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What does "kcal/mol" mean when speaking of enzyme catalysis?
After thinking about it, I'm confused by what the reaction barrier of an enzyme actually means.
Imagine a reactor containing enzyme and substrate.
If the enzyme in the reactor has a reaction barrier of 15 kcal/mol,
a) then when 1 mole of product has formed, that means 15 kcal have been consumed, independent of how much enzyme is present in the reactor.
b) then when 1 mole of enzyme is present in the reactor and 1 mole of product is formed, 15 kcal have been consumed.
Is it option a), b) or otherwise?

Let us imagine two companies A and B.
Both companies use very similar technical equipment to carry out a biotechnological process where a chemical reaction is catalyzed by an enzyme.
Company A uses an enzyme with a reaction barrier of, say, 15 kcal/mol, while company B uses an enzyme to catalyze the same reaction but this enzyme has an activation energy of only, say 12 kcal/mol.
For every Mole of product, company B saves 3 kcal worth of energy needed to drive the factory.
Does that make sense?

While a lower activation energy is beneficial, I don't think a difference in activation energy of 3kcal/mol will translate into 3kcal/mol energy savings. It all depends on what requirements you have for the kinetics (reaction speed) and product yield. If you want faster kinetics you will have to make more energy available, but this may also change the equilibrium conditions. When optimizing reaction conditions, you will likely have to make tradeoffs involving reaction kinetics, catalyst amount, catalyst price and reactor temperature, depending on the specific reaction and the reactor design.

Let's think of a first order reaction  in terms of rates. Say enzyme 1 has a rate of 1000$s^{-1}$ and enzyme 2 has a rate of 2000$s^{-1}$, it's clear that enzyme 2 will only require half the time (at the same temperature) to produce 1 mole of product. Do you agree? So I only need to heat the reaction volume for half the time as I would when using enzyme 1.

Yes, I agree, an enzyme giving a lower activation energy will generally give a higher reaction rate, and that will definitely affect the economics of the operation.

I guess then the most reliable way to do this would be to calculate the time required to produce 1 Mole of product (given the rate constants) and then calculate back to the activation free energy differences. From this also I guess one can say that the unit "kcal/mol" indeed refers to 1 Mole of product.

I'm not sure I understand you correctly. Could you perhaps give a calculation example?

I mean just by using $k(T) = \gamma(T)\frac{k_\text{B}T}{h}e^{-\Delta G^{TS}(T)/RT}$ (see here http://www.sci.ccny.cuny.edu/~gunner/Pages-422/PDF/section.1/catalysis/cat.truhlar.pdf) and from this getting back $\Delta G$.

If you already know the rate constant at a given temperature and all the other factors then yes, you can calculate the activation energy. I don't see why you would need to do that though? If you already know the rate constant, you don't really need to know the activation energy to calculate your energy needs, unless you want to use it to calculate the rate constant under different conditions.

Sure, the rate constant already is very informative. Still if you can assist me in this initial question: If all is equal between reactors A and B, except the activation energies, then after having produced 1 Mole of product, one reactor required dE less energy to arrive at 1 Mole of product where dE is the difference in activation energy. Do you agree? I'm assuming both reactors require the same amount of energy to be heated up to the same temperature.

No, and that's what I've been getting at. As mentioned, the activation energy is only "borrowed". To find out how much energy you need to input or remove from the reactor to keep the temperature steady, you need to look at the heat of reaction. See the difference in height of the line at "reactants" and at "products" in the figure in the answer by Chris? That's what matters. If you have further questions on this, I think you may find people on the Chemistry StackExchange who can explain better.

The reaction barrier (also termed activation energy) is the energy that is needed for the reaction to take place. An enzyme is "only" a catalysator which lowers the necessary energy (and/or makes the reaction possible under the conditions) but some energy to start a chemical reaction is still needed. See this image (from here):

To your questions: A and B are essentially the same - but the reaction time necessary with small amounts of enzyme is much longer than when 1 mole of enzyme is present. The amount of energy needed to catalyze the production of 1 mole of product stays the same.

Shouldn't we say - energy barrier of the reaction rather than that of the enzyme (as TMOTTM has written in the question) ?

It would be more accurate. But it still makes sense, since it is the energy for the reaction with the enzyme.

@biogirl you're right.. mea culpa.

The activation energy for a reaction is given for a given extent of reaction, typically per mole of product formed. In general, the amount of enzyme present in the reactor is irrelevant with respect to the activation energy. So option a) is closest to correct. However, note that the activation energy does not tell you how much energy is consumed taken up during the reaction, only how much energy is needed for the activation energy to be exceeded and the reaction to proceed. The kinetics of a reaction, is a separate issue from the thermodynamics of the reaction, which determines the equilibrium concentrations of substrate and product. What the enzyme does is lowering the activation energy, thus speeding up the kinetics of the reaction and allowing equilibrium to be reached. In practice, the activation energy in the absence of the enzyme may be so high that the reaction would not proceed at all, and thus equilibrium would not be reached.

I agree, the activation energy would give me the amount of energy consumed during catalysis alone. Heating up the mass would be on top of that. But one can imagine that this component remains constant for different enzymes.

I think there might (still) be a misunderstanding here? The heat of reaction doesn't come on top of the activation energy - they are two separate things - and a catalyzed reaction does not consume or produce more energy than an uncatalyzed reaction. Think of it like this: The activation energy is the maximum energy that is "borrowed" when the reaction happens.

I might have been unclear. I know that $\Delta_f H$ is an indication of how spontaneous the reaction is.
With regard to the word "consume": I respectfully disagree, because to form 1 mole of product, an uncatalyzed reaction does require more energy input.

Indeed, you need to have more energy available, but the energy you spend on reaching the activation energy you also get back, so I feel "consume" is the wrong word to use. I don't see much point in arguing about that though - thanks for clarifying.

Let me put it differently, please see edit of original post.

To better understand the activation energy concept my teacher had given us an excellent example.  Suppose you are driving a car and want to cross a mountain. You could either go to the mountain summit and then come down or you could directly cross it through a tunnel. What enzyme does is to construct a tunnel for the reaction to proceed.

I dont think I have a problem with understanding the concept of a potential energy surface, in fact I would be a bit careful with that analogy. But it is a good starting point. Rather than a tunnel, I would say the enzyme finds a rout which doesn't reach that high up as the summit. Speaking of tunnels can be misleading when talking about enzymes, so one has to be careful about the terms one uses.

@TMOTTM yes I agree. Tunnel is a bit too much.


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Effect of Aging on SA node's sympathetic fibers
I am trying to understand the effect of aging on the sympathetic fibers of SA node.
I know that aging shifts the vagal curve to left in frequency due to aging.
However, I am interested if aging has similar effect on sympathetic fibers.
In young heart, heart's intrinsic functions can work with simultaneous parasympathetic and sympathetic processes.
If there is no change in the sympathetic function, then those processes have to happen at different times.
I am having this kind of schematic picture in my mind:

where intrinsic functions occur in 100-110 BPM normally.
However, aging shifts V1 to V2, no intersection anymore between V2 and S1.
What is the effect of aging on the sympathetic fibers of SA node?

Aging reduces mHR by reducing iHR and thus by reducing the pacemaker activity of the sinoatrial node of the heart. The progressive decrease in iHR with age necessitates a corresponding increase in sympathetic tone in order to maintain rHR

A bit late to ask, but where does South Africa come into this?

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How would the human body adjust to sleep times if we were to live in a place with different day lengths?
You sleep at night and are active during the day that's how things work for humans, but theoretically if a human whose parents lived on earth were to be born in another planet resembling earth but the difference was that this planet has an 8.5 hour day, what kind of changes will this person undergo?if a human who grew up on earth suddenly had to move to this planet how would his body adapt? what would be the difference between a person who moves to this 8.5 hour day planet with the person that was born there? and would the person who was born on this planet be active for 4.25 hours and then sleep for the other 4.25?

This is a cop-out, but I think in practice, the circadian rhythm for civilized humans is only loosely coupled to the day/night cycle. Astronauts will probably spend their day indoors, with artificial light they control, which will be a bigger factor than the sun. Also, note that on Earth, there are people who live in areas such as Antarctica, where for days at a time there is no night at all.

It would be pretty ineffective to adapt to an 4.25-hour rhythm. The proportion of necessary, but not directly beneficial activities like driving to work or preparing a meal would rise to a very high level. I go with ThePopMachine ...

Humans have evolved for 24 hour days and our bodies would not adapt well to this short of sleep/wake cycles (whether or not they were born there, unless they have been there for many generations and have been able to evolve for the new time). Our bodies would still want to spend about the same amount of time sleeping and being awake.
If we tried to adjust our sleep cycles to this planet with 8.5 hour days, we would experience many of the stresses that occur during jet lag (Google Scholar search), which can cause depression. Jet lag is identical to experiencing one day which is shorter or longer than the typical 24 hours.
The sunlight helps set our circadian rhythm, but 8.5 hours would be too fast. I thought I heard for an experiment that used mice that supports this, but I still haven't found the reference yet.
Nbogard referenced the article Plasticity of the Intrinsic Period of the Human Circadian Timing System, which showed that the circadian rhythm in humans can be altered by up to 0.65 hours by the use of lights. This is consistent with what I mentioned that the sunlight helps to set our circadian rhythm.
The best way to adapt would be to use artificial lighting to keep your days about 24 hour days (artificial light during waking hours, heavy curtains during sleeping hours), as mentioned in ThePopMachine's answer.

Now we have two contradictory answers. Some sources to back up each view would be nice.

