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Why do we age? or Do we have a theory of senescence?
There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of telomere length during cell division.
My hand-wavey idea would be "wear and tear".
Are we anywhere near a consensus theory of senescence?

This is one of the subjects where -- in my opinion -- there can't be just a single dominating theory, at least not now. As in many other areas of biology, many different theories do co-exist here and the reality seems to be a mix-up of them all.

Can you explain why there can't be a single dominating theory? Your comment suggests that in the future we might have one. I find this a fascinating subject - since so many pathologies are age related, surely a "theory of senescence" should be one of the primary focuses of medicine..?

The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.
To set up the argument, we need two things:
First, each individual has got a 'reproductive potential' which is realised throughout life. This means a deleterious mutation which has an effect in early life, will affect reproductive value more than a mutation which manifests itself in later life, after the individual has already had offspring. Thus selection will act strongly on genes which are expressed in early life than on those which are expressed later. For that reason, there's no strong selection against diseases such as diabetes or cancer. This argument can be applied not only to occurrence of disease but also to decay of ordinary functions of the body.
Secondly, cells in the body are constantly renewed and defects such as telomeric breaks are repaired. Mutations in the soma are taken care of by the immune system and can be in principle avoided. The fact that they tend to accumulate in later life can be explained by the first point: selection is weaker to oppose telomeric breaks and mutations in later life.
I was trying to be brief here, but there are more sides to the argument (e.g. Williams' antagonistic pleiotropy). Modular Evolution (Vinicius, CUP 2010) provides a good overview of the evolutionary aspect of theory of senescence (and many other interesting evolutionary arguments).

Thanks @Greg Slodkowicz. Would it then be true to say that all sexually reproducing species age? I ask this because some bacteria do not exhibit senescence.

http://en.wikipedia.org/wiki/Turritopsis_nutricula is a famous example. In case of bacteria, they are said to be immortal as a colony, since they can divide indefinitely. But for single-cell organisms which reproduce asexually even the notion of an individual is blurred, since each cell splits to form two identical daughter cells.

I’ve never been completely convinced by the wear & tear argument: germ cells (and all unicellular organisms) are direct descendants of the “arch” cell. Not just genetical, but cytoplasmatic, through cell division. If the wear & tear argument were naively true, germ cells would long have ceased working. Now, it may be that preventing wear & tear is so expensive that metazoa have disbanded it in somatic cells (where it’s expendable). But I’ve never heard that mention.

Maybe recombination prevents the accumulation of defects that you would expect from germ cells by providing other alleles that may be functional.

Once could argue that we die because it is advantageous to get rid of mature individuals once they have reproduced.  Because mature individuals have no more offspring to convey beneficial genes, those offspring which will benefit from knocking off their ancestors will have an evolutionary advantage.

Actually, you want them to stick around long enough to take care of their offspring.

But not too much longer ofter that.  Any post-reproductive beneficial traits will not be selected for, and will die out.

@dar7yl Except for post-reproductive lifespan in women. Not sure how strongly it is selected for, but it clearly has an advantage. See here. Awesome results!

That doesn't explain why we don't just reach sexual maturity and then stop aging - it can't be the primary explanation, although it would be a selective pressure once aging existed in the first place.

There is a pretty good discussion on this topic in chapter 2 of Geriactric Medicine - An Evidence Based Approach (4th ed) by Cassel. This is the main reference for the info below which can hopefully add something to the answers already given.
In terms of views on ageing, there's evidence to support both:

general principles that may apply to it; and
it being a consequence of a collection of degenerative processes (this is apparently the more supported view).

Since almost all biological systems in the body degenerates with age and this happens seemingly at random, it's been difficult to identify particular catalysts that cause this. Consequently, biologists apparently steer away from a general theory or mechanism.
However, there are two classes of theories that have been floating around. That is 'loose cannon' and 'weak link'.
Loose Cannon encompasses theories that support the 'wear and tear' proposition. Two popular theories under this banner are free radicals and glucose.
Weak Link suggests that particular physiological systems are vulnerable during senescence and if a system fails, the whole body begins to decline. It's suggested that the neuroendocrine and immune systems are particularly vulnerable.
There is also a limit on the ability of cells to replicate - this is called the Hayflick Phenomenon (or limit). The reduction of the enzyme Telomerase, which lengthens telomeres during mitosis, is implicated in limiting a cell's ability to replicate indefinitely.

The link to springerlink.com is broken. I'm also unable to find any copy saved on the Wayback Machine.

"WHY" we age is a different question from "HOW" we age.  The "WHY" refers to ageing from an evolutionally standpoint, whereas the "HOW" refers to biology of ageing.  As for the "WHY" I would read a few papers on the antagonistic pleiotropy hypothesis (click here).  As for the "HOW", there is no definitive understanding of mechanisms of ageing.  However, the role of cellular senescence in ageing and age-related disease is a major player in the biology of ageing (click here for example).  When cells become senescent (due to either telomere shortening/DNA-damage) they can no longer divide to regenerate damaged tissue.  Additionally, senescent cells are highly pro-inflammatory and so have the potential to damage the surrounding tissue if the are not removed.  In younger organisms, senescent cells are most likely removed my the immune system, but as organisms age, the immune system also ages and can no longer effectively remove senescent cells.

I know this question has closed out, but I wanted add this recent reference.  The reactivation of telomerase (which inhibits telomere shortening) seems to have rejuvinated mice, including neuronal growth in the brain.  This is crazy awesome for a couple of reasons.
One being that we may all get to see our 140th birthday.
But since there were a reversal of aging from telomere extension, that implies that aging is adaptive and not a 'wear and tear' phenomenon, at least in animals like mice (and hopefully humans).  hard to believe.
i.e. If there was a mutant that turned on telomerase, why is it not a ubiquitous trait?

Interesting, but the Guardian article is not really a reference - better to go to the original  paper. Also, a concern with telomere-lenghtening strategies would be carncer surely.

cancer is mentioned in the article...

I was think about this. I have same idea, so i think to be immortal we should resolve cancer first. So i'm still researching about cancer...

are you aware of Aubrey De Gray?  His thinking is theoretical at this point, but well articulated. http://www.ted.com/talks/aubrey_de_grey_says_we_can_avoid_aging.html


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Why would diffusion be faster across a non-specialised tissue?
The standard protocol for a person experiencing chest pains is to chew a 300mg aspirin tablet, the argument being that chewing rather than swallowing the tablet results in the aspirin entering the blood stream faster.
From a biological standpoint, why is this the case?  Given that the stomach and GI tract are specialised tissues to allow for maximum diffusion, why would it be faster to pass aspirin across the gums (bucaal administration?) tongue and cheeks which are not specialised for this purpose?
It is not just a special case for aspirin either, as HypostopTM/GlucogelTM (acute treatment for hypoglycaemic shock, essentially concentrated sugar) is applied directly to the gums or cheek with a similar argument that in critical situations it is faster.
The only suggestion I could find was  very vague from the "Merck Manual":

The stomach has a relatively large epithelial surface, but its thick mucous layer and short transit time limit absorption
  Which I assume could mean that it is the reduced absorption rate in the stomach that makes the oral membranes faster, yet it also says that the delay in the stomach is brief.

I'd be really interested to know the biology behind this!

I don't have time to write a complete answer now. I will write one out later if no one beats me to it but note that the stomach is not specialized for absorption.  Only very limited absorption occurs upstream of the small intestine.  The key is that chewing greatly increases the surface area of the tablet, which speeds its dissolution and absorption across the mucosa.

Substances absorbed in intestine have to pass through the liver, maybe this cause the delay. See Wikipedia: Hepatic portal system

I had not even considered the mechanical action of chewing - how ridiculous!  However, it doesn't fully explain the difference as Hypostop is a gel and still preferentially applied directly into the mouth rather than being swallowed.

why would you by a pound of chopped ice rather than a single 1 pound cube of ice?

I think surface area is by far the dominant factor: the medical recommendation doesn't say you shouldn't swallow the tablet, only that you should chew it first. A well chewed anything is digested faster than an unchewed anything.

