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Is it possible to live without health problems sleeping one day and not the other?
Basically, I want to know if it would be humanely possible to sleep one day, skip the next, sleep, skip, sleep, skip, etc, with a 8 hour sleep time.
If you need any extra information, let me know.

What window of time are we talking about? 1 month, 1 year, lifelong?

It would be interesting to consider 6 years and lifelong.

You may be interested in Why do humans practice monophasic sleep cycles? biology.stackexchange.com/q/319/238

(too long to be a comment)
You may be interested in http://en.wikipedia.org/wiki/Phase_response_curve.
This graph shows how the body's circadian rhythm normally works: http://en.wikipedia.org/wiki/File:Body_Temp_Variation.png.  Body temperature decreases during the night (apparently due to more melatonin production.
I conjecture that the proposed schedule would interfere with the Circadian rhythm.  Melatonin is the hormone that regulates sleep--it causes drowsiness.  It is suppressed by blue light (because we get exposed to blue light in the daytime).
Aside from this, I am also very interested in the effects because I have personally wondered about the same question.  The thing I am worried about is significant immunosuppression.
A larger question might be--"Why is sleep necessary?"  Does it serve only to conserve food (which is very useful if you are living on subsistence) or does it serve a greater purpose? (whenever I have asked anyone about it, they always cite "regeneration" and some have cited the recycling of neurotransmitters.  Personally, I'm a little skeptical.)
One final study: there was a study by Dement on the effect of dream deprivation: he took several people and woke them up whenever they went into REM sleep.  Then, there was a period when the patients were not woken up.  He found that there was a "REM rebound"--that they would go into more REM sleep after they had been deprived of it.  This seems to indicate that dreaming, specifically, may serve a significant purpose.

I'm not aware of any study testing this hypothesis. I would surmise that adverse health effects are likely because the circadian clock operates on a 24-hour time frame, and because lack of sleep for ~40 hours every second day will alter hormone, cytokine and other measures to levels not normally seen in 8-hour sleep/16-hour wake cycle.

You may want to cite some paper showing that perturbation of sleeping results in significant perturbation of hormonal rhythms.

@nico Why don't you add an answer explaining that? And what about splitting 4hs each day?

@Peter Tamaroff: because I don't know any paper showing that (but I would be very interested in seeing one)!


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What is this super-fly?
This fly repeatedly buzzed in my girlfriend’s ear. Eventually got it from it being caught in her hair. I clapped it between my hands. It fell on the floor and twitched a bit as flies sometimes do. It started walking away again. I hit it hard with the side of my fist against the carpet. Still going. I hit it multiple times and it left a blood mark. I went to get some paper to collect it. And it’s walking away again! I pinched it in the paper. Still moving about. It’s now in a jar. I suspect it is actually a forward member of some kind of nation-state engineered nano invasion force.
I have a lot of experience with fly disposal but this thing is actually scarily hard! Also the fact it was ear-buzzing seems very mosquito-like behaviour. But it clearly isn’t a mozzie.
If you are a fly researcher and want the next breakthrough in self-healing psycho DNA give me a shout.
But what is it?
Location Yorkshire UK. Size about 6mm head to tail?

Please leave a comment if downvoting (snooze). This is my first question on this site so apologies for my layman’s effort.

@user338907 Haha no, we have a 2 year old so it’s kind of past that stage.

Welcome to the site. Links, particularly for images, within a question can age and rot, leaving the question unanswerable and not useful for anyone reading the post. Please make your question self-contained.

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In a sugar such as a disaccharide are both ends of the sugar known as reducing ends?
For example, in maltose (a disaccharide of glucose monomers) are both of the ends either side able to be opened to form an aldehyde group?

No, in dissacharides the reducing end is situated only on one monosaccharide which is having free anomeric carbon. This carbon does not take part in glycosidic bond formation and can form open chain.

Check out:
https://chem.libretexts.org/Courses/Sacramento_City_College/SCC%3A_Chem_309_-_General%2C_Organic_and_Biochemistry_(Bennett)/Text/14%3A_Carbohydrates/14.6%3A_Disaccharides

Your answer would be better if it indicated the reducing position in the monosaccharides and the disaccheride and did not contain material largely  irrelevant to the question. Perhaps you could consider drawing a diagram of your own.

okay..will do that

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Cause of Obesity
Considering that the sequestering of 'persistent organic pollutants' [POPs] by adipose tissue is now established (see Toxicological Function of Adipose Tissue: Focus on Persistent Organic Pollutants by La Merrill et al. Environmental Health Perspectives, 121, 2013, pp162-169; pdf available here), is there any evidence that the existence of such POPs within fat cells interferes with the function of leptin, in particularly with the normal suppression of appetite in the hypothalamus?
Were there in fact such evidence, could such a derangement in leptin function account for tendencies to obesity in populations exposed to POPs?

The normal function of adipose tissue is to stare triglycerides. Please quote a source for your statement about organic pollutants (and for goodness sake don't abbreviate them as POPs).

It seems fairly well accepted that part of the function of AT is to store fat soluble toxins such as OPs. [e.g. Env.Health Perspectives 121(2) La Merrill]. There is a Korean study citing numerous references and discussing the relation of OPs to obesity [Obesity Reviews 18(2) Y-M Lee]. However, I could find no study which proposes an underlying mechanism according to which, presuming that the accumulation of fat serves an entirely necessary--rather than erroneous--function in all cases, dysfunction in the leptin-mediated circuit induced by OPs in AT is implicated. If so, it would explain a lot.

How do you differentiate between "function" and "they happen to accumulate there because they are fat-soluble? I thought it was the P450 system that had the function of dealing with toxic compounds, the endpoint being elimination (not sequestering). Whatever the connection between modern organic pollutants and obesity, you should remove the assertion that the normal function of adipose tissue is to sequester these compounds.

Perhaps it is more pertinent to ask to what extent fat cells discriminate between lipophilic organic compounds; the point being that because in the general case they do not, it is not unreasonable to argue--without quibbling over semantics or even raising the philosophical issue of intention--that this capacity for AT to dissolve, thus temporarily sequester organic pollutants within the process of their eventual detoxification--if this is indeed possible--, therefore protecting vital organs from the harmful action of these compounds. I will elaborate a little in answer to the question.

@user1136 That is good editing, and resolves some of the earlier objections to the question. I don't think my own answer which was effectively prompted by those unfounded objections in order to clarify that question deserves its down-votes by the way; since in the main what it states is correct, while contention about its latter paragraphs--which need not have been included but were-- is essentially a matter of opinion.