Added link for sources. Also, clarified my answer, so that it is more apparent that our answers don't really contradict.

This is hard to back up with evidence, but I think jet lag has to do with synchronizing to the other people in your time zone, not the sun. Furthermore, if people on such a planet lived with 24 hour cycles anyway, would the effect on their psychology would be any different from graveyard shift workers?

Hopefully it is more clear now: I meant that adjusting our sleep schedules to the new planet (of 8.5 hours in each day) would be the same physiologically as jet lag ("repeated phase shifts of the biological clock"). Does that make more sense?

I think the important question is whether or not your circadian clock can adapt to faster day/night cycles. Jet lag is caused by a large shift in the 24-hour cycle, so it's unclear whether the effects would be the same or how long they would last.

Check this out: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1934931/

@nbogard, thanks, I added it into my answer. I still need to find evidence for more extreme changes to circadian rhythm.

Actually, for your example it would be pretty easy to adapt.  You just have a 25.5 hour day with 12.75 hours of day and 12.75 hours of night.  Except you have a 4.25 hour period in the middle of the day where you stay inside and use lights (like in the evening for most people on Earth) and a 4.25 hour period at night where you make sure your eye mask is on.
Added convenience: there are three different choices of when to call day so it's good for shift work and there's no problem with traffic.  Let's move there!

Most marine animals follow a 25.5 hour "day" because of tides. It is far more important to a barnacle whether it is submerged or in the air than whether it is day or night out. (That is just the most extreme example, of course. It still matters to mobile animals) Humans easily adapt to longer day lengths, as shown in cave research, but not to shorter.

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Is there a name for this principle in biological contexts?
This is mostly a question about usage.
There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was probably likely to do so.
This has been used in discussions about evolution, in which it is said that while we have trouble imagining circumstances in which self-replicating forms arise, the odds were probably in favor of their emergence when it actually occurred. And in discussions of the existence of intelligent life--it may be prevalent if we make the somewhat natural assumption (among others) that our own emergence was not highly improbable, given the existence of a suitable planet and so on.
Is there a name for this principle? I am familiar with the idea in the context of probability but have thought of it as an 'argument from likelihood' in biology. Also if there is a good description of the idea in a biological context a reference would be appreciated.
The tag is a little arbitrary. Thanks for any suggestions.

conditional probability?

@memming: Almost, except that it's a fallacy. To say that condition X existed because if it did then conditional probability would give a simple explanation for Y is backwards. So the idea is related.

It may also be called as Idea of maximum parsimony. It is used in phylogenetics to construct phylogenetic trees which require the least number of evolutionary events.

Max. parsimony is essentially Occam's razor. Maybe that's the best we can do.

@daniel Yes. I just wanted to give a specific example

@memming's comment above is also right. Occam's razor would work if we could assume anything about initial conditions. Then conditional probability gives the simplest explanation.

The principle of least effort / path of least resistance fit pretty well: animals, people, and systems (like evolution or a mechanical system like a machine) will naturally choose the path of least resistance or effort. The principal applies to chemistry (low energy states) and physics (the path an electrical current takes) as well. Occam's Razor fits somewhat too in an abstract sense in that nature favors simple solutions over complex ones. You may find something in thermodynamics as well.


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What kind of small insect is this?
Found in central florida in the bath tub. Its about the size of a pencil marking, very small. What is it?

This small hexapod appears to be a species of Springtail (or Collembola).  It is similar to the one below, with slightly different markings.

From the University of Florida:

Springtails are minute insects without wings in the Order Collembola. They occur in large numbers in moist soil and can be found in homes with high humidity, organic debris, or mold. Homeowners sometimes discover these insects occurring in large numbers in swimming pools, potted plants, or in moist soil and mulch. They feed on fungi, fungal spores, and decaying, damp vegetation, causing organic material and other nutrients to return to the soil; these nutrients are later used by plants. Occasionally, springtails attack young seedlings and may damage the roots and stems.

More information can also be found at NC State University Entomology Website:
http://www.cals.ncsu.edu/course/ent425/library/compendium/collembola.html
It is hard to say what species it could be, but it looks most similar to:
Isotomurus plumosus:

or Isotomurus tricolour from Rick Cowen:

It is hard to tell but it seems to be part of this genera, or is at least in the family Isotomidae, if not the exact species.
Their taxonomy is actually under debate, and they are in a group of hexapods that are no longer considered insects.


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Identical twins' biological sexes
Can identical twins have different genders (as in biological sex)?
I thought they should have absolutely the same genes. If they can, what caused it? I'd assume it MAY be because of errors in cellular division at conception.
Thank you.

Note that your question, and the accepted answer, seem to depend on the use of the term "gender" to mean "biological sex". You might consider rephrasing for clarity here, since "gender" is a rather more complex and nuanced social construct.

Done. Could you clarify what you mean by that? Or is it better if I post another question?

@WajihAziza These might get you started: http://en.wikipedia.org/wiki/Gender http://en.wikipedia.org/wiki/Transgender

Identical twins occur when a single egg is fertilized to form one zygote, which then divides into two separate embryos. Thus, identical twins are always the same sex unless there has been a mutation during development.
However, two identical twins expressing different sexual phenotypes does happen in some extremely rare cases due to environmental factors, deactivation of different X chromosomes in females, or aneuploidy. This is normally because an XXY Klinefelter syndrome zygote has split unevenly.
You are correct though, in that identical twins usually have hundreds of genetic differences early in fetal development which can be attributed to mutations in the DNA. But usually these differences do not result in twins with different sexual phenotypes, though it is possible.

There can also be many epigenetical differences between twins.

So theoretically, it's impossible to happen unless it was caused by an "error". That was enlightening. Thank you.

@WajihAziza Biology isn't at all my field so I may be off base here, but wouldn't the twinning event itself be considered an 'error' as that is outside of the normal?

Perhaps you want to rethink calling everything outside the norm an error.  It's needlessly pejorative.


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What is accumulation and release centre of neurohormones?
What is accumulation and release centre of neurohormones?
Is it hypothalamus?

Have you tried googling it ?

Incidentally yes.
I just want to be sure whether it is hypothalamus.

There are many tissues expressing and secreting neuropeptides and hormones. Certainly the hypothalamus and pituitary gland, but there are clusters of enervating through the brsinstem secreting GLP1, a host of enteroendocrine tissues to name a few. Are there some hormones in particular you are interested in?

The neurohormones in most mammals include oxytocin and vasopressin, both of which are produced in the hypothalamic region of the brain and secreted into the blood by the neurohypophysis (part of the pituitary gland).
A second group of neurohormones, called releasing hormones, also originates in the hypothalamus. The members of this group, however, are transmitted within the neural cells to a second locus in the brain, from which they pass in the bloodstream to the adenohypophysis, which also is a part of the pituitary gland. There they either stimulate or inhibit the release of the various adenohypophysial hormones.
A third group of neurohormones includes the enkephalins and other endorphins. The endorphins are effective in relieving pain, a property apparently related to their function as neurotransmitters, passing nerve impulses from one neuron to another. Their neurohormonal activity is manifested by their stimulation of the secretion of somatotropin and vasopressin by an indirect process involving a site (other than the secretory neuron) in the central nervous system.


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Strictly from a biological perspective, what is the functional expectation of a human being
Just like the title says: Strictly from a biological perspective, what is the functional expectation of a human being.
No religious or philosophy-based answers will be accepted, we are talking biology not religion or philosophy.
Answers involving excessive psychology will be frowned upon unless found to be exceedingly insightful. (The brain is a biological entity)
If you are considering claiming this to be too broad or unanswerable consider the hypothetical question "what are the functional expectations of human feet" which can be answered fairly easily by a child with no formal training in biology. In my actual question I simply ask about the feet and the other parts attached to them.
Edit: Originally this question was titled "Strictly from a biological perspective, what is the purpose of a human existence." To clarify the question i have changed it to "Strictly from a biological perspective, what is the functional expectation of a human being."
Despite the concerns raised with the use of the word "purpose" the question was serving its purpose with the answers I am seeing.  I did have  some reservations about the word "purpose" as well, but I thought I would try it and see what others thought.
So if a human stomach has the overall functional expectation of mechanically and chemically breaking down and digesting food, what would be the overall functional expectation of a human as a whole? I am looking for not so much of psychologically specific functional expectations and more of physical functional expectations.
For instance a house cat's functional expectations are generally considered to be sleeping, eating, reproducing, socializing, hunting, etc.

Adding the line "from a biological perspective" does not make this any less of a philosophical question. I would argue that the question "what is the purpose of feet" is also philosophical, but as shorthand most people will interpret that as 'what function(s) do feet serve the body' which is a biological question. It doesnt work for your question. What function do humans serve _____? Serve what? Serve themselves? Serve elephants? This question is too broad if biological, off topic if philosophical

Although "What is the purpose of human feet" and "What is the purpose of human existence" have the same word pattern, they are quite distinct English sentences, even before the biology question.  The first can be answered with what good feet do for people.  The second asks what good people do for  something (what?)  I would -1 this if I had the rep on this site (I have lots on math) Looks like a troll to me.  Biology and purpose rarely belong in the same sentence.

I think maybe the question is badly phrased.  You may want to rephrase without using the word "purpose", which implies a rationally-planned intention before the development of the item to which purpose is ascribed.  As biology does not accept that any such rational planning occurred, strictly speaking nothing can be said to have purpose in a biological context.

First you have to define "purpose"...