There are several issues here:
1) Any mucous membrane is a specialized tissue for absorption.
Mucous membranes are indeed not so good for passive diffusion, that makes them absolutely perfect tools for active absorption of certain substances, almost independently from the membrane type. To provide some examples: many drugs like cocaine are inhaled and absorbed in nasal cavities, whereas the rectum is also known and favorite delivery way for medicines.
Generally the absorption force of the mucous membrane is dependent upon how well it is vasculated, for after going through the basal membrane the substance directly enters the blood flow and quickly travels away, thus the concentration gradient on both sides of the basal membrane -- the main barrier in mucosa -- remains relatively high.
See  Bhat P. 1995. The limiting role of mucus in drug absorption: Drug permeation through mucus solution for an experimental model for this statement.
2) Mouth mucosa can absorb many substances.
There is a special term called "oral absorption" to describe the rapid drug absorption into blood flow from the mouth cavity. The mucous membrane is not specialized here, but small molecules are able to permeate here through all barriers.
3) Advantages of oral absorption.
There are some:

The mucous membrane in the mouth cavity is very highly vascularized. The whole mouth can be seen as a bundle of skeletal muscles and every muscle requires a lot of energy and oxygen, therefore they have one of the highest vascularity rates, having much less distance between single capillaries.
Blood flow is higher in the mouth cavity walls than in other inner organs. This is mostly because muscle contractions (during chewing) lead to increased propulsion of blood through capillaries and small vessels here.
Any substance that enters blood flow here bypasses the hepatic-portal system. This means that the substance does not have to wait until it is filtered by our liver, it is immediately distributed through the whole body.
There are special reflexes from oral mucosa to inner organs. Even not so important in case of aspirin, this is very important for some placebo drugs like methyl valerate (known as "Validol" in many countries) used a lot for treating angina pectoris whose only action is to activate the cold receptors in mouth and thereby leading to reflectory dilating of cardiac vessels.

This is why many drugs, like for example loperamid, are administered only as sub-lingual tablets. And this also explains why in emergency medicine many remedies are injected directly into the tongue.

"And this also explains why in emergency medicine many remedies are injected directly into the tongue." Ahhhh!

It would also be logical to note that a chewed tablet increases its surface-area-to-volume ratio for absorption relative to an intact tablet, for any absorptive tissue.

From an engineering point of view, if you chew it the surface area will be enlarged. For example, you take 2 containers with water and 2 tablets which will dissolve in this water. If you crumble one tablet, the take up rate (flux) will be much higher due to the enlarged surface area of the tablet. If you add mixing to the concept, the flux will increase even more. Therefore, in the same amount of stomach fluid there will be a higher concentration of medicine which can be taken up by the body.

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Is trembling an advantageous response during periods of anxiety?
I originally had planned to ask about whether there was any biological truth in the popular phrase "shivering with fright".  However, after doing a fair bit of googling it seems that there is a lot more medical reference to trembling as a result of anxiety (1) (though I would imagine the distinction to be fairly minor).
I was, after about an hour of fruitless searching, beginning to wonder if it was a phenomenon created only in literature (such as being 'frozen by fright') rather than genuine human physiology, however then a website described how many people often have minor trembling before exams, interviews or other high pressure situations - something I can attest to myself!
This hasn't really changed the biological purpose behind the question however - is there any advantage to shivering in a fight or flight situation or is it more a side effect of the release of adrenaline or another chemical response? I am struggling because I can only imagine it being a real disadvantage (consider for example an organism hiding from a predator - uncontrolled movement in a stressed situation can not be beneficial) so the only way that I can see is that the shivering must be linked to something that is a definite advantage in a high stress situation.  What would that be?

At low temperatures, trembling helps to heat up the body (as a result of muscle movement). I am not sure, however, what the link with fear would be.

It's interesting if research was done whether body temperature drops or changes in fear. That, in conjunction with @Nick observation, can explain trembling (2) fear reaction is probably is similar to stress reaction. Both are associated with hormone injection into blood, that changes many reactions in the body and brain (3) reaction of different people to fear is different. Some become pale, some flush, some tremble, some do not. This is known since Roman times.

@Andrei Well I suppose if we follow it through then we could hypothesise that adrenaline released in times of fear would raise heart rate which, if not coupled with vasoconstriction, would lower body temperature.  However I think I am correct in thinking that adrenaline also raises blood pressure which I assume is the result of the contraction of blood vessels?

http://www.medicalhealthtests.com/askquestion/141/does-body-temperature-increase-with-fear.html

@Rory Actually I think we heel sense of warmth when body temp is low, and we feel ambient cold when body temp rises. My personal observationDifferent from

@Andrei Ahh I thought you meant actual temperature change rather than perceived temperature change, apologies

Some assumptions made in the question.
There is an implicit assumption in your question which I don't think to be correct: you assume that any reaction of the human organism to stress (let's substitute "fright" by "stress" in your question) is a physiological reaction, meaning that this reaction somehow helps the organism to overcome the stressful situation. From medical viewpoint the reaction to any external action can be:

physiological one (i.e. the one that is expected and is considered "good", helping the organism to adapt to this action).
pathophysiological:

as a side-effect of physiological reaction
as a result of nervous/humoral system overlast and depletion
as a reaction to unknown action
as a reaction to something mistaken for known action that is indeed something else

Mechanisms of tremor.
From mechanical viewpoint our body consists of dozens joints that are absolutely not fixed and have from two (moving in one plane) to three (for free movement in 3D, for example coxofemoral joint), thus giving our extremities an incredibly high number of degrees of freedom.
In order to sustain a certain posture our joints are equipped with antagonistic muscles: muscles that move the joint into opposite direction. The muscles, again, by design are very badly adapted for isotonic action. That basically means they cannot keep the same pressure for long time and the only way to get a fix posture for the whole body is to keep sending repetitive pulses to antagonistic muscles so that none of them actually wins.
Normally the impulses are very short and frequent. They also have to come synchronously and out-of-phase, meaning that whenever one muscles contracts its antagonist should dilate and vise versa, so that no muscle rupture takes place because of the simultaneous contraction of two opposite muscles. This synchrony accounts for very subtle trembling of the body, almost not seen by a naked eye in healthy humans. This trembling is also called physiological tremor to designate its being normal, e.g. physiological.
There are two ways how this trembling can increase so that it becomes visible and sensible:

Due to impaired synchronisation between the pulses sent to the antagonistic muscles. Since these pulses are generated in brainstem nervous centers, the impairment of those (in case of Parkinson's desease) or some inhibiting input into them (as in case of cerebellar deseases) leads to desync of these pulses, the frequency goes down whereas the amplitude might increase, making the trembling visible.
Due to attenuated cell sensitivity to the incoming impulses. This happens if the muscle cells start to overreact to the normal impulses and respond with prolonged contraction (followed by longer refractory period when they are unable to respond any impulse, thereby missing frequent pulses and reducing the effective frequency). These is mainly caused due to special metabolic changes within and in the vicinity of the muscle cells.

The most common metabolic change within the cell is either the increased Calcium concentration within muscle cells, leading to much stronger contraction, or increased sensitivity for Calcium (via Ca and ryanodin receptors), that leads to much abrupter Calcium concentration rise in cells and results in the same.
The reason for Ca to increase within the cells might be the intake of some known Calcium liberators, like caffein, increased concentration of the humoral factors that use Ca as second messenger, like adrenaline, insuline, thyroid factors etc. Those, again, can be released during some stress conditions, during artificial or temporal low sugar level and other factors.
Shivering as a reaction to stress.
The shivering, or in medical terms tremor might appear due to the following mechanisms:

Massive release of adrenaline during the stress: both directly via the adrenaline receptors and indirectly by causing temporal hyperglycemia via the metabolic adrenaline receptors. The action of adrenaline is also increased due to concomitant release of corticosteroids.
(muss less probable in case of fright, however might be common in many other cases) Overlast of the hypothalamic/amygdalic/brainstem structures responsible for stress reaction with probable weakening of deep nuclei controls over the posture and muscle contraction.

Conclusion.
So, as you see, the tremor is rather a pathophysiological reaction when it appears as response to stress, a side-effect manifestation due to acute temporal increase in adrenaline concentration in blood. Funny enough, but exactly this tremor is referenced to as "physiological tremor" in medical literature, because this type of tremor is not indicative for any CNS or endocrine disorder, that is very common for other types of tremor (postural, intentional etc.).

What is the mechanism for #1? I mean, how does it cause tremors?

@nico: I editted my answer to address your question, I hope that this answers your question.

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Is there a photobleaching-resistant, cell-permeant viability stain in the far red part of the spectrum?
I am looking for a live-cell–impermeable dye for viability. (The cells cannot be permeabilized and fixed in this experiment.)  I would prefer with excitation and emission spectra similar to Cy5, but I can be flexible here as long as the spectra are far away from Hoechst.
I have tried TOPRO3, but it seems to lose its brightness after a few exposures, so I would like something more resistant to photobleaching.