Leptin is the satiety hormone produced in the body fat cells - increased blood leptin levels suppress appetite and decreased levels stimulate it.
Persistent Organic Pollutants (POPs) are man-made chemicals that are environmentally persistent, leading to bioaccumulation in the food chain. Examples include polychlorinated biphenyls (PCBs) and polybrominated diphenylethers (PBDEs).
In the only study I've found that mentions the direct relationship between POPs and blood leptin levels, the exposure to POPs was associated with decreased leptin levels in women but not men: Expression of Obesity Markers and Persistent Organic Pollutants Levels in Adipose Tissue of Obese Patients: Reinforcing the Obesogen Hypothesis? (PlosOne, 2014):

Our study revealed a negative association between leptin serum
  concentrations in women, and the levels of several PCBs and BDE153 in
  both fat depots. Remarkably, in men, none of the analysed POPs
  correlated with leptin serum concentration.

In another study, the exposure POPs was associated with decreased levels of leptin in breast milk: Association between Several Persistent Organic Pollutants in Serum and Adipokine Levels in Breast Milk among Lactating Women of Korea (Environmental Science and Technology, 2015):

Leptin concentrations in breast milk were negatively associated with
  ∑hexachlorohexane (HCH), oxychlordane, ∑chlordane, or
  2,2',4,4',5,5'-hexachlorobiphenyl (CB 153) levels in maternal serum.

Both studies suggest, directly or indirectly, that persistent organic pollutants can decrease leptin levels and thus stimulate hunger, but the studies were small and are not, at least for me, considered sufficient evidence.

Excellent work.You understand the question, the possible importance of its consideration and have given a good informative answer. I agree that there is little evidence of the association, but continue to believe that it deserves more investigation. Naturally it would be difficult to establish a direct relation between POPs sequestered in fat cells and leptin function deriving in those cells; first it would be interesting to find if POPs are in fact present in fat cells of the obese. As you see, someone is so offended by my answer that he repeatedly down-votes it without proper reason.

@jeremiah, leptin is present in the fat cells of lean and obese people. I'm not sure how much the leptin levels fluctuate within the fat cells and if this has any importance, but it's the leptin that is released into the circulation that affects appetite in the hypothalamus.

@Jan.I know that leptin is produced in fats cells; the point of the question is whether the presence of POPs in the fat cells of obese people interferes with the conformation of leptin rendering it less effective at the H/T or even inert. The first question is to ascertain whether POPs are present in greater degrees in the fat cells of the obese than in a control group; and if not, whether they nevertheless exert a deleterious effect on leptin synthesis. If the leptin isn't working, then that's 'leptin resistance' isn't it. You're a young researcher aren't you? Well, there you are.

@jeremiah, from what I understand from the linked studies, the higher amount of POPs in the fat cells is associated with lower levels of leptin in the blood. I assume this is due to decreased release of leptin from the fat cells into the circulation. I have no idea if POPs affect leptin when there are still in the cells.

That's a start; and it may end up being the principal effect. I haven't yet read the linked articles; but I'll get to it. Thanks by the way for your effort in uncovering them. One of the reasons this is important is to establish some cause for leptin resistance which is associated with obesity; not necessarily so that it may be redressed, but at least that obesity might be better understood as a condition of 'leptin resistance', rather than a syndrome of grievous gluttony and sloth as it is often portrayed.

Leptin resistance would occur at the target cells in the hypothalamus. In this case, blood leptin levels would not be likely decreased. It's like insulin resistance occurs at the target tissue cells and the insulin levels are actually increased.

Yes, the inference of these studies is that POPs would not account for leptin resistance if they correlate with reduced serum levels. It seems we must leave the question unresolved for the moment.

It seems that the answer to this question is at present no--and might remain so until or unless researchers dedicated to elucidating any such relation between leptin and obesity are prepared to subject some population of poor leptin-producing creatures to given organic pollutants, with the aim of determining any measurable effect on leptin capability--a difficult assignment to say the least.
Various studies seeking to confirm the so-called 'obesogen hypothesis' have not unreasonably argued a mechanism of 'endocrine disruption' by certain common organic pollutants, but these are neither comprehensive nor capable of resolving certain paradoxes in the relation between leptin and obesity: notably that leptin levels are routinely observed to be raised in cases of severe obesity.  The idea of some derangement in leptin function induced by a local cause therefore becomes attractive in explaining such 'leptin resistance'.
At the same time, it is probably negligent to blame rising levels of obesity merely upon the delinquent appetites and profligacy of affluent people, particularly when certain benefits of fat accumulation, apart from the sheer simple joy of being fed, have been observed: putatively there are diminished rates of neuro-degenerative disorders such as Alzheimer's disease in the mildly obese. (There are various studies drawing such conclusions). Possibly such effects also pertain to the capacity for adipose tissue (AT) to sequester organic pollutants.
Now the respondent to this question has objected to the characterisation of this latter effect as a 'function' of AT when it is clear that this capacity for fat cells to accommodate fat-soluble substances without the necessity for their elaborate discrimination is indeed inherently and innately part of the broader function of AT.  The inference of the question itself is in fact that the proliferation of fat cells and fat mass in obese individuals may serve precisely this purpose or function.
Such an assertion requires no troublesome incursion into philosophical or teleological dispute--regarding ultimate cause or intention--nor great excesses of the imagination--that for example we are essentially organic creatures increasingly immersed in the products of oil and other hydrocarbons, themselves loosed from the ancient abeyance of that essential nature--, only the understanding that part of the actual mundane function of fat stores is to hold in continuing abeyance those organic compounds, in particular those which are broadly derivatives of hydrocarbons, which the organism generally is unable either to accommodate elsewhere in its metabolism, as if effectively indigestible food, or successfully to excrete.
It might be emphasised here that the aim of any such inquiry into the relation between organic pollutants and obesity--possibly mediated by a derangement in leptin function--is not of itself to redress any such local cause determined empirically; since realistically such would come only with the inevitable obsolescence of oil and the derivatives of hydrocarbons generally: petroleum, plastics, organic pollutants etc.
The aim is to elucidate the nature of this phenomenon of modern obesity, that at least it might be understood as part of universal necessity, that indeed it must in principle serve some eventual 'evolutionary advantage', not of a family of reproducing organisms--although this is an aspect of it--, but of the universal entirety itself in eternity (which some are emboldened by a peculiar philosophical perspective of the absolute inviolability of such a universal unity to characterise as the 'Unitary Soul', for want of a better description of the singular dynamic and process which must enliven it).
I might add here that there has developed an obsession in the biological sciences with a theory of evolution based not only on the philosophically repugnant idea of 'chance'--which despite the fervour with which such a paradigm is defended cannot of course be quantified in any meaningful way; which incapacity of itself requires that the entire notion be removed from orthodox thinking--, but on the necessity to impute to some detail of formal biological reality an evolutionary advantage conferred by such happenstance (e.g. in the usual view, base mutations) within some limited context, the niche, of which it is in any event merely an aspect, when the ultimate parameters of such advantage, more especially in the greater spatial and temporal context are essentially unknowable.
This is not to dispute the absolute preeminence of an 'evolutionary principle' within universal reality; only to argue that this principle is entirely singular and simply inherent within the fact of existence itself; and most importantly that the ultimate parameters of such a principle can never be objectively discriminated or 'known' by those such as we mere humans entirely immersed within  the mechanics of an inviolate universal unity in eternity. No conception of an ultimate 'evolutionary disadvantage' may be formed without the possibility for knowledge of the ultimate intention of such a dynamic universal unity.
And for those who would object that such an 'a priori' postulate of universal unity is improperly metaphysical in character, it would be well for them to remember that the existing scientific and cultural ethos of a blind aimless nature--Dawkinsism--, and the preeminence of 'happenstance' as its primary impetus--which is to say the denial of singular universal cause and intention merely for want of the capacity to discern it--, is only the expression of a passing alternative school of philosophy and its guiding paradigm, essentially that of 'chaotic erroneous nature' groping its cruel meaningless way aimlessly in the eternal darkness awaiting only the guiding hand of Man to render 'order' within it.