Sorry guys I don't see any way of further modifying the question without changing the intent of the question. It is an important question and was answered well. Do whatever needs to be done.

I will start with a quote from François Jacob, a French geneticist:

The sole ambition of a bacterium is to make two bacteria.

The same reasoning can be extended to all life on Earth, including humans.
There is no purpose to human existence, in the same way that there is no purpose for life at all. Life is there because it can. It works, chemically, physically and thermodynamically, given the physical conditions present on Earth.
Biology does not give any moral reason for our existence. It only describes what is there. Using experimental techniques we can infer the purpose of the human feet. All we need to do is to remove the feet of a human subject and see what happens. The subject will be unable to walk, and therefore we will be able to infer that the feet's purpose is to enable locomotion. In biological research, we usually remove or silence genes or proteins from an organism to infer their purpose. We then observe the phenotype. Most of the time however, such an experiment does not give any information on the purpose of the gene because its function is not obvious enough to be observed.
In the same vein, one could remove humans from the Earth and see what happens. If something changes for the worse on Earth, then we would be able to infer that our purpose was to prevent such event from happening. Obviously, such an experiment is impossible to perform, therefore we will never know what is our purpose, neither will we know whether we actually have a purpose.

I would have given a two-word answer ("To reproduce."), but +1 for making the answer long enough to satisfy stackexchange requirements and even throwing in an apropos quote.

Purpose requires a sentient being to have intent.  There is no biological reason to suppose there is any purposeful intent behind life.
If you hold otherwise, perhaps inquire of the fellow or lady or other you suppose is responsible.
Just because a child can give an answer to a question doesn't mean that the answer is accurate, or that the question truly is well-formed enough to answer well.

+1.  That there is an evolutionary benefit to feet does not imply that they have a purpose, as purpose requires forethought.  The same can be said of life's tendency to reproduce itself: you can argue that it is a basic characteristic of life, but that doesn't elevate it to the status of a purpose, because purpose implies design and there is no scientific basis for believing that any such design occurred.

In the context of evolution, the only "purpose" that a thing can serve is the role it plays in the process of reproduction, selection and mutation.
So, "what purpose do feet serve"? Naively: the formation of part of the human body as feet serves to increase the likelihood of the survival and reproduction of humans, by supporting the way we move and stand. Even more naively, the child wouldn't talk about survival and reproduction -- to a child the purpose of something is whatever benefit it is seen to cause, so the purpose of feet would be "walking".
"What purpose do humans serve"? Naively: to survive and reproduce. With more nuance, since we know about symbiotic evolution: to increase the likelihood of the survival and reproduction of various species, including but not limited to humans. For example humans have been pretty bad news for North American magafauna, but pretty good news for wheat.
On this basis of symbiosis you could reasonably conclude that the "purpose" of animals (or at any rate most bilateral animals) is to serve as a habitat and food-gathering mechanism for their gut-flora. Or that the "purpose" of most eukaryotes is to do the same for mitochondria. Or less fancifully, that the "purpose" of living organisms is to provide a stable environment for RNA and DNA to reproduce.
It's ultimately a question of perspective and as such subjective. "Purpose" really implies intent, which absent religion or philosophy is pretty hard to pin down. But when talking about feet and other biological characteristics we use "purpose" as a shorthand for "benefit which explains their being selected for".
As such, providing an environment for DNA to reproduce is right up there as a candidate for the purpose of life in general, including humans. Humans then are a variation within this general goal, that seems to be doing OK for the time being. This is more or less the theme of The Selfish Gene. You can easily question Dawkins's views on religion and philosophy, but (despite some disagreement) his ideas on genetics were pretty well received as far as they went.

That all depends on the perspective from which you view the question. For example, from the perspective of a human being the purpose of human existence may be to make more humans. From the perspective of a herd of goats the purpose for human existence is for the humans to bring food and water, care for kids, shovel out the barn, talk nicely to them, scratch them behind the horns where they can't reach, and give them something to snicker at. Cats are much the same but will sometimes allow their bellies to be scratched, don't have horns, and are to the best of my knowledge unable to snicker.
And of course all this assumes, on what only be termed hear-say evidence, that humans exist. "Ah", you say, "but I am real - I have form - I have substance - of course I, and by extension the entire human race, and in fact the entire universe, exist!". Perhaps, but then again perhaps not. What if what you perceive as existence is merely the by-product of intestinal gas disturbing the slumbers of a god-like creature whose vagrant dreams can morph into something approaching reality, but which vanish like a popping soap bubble when the god awakes?


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When does exposure to an allergen increase / decrease allergy?
In immunotherapy a person is regularly exposed to an allergen to decrease the allergy. Yet apparently "repeated intranasal challenges ... induces robust allergic airway inflammation, " [0]
So when does exposure to an allergen cause allergy induction vs hyposensitization?
[0] http://www.researchgate.net/post/Which_is_the_best_way_to_sensitize_mice_to_house_dust_mites

Small or relatively small amounts of the antigen can cause an allergy, when you have IgE antibodies which fit to this antigen. They will then cause a local immune reaction and cause the secretion of histamine.
For the desensitation therapy large amounts of antigen are given (which is not without risk). The mechanism behind this therapy is not completely understood, but there are some good points.
The immunetherapy seems to induce class switching from the IgE antibodies which can trigger allergic reaction to IgG who can not do this. Furthermore the IgG will mark the antigen for uptake and degradation by the mast cells.
This seems to be induced by a shift from a Th2 immune response over to a Th1 response. This also leads to the production of a different set of cytokines which are anti-inflammatory (IL-10 for example) and the already mentioned different secondary immune response. The immunetherapy reduces the amount of mast cells, basophils and eosinophils which are recruited into skin, nose, eye and the bronchial mucosa. These cell usually support the reaction to allergens in this tissues after the exposure.
See these papers for more information:

Allergen immunotherapy.
Allergen-specific immunotherapy


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How does regurgitated food go to the 3rd stomach chamber instead of going to the 1st?
Ruminants are known for their regurgitation of food; the food goes through the 1st and 2nd stomach chambers, then returns to the oral cavity in cuds. The cuds then come back into the stomach, but this time they go through the 3rd and 4th chambers, instead of going to the 1st and 2nd again.
How is it ensured that the regurgitated food doesn't go through the 1st and 2nd chamber by a mistake?

Your question supposes a very linear version of the flow of stomach contents of:
1->2->mouth->3->4
In reality, it is not so linear. Firstly some background: The rumen and reticulum form the first two parts of the four, and are in fact a single chamber/organ (collectively known as the reticulorumen). They have different wall structures, and perform initial digestion of different particles (mostly heavier particles in the rumen such as grain and more digested hay). This reticulorumen chamber is where the initial microbial fermentation of the feed occurs. Matter passes from rumen to reticulum and back regularly by means of two distinct muscle contractions.
To aid in the breakdown of the feed, the cud is regularly regurgitated, chewed and then re-ingested. The re-ingested cud returns to the reticulorumen. From there, in order to advance down into the later stages of the digestive tract, it must pass through the reticulorumen orifice into the third compartment - the omasum. The orifice allows particles up to 4mm in size in cattle.
The omasum chamber removes water and some nutrients. The contractions of the omasum remove water and move solids through the system, and the contractions are speculated to filter out any larger particles and return them to the reticulorumen. Matter that has been processed by the omasum is passed along to the fourth chamber, the abomasum.
So to answer your question in brief, after mastication the cud returns to chambers one and two, potentially going round this loop several times until it is sufficiently broken down by chewing, saliva and bacterial action, and then it can proceed from there to the third chamber.
The "digesta circulation and reticulo rumen motility in the ruminent" paper (C. Poncet, C.H. Malbert, R. Baumont) has this to say:

The outflow of digesta, allowed by the opening of the ROO [reticulorumen orifice] during the second phase of the reticular contraction, is highly selective. The effluent does not contain particles greater than 2mm in sheep and 4mm in cattle. This is due to the buoyancy of the large particles in the reticulum, to the self filtration of the digesta during the passage through the ROO and perhaps to backflows from the omasum to the reticulum.

You may find it useful to get a copy of this collection of papers (quote from p.366): http://books.google.co.uk/books?id=Bcsa8Z4u-E4C&printsec=frontcover#v=onepage&q&f=false

Thanks. Just to make sure I understand, do you mean that the large pieces of food simply cannot get through the passage to the 3rd chamber, and only the ingested, chewed-into-small-pieces food manages to get through?

In the main yes, although all digestion will be a little inexact - the odd larger particle could in theory get through I would guess. The size of the reticulorumen orifice would place an upper limit on the size of particle that could pass, and it is believed that the omasum will pass back some larger particles - the omasum contracts to expel water and move matter, and this may work in both directions.


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How were the first primers made?
I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about 20-30 bases long.
However, how were the first primers developed? Somewhere, someone needed to come up with a 20-base sequence that bound to a specific part. Aren't there 4^20 such combinations? That's a lot of potential options to test.
How was that done?

When you don't know what primer to use, you can use random hexamer primers. They have a rather low specificity but they make it possible to get some information that you can use as a starting point. Alternatively you can also use the known parts as a poly-A tail in mRNA and start from there. Or you add an adapter to your DNA to be sequenced with a known sequence and use primers from this adapter (this is what is done for NGS).

The process of sequencing was, and can be, assisted by cloning a DNA fragment into a plasmid and using primers that bind to known sequences (in the plasmid) that flank the cloning site.  (and what @Chris said)!

+1 for PlaysDice - this is why the primers that were used in Sanger sequencing were called universal primers. @PlaysDice you should write this as an answer.