You could try SYTO Orange. Unlike SYTOX, which is a fixed-cell marker, SYTO works with both live and fixed cells.


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How is temperature sensed?
Can anyone summarize the mechanism by which when an object of a given temperature is placed in contact with, say, the skin on a human fingertip, the average speed of the particles of the object is converted into nerve signals to the brain?
If you can answer that, how about the format of how the temperature is encoded in the nerve signals?

In the periphery (e.g. on our fingertips), our body senses external temperature through nerve terminals, expressing certain TRP channels. These are ion channels that are sensitive to temperature (note that TRP channels can be sensitive to several things, such as pH, light, and stretch) and allow entrance of cations in the cell when the temperature is higher or lower than a certain threshold.
Six TRP channels have been described as been involved in sensing different temperature ranges1,2:

TRPV1 is activated at >43 °C
TRPV2 at >52 °C
TRPV3 at ~> 34-38 °C
TRPV4 at ~> 27-35 °C
TRPM8 at ~< 25-28 °C
TRPA1 at ~< 17 °C

Not surprisingly, TRPV1 and TRPV2 are also involved in nociception (=pain perception).
The exact molecular mechanisms by which different temperatures open different TRP channels are unclear, although some biophysical models have been proposed.3
I am not sure of the exact "format" in which sensory fibers encode different temperature, but I would assume that the neuron would fire faster the more the temperature is distant from the specific threshold (hot or cold).

1 Thermosensation and pain. - J Neurobiol. 2004 Oct;61(1):3-12.
2 Sensing hot and cold with TRP channels. - Int J Hyperthermia. 2011;27(4):388-98.
3 - Thermal gating of TRP ion channels: food for thought? - Sci STKE. 2006 Mar 14;2006(326):pe12.

How are objects of temperatures in the middle of the 18-24 °C sensed?  Is it expected that further channels will be found?  I really enjoyed your answer - it's particularly interesting to me to have discovered, as a by-product of following your links, how the burning effect of chilli peppers is as a result of TRPV1.

@Rory: 18-24 is covered by TRPM8

Also, about the chillies: that is a very nice example of a "false sensation". Chillies don't really burn you, but as capsaicin is detected by the same receptors as high temperatures your brain cannot distinguish between the two.

What is the mechanism by which the cell allows entrance of cations at a certain temperature?

@user1997744 I'm not an expert on this topic, but an educated guess would be that the structure of the channel changes with temperature.
Aside from reference #3 in my answer, this review also seems to go in quite a detailed description (in the "Activation mechanisms" section there is a "Heat" subsection).

To complement on nico's answer (I don't have enough rep to comment), TRP channels seems to be also sensitive to increment or decrement of temperature as reported recently in a paper by Gallio et al1.
Probably that channels have incomplete adaptative behavior that make them sensitive both to increment and absolute temperature values.

[1] Gallio M, Ofstad TA, Macpherson LJ, Wang JW, Zuker CS (2011).  The coding of temperature in the Drosophila brain. Cell 144: 614-624.


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Is Batesian Mimicry a form a parasitism? To what extent is the species with real defenses harmed by the defenceless species?
It seems like Müllerian mimicry would be an example of mutualism because both species would end up being eaten less by predators that only have to learn one pattern of warning symbols. But to what extent is Batesian mimicry a form a parasitism? It seems like predators who ended up consuming the harmless species would lose some of their conditioning to not eat prey that resembled it, thus harming the species that is actually protected.
How often might this happen in ecosystems where Batesian mimicry is present? Does the presence of a similar unprotected species cause the protected species to be a more common target for predators?
Difference between Batesian and Mullerian mimicry on wikipedia

In my own opinion, I would not classify this as parasitism, as more unpalatable species are eaten with Batesian mimicry (and eating causes death). Parasitic organisms often do not kill the host, whereas in this case, it does. However, you are correct in stating that a unpalatable species with aposematic coloring is detrimented by the presence of a palatable Batesian mimic.
Predators often recognize the aposematic coloring of an unpalatable or dangerous species. They "train" themselves not to eat that particular prey, as it is detrimental. The presence of a Batesian mimic which is palatable or not harmful, in simple terms, "untrains" predators of the harmful nature of that particular aposematic coloring. Predators are "confused", and are thus more likely to eat preys with that aposematic coloring, and results in more death of the species being mimicked, while providing protection to the species that is mimicking.
As far as I'm concerned, within an ecosystem, this phenomenon happens with any Batesian mimicry to some degree. Factors that may influence this degree is the recognizability of the aposematic coloring, as well as the ability of a predator to recognize this coloring.
I hope this clears things up.


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Are these Gram stain substitutions acceptable?
In the context of a Gram stain on a blood smear:
Are the following acceptable substitutions and/or what differences could arise by substituting them?

Using methylene blue instead of crystal violet
Using carbol fuchsin instead of safranine

I've seen text implying they are OK substitutes, but didn't find anything saying the if, why, or problems associated with replacement.

I'm not a biologist.
From a chemist's point of view, these molecules should have similar polarity. Their structure is very similar, actually.
Considering your replacement rule is correct, I would say there wouldn't be much effect other than observing different colors. What is also plausible is that you'd have to reverse the interpretation of your results, e.g. methylene blue stains X, but crystal violet stains Y whereas carbol fuchsin stains Y and safranine stains X.
Was that clear?


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Has there been any observation of species adapting the evolution process?
I am very interested in the evolution of the evolution process itself. There are of course a lot of things that influence how evolution will work, but for this question, I am interested in things that are only related to the evolution process. Examples could be increase chance of mutations in newborns, change in reproduction age, and similar. I am specifically interested in observation where the evolution process itself has adapted to a change in the environment.

Nick's answer here is a bit off base. You could look at cells of the immune system as doing something similar to evolving (there is selection, etc.). But these changes are not passed on to progeny through the germ line.

I think humans have changed their reproduction age back and forth several times during their evolution. I recall hearing about geographical differences for entry into puberty age as well.

Species with parthenogenesis come to mind. Not observed but obviously adaptation from loosing all the males.

Bacteria such as E. coli are known to increase their mutation rate (by switching to a more error prone polymerase among other things) when under stress. This can mean being placed in a medium where it's not adapted to grow (http://www.micab.umn.edu/courses/8002/Rosenberg.pdf) or when treated with antibiotics (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088971/?tool=pmcentrez).

The "change in reproduction age" you mention is one major aspect of life history evolution.
A massive literature exists on this topic, including several books: e.g., The evolution of life histories: Theory and analysis (Roff, 1992) and The evolution of life histories (Stearns, 1992).
Reznick and various colleagues have carried out extensive studies of experimental life history evolution in Trinidadian guppies going back ~30 years. For example:

Reznick, D.N. and Endler, J.A. 1982. The impact of predation on life history evolution in Trindadian guppies (Poecilia reticulata). Evolution 36:160-177.
Reznick, D.N. and Bryga, H. 1987. Life-history evolution in guppies. 1. Phenotypic and genotypic changes in an introduction experiment.  Evolution 41:1370-1385.
Reznick, D.N. 1989. Life history evolution in guppies. 2. Repeatability of field observations and the effects of season on life histories. Evolution 43:1285-1297.
Reznick, D.N., Shaw, F.H., Rodd, F.H. and Shaw, R.G. 1997. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata).  Science 275: 1934-1937.
Reznick, D.N. 1997. Life history evolution in guppies (Poecilia reticulata): guppies as a model for studying the evolutionary biology of aging. Experimental Gerontology 32:245-258.

Life history evolution has also been documented in response to human pressures. Fisheries stocks are evolving in response to overfishing. For example:

Walsh, M.R., Munch, S.B., Chiba, S. and Conover, D.O. 2006. Maladaptive changes in multiple traits caused by fishing: impediments to population recovery. Ecology Letters 9:142-148.
Conover, D.O., Arnott, S.A., Walsh, M.R. and Munch, S.B.. 2005. Darwinian Fishery Science: lessons from the Atlantic silverside. Canadian Journal of Fisheries and Aquatic Science 62:730-737.

I think this falls into your criteria but correct me if i'm wrong :).
The HIV reverse transcriptase protein has evolved to have relatively low fidelity (leading to a high mutation rate in replicated virus particles).  Reverse transcriptase is also recombinogenic, ie. it can switch templates during replication leading to even more variability.  Combined, these two properties lead to each individual having a large number of variant viral genomes, which leads to increased resistance to antiretroviral drugs etc.
EDIT:
I thought of influenza as a second example.  The viral genome has evolved to be fragmented into 7-8 pieces of RNA, which can be swapped with other strains during co-infection of a single cell.  This can lead to more virulent or transmissible strains of influenza; these can also be helpful to create new strains that influenza vaccines are no longer useful against.