This answer is frankly terrible and one of the worst ones I have seen on this site. I would normally recommend adding references but I don't think even that can save it from all the illogical tangents and wrong statements. Universal unity? Unitary soul? A complete lack of any understanding of evolution?

@user1136. The reason for the post was to ascertain whether this was an original idea; since my suspicion is that it seems too obvious a connection not to have been conceived and studied previously; there were no references which I could find.  As such, the reference from a 2014 paper demonstrates that it is neither a novel idea nor without foundation, in spite of the previous reception of the question here. Moreover, there would seem considerable potential to investigate the idea that it is such a derangement in leptin metabolism which is at the root of obesity, if only to understand it.

Of course the hypothesis is unproven, nor have I supposed or stated otherwise; but I believe that part of the purpose of forums such as this is to air such ideas among those with the where withal and inclination to pursue them.  That latter part of my answer is intended only to express a particular philosophical perspective--just a form of old-fashioned determinism really, newly expressed--, the implication of which is that whatever mechanism is finally established for the effect that in the modern day, there are some who simply cannot satisfy their appetites, it is nonetheless an entirely..

..an entirely necessary and intrinsic part of nature: in this view nature, reality itself, simply CANNOT EVER be in error, regardless of how things may appear locally or temporarily. What appears as a error or deficiency in one aspect of a Unitary Universal Principle represents only the incapacity on our part to determine its greater context. Neither is this a new idea; anyone familiar with Schopenhauer for example, to cite a modern thinker, knows this. However, in modern times, the implications of such a view are far more troublesome to an ethos of scientific manipulation than previously.

@BryanKrause. The gulf between our views is probably too great to bridge here; however, since it is essentially philosophical, I would humbly request that you regard it as such.

The answer is carefully written to separate the quite plausible rational if also arguable idea that some recent modern influence apart from the ready availability of KFC etc. might be responsible for what is undoubtedly an epidemic of obesity in Westernised societies--for example, some disruption in leptin function which may at the same time amount to the establishment of an evolutionary advantage in dealing with POPs--, from the later expression of a philosophical view of the circumstance itself of such a condition.That view does not deny the operation of an evolutionary principle, for what..

..for what other reason does reality exist? It simply conceives of that operation in another way. It does not for example understand base mutations to be other than orderly transitions in the configuration of DNA conforming to the exigencies of that principle which indeed also tend to preserve the basic structure of that genome. Nor does it separate organism and niche in the ordinary way;affording a much greater importance to epigenetic function, and therefore to the heritability of genetic potential, thus 'adaptability' which is inseparable from the memory of environment continuous with it.

So, I suppose what I'm trying to say is that while I can appreciate the traditional theory of evolution, I simply cannot accept it philosophically; and am therefore compelled to take a broader view; which happily leads to what I find to be a more satisfactory explanation of phenomena, and of the intricacies of empirical observation; in particular the structure and function of DNA, and its dynamic of replication and transcription. Eventually, the underlying physics itself of that dynamic will be demonstrated to conform to that of a 'unitary universal wave principle' operating ubiquitously.QED.

@jeremiah I think you misunderstand the purpose of this stack. It is not to propose philosophical ideas, but rather to answer specific questions with referenced, scientific answers.

@Bryan Krause. With respect, sometimes an answer requires a different philosophical perspective, particularly when the principal foundation of the traditional answer is merely a prevailing philosophical view. At the same time, it is not my intention here to expatiate thus.In this case, a good well considered question was asked and because it was roundly derided, I answered it myself in the hope of elucidating the idea. As you now see, there is good evidence that the idea has merit. I do wish therefore that you would please not continue to attack this and other questions; rather answer them.

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Standard Free energy of hydrolysis of phosphoenolpyruvate (PEP)
In ATP we have two anhydride bonds, each with a Standard Gibbs free energy of hydrolysis ~ -30 kJ / mol and one phosphoesterbond of ~ -20 kJ/ mol, if my notes are correct.
In phosphoenolpyruvate (PEP) we also have a phosphoester bond, but the Standard Gibbs free energy of hydrolysis is three times higher, at ~ -62 kJ / mol.
How does the double bond / enol form contribute to this high free energy of hydrolysis?

I have edited your question so that it is clear that it refers to free energy of hydrolysis. Chemical compounds do not have energy in isolation, so the term "high energy" should be avoided.

An answer to this is given in the online version of Berg et al.

Why does phosphoenolpyruvate have such a high phosphoryl-transfer potential? The phosphoryl group traps the molecule in its unstable enol form. When the phosphoryl group has been donated to ATP, the enol undergoes a conversion into the more stable ketone—namely, pyruvate.

Thus, the high phosphoryl-transfer potential of phosphoenolpyruvate arises primarily from the large driving force of the subsequent enol-ketone conversion

Note that Berg et al. use the term “high phosphoryl-transfer potential” or “high phosphoryl group-transfer potential”, as explained in sections 14.1.4 and 14.1.5. These sections are worth reading, and this terminology is worth following.

Thank you very much and also tomd for the adding comment!

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ATP Hydrolysis to AMP in the Urea Cycle. What is the Free Energy Change?
How is the hydrolysis of ATP into AMP and PPi in making arginosuccinate equivalent to the hydrolysis of 2 ATP?

Please provide a source for the statement you are querying. This will provide a context for us to interpret it and provide an appropriate answer. @user1136 had provided a comprehensive quantitative answer, but I wonder if your original source is making a more general qualitative point. At the moment your question is unclear and is likely to be deleted.

