biochemistry - Basic Amino Acid Residue Binding Mechanism to DNA

This question has no particular answer. There are several families of DNA binding proteins, some of them bind specifically (e.g. restriction enzymes like EcoRI which binds to and cuts GAATTC or transcription factors like lac repressor which binds a particular point of the e coli genome about 25 base pairs long) and some of them bind semi-specifically (e.g. zinc fingers which bind GC rich regions), others non specifically (e.g. the sliding DNA clamp).

For all of these proteins, they will have a tendency to have positively charged amino acids facing the DNA because the DNA's phosphate backbone is negatively charged. There are lots of protein motifs (like the helix turn helix motif) that fits into the major or minor groove of the DNA. The lysine and argenine are important because they are the positively charged amino acids. Histidine is also positively charged, but it is not as long and flexible, and doesn't seem to fit as often or as well.

http://en.wikipedia.org/wiki/DNA-binding_protein

cell biology - RNA or ribosome, which one moves during translation?

The ribosome moves relative to the mRNA by, in effect, pulling itself along it. If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses.

(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)

As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton. Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.

Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand. That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.
Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it. And I really have no idea how negligible the interactions with the tRNAs and so on are. It's a mess, but my guess would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).

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Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a gedankenexperiment. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls. Then get in, grab the rope with your arms and legs and try pulling yourself along it. While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)

genetics - Could Junk DNA be used as a Turing Machine by nature?

By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus. The answer is "no" for both. Well, sort of.

Does noncoding DNA contain information? By definition, no. There are probably many regions of the genome that appear to have no information, only later to be found to contain introns, regulatory elements such as enhancers, boundary element, MAR/SARs, targeting sites, etc. Even functional tests (such as removing the region) may not reveal anything because the effects could be minor, or only evident under special conditions. But arguably, if you remove a region and it has an effect on the organism, then it's not really a noncoding DNA, it's just you didn't see the coding before hand.

As for the latter, can it altered, the answer is again "no," or at least "apparently not." Intergenic regions (those stretches of DNA that do not contain obvious or characterized transcribed regions or their control elements) are very stable between organisms and even between species. They seem to have a mutation rate expected for having no information, and thus free to mutate slowly without being swept away. There is no evidence (as far as I know) of any region of the genome being purposefully altered, with the exception of a handful of specific genes whose regulation is controlled by DNA nicking or some such.

Perhaps I am missing your question, being a biologist and not really knowing what a "Turing Machine" is. If I misunderstood, please clarify.

life history - Has there been any observation of species adapting the evolution process?

Pigliucci gives a good review of some aspects of this topic in "Is evolvability evolvable?" (2008). He sees what you're asking about, which he calls "evolvability", as one of the key topics for the future of the study of evolution.

It's very conceptually dense evo-devo-theory, so I'll probably do a poor job trying to explain it, but he tries to set up a framework that deals not just with things like life-history (per kmm's answer) and mutation/recombination rate (low fidelity in HIV per GWW's answer, and, I suppose, the evolution of sex itself), but also with constraints that evolve at various levels to "positively channel" mutation (that is, the understanding that while mutations are effectively random, the phenotypes that emerge, and are acted upon by natural selection, are not random, but are channelled by the developmental system of the organism).

He also includes the role of development in opening up "phenotypic space" into which a lineage may evolve. For instance, single-celled organisms have a limit on size and complexity, the evolution of multicellularity opens up this huge zone of evolvability. In a sense, this is also the "evolution of evolution".

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Time from stimulus to gene expression

My understanding is that gene expression, in response to some stimulus, generally occurs on the order of minutes. I'm curious about the extremes...the quickest and the slowest cases.

What is(are) the fastest time(s) recorded for genes being expressed in response to a stimulus? What are the slowest times?

botany - What is the lowest pressure at which plants can survive?

I like your question!

Low surface pressure on Mars (averaging 600 Pa or about 1/170 of Earth's at sea level) is only one difficulty that an organism would have to contend with. In addition, mean surface temperatures are ~210 K (-63 C), the surface ultraviolet flux is extremely high (no ozone layer) and an aridity comparable to the Atacama desert. On the plus side, a 95% CO2 atmosphere might promote photosynthesis.

So, higher plants are extremely unlikely to prosper on Mars. Purely in terms of pressure, experiments suggest that at 1/10 Earth atmospheric pressure vascular plant transpiration increases significantly. So much so that they enter into a drought response which often leads to plant death.

However, lichens may be another matter. These are often adapted to low precipitation/pressure environments such as high mountains. Indeed, this article addresses exactly your question (sadly it is not open access). The authors suggest that the lichen Xanthoria elegans experiences no loss in vitality after 22 days exposure to laboratory Mars-like conditions (low pressure, low temperature etc.)!

Having skimmed this article I am frankly amazed (and slightly dubious) at the result. However, it should be noted that they only ran the experiment for 22 days, applied no ionising radiation (to simulate the high UV flux) and make little mention of the precise metabolic state of the lichen. If it has entered into cryptobiosis (cessation of metabolic processes) then it can't exactly be regarded as prospering.

• de Vera et al., 2010, Astrobiology, 10, 2, Survival Potential and Photosynthetic Activity of Lichens Under Mars-Like Conditions : A Laboratory Study

digestive system - Is it the sphincter that flexes when a human pushes a bowel movement?

Of course the sphincter muscle is at the exit point. To use a toothpaste tube analogy, if I want to squeeze out some toothpaste, it does me little to no good to jostle the nozzle; I need to squeeze the tube (which is analogous to the colon) to get the paste (payload) to come out.

So when a human is sitting on the toilet squeezing, is that squeezing flexing of the sphincter, or squeezing muscles along the sides of the colon pushing on it as one's fingers push on the tube to get toothpaste to come out.

If it's the sphincter that's getting flexed, how is that helping get a big log out?