Species have been observed in controlled experiments to use different sources of energy, for instance axenic E. coli cultures picking up citrate metabolism in Lenski's Lab at MSU.  They have also shown that mutations to the mutator gene mutT can accelerate the process of evolution, though it's evolution directed by fitness in a very specific setting.

How about species actively changing the factors that play a role in the selection process?
Humans are a species that have heavily modified this process. In the western world, we have gone away from selection by survival skills and genetic fitness to move to a social selection, where genome is secondary to social skills and adaptation to fashion, which are acquired skills.

I don’t think this entails a change in the underlying mechanism. At least, not one that has been demonstrated yet. “social selection” is a very diffuse term. Does it actually differ from natural selection? Personally, I doubt it: it can be readily explained in terms of natural and sexual and kin selection so this would be the most parsimonious explanation.

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".

 Pigliucci M. 2008. Is evolvability evolvable? Nat Rev Genet 9: 75–82. Behind paywall, but free pdf here

If you look at the adaptive immune system, the process of B-cell recombination, clonal expansion and somatic hypermuation is, in essence, induced evolution.

The following paper published on August 25, 2015 claims that there are indeed directed mutations.
Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005477


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Can oxygen diffuse out through the lungs?
Let's say you accidentally walk into a room pressurized with pure nitrogen (or you're jettisoned into space). Within a couple of seconds, the partial pressure of oxygen within your lungs drops to 0. But there's still a (small?) reserve within your bloodstream.
Now, will the oxygenated blood travel to your lungs? If so, will the usual gas exchange reverse, with oxygen going from your blood to the oxygen-poor environment?

Yes.  Blood will continue to circulate (as long as you're alive and your heart is beating), so will eventually come in contact with your lungs.  Once there, the gasses (O2, CO2) will cross out into the lung and be exhaled.  All diffusion is driven down a concentration gradient.

Okay, two questions I think need to be explicitly asked: (1) In my basic research I read here that something goes on with 2,3-BPG near the heart which allows deoxygenated RBCs to be separated from the oxygenated ones – does that play a role here? (2) Can the concentration gradient just flat-out strip the oxygen from hemoglobin?

There are many factors - BPG concentration, hydronium concentration (i.e., pH), cooperativity - that modulate the actual Kd for oxygen of hemoglobin (described here http://employees.csbsju.edu/hjakubowski/classes/ch331/bind/olbindhemoglobin.html as well as other places), but the physics/chemistry is unavoidable: if one moves to an atmosphere devoid of oxygen, oxygen will leech out of the blood.  http://www.olemiss.edu/depts/chemistry/courses/chem471_99/L12_6.pdfhas some graphs that show binding as a function of pO2.


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Online repositories of scanning electron microscope photographs?
I have looked at every single Wikimedia commons photo in the category 'scanning electron microscope'. Unfortunately, I could not find any other repositories of such photos, but I would readily look at every single photograph there as well. It strikes me that such repositories are also bound to be useful to biologists and biology students. A simple Google search did not yield much. Can anyone help out?

Are you looking for images for your personal use, CC or similar licensed images or commercial photos? =)

@Rory i'm looking for anything and everything. what people have posted so far is great.

micrographs, not photographs. Photons are not involved in the generation of SEM micrographs (well, they CAN be for some techniques, but those are afaik mostly used to study certain mineral deposits etc.).

First off I'd like to reccomend the University of Dartmouth's publicly available collection located here.  They have both SEM and TEM images of a wide range of organisms and cells from algae to see urchins through everything from cholera to mammalian cells.  Images are high quality, fully captioned and properly attributed.
I'm a little confused as to the problem you're having with google - see my original comment on your question.  However I have looked at the photos of Wikimedia Commons in the SEM category and see that they are either images taken with, images of SEM Microscopes or technical drawings regarding their function.  I assume that you're looking for the images taken with SEM.
I was able to find a great number of similar images to those in the commons with a Google Image search - I read above that you were having problems with this approach so perhaps try the search term "SEM images" in image search (or this search to avoid duplications from images you have already seen on Wiki Commons)?
Examples found on just the first page:

thanks for those recommendations. the trouble with google image search is that it doesn't search everything, doesn't know about everything -- and how can it? not everything has top-down categorically descriptive text attached. there's just no way to find out about repositories of images like the ones linked to here without asking people.

I know exactly where you're coming from, hope Dartmouth helped though =)

David Orloff's The Cell – an Image Library has thousands of SEM images.

very nice. i have a hard time deciding whether or not i like the dartmouth images better or i like the cell images better, and that's an excellent predicament to be in.

Have a look at:

XTALENT Image Gallery, more than 600 images, last updated in 2006, though.
Dennis Kunkel Microscopy, Inc., "scientific stock photography library of light microscope pictures and electron microscopy images featuring science and biomedical microscopy photos".
Iowa State University SEM library, includes pictures submitted by students from around the state of Iowa.

Take a look at my website which has a section called Images.  http://www.hssemgroup.com/
There are more than 13 sites listed which have hundreds of SEM images posted

Specifically http://www.hssemgroup.com/students-enjoying-their-sems/resource-urls - looks like a very helpful resource.


text:
What effect has changing pH and salt concentration on protein complexes?
I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt concentration have and what is the physical basis behind this?

I submitted an edit to your question, it was not entirely clear to me if you ask about proteins alone or protein complexes and interactions. If I got it wrong please just edit your post again.

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into chaotropes ('disorder-making'), which destabilise protein structures and kosmotropes ('order-making'), which stabilize them. [1, 2]
Chaotropic salts interfere with intramolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which, at high cosolvent concentrations, results in protein denaturation.
Kosmotropic salts, on the other hand, cause water molecules to favorably interact, which also stabilizes intermolecular interactions in proteins. The salt molecules readily interact with water from the protein's hydratation shell and remove it from the protein surface, which produces thermodynamically unfavourable interactions that are reduced when proteins associate to form complexes. With increase in salt concentration the protein precipitation (salting out) increases.
Both cations and anions have been ranked separately by their capacity to precipitate proteins, to form a Hofmeister series [3, 4] (first set in 1888 but still hotly debated), e.g.:
SO42− > H2PO4− > CH3COO− > Cl− > Br−
At large salt concentrations protein solubility is given by the empirical Cohn equation [6]:
lnS = α − βc
where S is the protein solubility, c is the salt's ionic strength, α and β are empirical constants characteristic of particular salt.
Salting-out agents are very widely used in protein purification (to concentrate proteins eg. with ammonium sulfate), chromatography or crystalization.
The influence of pH on protein-protein interactions in solution works through altering of the electrostatic properties of protein surfaces. At pH equal to the protein's isoelectric point (pI), where its net charge is neutral, charge repulsions of similar molecules are relatively low and many proteins will aggregate. Very low and very high pH will case proteins to denature; during digestion, for instance, proteins are in extremely low and then extremly high pH that exposes their backbones for enzymatic degradation.
For more information, please refer to:

Martin Chaplin, Kosmotropes and Chaotropes, http://www.lsbu.ac.uk/water/kosmos.html
Zangi R. Can salting-in/salting-out ions be classified as chaotropes/kosmotropes? J Phys Chem B. 2010 Jan 14;114(1):643-50.
Pace CN, Treviño S, Prabhakaran E, Scholtz JM. Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc Lond B Biol Sci. 2004 Aug 29;359(1448):1225-34; discussion 1234-5.
Shimizu S, McLaren WM, Matubayasi N. The Hofmeister series and protein-salt interactions. J Chem Phys. 2006 Jun 21;124(23):234905.
Zhang Y, Cremer PS. Interactions between macromolecules and ions: The Hofmeister series. Curr Opin Chem Biol. 2006 Dec;10(6):658-63. Epub 2006 Oct 10.
Ruckenstein E, Shulgin IL. Effect of salts and organic additives on the solubility of proteins in aqueous solutions. Adv Colloid Interface Sci. 2006 Nov 16;123-126:97-103. Epub 2006 Jun 30.


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How do CpG islands remain unmethylated?
In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted genes.
What are the current theories on the mechanisms involved in this preferential demethylation?

Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled because of gene regulatory control, especially at the famous H19/Igf2 locus[1]. Here is a generally good recent review[2], note they mention that DNA methylation does not cause transcriptional silencing, and likely methylated promoters are probably more active than unmethylated, they just create silencing RNAs when methylated (resulting in an apparent silencing).  This may help explain some of the story[3], but note how old that paper is, yet generally I'd say few people know of its existance.
The exception seems to be transposable elements[4], but their control is probably also controlled by silencing RNAs.
References:

 Zampieri M, Guastafierro T, Calabrese R, Ciccarone F, Bacalini MG, Reale A, Perilli M, Passananti C, Caiafa P. 2012. ADP-ribose polymers localized on Ctcf-Parp1-Dnmt1 complex prevent methylation of Ctcf target sites. The Biochemical journal 441: 645–52.
 Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes & development 25: 1010–22.
 Rountree MR, Selker EU. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes & Development 11: 2383–2395.
 Bourc’his D, Bestor TH. 2004. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–9.

This came out mere hours ago ( http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002422 ). Imprinting of the maternal SNRPN allele (which is unmethylated) requires transcription, again underscoring that methylation is a consequence of transcriptional silencing, rather than causal in gene silencing.


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Where can I find the common names for the zoology taxonomy?
Forgive me if my question does not belong here or if I'm using incorrect terms, but I'm not educated in biology at all. I'm investigating the workings of the biological classification system.
I was wondering if there is a list somewhere of all kingdoms, orders, classes, etc., both in Latin and common names?

That list is called Wikipedia. ;-) … Seriously, (almost?) all Wikipedia articles on animals carry both the common and the scientific name.

True, and in fact Wikipedia is my source, but I'm looking for a more convenient format, a list on a single page.

The Tree of Life project has a browse-able tree of all major taxa, but not necessarily all species. You can start at the root of the tree here. Tree of life uses modern phylogenetic nomenclature rather than more traditional Kingdom-Phylum-Class-etc.
Part of the problem that you will run into is that common names differ across regions/countries/languages. This is the point of species binomials. They are language-invariant.

Thanks, thats a very useful site. The information there is largely what I need, I only require english common names. The format isn't ideal for my purposes but I'll find a way to parse it.

Wikispecies might help with common names: http://species.wikimedia.org/wiki/Main_Page

Kingdoms
The UK accepted system has five kingdoms, for some it's hard to describe a single word common name so I hope you don't mind that I have written brief summaries too:

Animalia are multi-cellular organisms that have adaptations to allow them to move within their environment.  They have membrane bound organelle but not cell walls or chloroplasts. They must absorb nutrients by ingestion.  Common name is animals ;-)
Plantae are multi-cellular organisms that use photosynthesis to harness energy from sunlight.  Their cells contain cell walls & chloroplasts (where cells are exposed to the sun).  Common name is plants
Fungi are multi-cellular organisms with no adaptations to move independently.  They range in size from microscopic to the size of mushrooms (literally, of course).  They absorb their nutrients from their surroundings.  Common name could be mushrooms & molds
Protista are marine organisms that are eukaryotoic (have membrane bound organelles) and some can photosynthesise.  Common name could be algae
Prokaryota (a.k.a. Moneara) are single celled, with a cell wall but with no membrane bound organelles (i.e. they have no smaller 'bits' within the cell separated by a membrane).  They absorb nutrients directly across their membranes or can photosynthesise to make their own nutrients.  Common name could be said to be Bacteria.

Sources: 1, 2, 3 (for Protista)
Phyla and Below
You may wish to try the following website:
ITIS Database - enter a scientific or common name of an organism to get it's full taxonomic tree.  For example the tree for the Panthera leo (Lion).  This site also gives common names of Phylum, Class, Order & Genus - for example the lion is a member of genus Panthera ("roaring cats"). It may be slightly cumbersome but it is a way to get the info you want and is actually quite interesting once you get going, particularly if its just for your curiosity!
Additions after comments by OP
Have been hard at work, however it seems that a centralised repository is certainly elusive!  I've found some sites which go a little of the way to amalgamating scientific and common names on a single page but I'm doubtful that you will be able to get much further than Phylum without having to write a script to harvest data from sites such as ITIS

List of all Phyla for the Animalia Kingdom with common names.
As above for Kingdom Plantae
As above for Kingdom Fungi
As above for Kingdom Protista

Thanks. What you did is to describe the kingdoms in a language common people understand. That's what I'm looking for, but I'd like that kind of information for lower taxonomy levels as well, ideally in a single list. I know I can find the common names of every level using various resources (ITIS,EOL,Wikipedia), but I'm looking to automate parts of this.

@Ferdy Well I've gone back and got you as far as phylum for four of five kingdoms (apparently there is some contention over prokaryota).  I'm beginning to get the impression that the data simply doesn't exist as one long list - sorry, I tried =)

"Protista are marine organisms that are eukaryotoic (have membrane bound organelles) and some can photosynthesise. Common name could be algae" - not all protozoans are marine organisms, and not all of them are algae (conversely, not all algae are protists).

"Animalia are multi-cellular organisms that have adaptations to allow them to move within their environment." - sponges and a few other sessile marine organisms are still treated as animals, no?

I just wanted to note that the Five Kingdom classification (Whittaker) system pre-dates the currently accepted three-domain system (Woese) introduced with 16S rRNA-based classification in 1990.

EOL has large collections of common names, and a pretty comprehensive API which should be able to access them somehow (I haven't tried specifically downloading commons name before, though, so I can't promise that it'd work). If you need a list locally, ITIS has downloadable pipe-delimited files containing scientific names and common names (although you'd need to do the mapping yourself). Hope that helps!

EOL gets some of their common names from uBio, which exists explicitly to serve names. I don't know how their API is compared to EOL, but it would be worth checking out.


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Abiogenesis: Beyond the research journals as a lead in to discussions on evolution
I just came across this abstract:

Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are
  necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two
  classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the
  terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here,
  an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the
  mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive
  binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the
  reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby
  providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is
  a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the
  codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be
  charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the
  codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

Granted, this is a few years old, but I often find myself having to admit that "I don't know" when at the root of discussions on evolution.  That is, once abiogenesis has occurred, we can go on and explain the rich diversity of life, but sadly we really don't know much before that critical step.  Generally, those satisfied with "magic" as an answer posit their myths and fables, whereas I'd rather try to actually find out what happened.  Sadly, as the abstract shows, you actually need a level of education to understand papers such as this that is generally well beyond those who would deny the reality of evolution.
Does anyone have a collection of papers on abiogenesis that are more accessible and understandable to laypeople?

The fascinating field of abiogenesis is, as Nick Lane put it, "a wild west of ideas, theories, speculations, and even data". The stories we have involve a plethora of assumptions, there is no hypothesis where all or most of the pieces would fit together. Usually scientists agree it was RNA that played central role in the process, as the molecule could both carry the genetic code, necessary for hereditary natural selection, and catalyze basic biochemical reactions. Where the energy came from and how it was harnessed to maintain RNA (a rather unstable molecule) and perform work is still debated. A fermentation in a 'primordial soup' or a primitive form of respiration, perhaps through a thin iron-sulphur membrane, have been proposed as possibilities. The second gave a start to the iron-sulphur world hypothesis. Iron-sulphur minerals could catalyse the first organic reactions to synthetize sugars, amino-acids and nucleotides, and eventually RNA world, where natural selection could take over. Theories abound.
Usually reviews will give you a sound and approachable picture of the current thought on the matter. Take a look into Nick Lane's book and these articles, too.

Lane N., Origin of Life in: Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press, 2005. p. 94-104.
Russell, Michael (2006). First Life. American Scientist 94 (1):32.
Van Noorden R., RNA world easier to make - Ingenious chemistry shows how nucleotides may have formed in the primordial soup. Nature 2009
Check Hayden E. A never-ending dance of RNA - The recreation of life's origins comes a self-catalysing step closer. Nature 2009.
Cech TR. Exploring the New RNA World. Nobel Prize articles
Müller UF. Re-creating an RNA world. Cell Mol Life Sci. 2006 Jun;63(11):1278-93.
Lazcano A, Miller SL. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell. 1996 Jun 14;85(6):793-8.

Hypotheses abound, not theories.


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Why do Humans not produce Vitamin C like other mammals?
Why do most mammals produce their own Vitamin C?
Why do Humans not?

See the last two paragraphs of https://en.wikipedia.org/wiki/L-gulonolactone_oxidase#Consequences_of_loss for two alternate hypotheses.