The answer, I reckon, is that as stated it isn't.
However,the hydrolysis of ATP to AMP and PPi yields considerable more free energy than does the hydrolysis of ATP into ADP and Pi.
That is, the free energy change for the hydrolysis of  ATP into AMP and PPi is considerably more negative that that for the hydrolysis of ATP into ADP and Pi and for the hydrolysis of ADP into AMP and Pi.
If we consider the the free energy change for the reaction ATP  = AMP + 2 Pi  (where, say, the pyrophosphate (PPi) produced by  argininosuccinate synthetase is broken down by a  pyrophosphatase), then  it is the equivalent to  the  hydrolysis of 2 ATP to ADP and Pi and (more or less) to  the hydrolysis of 2 ADP to AMP and Pi.
When dealing with ATP hydrolysis, we must take the 'chemical environment' of the phosphate group into account, not only in determining whether the bond is 'high energy' (in the Lipmann sense) or 'low energy', but also when considering the amount of free energy released by hydrolysis of a  'high energy' linkage: not all pyrophosphate linkages yield the same free energy on hydrolysis.

Cleavage of the 'inner' pyrophosphate linkage in ATP (to give AMP and PPi) 'releases' considerably more free energy than cleavage of this linkage in ADP (to give ADP and Pi).
Cleavage of the 'inner' pyrophosphate linkage in ATP  (to give AMP and PPi) releases considerable more free energy than the cleavage of the 'outer' pyrophosphate linkage (to give ADP and Pi).

If  one 'unit' of free energy is considered to be about 32 kJ mol-1 then:

The hydrolysis of ATP to ADP and ADP roughly releases 1 unit
The hydrolysis of ADP to Pi and AMP roughly releases 1 unit
The hydrolysis of ATP to AMP and PPi roughly releases about 1.4 units
The hydrolysis of PPi to 2 Pi roughly releases about  0.6 units
Hydrolysis of ATP to AMP and 2 Pi roughly releases 2 units.
Hydrolysis of AMP to adenosine and Pi roughly releases 0.4
units.

The question posed by the OP may now be answered as follows.
Hydrolysis the inner pyrophosphate linkage of ATP (to give AMP) rather than the outer linkage (to give ADP) provides a 'thermodynamic pull' of 0.4 'free energy units' to the  argininosuccinate synthase reaction.  If the  PPi is hydrolyzed by a pyrophosphatase an extra 0.6 'free energy units' are obtained and the free energy change for the combined reaction (that of argininosuccinate synthase and the pyrophosphatase) is equivalent to 2 'free energy units' (about -70 kJ mol-1).

As pointed out by Frey, & Arabshahi (1995), hydrolysis of the $\alpha$,$\beta$-phosphoanhydride of ATP, rather than the $\beta$,$\gamma$ linkage, is a common strategy in biosynthetic reactions.  To quote the final line of this paper: Cleavage of the $\beta$,$\gamma$-phosphoanhydride bridge in ATP takes place in metabolic reactions in which a smaller driving force is required.
A Small Piece of History
It was not always accepted that the hydolysis of ATP to AMP and PPi proceeded with a more negative free energy than for the hydrolysis of ATP to ADP and Pi.  To quote from  Standard Free Energy Change for the Hydrolysis of the $\alpha, \beta$-Phosphoanhydride Bridge in ATP , by Frey & Arabshahi (1995).

It  appears to be common knowledge in biochemistry  that the standard free energy change $\Delta G^{'o}$ for the hydrolysis of ATP to AMP and PPi is -7.7   to  -8.4 kcal  mol-1 [-32 to -35 kJ mol-1].  Most textbooks of biochemistry  list  values  in  this  range (Zubay, 1993; Lehninger et al.,  1992; Garrett & Grisham, 1994; Voet & Voet, 1990; Matthews & Van  Holde, 1990). Moreover, many  textbooks  also  list  the standard free energy  for  the hydrolysis of  PPi as  $\Delta G^{'o}$ = - 7.9 to  8.0 kcal  mol-1.  [-33 to -33.5 kJ mol-1]. However,  the  true  value for pyrophosphate  hydrolysis is significantly less negative (Flodgaard & Fleron, 1974). Therefore, the standard free energy change for the hydrolysis of ATP to AMP and PPi must be more negative  than 8 kcal  mol-1 [ 33.5 kJ mol-1]  as is explained in this paper

This reminder should not have been necessary.  The correct value for the free energy change in the hydrolysis of ATP to AMP and PPi is given by Schuegraf et al (1960)  , a paper co-authored by Sarah Ratner
The hydrolysis of UDP-Glucose
$\Delta G^{'o}$ for the hydrolysis of UDP-glucose to UMP and  glucose-1-phosphate is about - 43 kJ mol-1 (- 10.3 mol-1) [Frey, & Arabshahi, 1995], also considerably more negative that that for the hydrolysis of ATP into ADP and Pi
Specifics

The standard free energy of hydrolysis ($\Delta G^{'o}$) of the $\alpha$,$\beta$-phosphoanhydride of ATP to give AMP and PPi is about - 45 to -50 kJ mol-1

The standard free energy of hydrolysis of the $\alpha$,$\beta$-phosphoanhydride of ADP to give ADP and Pi is about -30 to -34 kJ/mol

The standard free energy of hydrolysis of the $\beta$,$\gamma$-phosphoanhydride of ATP to give ADP and Pi is about -32 to -36 kJ/mol.

The standard free energy of hydrolysis ($\Delta G^{'o}$) of PPi to 2 Pi is about 20 kJ mol-1

The standard free energy of hydrolysis ATP to AMP an 2Pi about -70 kJ mol-1.

The standard free energy of hydrolysis ($\Delta G^{'o}$) of PPi to 2 Pi is about 20 kJ mol-1

The standard free energy of hydrolysis ATP to AMP an 2Pi about -70 kJ mol-1.

(For a diagram illustrating the  nomenclature of the $\alpha$, $\beta$ and $\gamma$ phosphates of ATP, see here).
Notes

Following Alberty (2000), all equations are written as 'biochemical equations' where everything is balanced except hydrogen ions.