@PlaysDice I want to understand more about it! Please write it in an answer.

@AlanBoyd.  By popular demand..added ;)

The MIT synthetic chemist Gobind Khorana won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids.  The chemistry was difficult at the time but he won the prize for making specific sequences of RNA bases which were then fed to cells, resulting in specific amino acid chains, which ultimately deciphered the specific base to amino acid correspondence of the genetic code.
Khorana was only one of the chemists who worked on nucelotide synthesis, but the technique overall is simple and since nucleic acid polymers are only unbranched polymers,
any sequence combination is easily obtained.  Each sequential reaction adds one base.  Repeat the reaction as many times as needed.

The chemistry Khorana devised was refined and easily extended to DNA polymers since the linkages are identical, the difference between DNA and RNA is only a single alcohol (-OH) group, which is not directly involved in the bond between the nucleotide bases.
By 1983 when Kary Mullis concieved the idea of PCR, short sequences of DNA and RNA could be synthesized on commercially available machines.  In fact Mullis was responsible for just such a machine at Cetus Pharmaceuticals and had been trying to find a way to increase demand for his services.
The PCR oligos were the easy part of the operation.  To prove the concept, the team at Cetus used a conventional DNA polymerase and add it to the PCR mix after every cycle.  By 1986 the Cetus team had succeeded in performing PCR a heat tolerant DNA polymerase from Thermus aquaticus, a bacterium from a hot spring, which basically made it the technique we still use today.

The process of sequencing was, and can be, assisted by cloning a DNA fragment into a known site in a plasmid designed to help sequencing. That cloning site is flanked by a known sequence(s) that can use standard primers

In the figure "A" and "B" are just reference points on either side of the Cloning site.  Of course, the plasmid extends on either side of the shown region.  The plasmid is first cut open at the cloning site (upper step) and the unknown DNA fragment ligated in (middle step). Then the known 'forward' sequence can be used, with a complementary primer (shown as the arrow), to prime a sequencing reaction (lower step, dashed line).
Additional modifications include (per @Chris) preparing the insert with adapters or using a plasmid with sequence that binds a 'reverse' primer (on this figure, that would be an arrow on the right hand side of "B" and pointing to the left).   The reverse primer allows sequencing of the opposite strand to the forward primer and gives access to the 3' end of the inserted unknown sequence.   In the early days of Sanger sequencing read lengths were quite short and often were unable to run the length of a larger insert.
Sequencing plasmids are designed so that their forward and reverse primer binding sites are unlikely to contain any sequences that may be found in the insert.   Because these known primers can be used in this manner to sequence almost any insert, they are often called Universal Primers (per @AlanBoyd).


text:
What is meant by single molecule sequencing?
When sequencing papers refer to single molecule sequencing, what is their definition of a "molecule". Are they saying base by base? The entire DNA chain in a chromosome can also be though of as a "molecule". In that case, that's a much larger read. What's the default interpretation?
For instance, is the Illumina sequencing "single molecule" as they fluoresce one base at a time?
Thanks!

For the classic Sanger sequencing you need quite large amounts of DNA to be able to run the sequence reaction. This is a problem when you want to sequence whole genome since the DNA needs to be amplified then, which for some sequences can cause problems, introduce errors or cause bias.
Single molecule sequencing is a huge step forward here, since only one molecule of DNA is used for sequencing. There are different sequencing technologies based on this principle.
The system of pacific biosciences uses a polymerase bound to a small well which binds a singlestranded DNA and begins to make the opposite strand, when nucleotides are present.
See the image below or this video, which explains the technique quite nicely.

Illumina binds singlestranded DNA molecules to the surface of the reaction chamber and starts amplifying them there. The use of fluorescently labelled nucleotide allows to monitor the reaction. This looks like the following (left side of the figure from the review mentioned below):

An illustration from Illumina which is more detailed, can be found here.
Although it is a bit older (and the technology develops fast), this review is a nice introduction: "Sequencing technologies - the next generation."

Nanopores typically use an unlabelled oligo. Your figure is Pac Bio's immobilized DNA polymerase approach that uses the wonderfully named Zero Mode Waveguide to visualize a 20 zeptoliter volume and observe each labelled oligo being incorporated by the polymerase.

Yep, thats right. Have a look at the video, it is about the same method.

But it doesn't use a pore.  Its a well.  My comment was that a 'true' nanopore approach like Oxford Nano doesn't use label.  Both are examples of single molecule analysis.

I'd +1 if you add a sentence about nanopores or other single molecule approaches and answer OP re Illumina.

@Chris: So for some of these methods, they say "1 molecule = 1 count". So say they had a read count of 100 for a gene. What exactly does that mean? There were 100 reads from that gene? 100 reads of bases from that gene? Something else?

@Chris Is this same as what is called - Sequencing by synthesis ?

@biogirl Yes, as far as I know this is one of the other names for it.


text:
How is nutrient uptake in humans measured?
There are many claims made about nutrient absorption, eg "Juicing helps you absorb all the nutrients from the vegetables".  I'm curious to know how nutrient uptake is measured.
Eg is it a pure nutrients in vs nutrients out equation?  Or are blood levels of nutrients measured before and after consumption?
What ever the methods, are they reliable enough to support claims made about relative absorption rates of certain diets or eating practices?

Depends on the nutrient type. Typically you would need an distinct assay or a molecular sensor for each nutrient type.


text:
Is a naive immune system equally able to handle new antigens as an educated one?
This is a variation of the "does the immune system run out of memory" question.
Here's a (possibly imperfect) thought experiment: You take two twins. One of them lives in a bubble from birth. One of them is Mike Rowe from Dirty Jobs, and gets exposed to all sorts of antigens as well as vaccines. When they are 30 years old, you expose both of them to an antigen that neither has seen before. What happens?
PS: Note that while this example is illustrative, my question is really about whether there is any way at all in which the response of a naive immune system to a novel antigen is different from that of a very educated immune system (which has also not seen the antigen before). For instance, would the same amount of antigen be required to stimulate the immune system? Would the antibody count several months or years post-exposure differ?

Of course, we've never done this experiment (bubble boy without an immune deficiency), but I'd speculate that the regulatory environment for the immune response would be quite different. It's hard to say whether the 30 year old immune virgin would react to exposure like an infant, or something different entirely, but you can't just consider the novel antigen and the immune cell that recognizes it. In vitro, in standardized conditions, you would expect a naive B or T cell from either brother to react to a novel antigen in the same way, but that's not what you're asking.

They will both go through a primary and secondary immune response. So first low affinity antibodies will bind, the corresponding b cells will undergo affinity maturation, somatic hypermutation until high affinity (perfectly fitting) antibodies are available and these antibodies will finally undergo class switching.
Depending on the antigen an innate immune response will also be triggered as part of the first line of defense. There is no difference in the immune response between these two hypothetical brothers.

While the initial response would be the same because neither person has corresponding antibodies, would there be a difference in the amount of time that it takes the killer T cells to respond and destroy the antigen? Bubble boy never uses his killer T cells and Mike Rowe would use them all the time. Would that make a difference in response time or the quantity of killer T cells?

Not when we assume that both have never seen this antigen.

I think this is the right answer, barring cross-reactivity. In other words, Brother Ed (educated) may have not have seen a specific new antigen, but he may have been educated with another antigen such that his antibodies cross-react with the new one.  So, on balance, I'd err on the side that Ed might indeed react.  Feel free to add if it helps.

This answer neglects the general changes that occur in immune cell and antibody populations resulting from 30 years of exposure to the environment. Cross reactivity is one issue. There are many others, e.g., the regulatory effect of the entire population of the gamma fraction of plasma, and changing populations of $T_{reg}$ and Th17 cells. The adult immune system is quite different from an infant's immune system, and much of this appears to be related to cumulative exposure to non-self antigens. It's not as simple as whether or not you've been exposed to a specific antigen.


text:
Gel Electrophoresis - loading dye and more
I'm a student new to molecular biology coming in from an eco-evo background looking for tips from you molecular pros! It seems that I'm running quite a few gels. The loading dye I'm using is Gel Loading Dye, blue (6X). The supporting document calls for 5uL:25uL reaction and 10uL dye:50uL reaction. Here's the problem: I'm trying to get my PCR to work and so I'm doing a lot of 'just checking' trials where I only load 2uL of reaction to each well from different 20uL PCR reactions. What volume of Gel Loading Dye, blue (6X) should I use when running only 2uL of PCR product
My goal now is to learn to do a DIG in situ hybridization to localize the distribution of mRNA of a gene I'm interested in so any tricks and tips would be greatly appreciated!

The loading buffer you add to your samples for gel electrophoresis has a few different purposes, but the exact amount does not really matter. The purpose of the loading buffer is

to make the sample heavier so it is easy to get into the pocket and stays there
to visualize how far the gel has run
to denature the sample (only for denaturing gels)

Sample buffers for agarose gels usually use something heavier than water like glycerol or sucrose together with a tiny amount of a dye like bromophenol blue.
So in general there is no issue with using too much dye, but using not enough could lead to the sample being not heavy enough and problematic to pipet, or the sample not being properly denatured. I'd either use 1 ul of the sample buffer (smaller amounts can be annoying to pipett) for your sample, or dilute the sample to 5-10 ul and use the regular amount.

When using small sample volumes, it is advisable to use water to increase the volume and make handling and mixing with loading dye easier. For example, you may mix 2 uL of your sample with 1 uL 6X loading dye and 3 uL water for a final volume of 6 uL.


text:
Why is oxygen used up in eutrophication?
This probably sounds pretty dumb, but wouldn't algae blooms produce a lot of oxygen? Although they would die out and decomposers would use up oxygen, is that more than what the algae produced?