Humans do not produce Vitamin C due to a mutation in the GULO (gulonolactone oxidase) gene, which results in the inability to synthesize the protein.  Normal GULO is an enzyme that catalyses the reaction of D-glucuronolactone with oxygen to L-xylo-hex-3-gulonolactone.  This then spontaneously forms Ascorbic Acid (Vitamin C).  However without the GULO enzyme, no vitamin C is produced.
This has not been selected against in natural selection as we are able to consume more than enough vitamin C from our diet.  It is also suggested that organisms without a functional GULO gene have a method of "recycling" the vitamin C that they obtain from their diets using red blood cells (see Montel-Hagen et al. 2008).
A 2008 published study (Li et al. 2008) claimed to have successfully re-instated the ability to produce vitamin C in mice.
Simply as trivia: other than humans; guinea pigs, bats and dry-nosed primates have lost their ability to produce vitamin C in the same way.

References

Li, Y., Shi, C.-X., Mossman, K.L., Rosenfeld, J., Boo, Y.C. &
Schellhorn, H.E. (2008) Restoration of vitamin C synthesis in
transgenic Gulo-/- mice by helper-dependent adenovirus-based
expression of gulonolactone oxidase. Human gene therapy. [Online] 19
(12), 1349–1358. Available from: doi:10.1089/hgt.2008.106 [Accessed:
31 December 2011].
Montel-Hagen, A., Kinet, S., Manel, N., Mongellaz, C., Prohaska, R.,
Battini, J.-L., Delaunay, J., Sitbon, M. & Taylor, N. (2008)
Erythrocyte Glut1 Triggers Dehydroascorbic Acid Uptake in Mammals
Unable to Synthesize Vitamin C. Cell. [Online] 132 (6), 1039–1048.
Available from: doi:10.1016/j.cell.2008.01.042 [Accessed: 31 December
2011].

Comments are not for extended discussion; this conversation has been moved to chat.


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Can scientists create totally synthetic life?
This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.

This is a great question, and Larian LeQuella answered pretty thoroughly to it. I just wanted to add that it is exciting time to be a synthetic biologist. Scientists have now the tools to build anything they have ever dreamed about.

In 2010, Dr. Craig Venter actually used a bacterial shell and wrote DNA for it.

Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved.
(Snip)
The new organism is based on an existing bacterium that causes mastitis in goats, but at its core is an entirely synthetic genome that was constructed from chemicals in the laboratory.

Keep in mind, this is only a synthetic genome, not a truly unique organism created from scratch.  Although I am confident that the technology will become available in the future.  As has been pointed out, the entire genome wasn't built de novo, but rather most of it was copied from a baseline which was built up from the base chemicals with no biological processes, and then the watermarks were added (still damn impressive since they took inorganic matter and made a living cell function with it). But they are working at building a totally unique genome from scratch (PDF).
This is actually quite an emerging field, so much so that the MIT press has set up an entire series of journalsfor this.  As far as to the purpose of these artificial organisms, most research funded by companies are meant to be for specific purposes that biology hasn't solved yet (such as a bacteria that eats a toxic waste or something).  Although, a lot of people are concerned about scientists venturing into the domain of theology.
In terms of abiogenesis, there are many resources to learn more about this.  Here is a list of 88 papers that discuss the natural mechanisms of abiogenesis (this list is a little old, so I am sure that there are many, many more papers at this time).
I also found this list of links and resources for artificial life.  I cannot verify the usefulness of this since the field is a bit outside my area of expertise.  However, it does seem quite extensive.
EDIT TO ADD:  Now we have "XNA" (a totally synthetic genome) on the way.

Note that the answer was originally posted at ScepticsSE (Can scientists create a life-form yet?).

@fileunderwater Yep, and I thought it was something that belonged here as well (from the purely biological perspective).  This is two years old now, so I wonder what advances in this field have been made (I haven't kept up)?

In principle it is possible. Life doesn’t contain some divine or intrinsically spiritual element that we would have to add to our artificial organism potion to breathe life into it. At this moment we are limited by gaps in our knowledge and by the current state of technology.
We first have to better understand fundamental principles of life on a multi-level scale: from quantum mechanics, through biochemistry, structural biology, molecular evolution, to macroscopic function and behavior on the organism level. This, together with development of enabling technologies, will require decades of research but some steps have already been taken.
One of the promising approaches is re-writing, as exemplified in this work:

We redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. (...) The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.

or a minimal cell synthesis project:

Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. (...) Completion would yield a functionally and structurally understood self-replicating biosystem. (...) Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.

So, technically it’s very difficult but definitely can be done, which is really exciting.

I would like to add a lecture on Synthetic Biology by Andrew Hessel, who introduces the open source synthetic biology field, compares it to computing, and gives an overview of what are its applications, like the creation of the first synthetic organism.
I also stumbled upon a talk from the famous physicist Michio Kaku, who shares his vision about the world in 2030, when synthetic biology will change every-day-life.
Enjoy!

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Is "exhaustion" of the Hodgkin-Huxley membrane at constant stimulation a real phenomenon?
I was playing around with a simulation of the Hodgkin-Huxley model using their original parameters for the squid giant axon.
By applying a constant stimulation current to the model in resting state, an infinite train of action potentials is triggered, which seems reasonable. However, if the current exceeds a threshold, these APs die off very quickly as both the membrane potential and the ion conductances reach a steady state.
What is this phenomenon called? Is it a real phenomenon, or just an artefact of the Hodgkin-Huxley model?

Just for my own ability to reproduce your results, did you use one of the online simulators or did you code your own?

@jonsca: It's based on one from a university course. I shouldn't share it publicly, but could email you the Matlab code (tim@gurka.se). It's a naïve DE solver that directly approximates the differentials in time steps of 1e-3 ms.

This phenomenon is called depolarization block and it occurs in real membranes in current-clamp experiments.
The key mechanism is that the membrane has not been allowed to repolarize sufficiently to relieve the inactivation of sodium channels. The Hodgkin-Huxley model reflects this in the "inverted" voltage-dependence of the h gate (sodium inactivation gate)--inactivation is greater at higher voltages. This means that sodium channels cannot open again, or trigger another action potential, until the membrane is repolarized. Canonically, the need to relieve inactivation of sodium channels is the reason for the afterhyperpolarization phase of an action potential where the AP downstroke becomes transiently more negative than the resting potential.
The relevance of depolarization block in in vivo physiological conditions is not well studied. It is not likely that depolarization block occurs in well-behaved neurons under physiological conditions. However, it's possible that it does occur during pathological states.

(I probably ought to have a pat answer to this on the tip of my mind, but since I don't I'm going to wing it. This is probably just an opportunity to make an utter fool of myself. Please treat everything that follows with extreme suspicion.)
I think this is effectively an artefact of the model. That may not be true in the strictest sense -- it is possible such behaviour could be produced in real experimental preparations -- but it would require driving them in drastically non-physiological ways. I am not aware of this having been done, but I'm sure that's just my ignorance -- I would be surprised if nobody has tried.
In physiological terms, though: where would such a large constant current come from in a real cell? Where would the charges go? How would that be sustained with realistic boundary conditions?
While it is possible that such an effect can come into play very transiently in living systems, it seems unlikely that a true steady state of this kind could ever be reached.

Thanks for your input. I'm interested in what would happen to a real membrane, though, not whether the situation is likely to occur naturally.

@Tim In which case you probably need to be more specific about the experiment you're proposing. Your question seems to boil down to how fully the H-H model describes the behaviour of an actual axon membrane propagating APs. (There's an auxiliary issue of how well your sim implements the model, but let's shelve that for now.) Not having done the experiment, I can only guess. My intuition is that it would be possible to drive a real membrane to steady state if you're sufficiently aggressive about it, but that doing so would not demonstrate anything meaningful.

The question is rather how well the model describes reality in one specific aspect. A way to check would be to clamp a squid giant axon the way Hodgkin and Huxley did, apply a constant current of sufficient amplitude, and measure the membrane potential.

I don't find it improbable that this could be a known problem with the model or a known behaviour of the real membrane.

@Tim For that experiment, I broadly stand by my guess. With sufficient current injection you could overwhelm the oscillatory behaviours of the channel population. It would, however, be interesting to see how closely the real current needed for that matched the model prediction.

From my point of view, whether or not this phenomenon requires non-physiological input to the cell is not relevant to the question. This is not an artifact of the model. In fact, the model predicts the behavior of a real neuron.


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What are the variables that control/influence the color of oranges(Citrus sinensis)?
I hear that Oranges cultivated in tropical areas of the world tend to be greener when ripe, is that correct?
Even the same type of Orange differs in color if cultivated in California or Florida. I hear that's because of the climate (colder nights == oranger oranges)
But, at the same time, oranges tucked in between the tree leaves tend to be greener, for they need more chlorophyll to make the most use of less access to sun rays.
Could someone correct my assumptions? Also, if possible, list the pigments and processes involved?