$\Delta G^{o'}$ for the following reaction is about -50 kJ mol-1 (-12 kcal mol-1)

$$ ATP + H_2O= AMP +PP_i $$

[1 ]  Frey, & Arabshahi (1995) give a value of -45.6 kJ mol-1 (-10.9 kcal mol-1).
[2] Dixon et al  (2000) give a value of  -48.5 kJ mol-1 (-11.6 kcal mol-1).
[3] Schuegraf et al (1960)  give a value of  -43 kJ mol-1 (-10.3 kcal mol-1).
[4 ] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1) of -50.2 kJ mol-1 (-12.0 kcal mol-1)

$\Delta G^{o'}$ for the following reaction is about -36 kJ mol-1 (-12 kcal mol-1)

$$ ATP + H_2O= ADP +P_i    $$

[1] Frey, & Arabshahi (1995) give a value of -32.6 kJ mol-1 (-7.8 kcal mol-1).
[2] Rosing & Slater, 1972 give a value of -31.5 kJ mol-1 (-7.53 kcal mol-1).
[3] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1 ) of -36.6 kJ mol-1 (-8.8 kcal mol-1)

$\Delta G^{o'}$ for the following reaction is about -34 kJ mol-1 (-8.1 kcal mol-1)

$$ ADP + H_2O= AMP +P_i $$

[1] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1) of -34.04 kJ mol-1 (-8.13 kcal mol-1)

$\Delta G^{o'}$ for the following reaction is about -71, kJ mol-1 (-16.9 kcal mol-1)

$$ ATP + 2 H_2O = AMP + P_i  + P_i$$

[1] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1) of -70.68 kJ mol-1 (-16.9 kcal mol-1)

$\Delta G^{o'}$ for the following reaction is about -13.7 kJ mol-1 (-3.3 kcal mol-1)
$$ AMP+ H_2O  =  Adenosine  +P_i $$

[1] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1) of -13.74 kJ mol-1 (-3.28 kcal mol-1)

$\Delta G^{o'}$ for the following reaction is about -20.5 kJ mol-1 (-4.9 kcal mol-1)

$$ PP_i + H_2O= P_i +P_i $$

[1] Frey, & Arabshahi (1995) give a value of -19.24 kJ mol-1 (-4.6 kcal mol-1).
[2] Calculation from the tables supplied by Alberty (2000) gives a value (25oC, pH 7, ionic strength of 0.1) of -20.5kJ mol-1 (-4.9 kcal mol-1)


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Are DNA molecules negatively charged at low pH values?
We know, that for each monomer of DNA, phosphate groups are having -1 charge because one of the oxygen is negatively charged (2nd oxygen participates in the phosphodiester covalent bond), but isn't it really depends on PH level? and if it does, for some PH level of X, for every N base pairs of DNA, how many phosphate groups are charged?
To better interpret what I mean, let me draw this scenario: If the solution contains too many protons (so PH is very low), would DNA still will be charged? why the negatively charged oxygens would not take these hydrogen ions, and makes them bond as hydrogens by sharing additional electron?

You are right. At a ph<5 which is where the PI of DNA breaks down, the phosphate group will bind protons, while the nitrogenous bases will become positively charged owing to the acidic environment.


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If red blood cells have no mitochondria how are they able to metabolize glucose?
I have read that red blood cells (RBCs) metabolize glucose. However they don't have any mitochondria because there is just so much hemoglobin that there is no room for mitochondria without expanding the cell.
So how is it possible for them to metabolize glucose if it is mainly O2, CO2, H2O, fatty acids (in cell membrane), and hemoglobin?

What exactly do you mean by "metabolize glucose"? Glucose is mostly converted to lactate in red blood cells, but some is oxidized to CO2 by the pentose phosphate pathway. Are you askiing about metabolism to CO2?

I mean metabolism to atp and co2.

In humans (and all mammals), red blood cells lack mitochondria and therefore has no functional TCA cycle. They metabolize glucose mainly via glycolysis, forming lactate which is released from the cells; this yields 2 ATP for each glucose molecule, much less than complete oxidation (ca 30 ATP), but enough to support the red blood cells' energy needs.
There is some oxidation of glucose to CO2 in red blood cells though. This occurs mainly in the pentose phosphate pathway or "shunt", where 1 carbon of glucose is released as CO2, and the energy extracted is used to reduce NADP to NADPH, which functions as an antioxidant. The resulting 5-carbon sugars (pentoses) are then rearranged to a 3-carbon sugar (glyceraldehyde phosphate) which enter glycolysis again. Hence the term "shunt": 5/6 of the glucose carbon that enter actually comes back to glycolysis again.
By varying flux through the PPP, cells can balance the use of glucose for ATP (energy) or NADPH (antioxidant). Studies estimate that in human red blood cells, 10--30% of hexokinase flux is diverted through the PPP, and the remainder through upper glycolysis (see this and this article). This corresponds to 2--5% of glucose carbon released as CO2, and the remainder metabolized to lactate.
Note that the above apply to mammalian red blood cells. Red cells of other vertebrates, including birds and fish, retain both their nucleus and mitochondria, and their metabolism is different.

While hemoglobin makes up about 90% of the protein in an RBC, there are many other proteins present as well, including enzymes in the anaerobic pentose phosphate pathway, which is responsible for metabolizing about 90% of the glucose entering the cell (the aerobic pathway takes care of the other 10%). There are also proteins responsible for maintaining the oxidation state of the hemoglobin-bound iron atoms. The iron in oxidized hemoglobin, or methemoglobin is in the $Fe^{3+}$ (ferric) state, which is unable to bind oxygen. The NADH-dependent enzyme methemoglobin reductase converts the iron to the $Fe^{2+}$ ferrous state, which binds $O_2$. NADH just happens to be one of the most important products of the pentose phosphate pathway, along with ATP and 2,3–BPG, which helps regulate $O_2$ release from hemoglobin. NADPH is also produced by the anaerobic pathway, and is a cofactor in the reduction of oxidized glutathione, acting as one of the major reducing agents in the cell to protect against oxidative stress. Other enzymes such as superoxide dismutase, glutathione peroxidase, and catalase also help prevent or reverse oxidation. All of the oxygen moving to and fro results in the formation of reactive oxygen species such as superoxide and hydroperoxyl radicals ($\cdot{O_2^-}$ and $HO_2\unicode{x22c5}$) and peroxides like hydrogen peroxide ($H_2O_2$), necessitating the presence of these defensive proteins.

where do you get your numbers from? I've never seen any cell metabolize 90% of its glucose through the penthose phophate pathway. Typical numbers are more like 10--30% of hexokinase flux diverted through the PPP, and the remainder through upper glycolysis (see for example http://www.sciencedirect.com/science/article/pii/S0165022X99000056). In terms of carbon, this corresponds to 2--5% evolved as CO2, and the remainder metabolized to lactate.

I thought most of the anaerobic metabolism comes from glycolysis and lactic acid fermentation(which unless you are talking about fructose eventually turning into glucose or DNA or RNA does not involve the pentose phosphate pathway).