Algae produce $O_2$ in the upper layer of water but when they die they stop producing $O_2$. They sink to the seafloor and most get decomposed by bacteria on the seafloor. In this process, bacteria use $O_2$ contained in the bottom layer of water which decreases the dissolved $O_2$ concentration in the bottom water.
These concepts (and much more!) are well described in the excellent open-access paper by Rabalais et al. (2010) Dynamics and distribution of natural and human-caused hypoxia. It also includes case-studies of areas affected by hypoxia and eutrophication around the world. A must read if you're interested in this topic!

thanks for your contribution to BiologySE! Are you able to put some references to your answer? We prefer answers with references on this site, as anonymous users can claim to be an expert in anything... and having references allows other users to read more about your answer in the context of the question

@VanceLAlbaugh that's definitely an excellent idea, thanks for pointing this to me. I edited my answer with one of my favorite paper on the topic.

As you surmise, the oxygen is consumed by decomposers. From the Wikipedia page on Eutrophication:

Phosphorus is a necessary nutrient for plants to live, and is the
  limiting factor for plant growth in many freshwater ecosystems. The
  addition of phosphorus increases algal growth, but not all phosphates
  actually feed algae.[2] These algae assimilate the other necessary
  nutrients needed for plants and animals. When algae die they sink to
  the bottom where they are decomposed and the nutrients contained in
  organic matter are converted into inorganic form by bacteria. The
  decomposition process uses oxygen and deprives the deeper waters of
  oxygen which can kill fish and other organisms.

Does the oxygen produced by the algae while they are alive evaporate away or what? Is it a question of producing O2 at the surface and consuming it at the bottom of the water column, where fish live? If the algae still have carbon-containing bodies there must be surplus O2 somewhere that they made while alive. As a continuous process why isn't the oxygen produced by new algae used to decompose the old algae? Does it just escape into the atmosphere?

As the question is tagged as "marine-biology", your answer is not completely correct. Most marine ecosystems are nitrogen-limited, not phosphorus.

Much like how planes fly, a proper explanation to this question is more nuanced and complex than first appears...
The total algae lifecycle is oxygen neutral
When any plant or algae grows sunlight is stored as chemical energy (oxygen + organic compounds). After the autotroph dies decomposers consume this energy and we are back to square one.
Would burying dead biomass keep the oxygen from being used up? Doing so oxygenated Earth in the first place (and oxidized soluble iron II into insoluble iron III). However, it only took a tiny fraction of fossilization to build up oxygen over geological time. Thus we can ignore burial in most ecosystems.
Water can't store enough oxygen
Water contains very little oxygen, even less if it is warm. Freezing water which is fully oxygenated (has been well-aerated with air at sea-level) will have about 14ppm of oxygen. This compares to 20% oxygen (200000 ppm) in the air. Water holds at most 1/10000 oxygen by mass and 1/10 by volume as air! This is also probably why no fish or shark is as big as a blue whale.
During the bloom oxygen rapidly exceeds the amount water can hold. It may seem strange that water with only, say, 25 ppm oxygen will give oxygen to the air. But the rule that "solutes move down their concentration gradient" assumes that the solvent they are dissolved in stays the same. When we consider multiple solvents we need to factor in the partition coefficient.
Even if air was pure oxygen, only 40ppm would dissolve in warm water. When shallow water exceeds this threshold bubbles of oxygen appear and rise to the surface.
Algae blooms are followed by a population crash once whatever nutrient caused the bloom (usually nitrogen, iron, or phosphorus) is used up. Such crashes are common with fast-growing species. Since most of the oxygen produced by the bloom has been lost the water will end up with less oxygen than it started with. Anoxic water is quite unpleasant.
Decaying biomass sinks
Algae blooms produce oxygen near the surface. The cells then die, lose buoyancy, and sink. The whole lifecycle of growth and decay has the effect of pumping oxygen out of deeper water and into the air. This can create near-permanent dead-zones in deeper water.

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


text:
PCR master mix contents
I am running PCR reactions with different sets of degenerate primers and I want to know what should go into the master mix

My usual master mix:

DEPC water
PCR buffer (-Mg)
25mM MgCl2
10mM dNTPmix
cDNA

On ice I add my forward and reverse primers to the appropriate PCR tubes, add master mix to each PCR tube, then right before I pop them into the thermal cycler I add taq and mix.

Is this a proper way of doing it? I get product but I'm thinking maybe I can improve it by changing what I add to the master mix. For example, is it better to add taq instead of cDNA to the master mix and then add cDNA before I start the PCR? Is it okay to add both cDNA and taq to the master mix together?

I always add the Taq to the mastermix. First it makes the handling easier and it avoids pipetting steps which can cause contamination and can also be forgot. Then the enzyme is very stable and will even tolerate room temperature without problem. Since we are going to heat this 30-40 up to 95°C, so this is clearly not problematic. Since the reaction mix is cooled, you reaction will not start. And even if it does, there wouldn't be much amplification due to the low temperature.
I usually add everything which is the same for all reactions to the mastermix (this can include the DNA as well). If I use more than one DNA I split the mastermix in half. This way you are not going to make different pipette errors for the template, which is especially important for realtime-PCR. I usually dilute the primers slightly so I can pipett bigger volumes (simply use a part of the water used to balance the PCR reaction). You can also premix primer pairs, if you want, I have never seen problems doing this.


text:
What is Saccus in Embryology?
The word seems to be of German origin.
I have it here

Saccus lymphaticus inguinalis,
  Saccus lymphaticus jugularis,
  Saccus lymphaticus posterior,
  Saccus lymphaticus retroperitonaealis.

I would like to use the word "sinus" instead.
However, Google search does not give good results for it.
What is the meaning of the word "saccus" here?

From the Latin saccus, bag, which is in turn from the Ancient Greek sakkos, sack or bag.

Saccus simply means sac or bag and is is closed cavity. The lymph nodes develop from the structures, see this image:

Superior cardinal vein (jugular vein)
Jugular lymphatic sacs
Right subclavian vein
Axillary lymphatic sacs
Left brachiocephalic vein
Thoracic duct (bilateral)
Lumbar lymphatic sacs
Iliac lymphatic sacs

The image is taken from this webpage, which should be interesting for you.


text:
How much of the jejunum is bypassed during gastric bypass?
There is both long and short limb gastric bypass surgeries (along with several other variations on intestinal bypass procedures). How much of the jejunum is bypassed with a long-limb and short-limb gastric bypass?

One of the most used surgical technique is Roux en-Y where the small intestine is divided approximately 40-50 cm below the lower stomach outlet and is re-arranged into a Y-configuration.
The portion of intestine (jejunum) from the upper stomach is called the "Roux limb". It has a total length of 80 - 150 cm.
So the Roux en-Y technique "bypasses" only the duodenum and a small portion of jejunum - no more than 50 cm, that's about 7-10% of total length of small intestine.
"Total gastrectomy with Roux-en-Y" by ignis - Own work. licensed CC BY-SA 3.0 via Wikimedia Commons.
Reference: Wikipedia contributors, "Gastric bypass surgery," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Gastric_bypass_surgery&oldid=606081291 (accessed June 27, 2014).


text:
Advantage of cup-like shape of blood cells, spores?
Mold spores sometimes have the same shape as platelets in blood. If I were designing a spore it would probably be spherical. Is there any advantage to this cup-like shape?
Maybe there is some advantage in flow properties in fluid or air? And maybe the physics of structures on that scale differ from that of everyday objects?
Thanks.

The functional implications of the biconcave shape of human red blood cells are not fully understood. Several hypotheses have been suggested as explanations, including bending energy (1) and effects on oxygen transport (2). More recently, it has been hypothesized that the shape is important for the flow properties of the blood cells in capillaries. Uzoigwe (3) states that

The deleterious nature of turbulent flow on the cardiovascular system
  suggests that the biconcave disc form has evolved out of a necessity
  to maximise laminar flow, minimise platelet scatter which in turn
  suppress atherogenic activity in the large vessels.(...) The biconcave
  profile of the discocyte means that much of the mass is distributed in
  the periphery. This increases the moment of inertia of the cell and
  subsequently renders the erythrocyte less prone to rotation during
  flow in the large vessels. Here it is suggest that this reduction in
  rotation promotes laminar flow and discourages platelet scattering by
  minimising the "Eddy currents" and it thus anti-atherogenic. A number
  of pathological mutations result in the red blood cell adopting a
  spherical shape as opposed to the biconcave disc profile. The sphere
  has a smaller moment of inertia when compared to the discocyte, as
  much of the mass is distributed round the centre. The spherocyte is
  hence much more prone to rotation during flow in the large vessels.

The advantages of various structures do depend on the scale of the system, as you say. For red blood cells, the size of capillaries and veins are of importance. The shape of red blood cells differ in animals that have blood transport systems with different structures than humans. Thus, the red blood cell shape is likely optimized with respect to movement in the human blood transport system, with oxygen diffusion also being a possible factor. To determine what advantages a specific shape of spores would give, you would need to consider the expected environment the spores would live in and their typical lifecycle.


text:
Ideal lab glassware cleaner for molecular biologist
I'm using Alconox powder detergent to clean my laboratory glassware, the powder is a pain to store near the sink and to use. Would like to make a   concentrated liquid to use in its stead.
I have tried a few things, obviously just water and mixing, even up to overnight. It really doesn't go into solution very well, even at seemingly low concentrations. Ive got it up to about 20% w/v but I've tried heat, glycerin, adjusting pH to ~8.8, adding EDTA. I have not added these things in any scientific way, just kind of pouring glycerol or EDTA in.
Wondering if anyone in here has experience with detergents like this , or has done something like this before. Thanks in advance!

for usual cleaning a regular liquid detergent should be sufficient. I subsequently wash it thoroughly with milliQ water. Unless you are doing some sensitive experiments such as mass spectrometry, the minute amounts of residual detergent should not be a problem. For what purpose do you use Alconox ?