Naturally, ripe orange skins are usually green-yellow. In colder climates, they will turn orange over winter, since in the cold the chlorophyll will start degrading and stop masking out yellow/orange carotenoids in the skin. If the fruit is picked in fall (and not let ripen or degreened) they will have green color.
Ehtylene gas, which is a natural plant hormone, is sometimes used to give them more uniform, orange color (degreening). Also, some oranges cultivated in the US are dyed with Citrus Red 2 to make their peels orange.


text:
What causes REM atonia to be lost in sleepwalking?
I understand that in normal REM sleep the voluntary muscles are in effect paralysed in order to prevent an individual acting out their dreams.  This paper indicates that there are likley to be multiple causes of this atonia. I am interested to know what are some of these methods by which natural atonia is achieved by the body in periods of sleep?
Furthermore, what causes these mechanisms to fail in individuals who suffer from sleep-walking?

I don't know if this will help you find the right answer, but a related process is 'sleep paralysis', in which a person continues to remain paralysed after waking up from REM sleep. It's happened to me once or twice (for less than a minute each time); scary stuff: http://en.wikipedia.org/wiki/Sleep_paralysis

There's an excellent, comprehensive review article on the entire process of REM sleep:

Vetrivelan,R, Chang, C, Lu,J (2011). Muscle tone regulation during REM sleep:
  neural circuitry and clinical significance. Archives Italiennes de Biologie, 149 [DOI] [Free PDF]

Projections from the sublaterodorsal nucleus (SLD) of the Pons in the brainstem are responsible for the suppression of the spinal motor output/movement (for an anatomical schematic, see the article).

Descending SLD glutamatergic projections activating the premotor neurons
  in the ventromedial medulla and spinal cord interneurons bring about muscle atonia and suppress phasic muscle twitches in spinal musculature.

Lesions in this area in rats have resulted in REM sleep without atonia.

Many studies have
  suggested that the ventromedial medulla (VMM),
  which receives glutamatergic inputs from the SLD,
  may be the relay site for the pontine inhibitory area
  on spinal motor neurons

The SLD axons relay through the VMM, but also directly projects onto interneurons within the spinal cord, directly inhibiting their activation.
Most of the knowledge we have about this subject comes from animal studies, so it will take some time to verify whether these same mechanism and relays are the same in humans.
The area that is lending the most credence to these issues of REM atonia is not sleepwalking as much as REM sleep behavioral disorder (RBD).  In this condition, sufferers act out their dreams and generally lose atonia during REM sleep.
Evidence points to the fact that such behavior is often seen decades before such conditions as Parkinson's and Lewy Body dementia.

Ferini-Strambi,L (2011) Does idiopathic REM sleep behavior disorder (iRBD) really exist?
  What are the potential markers of neurodegeneration in iRBD? Sleep Medicine 12, S43–S49 [DOI]

They summarized two studies which explored these anatomical changes:

[Diffusion tensor imaging, a type of MRI scan] changes have been reported in the
  brainstem (pons, substantia nigra) as well as the fornix, the right
  visual stream, and the left superior temporal lobe suggestive of
  brain tissue disintegrity[1]
significant decreases of [fractional aniosotropy] in the tegmentum
  of the midbrain and rostral pons and increases of [mean diffusivity]
  within the pontine reticular formation overlapping with a cluster
  of decreased [fractional anisotropy] in the midbrain [2]

So, the answer is, we don't know for sure, but we have some clues from the animal models as to what stages of the signals to suppress movement are interrupted.
[1]Unger MM, Belke M, Menzler K, et al.(2010). Diffusion tensor imaging in idiopathic
REM sleep behavior disorder reveals microstructural changes in the brainstem,
substantia nigra, olfactory region, and other brain regions. Sleep,
33(6),767–73.[FREE PDF]
[2]Scherfler C, Frauscher B, Schocke M, et al. (2011) White and gray matter abnormalities
in idiopathic rapid eye movement sleep behavior disorder: a diffusion-tensor
imaging and voxel-based morphometry study. Ann Neurol,69(2),400–7. [DOI]

Failure of maintaining atonia does not lead to sleep-walking but to REM sleep behavior disorder. Sleep-walking is a mixture of NREM and wakefulness.
Mahowald, M. W., & Schenck, C. H. (2005). Insights from studying human sleep disorders. Nature, 437(7063), 1279–85. doi:10.1038/nature04287


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Are Schwann cells the sole source of myelination in PNS?
Are Schwann cells the only source of myelin for axons in the peripheral nervous system, or are there other neuroglia or other processes that result in myelination of PNS axons?

Schwann cells seem to be the most common type of glial cells outside of CNS, and the myelinating Schwann cells are the only known source of myelin in PNS. Other types of neuroglia in PNS, for example non-myelinating Schwann cells and astrocytes-like cells do not seem to take part in myelination, neither in CNS nor in PNS.

With "seem", are you talking about what you believe, or what the medical community believes? This answer seems a bit vague.

With "seem" I mean that there is no known evidence about it in the research publications available to me. There is no way to prove that something does not happen, we can only prove something to happen by observing it under certain conditions (in vivo or in vitro), that is why I can't be 100% sure that this is true, but this is the common belief in neuroscience that fits into the general schema about neuroglia functions.


text:
What would be the conduction speed of A-alpha fibers, were they unmyelinated?
It's known (Hursh 1939) that myelinated axons exhibit the behavior $v = 6d$, where $v$ is the propagation speed [m/s] and $d$ is the axon diameter [μm].
A related relation for unmyelinated axons is (Malmivuo & Plonsey, eq. 2.1):
$$v = \sqrt{\frac{i_\text{Na max}}{r_i c_m^2 V_\mathrm{th}}}$$
I want to approximate the propagation speed that A-alpha nerve fibers would exhibit, if they were unmyelinated. How could I find values for the constants in the above equation? Is there an easier way to conduct these calculations, or has there already been a study done on this?
For the (myelinated) A-alpha fibers, d = 13-20 μm and v = 80-120 m/s according to Wikipedia.

The provided relation for unmyelinated axons only holds up to certain diameter value of the axon and is valid only as long as the sodium conductance iNa is uniformly distributed along the cross-section of the axon. This explains why non-myelinated fibers are so thin, being only 0.2-1.5 μm in diameter.
In axons having a larger diameter the axon potential can only move between Ranvier nodes. If this fiber gets unmyelinated the axon potential just stops propagating, due to several reasons:

Sodium concentration through the complete axon surface is too high so that it diffuses internally along the axon and reduces the concentration gradient in the direction of AP propagation.
AP is propagated not only along the length of axon but also laterally, that leads to its flatenning over the axon surface, decreasing its amplitude etc.

Unfortunately I couldn't find the reprint of the original publication in Biofizika referenced by the webpage you provide the link to, so I cannot investigate the constraints of their model for AP propagation.
In order to estimate the propagation velocity in unmyelinated axons of large diameter I would take some theoretical papers investigating the properties of nerve fibers undergoing demyelination. Z. J. Koles and M. Rasminsky "A computer simulation of conduction in demyelinated nerve fibres", J Physiol. 1972 December; 227(2): 351–364. seems to be one of the earliest publications on this topic and it is freely available online.
In this paper the authors tried to simulate the conductance of demyelinated motor axon with diameter of 10μm and 5μm myelin sheath. They gradually decreases the amount of myelin width until 2.7% of the initial value where they saw the abolishment of AP propagation. The propagation time was 12.5 times higher than in normally myelinated fibers (for the distance where AP could travel). If we consider the initial propagation velocity being 80-120 m/s then after demyelination it is reduced down to 6-10 m/s and fade after a short travel.

Is mkm being used as Micrometre (μm)?

Yes, thank you for your comment: I used it to copy the μ-symbol and substituted it in my answer! ;-)


text:
What is the mechanism of transgene integration (from expression vector to the host genome)?
How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium).
I already cut some parts (NdeI-PciI) of the vector (pUC18) and wondering if it affects the integration procedure. Is there any recombination-like procedure same as gateway?