@MattDMo, also NADH and ATP is not produced by the pentose phosphate pathway, but NADPH is. On the other the "anaerobic pathway" (I assume you mean glycolysis?) does not produce NADPH, but does produce NADH and ATP. It seems like you have mixed up the names of the pathways?

@Caters, glycolysis and the PPP are interconnected, but yes, most glucose carbon in red cells is processed "straight" through glycolysis and converted to lactate. The PPP can operate to yield NADPH without producing ribose for RNA/DNA though. I posted an answer to clarify the details.

@Roland I apologize for not including all my sources - while a lot was found in the links I gave, I also based some of the answer on this page from the Children’s Hospital & Research Center Oakland.

@MattDMo I see, it really looks like you have mixed up glycolysis and the PPP as your description is pretty much exactly the opposite of that given on the page you're citing. I would suggest you edit your response for correctness.


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What are some of the known fungi with heat resistant spores
Are there any fungi whose spores can survive 100+ degrees for 15 minutes and grow in a sugar-deprived medium?

According to Sterflinger, some black yeasts may qualify: http://www.ncbi.nlm.nih.gov/pubmed/10081587

Rock inhabiting meristematic fungi are extremely tolerant against high
  temperatures, desiccation and osmotic stress. Their temperature
  tolerance increases with increasing dehydration of the fungal thallus.
  Air dried mycelia of black yeasts stand temperatures up to 120 degrees
  C for at least 0.5 hours

More recently, Suryanarayanan et al. (http://www.ncbi.nlm.nih.gov/pubmed/21872180) have published the discovery of several fungal environmental isolates able to survive dry heat sterilization for 2h at 100+ degrees C. Growth testing was done on Potatao Dextrose Agar (PDA).

Among 25 species of Ascomycota isolated from leaf litter, nine were
  able to grow after incubation in a drying oven for 2 h at 100 °C; the
  spores of two of these species survived 2 h incubation at 110 °C, and
  one survived exposure to 115 °C for 2 h." (...) Craphigera and Phoma sp.
  survived 2 h incubation at 110 °C; the conidia of Bartalinia sp. were
  the most resistant and survived exposure to 115 °C for 2 h

The isolates which survived at least 2h at 100 C were:

Bartalinia sp. (NFCCI 2307)
Chaetomella raphigera (NFCCI 2308)
Curvularia sp. isolate 2 (NFCCI 2311)
Drechslera halodes (NFCCI 2312)
Leptosphaerulina sp.
Pestalotiopsis sp. isolate 1 (NFCCI 2309)
Pestalotiopsis sp. isolate 2 (NFCCI 2313)
Phoma sp. (NFCCI 2310)
Pithomyces sp. (IMTECH 9398)


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Gene transfer between Gram positive and Gram negative bacteria?
How does transfer of genetic material occur between Gram positive and Gram negative bacteria?

By horizontal gene transfer.. but would you add more details to your question ? then the answers can be specific.

Do you want the exact mechanism ?

Have a look at this two links:

Exchange of genetic information
and
Gene transfer between distantly related bacteria

Especially the second should answer a lot of questions.


text:
Can a dNTP be built into a RNA strand?
DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two molecules differ in the hydroxy group in the ribose which is only a single proton in the deoxyribose. This part of the sugar molecule is not directly involved in binding reactions, nevertheless it causes the whole difference in RNA and DNA.
I wonder: could a dNTP be used in an RNA strand (or vice versa)? Is it chemically possible that we have a RNA molecule that contains a dNTP next to its NTPs?

Are you interested in whether this happens naturally, or if we can do it in the lab? And depending on which interactions you mean, it's not really correct to say that the 2'-OH is not involved in binding.

I'm interested in both -- if we can do it in the lab, it's technically feasible and this would be interesting. But if it is possible, could it even happen naturally? And you are of course right, the 2'-OH is involved in binding, I tried to say that it is not used to form a new bond (therefore not directly involved).

This is rather easy to do if you synthesize oligonucleotides chemically and not enzymatically. This is typically done using phosphoramidite chemistry, and it allows for the synthesis of chimeric RNA/DNA oligos. You can even incorporate modified nucleosides like 2'-O-Me or LNA.
This is typically done if you want to change the properties of an oligo, e.g. if you want to make it resistant to degradation by enzymes.

That plus the paper Alan Boyd posted below answered my question. Thank you!

All DNA polymerases use an RNA primer during DNA replication - they cannot begin a DNA molecule de novo. Before the primer is removed the newly synthesised strand is an RNA-DNA hybrid. The first deoxynucleotide to be incorporated into the new DNA is added to the 3'-OH of an RNA.
Does this count?
Added later:
this looks like a place to start reading

It counts. But I still wonder if it is possible to find a deoxynucleotide in the middle of an RNA strand. BTW: thank you for correcting the question :-)


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Primer design for Gibson assembly
I'm trying to design a primer for Gibson assembly.  My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid.
I am unsure how to design my primers for PCR. I know that I need 2 sets of primers (4 total).

Backward and forward primer to copy my gene out of the plasmid that holds it.
Backward and forward primer to copy the plasmid.

I also know that I need to create complementary regions of overlap between my gene and the plasmid I want to put it in.  How do I do this?
Here is the plasmid and the gene. I want to place the gene in between the biobrick prefix and suffix.
Here is what primers I think I need:
For the plasmid I want to put the gene in, my primers should be

Forward: ATTCGCGGCCGCTTCTAGAG
Reverse: CTGACGCGGCCGCTACTAGTA

Primers to copy gene and add overlap

Reverse: ATCATTTCAAATTCGTCCATCTCTAGAAGCGGCCGCGAAT
Forward: AATTAGAAAGAGATTATAATACTAGTAGCGGCCGCTGCA

Here is the gene

IodoY TyrRs

Here is the plasmid I want to put it in. I am using geneious, but I think for this purpose, word works just fine.

your gene is 5kb long.. you cant assemble it with 4 primers..
BTW.. why do you need to assemble it ? you can do a normal PCR.. easier

@WYSIWYG the TyrRs gene is just 1920 bp of the plasmid in the linked file.

@AlanBoyd.. that would still require more than 4 primers to assemble it.. To assemble a ~320bp fragment I used four 90mers..

Marco... I think what you want to do is a nested PCR.. in gibson assembly you assemble the entire DNA fragment using several small oligos..

Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two 20 bp segments of each 40mer.

Here is a good overview of primer design considerations when using Gibson assembly.
http://j5.jbei.org/j5manual/pages/22.html

it says can linearize the plasmid by cutting it and so you'd only need 2 primers to clone the insert.  what advantage is there clone the vector as well?  I guess it saves a miniprep, but 2 oligos cost more than a miniprep does..