Obsessive compulsive disorder mostly. I like having clean glassware. I pulled up msds on alconox and liquinox. They are very different chemicals. Would have been  nice to be able to make a viscous concentrated liquinox out of all the powder alconox we have though.

Have you considered bleach to clean things, and then a general purpose liquid detergent to help carry away the residue if any remains? A nice bleach soak will destroy everything biological.

SparKleen because the name is awesome

If you're just using it for hand washing, you probably don't need an ultra-concentrated solution. A very small amount of detergent goes a long way. (Think about it - what would you do with an ultra-concentrated solution? Probably squirt a small amount on the glassware and then add water.)
What I've seen done is to make your "dilute" solution of Alconox, put it in a squirt bottle, and then use a healthy squirt of it when washing. In fact, you probably find you don't even need a healthy squirt of it. A small amount of even the dilute solution is fine.
The approaches I've seen have been rather cavalier - basically just throwing a bunch of the powder in the squirt bottle and filling it with water. You quickly get a sense of how much will dissolve, and if you use a squirt bottle with a drop tube that doesn't go all the way to the bottom, you don't need to worry if not all of it dissolves.
Alternatively, as you you seem the fastidious type, you can fill another (non-squirt) bottle partway with Alconox, the rest of the way with water and let that sit (perhaps with occasional mixing). This should give you a saturated Alconox solution, which you can use to fill the squirt bottle, being careful not to transfer residual powder from the bottle. Then you can add more Alconox powder and water to the stock bottle, let dissolve, and you should be ready for the next time.
Again, this may only give you a 10-20% solution of Alconox in water, but that should be more than sufficiently concentrated for most usages.

In our labs we just use something like palmolive or bleach followed by a 95% EtOH rinse and finally rinsing with DI water.

this has nothing to due with my question


text:
introduction to Chip Seq
I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've been looking at Chip Seq data. But to make sense of the Chip Seq data I wish to understand how the experiment is first performed.
Basically my question relates to step 1 of the following diagram:

Now my main question is how come the reads are overlapped? Where did we get so many of the (almost the) same reads?
My "understanding" is that:
1) They take a DNA sequence and crosslink the protien of interest. Then they get rid of the DNA sequence surrounding this area of interest so now we have a "small" sequence of DNA and in this small DNA is somewhere where our TF binds. Now we make copies of this small DNA seq and run it through a sequencing machine. Is this correct?
2) They take a bunch of cells = bunch of DNA sequences. Then they do the same procedure above (by crosslinking and getting a "smaller" DNA sequence of interest). Since they had many cells to begin with, this means they had many DNA seq to begin with. Now they shear the DNA seq and we have fragments. Then we align these up with the reference genome.

The basic steps of ChIP-Seq are:

Crosslinking proteins to DNA - this fixes the proteins in their natural positions
Nuclease digestion - this removes regions that are unbound to protein; nucleases are sterically hindered from digesting protein-bound DNA
Immunoprecipitation - this allows isolation of the target protein by binding it to a selective antibody
Sequencing to determine the bound DNA sequence
Mapping the reads to the reference genome

Why so many reads? They are taking many reads from different cells. Why are the reads so short? Many modern next-gen sequencing methods are limited to ~30 bp reads. Thus, the reads you see are not actually the entire protected sequence but rather just a shorter fragment from the 5' end (where sequencing starts from). The why behind this is explained by Jiang and Pugh, 2009 (Nucleosome positioning and gene regulation: advances through genomics):

Three DNA sequencing technologies have been used to map nucleosomes. Pyrosequencing using the Roche 454 GS20/FLX
  sequences nucleosomel DNA end-to-end, allowing both nucleosome
  borders to be linked in a single sequence. This method provides the
  greatest mapping accuracy, particularly in genomic regions of low
  complexity. By contrast, other platforms, such as those provided by
  the Illumina-Solexa Genome Analyzer and Applied Biosystems SOLiD,
  generate only 25-35 by sequence tags, requiring both nucleosome
  borders to be inferred. Nonetheless, these short-read technologies
  produce >100 times the number of sequence tags at a similar cost as
  the long-read technologies, and so the short-read technology is
  currently the only practical technology for mapping nucleosomes in
  large genomes. The higher tag count of the short-read technology
  enhances mapping accuracy and thus provides a practical way of
  mapping nucleosomes.

Why are the reads overlapped? I can think of a few explanation for that. For starters, Protein-DNA binding is variable in its specificity. In other words, a given protein might bind at the exact same site every time or it may bind 'around' a site or it may bind randomly. A protein that binds an exact sequence would be expected to produce reads that are more in phase that one that binds more variably. Next, the nuclease digestion process is random (or at least expected to be). Thus the DNA cleavage point relative to the protein is variable and your reads start from different points. Again, from Jiang and Pugh:

At any given genomic locus, the preferential positioning of nucleosomes--called phasing--can be described. At most loci, there is an approximately Gaussian (normal) distribution of nucleosome positions around particular genomic coordinates, ranging from ~30 by for highly phased nucleosomes to a random continuous distribution throughout an array. How much of this variation is due to genuine positional heterogeneity and how much is an artefact that is caused by overtrimming or undertrimming of the DNA at nucleosome borders by micrococcal nuclease during sample preparation remains to be determined.

Does that answer your question? Basically the reads are overlapped because there are many of them and they may differ either because of actual variance in the DNA binding site (which is biologically significant) or because of variance in the DNA digestion site (which is a methodological flaw). As with any biological experiment, you must perform many replicates to statistically determine the source of the variance and this is done by taking many reads. I recommend you read the article I quoted from, it is a good overview of histone mapping with ChIP and is likely also applicable to what you're studying.
Also, do you know why there are two sets of reads (red and blue)? I would venture a guess that they are taken from opposite strands. In other words, they are reads of the same DNA region taken from different directions. That might help clarify what's going on.
To conclude:

DNA is not extracted from a single cell. In usual procedures it is
always from a collection of cells or from tissues.
The overlap in TF associated reads arises because of the TF bound
sequence coming from different cells in this collection.
Each DNA piece is amplified and clusters are formed in the NGS
sequencers (for the ease of detection);
In a homogeneous cell collection i.e. all cells are of same type, the
variability in the read position usually arises because of
flexibility of binding sites (i.e TF wont exactly bind to at a
certain locus). Also, as previously mentioned the variability can
arise during the technical procedures.
In case of heterogeneous tissues the variability arises because of
different biochemical status of different cells. Strictly speaking
there is always some heterogeneity even in an apparently homogeneous
tissue but tissues such as brain are highly heterogeneous
In the case of nucleosomes the positioning is not exact because the
sequence contribution to the position is very minimal. Certain
nucleosome positions are tightly maintained for e.g. around the TSS
(transcription start sites) whereas in other regions the positioning
is fuzzy because of the dynamic nature of the chromatin.

I added conclusions to summarize your answer.

Thank you. I think was missing is that a TF may bind 'around' a binding site. I was thinking suppose you have a DNA seq ATGCGCTATATCGAT but you have a thousand of these since there are 1000 cells. TF binds to TATAT so when we crosslink and "digest" we get rid of everything surrouding it. Then we have TATAT left. Then we can break this up to TA, TAT since NGS readers can't read long seq. Now we have a bunch of TA, TAT floating around. If we align all of them up, we shouldnt see the picture I posted, but we should see a "ladder". This is not true, but do i have the process right?

Your transcription factor may bind to TATAT but it may protect much more than that. For example, prokaryotic RNAP binds the core promoter at -10 and -35 (which is about 29 bp) but protects about 70 bp of DNA. Thus, you'd likely get more than just TATAT. Also, I expect that no NGS could actually sequence a fragment so short. Maybe I'm not understanding what you're getting at.

The example seq I used was supposed to be a very long DNA sequence. The binding site TATAT was supposed to be 150 - 900bp long. Still too long for NGS, so we breakup TATAT into shorter fragments TA and TAT.  And I wanted to see where my understanding had gone wrong.

So that's not quite how ChIP-Seq (Chromatin ImmunoPrecipitation and Sequencing) works. First, you start out with a large number of cells per sample (preferably on the order of 107 or more - the more sample, the more immunoprecipitations you can do to different targets) and do whatever it is that you're going to do to induce transcription factor binding - expose cells to drugs, treat with cytokines, grow in different conditions, or simply compare two types of cell populations - normal vs. cancer, etc. After a certain period of time, determined by your experimental setup, you cross-link the cells with 1% formaldehyde, which fixes everything in place, including transcription factors bound to DNA. The cells are then broken apart by incubation in a detergent-containing buffer, and nuclei are harvested. After washing, the nuclei are either incubated with micrococcal nuclease (MNase) to digest DNA into strands of 1-5 nucleosomes in length (150-900 bp), or sheared by mechanical ultrasonication, hopefully leaving strands of the same length.
Once you have your DNA strands, you add antibodies to specific targets - either certain forms/post-translational modifications of the histone proteins that make up the nucleosome, or to specific transcription factors or TF families. The antibodies bind to their targets, and are enriched by incubating with (generally magnetic) beads that have the antibody-binding protein Protein G covalently attached to their surfaces. The beads are washed with low-salt and high-salt washes, then the formaldehyde cross-links are reversed and the chromatin is eluted from the beads in an elution buffer at high temperature (65°C) with vortexing in a thermomixer. Any remaining protein is removed by digesting with Proteinase K, the DNA is purified using a spin column, and you now have your enriched, purified DNA sample ready for sequencing.