What is your host in this case? For integration into the genome of a bacterium, you would need to use an "integration" vector. Most commercial vectors (such as pUC18) will be maintained without integrating into the host genome.
Here is a description of an integration vector from the Bacillus Genetic Stock Center to give you an idea of how foreign DNA would be integrated into a Bacillus genome:

Integration vectors are plasmids that feature conditional replication
  coupled with a selectable marker. If the plasmid is transformed into
  an appropriate host under conditions that select for the plasmid’s
  presence but restrict its replication, all transformants will have
  integrated the plasmid into their chromosome (or some other resident
  DNA capable of replicating under the selective conditions). In
  practice, the selectable marker usually specifies antibiotic
  resistance. Conditional replication usually means that the plasmid has
  replication functions that work in E. coli but not in gram-positive
  bacteria, such as B. subtilis. Sometimes a temperature-sensitive
  replication phenotype is employed instead. Integration is targeted to
  a particular locus on the chromosome by including identical sequences
  on the plasmid. If there is a single homologous sequence, a single
  crossover will integrate the entire chromosome into the target locus
  by a Campbell-type mechanism. If there are two homologous sequences,
  and they are relatively close together on the chromosome, then a
  double crossover will result in a cassette integrating between the
  chromosomal targets. (source)

For most routine molecular biology labwork, there is no need to integrate genes into the E. coli genome. Integration is usually used to generate "knockout" cell lines to study gene function in the bacteria of interest.

Thanks for your time and consideration...but the host is microalgae (a eucaryote microorganism).


text:
Alternatives to ethidium bromide for staining small nucleic acids?
While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.
What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.

A list of dyes is available here and a list of dyes specific to nucleic acids is available here. I think you have two choices the SYBR Gold nucleic acid gel stain (S11494) which can be detected under UV light (not sure if it can be used with polyacrylamide gels). Your other option which can be used with polyacrylamide gels is the SYBR Green II RNA gel stain (S7564, S7568, S7586), this stain can be detected with UV light post-electrophoresis. It states RNA in the name but it can also be used for ssDNA.
Hope this helps

I would think GelRed or GelGreen would be an option too.  They claim to be more sensitive than EtBr and certainly less toxic (even moreso than SYBR Green).  I haven't personally used them against such a small bp product though.  GelRed has basically the same excitation/emission wavelengths as EtBr so no equipment change is needed.
Product sheet
Store link

I have heard several people complaining about GelRed being less sensitive than EtBr. Also, an interesting blog post about the toxicity of EtBr and SYBR Green: http://rrresearch.fieldofscience.com/2006/10/heresy-about-ethidium-bromide.html.

Interesting. I haven't done a comparison so I can't speak one way or the other.  But I do remember a similar article sometime back saying a similar thing (EtBr is not as bad as you think, and SYBR Green really isn't a "safer alternative" as advertised).

There's no such thing as a "safe" DNA fluorescent stain. The dye works by intercalating between nucleotides in DNA and it stays there. If that segment of DNA later gets copied or read, it will cause errors. Aside from this, one molecule of EtBr intercalates on average, between one of three nucleotides (1 EtBr/3 bases). Signal strength for EtBr or other dyes is directly proportional to mass and length of DNA.


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Why do we get runny noses in the cold?
The most annoying thing for me about being cold is a runny nose. Is there an advantage to having a runny nose when cold? What does having a runny nose achieve?

possible duplicate of What causes a 'stuffy' or 'runny' nose when you have a cold?

I added a duplicate badge to this question because I think the other question is better formulated. We do not get runny nose in the cold. We get runny noses when we have a cold. That is a big difference. I see this question as a very simplified question in Physiology which aims to explain difficult concept in Pathophysiology by concepts in Physiology.

I'd have to disagree with that. I get a runny nose when it's cold, even if I don't have a cold.

@jarlemag Yes, I agree that some people do get easily runny nose in the cold. Badly formulated sentence from me. My point is that the cause is not the cold weather. It is a secondary thing for the runny nose. Some people however do not get runny nose in the cold. The cold weather is not the cause itself - only a mechanism or a condition that triggers the runny nose.

Well, the important thing is that we both agree that someone can get a runny nose, when they are in a cold environment. I don't see a need to argue about the semantics of "triggering condition" vs. "cause". :-) Anyway, I vote to keep open as not a duplicate.

There are two reasons for this:

Nasal mucus helps warm inhaled air before it reaches the lungs. In cold weather, the mucus tends to dry out, so the membranes increase their production.
At the same time, exhaled air is warmer than the surrounding air, so it contains more moisture than the outside air can hold. This moisture condenses around the tip of the nose.

Explanation found here.
So there's no particular advantage to getting a runny nose; it's just a normal reaction occurring in extreme conditions.

Just to add, cold air has a lower capacity to solve water. Hence why cold air tends to be drier than warm air.

I do not agree with this answer. These are mechanisms, not the cause. I added a duplicate badge to this question because I think the other question is better formulated.

Rhinorrhea, or runny nose is a response used by our nasal membrane to get rid of foreign particles including pollen dust and infection. As such we get runny noses when we have a cold, allergy or are exposed to high densities of air-born particles. Cold air may irritate our nasal membranes, both because of temperature differences relative to our body and due to the lower amounts of moisture cold air holds. Cold air thus also results in a runny nose.

It would be great if you added some references to support your response!

There are definite advantages to getting a runny nose in cold weather. Rhinoviruses prefer cold weather and deploying large amounts of mucus is a good way to trap them (instead of letting them get in to infect the nose). Additionally, severe dry nose can cause nosebleeds and the mucus helps prevent this from happening.


text:
What is the mechanism behind "acquired" alcohol tolerance?
I can understand natural variation in alcohol dehydrogenase (ADH) in a population leading to variation in rate of inebriation (after controlling for other variables -- e.g., mass, food consumption, etc.).
But what physiological (adaptive?) process leads to increased alcohol tolerance over the long term in a single individual?

Are you asking about individual variability in alcohol tolerance or you mean the characteristical symptome of the Alcoholistm II: increase of alcohol tolerance?

[Untested] If I have 1-2 drinks per day 3-4 times a week. Assuming all other factors are equal, after some period of time (months?), I will be able to drink 3-4 on one day without feeling inebriated. How does this adaptive tolerance work?

The subject of alcohol tolerance is broader than it might appear. However, in most cases people refer to what is called metabolic alcohol tolerance. Based on your response to the comment made by Alexander Galkin, I assume that you also refer to metabolic alcohol tolerance.
Metabolic alcohol tolerance is the result of drinking significant amounts of alcohol over a period of time as you describe. Both the amount of alcohol and the duration that it takes to develop an increased metabolic tolerance towards alcohol differ from person to person.
When most people drink alcohol, the liver will responds by activating alcohol degrading enzymes that break down the alcohol molecules, which results in the elimination of the intoxicating effect. The activation of those enzymes occurs much faster with people who have developed metabolic alcohol tolerance and the concentration of those enzymes is generally higher. This means that those people can break down alcohol faster than you and me, that is, they can "tolerate" more alcohol in the sense that they simply get rid of it much quicker.
On a final note, being more alcohol tolerant is not exactly correct as metabolic tolerance doesn't necessarily mean that the organs affected/intoxicated (such as the brain) by alcohol aren't necessarily more tolerant. The alcohol is simply broken down much faster and can therefore have a limited impact.

So, judging by your answer to my comment you are most likely talking about so-called consumption-induced alcohol tolerance, that one might develop by regular drinking of alcoholic beverages.
We can group the reasons for increased tolerance to the following groups: better adaptation for the elevated concentrations (functional) or increased break-down (metabolic).
Functional tolerance.
This means that your body and its organs, especially your CNS, adapt to compensate for the increased alcohol concentration and manage to sustain its functioning despite the elevated blood alcohol concentrations (BAC). So, the dose of alcohol which previously led to trembling and disorientation now evokes only some coordinatory disturbances.
The physiological mechanisms involved here are:
1. Desensitization of the alcohol-sensitive (primarily GABA-ergic) receptors in CNS.
2. Changes in the neuron firing rates (to compensate for the deterioration of the GABA-ergic inhibition).
Metabolic tolerance.
This condition is characterized by the increased alcohol break-down by the liver, that slows down the increase of blood alcohol concentration (BAC) upon its consumption leading to the attenuation or complete disguise of alcohol intoxication (inebriation).
The main enzyme that is responsible for alcohol transformation is the so-called  alcohol dehydrogenase (ADH), that represents a group of substances catalyzing the alcohol oxidation to aldehydes. This enzymes are located in the liver cells (hepatocytes) and the increase in their activity (and most likely also the absolute amount) is not well understood. It happens, by the way, not only on alcohol consumption: the intake of barbiturates also leads to the increase of ADH and tolerance.
Here you can find much more information about acquired alcohol tolerance, but mostly from the behavioural viewpoint.