Well the downside to cutting the vector is that a restriction site must already exist at the junction. This is a major limitation that Gibson overcomes. The potential downsides of using PCR to amplify the backbone: you might have problems getting PCR to work (always a potential problem), and there is a minimal risk of introducing mutations during PCR (but phusion polymerase should give very few mutations).

Most vectors do have convenient cut sites, but I can see that this is convenient in a lot of ways and it would be quick to order new oligos for the vector.  i really want to try this in the lab...

@MarkB would you be able to [edit] your post to summarise some of the content of that link in case it is not around in the future?

This link helps to answer the question, but on Stack Exchange we prefer answers which don't depend entirely on a link to another website


text:
Enzyme kinetics
I can't understand how to study enzyme kinetics. Say I have a lipase and want to study the kinetics of this lipase using a fluorogenic substrate, how would I do this? From what I understand I would use a 96 or so well plate and in each increase the amount of substrate or increase the amount of enzyme and use a fluorescence microscope or a spectrophotometer?

A basic biochemistry textbook (or Google) will be very useful in answering this.

I'm going to try to lay out some basic definitions here in as plain language as I can find.
Its difficult to study enzymes when they are outside the cell, where they may behave quite differently in different contexts.  We categorize a given enzyme in its class by kcat, Km and by mechanism (the sort of reaction they catalyze.
kcat is sort of a maximum velocity of the enzyme - when there is a lot of substrate around - what is the rate of catalysis.  Ideally there will be zero product present.
Km is sort of the inverse affinity of the enzyme for its substrate, but at half the maximum velocity of the reaction.
The mechanism, which has a couple of definition basically asks how many substrates are bound and in what order, which products are released and in what order, and any intermediates in the reaction which might appear, and in what order.

e.g.: A -> A* -> B* -> B
  A + B -> C + D

I say 'sort of' because you might never see an enzyme operate at maximum rate in living cells.  Substrates are usually rate controlled there - they only have enough of any given compound as they need.
The context that all of these numbers and designations are used is often taxonomical - that is to say you can categorize and sort, and describe what the enzyme does.  In practice large differences in the numbers can describe how useful one enzyme is over another, but it doesn't necessarily tell you how an enzyme will definitely behave in vivo or entirely how it will work in an industrial application.  Its just a start.


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What is itching?
What exactly at the molecular level is itching? What physiological function does itching serve, if any? I cant remember the reference but a PLCb3 null mice lost the itch phenotype, so presumably it is mediated by the Gq-PLCbeta pathway through a cell surface GPCR. Since a physical action of scratching relieves it, could it be a case of a mechanosensitive channel at work?

I have seen two answers posted and then "disappear" after a couple of days.. Can someone tell me whats happening or was I dreaming? :-)

one was just a link to the wikipedia page about itching, was deleted by a mod as it was not an answer. The other was deleted by the owner (see my comment in the current answer).

Just for the record: as a comment to one of the deleted answers I linked to this article: The neurobiology of itch - Ikoma et al., Nat Rev Neurosci 2006. I think it could be a good starting point for an answer (I do not really know the subject and at the moment do not have much time to write a proper one, but I thought I would put the link again here)

Regarding physiological function. I was always of opinion thst purpose of itching reflex is to drive away insects that are drilling or biting or clinging to hair or skin. Given that insects transmit diseases and damage skin, the reflex makes perfect sense. It works for me :-) as it works for dogs, cows, etc.

Like all tough questions, this one has no well understood answer.  Itching "is one of the most poorly understood sensations."
The obvious facts: The urge to scratch part of your skin is the result of stimulus of the skin which causes some of the nerves to register an irritation (you can get an itch in internal organs too - which sounds excruciating).
Biochemically, following the effects of poison Ivy oils, the cathechols break down to orthoquinones and may stimulate local mast cells to release histimine.  So in this case you can see that itching, like many irritations are linked to the immune system which is highly variable from one individual to another, as such it is still a bit of a black box.
The histamine pathway is well studied and histamine stimulates an ion channel protein in nerve cells called TRPV1, which is also known as the capsaicin receptor, which means it is also related to sensing heat.  This explains why itching can be relieved (temporarily) by exposing the skin to water that is as hot as the patient can stand without burning them.  This is one of the ways pain and itching are highly intertwined.
Still, not all itching is stimulated by histamine release; that isn't the whole story.  Antihistamine allergy pills don't help itching.  Other nerve channel proteins can be activated to stimulate itching.  One example found in an itchy mutant strain of mice is TRPA1, and maybe the G protein coupled receptor, Gastrin Releasing Protein Receptor (GRPR). Its hard to imagine that there will not be more mechanisms discovered later.
Mediated both by immune systems and nerve cells, which literally have a mind of their own and whose signal processing is highly individualized and sensitive to local conditions in the body make itching a fairly mysterious phenomenon.  Its also likely that itching can be entirely initiated as a mental condition (Pruritus), so it is not entirely a biochemical phenomenon, which only serves to illustrate the point I guess.

i'll just +1 you for mentioning it  :)

It has also been related to nociceptive receptor based pathways too! That related the inflammatory pain and nociceptive pain pathways in a weird and interesting way!


text:
Why is GTP gamma S non hydrolyzable?
GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving Phosphate group. However, this is not the bond that is hydrolyzed (dashed line). What makes it non-hydrolyzable then?
GTP:                    GTPgS:

Indeed a good question. Bet it's got something to do with electronegativity XD

I'm almost certain its got something to do with the amino acid in the P-loop that contacts the gamma phosphate, however without a reference I am not going to post it as an answer yet. I can ask my PI but then its more fun to find it out myself ;)

"more fun to find it out myself" - ~asks on Bio.SE~

Gamma thiophosphate-analogues of nucleotides were first synthesized in the 70s (Goody and Eckstein, J. Am. Chem. Soc., 1971) and have been used to decipher many intracellular pathways.
To understand why GTP-γ-S is not (or very slowly) hydrolysed by GTPases, we can look at the structure of a GTPase-GTP complex.
GTP binds to various sites on GTPases. This is the binding of GTP to Rap2A, as described in (Cherfils et al., EMBO J. 1997).