Source
Antibody binding and enrichment of known sequences is often first analyzed by regular PCR, just to ensure that everything worked. Once your sample has been validated, it is then prepared for next-gen sequencing. We are now near Step 1 of your illustration above. The read lengths of some instruments may be shorter than the average length of the fragments you prepared during the ChIP step (150-900 bp), so during the library construction phase they are further broken down into shorter strands before having the common primer templates ligated to them (if that's the technology you're using). Even if the instrument allows you to use the full length of your DNA strands, you need to remember that the sample is the aggregate DNA from millions of cells, and they didn't all break after MNase digestion in exactly the same way.
After amplification and reading, you are then left a large number of short sequences, which need to be compared to a reference genome and aligned:

Source
Since we've already enriched for certain regions of DNA by using the antibodies which bind to DNA-bound or -associated proteins, there will be a larger number of similar overlapping reads in enriched areas, allowing us to tell where the histone, transcription factor, or other protein was bound when the sample was originally cross-linked.
Hopefully this all makes sense to you. I based my description of the ChIP protocol on Cell Signaling's SimpleChIP products, which I've found to be of quite good quality and reproducibility (no, I don't work for them!).

Thank you. I can not express my sincerity and appreciation for typing that out for me. Just a couple of questions: 1) what does " enriched by incubating with..." mean? In other words, what does enriching the DNA do?

When you introduce the antibodies to the sample, they bind the target protein but the complex is still in solution. The beads allow effective purification of the complexes by concentrating them on the beads, which are easily isolatable. 2) The NGS reads correspond to the red regions in the bottom image. Each 'line' is a single isolated DNA fragment which is sequenced from both ends to produce the 35 bp reads and then aligned to the genome. 3) That's essentially correct.


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Role of isopropanol in plasmid isolation
In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? How does it not renature every other macromolecule?

In a standard DNA preparatory procedure, isopropanol is used to precipitate the DNA. Nucleic acids are insoluble in alcohols, and bulk or stick together. This sticking together can be further enhanced by increasing the ionic strength such as through addition of sodium acetate.
alcohols in fact don't really denature the DNA.


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Why doesn't the cytosol dissolve the polar structures?
we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why it doesn't dissolve the proteins and enzymes which are most polar and ionic and they still form structures,organelle and function and suspended in water?

Many cell components are not simply hydrophobic or hydrophilic, but have dual affinities. Proteins typically have structures which result in the interior of the protein being hydrophobic and the exterior, which is exposed to the water in the cytosol, being hydrophilic. Thus, differences in polarity between different regions allow proteins to be dissolved in the cytosol while still maintaining a stable structure.
Similarly, the lipid bilayer is composed of phospholipids, which can be described as "tails" of hydrophobic carbon chains connected to hydrophilic phosphate "heads". The phospholipid bilayer is organized so that the phosphate heads are on the surface of each side of the bilayer, with the carbon chains from each side of the bilayer intertwined with each other in the interior.

ADDENDUM
Water can disrupt the intramolecular hydrogen bonds by bonding to the donors/acceptors. However, water in many cases can also act like a bridge and stabilize the protein structures. As already pointed out by jarlemag, the hydrophobic residues can push the water out of the pockets where intramolecular hydrogen bonds are to be formed. You may notice that the cores of the proteins are mostly hydrophobic while the surface is hydrophilic. So water plays an important role in the maintenance of the structure. Therefore many proteins need the assistance of chaperones to fold into a stable structure; once folded they maintain their structure while remaining suspended in water (I use the term suspended because proteins don't form true solutions: they form colloidal mixture). Chaotropic agents like urea exert their denaturating effect by disrupting hydrogen bonds as well as by increasing the entropy of the water molecules around the hydrophobic regions and thereby reducing the net hydrophobicity.
(I hope it is clear now)

This answer doesn't add anything to the others, but is an attempt to explain using different language.
"my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer"
In a sense, it does. See my diagram below The bilayer is composed of phospholipids, classic amphiphiles with a polar head group and a nonpolar tail group. The polar head group can interact favourably (in a thermodynamic sense) with the cytosol through hydrogen bonds. In contrast the hydrocarbon tails cannot interact with water through hydrogen bonds. This means that they force a structure on the surrounding water which decreases entropy of the system (unfavourable). The thermodynamic solution to this is for the bilayer to form - this maximises the interactions between the head groups and the aqueous surroundings and minimises the unfavourable interactions between the tail groups and the solvent. A beneficial side effect is tha the close packing of the tail groups maximises van der Waals interactions between them.
On balance the 'ordered' nature of the bilayer is stable because it is paid for by increased disorder of the solvent and favourable interactions between the hydrocarbon tails.
Exactly the same arguments apply to proteins: proteins fold to minimise the exposure of nonpolar amino acid side chains.


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Width of vein in finger
I am working on my bachelors thesis, where one part of it is to find width of vein in fingertip. I use database images and extract vein patterns from it, but i have to calculate the width of vein and I have no comparison of how many pixels in pic refers to how many milimeters in real.
I would like to ask how wide is the vein approximately in fingertip or in finger.
Thanks a lot, it would be really helpful.

Here is an image. My best guess is its in the order of 1-3mm.  The challenge you face is, absent any other features that provide scale, you don't know the  size of each hand in those stock images.  So you have two (too many) variables..(i) hand/finger size and (ii) vein width as a proportion of finger size.  I don't see how it can be done.  Imho, safest would be to image your classmates hands, beside a scale, and choose illumination that shows veins.

"Database images".  Provided these were acquired systematically in a lab using fixed imaging conditions (eg camera distance) then you can stick with pixels as your size unit for computation.  If you have access to the imaging setup, go ahead and image a scale.  I'd also just make a plot of your complete dataset for finger length and width and look for a 'biological' -type distribution without skew or  bumps. And the image files themselves may have camera meta-data such as aperture and exposure, also useful for quality assurance.  But images without scale, not ideal, for sure...

Thank you for your answer @PlaysDice.Unfortunately, I dont have access to image setup or the sensor, I used the database I found on the internet.Neither I have device capable of providing images link.I tried to build one, but didnt have proper LEDs(couldnt shine through the finger with my LEDs).
My results are between 1.2mm to 1.8mm and i used my finger as ethalon taken as normal image from approx. same heigh as in databse. Its not as good as it could be, but didnt come up with anything better.
Thx for post

Venous anatomy is highly variable from the start, there will also be changes with age and activity - I think this will b to calculate


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What's the difference between naive and memory B cells?
I understand that when naive B cells are exposed to antigens, they become memory B cells, but what is the functional difference between the two? I've looked at the quite a few article on B cells, but none of them stated the difference clearly enough for me to understand.

The main difference is that memory B cells start an immune reaction much more effective and faster than naive B cells. The reaction is also specific towards the antigen.
The memory B cell has a specific membrane receptor for an antigen. It produces specific antibodies only when exposed to the antigen.
References:

Tangye SG, Avery DT, Deenick EK, Hodgkin PD. Intrinsic differences in the proliferation of naive and memory human B cells as a mechanism for enhanced secondary immune responses. J. Immunol. 2003 Jan 15;170(2):686-94. PubMed PMID: 12517929.
Wikipedia contributors, "B cell," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=B_cell&oldid=612990219 (accessed June 26, 2014).

Naive B cells have not yet been trained by the immune system to recognize specific antigens -therefore the term "naive". Prior to antigen exposure, they must be trained in the bone marrow to recognize certain antigens.
Memory B cells, on the other hand, are formed after antigen exposure and clonal selection. As stated above, they have specific receptors for antigens and can produce antibodies.

They are actually not trained in the bone marrow, but in germinal centers in the lymphatic tissues.


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What is reductive deamination?
This presentation on anaerobic digestion mentions (pg. 19) two major pathways for the digestion of amino acids: Stickland reaction and reductive deamination. While I find some info on the former, what is reductive deamination? What is a representative reaction and what partners are needed?

Amine is already a reduced state and therefore the reduction part is not of the amine. In chemical process of reductive deamination the arylamine is first converted to an intermediate, usually by sulphonylation of the amine nitrogen [ref], which in turn is reduced.
$ArNH_2 + CH_3SO_2Cl \ \ \  _{\overrightarrow{pyridine}}\ \ \  ArNHSO_2CH_3 \ \ \  _{\overrightarrow{NaH+NH_2Cl}}  \ \ \ ArH$
Biochemical anaerobic reductive deamination is reported but not for amino acids (I couldn't find any). It is reported for anilines which probably proceeds via a carboxyl intermediate [1, 2].
This article says that the non-classical amino acid $ornithine\ \ $ is converted to $\delta-aminovaleric acid\ \ $ via a $\ proline\ $ intermediate but no mechanism is described.
I don't think this answers your question completely; the best solution would be to ask the author of the presentation for the exact reference.


