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)

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?

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   

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.

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?

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)

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

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).

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.

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!

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?

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!