure out what its active sites are (like the DNA binding site). Once we know that, the whole nanobot thing looks more promising. But keep in mind, that protein binds to a specifc site of DNA. Looking a Peice of DNA and figuring out what amino acids you need to build a binding site is still scifi. Mainly because, we know that a site on a protein binds to the DNA, but we're not totally sure of the actual physical chemistry and interactions between the two (like is it ionic? Do H bonds form? Does it cause a structural change in the Protein? If so how? what Other structure of the protein are used in a secondary fashion durring the binding? are they required for the nanobot?, etc etc). We are learning more every day, so I would expect in teh near future, for many of these questions to be answered.



Yeah sorry about that - I prolly got a little excited. And it seems to have happened again here - But I really hope it helps and gives us some food for thought. That and I'm going away right after academy gets out tomorrow for a few days (yay mini-Vacation), so I'm really just trying to distract you until I return!

i for one have no objection to lengthly posts. my honor's thesis was an 80-page ethnography on body art and modification, which i almost completely re-wrote 3 times. that means i had to read the whole thing through at least 3 times (it was more like a couple dozen). and yes, much food for thought. i'll finish digesting it tomorrow (had a mini-vacation tonight myself, to the bar, which was actually to celebrate a trip i'm planning next year to scotland to get in touch with my ancestry).