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Is there a protein in the eye that gets kinked by photons and shipped down to the liver to get un-kinked?
My friend made the claim that there exists a protein in your eye responsible for vision. This protein is sensitive to different wavelengths of light, and when it gets hit by the right wavelength, it kinks. In order to be un-kinked, he claimed, it has to be shipped down to the liver, and then back up to the eye.
He teaches organic chemistry at UCLA, so I trust him a little bit. But I couldn't find this with a quick search. Anyone know if this is legit?

Luckily, the unkinking can happen outside of the liver, and much quicker. You know how, if somebody suddenly shines a flashlight into your eyes, you go blind for a couple of seconds after the light is gone? The reason is that all your protein storage in the eye is already activated and needs to be brought back to the unkinked state before you can see again. Imagine how it would be if this process required several heartbeats for transport to the liver, then an enzymatic process straightening the kinks, than shipping back: the blinding will be longer by at least one order of magnitude.

The protein is called rhodopsin and the bit that gets kinked up is called retinol.   Normally when light hits it, it does trans to cis isomerization at the 11th carbon.  'kinks up' is a pretty apt way of describing it.

I'm not familiar with the shipped down to the liver part, but I'm guessing that the photo reaction of the retinol with itself or the protein must occasionally make the rhodopsin-retinol complex unfunctional - perhaps by the double bonds cross linking to other atoms in the retinol or to the protein.  As I understood it the retinol just straightens out again.  This reference shows that in the presence of rhodopsin, 11-cis retinol will become all trans again normally.
There should be enzymes in the liver that can recycle some messed up retinol configurations.  Its probably not the main route through your body. Retinol is stored in the liver from dietary intake, and then shipped via retinol binding proteins to the eye. So that is the organ which is the source of retinol in the human body (and probably most animals).  It should catch damaged retinols and refurbish them the same way it does those taken in via the diet.


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is there a way to do batch download for all gene pathways?
I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package.

in what format do you want the pathways? You can bulk download the SBML files. Also, please clarify what you mean by "download the genes of each pathway".

What pathways? From which database? What species?

Try using KEGG REST.
http://rest.kegg.jp/link/pathway/hsa ## list of all genes and pathways in Humans

Do you mind showing me how you got this file?

You can find it in the rest page.

If you're working with BioCyc pathways you can use their REST-API for batch-downloading all genes for their pathways. You can run a wide range of queries including BioVelo-queries for all genes/compounds in a specified pathway, all pathways in organism etc. A query for all the pathways in B. subtilis would look like:
http://biocyc.org/xmlquery?[x:x%3C-bsub^^pathways]
Where you get an XML with the Cyc-IDs for the pathways which can be used to search for the genes. A query for all genes in the Arginine synthesis pathway in B. subtilis would then look like:
http://biocyc.org/xmlquery?[x:y:=bsub~argsyn-pwy,x%3C-%28genes-of-pathway%20y%29]&detail=full
Which returns an XML with information regarding the genes, start and end positions including (i.e. gene length). Since I don't work very much in R I don't know if there exists an R-package. But it is very straightforward to write Python scripts for downloading and XML-parsing.


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phylogenetic Independent contrasts with unresolved tree
I have a dataset containing morphological and performance measures of species from various groups, including insects, lizards, frogs, spiders etc, and want to analyse the relationship between these measures and the animal's body size  via regression methods, while controlling for common ancestry, similar to what has been done in this work:
Peattie, A. M. & Full, R. J. Phylogenetic analysis of the scaling of wet and dry biological fibrillar adhesives PNAS, 2007, 104, 18595-18600
http://www.pnas.org/content/104/47/18595.abstract
For most of my species, statistically supported branch lengths are lacking, and I was thus wondering what the best way to conduct my analysis would be, and I would be grateful for any hint.

Look also into PGLS. Either way, one thing you could do--it would be ugly--would be to set all branch lengths to 1. Additionally, you could smooth the tree with penalized likelihood, e.g. chronopl() function in ape package in R. Again, this is an ugly solution and look into PGLS (it won't solve the ugly phylogeny part).


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What are the internal surfaces of body cavities actually made of?
In Ross's book of histology it says that the mesothelium that includes all body cavities is made of simple squamous epithelium but in other places it says that in the gastrointestinal tract it is made of simple columnar epithelium. Is it that the trachea and the the gastrointestinal tract are not classed as cavities?

It is correct to say that the trachea and GI tract are not classed as cavities, yes.

The peritoneum, the pleura, the pericardium, the tunica vaginalis testis and the tunica serosa uteri are made of mesothelium (simple squamous epithelium) [1].
The GI tube is made of a specialized tissue composed from four layers: mucosa, submucosa, muscularis externa and adventitia. The innermost layer (mucosa) has an epithelium that is stratified, squamous and non-keratinising, for protective purposes. The internal organs in the peritoneal cavity are covered with the visceral sheet of peritoneum which is the adventita layer [2].
Trachea is made of respiratory epithelium, which serves to moisten and protect the airways. It is lined with pseudostratified columnar epithelium with goblet cells that produce mucus [3].
Trachea, stomach and intestines are considered cavitary organs as opposed to parenchymatous organs (lung, kidney, liver).
References:

Wikipedia contributors, "Mesothelium," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Mesothelium&oldid=598055771 (accessed June 26, 2014).
Wikipedia contributors, "Gastrointestinal wall," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Gastrointestinal_wall&oldid=598338180 (accessed June 26, 2014).
Wikipedia contributors, "Trachea," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Trachea&oldid=613017631 (accessed June 26, 2014).


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tetrads in meiosis are held together by what
This is from SAT subject biology test practice question. The answer it gave me was both chiasmata and centromeres. I can understand they are held by chiasmata but why also centromeres? I looked it up, I didn't find anywhere mentioned that they are held by centromeres also, only synaptonemal complex and chiasmata.
tetrads are truly held by spindle fibers on centromeres too, but isn't the question asking what hold them together? Even without spindle fibers, they can still be held by chiasmata I guess.

A recombinase only active during meiosis - Dmc1 and a general recombinase Rad51 coat the single-stranded DNA to form nucleoprotein filaments. These filaments hold the homologs together at the chiasma, the point of attachment during crossing over.

It may help to think of the question in this way. Within a tetrad (that is 2 bivalents) there are 4 strands of DNA (really chromatin). Only the 2 inside strands are held together by the chiasmata. The outside strands are attached to the tetrad by it's centromere. Each pair of sister chromosomes are held in place at the centromeres during meiosis I. The sister chromosomes segregate together because the attached microtubules are oriented towards the same pole. They separate at the centromere at anaphase II to form the haploid gamete.


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Do invertebrates dream?
From Wikipedia:

Studies have observed dreaming in mammals such as monkeys, dogs, cats,
  rats, elephants and shrews. There have also been signs of dreaming in
  birds and reptiles.

Have there been such signs in any invertebrate species?

Do they even sleep? http://www.straightdope.com/columns/read/1646/do-insects-sleep

Belongs on cognitive science SE


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Does Sympaticus and lymphatic circulation cause feeling of thirsty after short shower?
I have been reading blogs, Guyton and Pocock about what triggers the feeling of thirsty.
I am not convinced that is the fact of

warm water
time is short so not much water lost

Assume that the water's temperature is the same as body's temperature.
Of course, there is little temperature change caused by air and water, but I think it is not that much.
I think more important is the steady, continous irritation of skin as a mechanism.
I wrote my suggestion for the answer below.
Do sympaticus and stimulation of lymphatic circulation cause feeling of thirsty?

I think the mechanism is the stimulation of the skin systemically i.e. the most important endocrine organ which we have.
The irritation of skin in the shower is

mechanical turbulent stream of water in acceleration

1) hitting (start) your skin from different directions (many flows) in many different flows
it's you who causes the systemic stimulation effect!
water steam in acceleration all the time; moving its direction; in ellipsoidal tracts
water stream flowing slowly on your skin towards periphery mostly
causing smooth but continuos irritation of your skin

activation of smooth muscles in synchronous order which boost lymphatic circulation

mechanical turbulent stream of air (temperature change of skin)

this one is not in accelerative move, since there is no forces which keep the subsequent air and skin together
very little impact, unless extreme situation (etc in Alaska)

I would think that the increased lymphatic circulation irritates the walls of lymphatic circulation which causes an increase in the need of water there.
So water would diffuse from vascular space inside blood vessels (extravascular space) into the lymphatic system.
The decrease in blood pressure through baroreflexive arch and hypothalamus (some nuclei too) would then be sensed as the feeling of thirsty.
Water in shower on the skin accelerates, since it changes its direction all the time from the beginning of the stream until the end.
I think it is the steady change of irritation's location in ellipsoidal tracts that stimulates hypothalamus.
I think it is not the strength of the stream but the changing direction that is cause of the irritation.
Of course, there is little changes in the strength of the total stream.
I think this is not so significant than the change of the direction of the water flow causing the irritation.
In short, I say that accelerative water streams massage lymphatic system in ellipsoidal tracts.


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Crusty eyes in the morning
Often, after waking up from a night's sleep hard, flaky, pale yellow crystals are deposited around the eyelids (which easily wash off with water).
What are these? Why are they yellow? What are they made of? Is their amount proportional to the length of sleep?

This is quite common. It is most likely dried rheum (also know by slang terms such as "sleep", "eye boogers", "eye crusties", etc.).
Rheum is the result of dried mucus, tears (and the salt and minerals therein), as well as dead blood and skin cells.
Essentially it is all the stuff that’s normally in your eye that eventually dries up making the contents more condensed giving it a light yellow color. When all that stuff is in your tears it is spread out enough that your tears are still mostly clear.