As you can see four different sites bind to the γ phosphate.
From the paper:

The interaction of Tyr32 with GTP suggests that its general conservation in small G proteins may have structural or functional advantages. Tyr32 is located three amino acids upstream of a threonine (Thr35 in Ras) which is extremely conserved in most G domains. The alpha subunits of heterotrimeric G proteins have a conserved arginine equivalent in sequence to Tyr32, which was shown from crystal structures to interact with the γ-phosphate of GTPγS

In particular, the position of Tyr32 is different, when Rap2A is crystallised with GTP-γ-S. This figure shows the position of the Tyr32 with GDP (A), GTP (B) and GTP-γ-S (C)

Crystals of Rap2A–GTPγS, whose structure we also report at 3Å resolution, are isomorphous to the Rap2A–GTP crystals. Both structures are essentially similar, except that Tyr32 no longer forms a hydrogen bond with the corresponding atom of the γ-thiophosphate, which is probably the sulfur atom. The Tyr32–γ-thiophosphate distance is 7.2 Å. The conformation of switch I and II and their interaction with the nucleotide are otherwise identical. Thus, the Tyr32–γ-phosphate hydrogen bond forms only in the presence of the true ligand, but is probably not essential for the triphosphate conformation of Rap2A nor for proper binding of the nucleotide. In particular, the position of Thr61 compares well between the GTP and GTPγS complexes.

The author conclude that:

Our study shows that the complex with the natural ligand GTP is similar to the complex with GTPγS, and thus justifies most conclusions obtained from previous structures of G proteins with GTP analogues. However, the structure of Rap2A with GTP reveals a novel interaction of Tyr32 with an oxygen of the γ-phosphate of GTP and with the amide group of Gly13. In the GTPγS complex, Tyr32 is shifted away from the corresponding atom. The Rap2A–GTP and Rap2A–GTPγS complexes are otherwise identical, and form isomorphous crystals. Thus, the interaction of Tyr32 with GTPγS is prevented solely by the presence of the gamma-sulfur, but the conformation of switch I and II is similar whether GTP or a GTP analogue is bound. GTPγS probably introduces a different charge distribution on the gamma-(thio)-phosphate and/or modifies the polarizability of the β–γ P–O bonds as compared with GTP


text:
Human sleep cycles and dream times, what influences the timing and intensity? Sleep history included
I'm doing sleep and dreams research and have developed an iPhone application to help me track my bedtime, rise time, sleep onset and also mark dreams. The app also monitors overall activity overnight as an Actigraph, recording periods of elevated motion and inactivity.
I have a lot of sleep cycle data that I have trouble analyzing.
I know that circadian rhythm is at play with 90-110 minute sleep cycles ehxibited over the course of the night, each one is a progression of various sleep stages, from NREM to REM. REM is more likely to result in a dream reported if awakened during REM.
What I'm seeing is a bunch of orderly patterns, and a lot of chaotic behavior that I cannot explain. Particularly the times of going to sleep and awakening, while dreams exhibit more orderly behavior, with dreams reported at similar times on subsequent days.
I'm also interested in any insight as to what's causing me to wake up at certain times and report dreams. What could be involved in this kind of behavior? I saw research about deuretic hormones not being suppressed for the night, causing the urge to urinate to awaken the dreamer.
Right now I have 90 days of sleep onset and dream data that looks like this:

Complete 90 day sleep history

In this case, each black marker indicates the sleep onset time for
the night
The orange marker indicates the time of getting out of bed
The green markers are dreams that I report upon awakening from a
dream, so dreams occur prior to the marker's location.
Each green
    marker's brightness indicates more clear dream content remembered
    and    recorded.
Cyan markers are lucid dreams, where I was aware
    that I was    dreaming within a dream.
Cyan color of a marker
    indicates that I    could control the dream's content from within a
    dream.
Red markers    are periods of insomnia.
The cyan line is
    number of hours after    bedtime
The purple line is sleep cycle
    approximation (90 minutes).

The data is stacked with each row being a day of data. You will notice that your eyes start to automatically seek patterns within the vertical arrangement of markers. Because each marker is a dream reported upon awakening, they roughly trace the sleep cycles over the course of the night.
I'm interested in learning what influences the desire to go to bed at a particular time?
What influences the getting out of bed times?
is there some sort of analysis I can perform to understand the pattern within the sleep cycles as it evolves over multiple nights?
Any input is appreciated!

I'm interested in learning what influences the desire to go to bed at
  a particular time? What influences the getting out of bed times?

It is the circadian rhythm. Circadian rhythm is mediated by the suprachiasmatic nucleus of hypothalamus, which gets afferent nerves from optic nerve. So, the circadian rhythm is mediated by light. Initiation of the NREM Stage 1 sleep is controlled by the lateral preoptic nucleus, which is another area in the hypothalamus, so it is mainly the absence of light which starts sleep.

I'm also interested in any insight as to what's causing me to wake up
  at certain times and report dreams.

Sleep is not equal to absence of consciousness, it is just an diminished state of consciousness. Sleep consist of mainly 4 stages, NREM-1, NREM-2, NREM-3 and REM. Every stage, the "depth" of sleep, or the level of the decrease in your consciousness changes. REM is the stage in which dreaming most frequently occurs, and also it is the sleep stage where your consciousness is highest, so you are more likely to awake because of the stimulus coming from the environment.

Circadian rhythms persist in the absence of light. Although light cues can entrain the rhythm, I would not say they are its mediators.

Light is not the only, but one of the main mediators of the circadian rhythm. There are many circadian rhythm abnormalities reported in totally blind people.


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Breaking of fats
There is a question I encountered.
Why is fat harder to digest ?
A) It has ester bonds.
B) It is not easily soluble in water.
Which is the most appropriate answer?

Not everything in biology is black or white (in fact, almost everything is gray). A combination of these factors and others play a role in the observation.

I think that the main reason (but probably not the only one) is because fats are hydrophobic, while the environment of the digestive tract is aqueous. Most of the fats in the diet are triglyceride and in hydrophilic environment they form globules. Triglycerides must be hydrolysed to be absorbed by the duodenum and this work is done by pancreatic lipase, that is a water soluble enzyme and can only hydrolyse the esteric bonds at the surface of fat globules.
Therefore, during the digestion amphipathic molecules such as bile salts and phospholipids emulsify those droplets in smaller ones, increasing the surface area where lipases, together with colipase can digest.

Fats are not metabolized in the digestive tract.  The metabolic pathways that break down and utilize fat turn fats into glycerol which is much easier to obtain from carbohydrates.

My Lehninger principles of biochemistry says that "products of lipase action [(monoacylglycerols, diacylglycerols, free fatty acids and glycerol)] diffuse into the epithelial cells lining the intestinal surface".
Is this incorrect or maybe I didn't explain myself well? I omitted this last part of the process because I thought that it was superfluous.

You might be right. I'd thought that the question is about metabolizing for energy.


text:
PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?
I am conducting a biochemistry-related experiment and I have been unable to understand a step which is commonly performed.
My aim in this step is to apply a PEG (Polyethylene glycol) silane layer.
After immersing indium tin oxide (ITO) slides in a PEG-concentration, the slides are incubated for 18 hours at a temperature of 60 degrees Celsius.
Can you tell me why the incubation is performed? And why for 18 hours and at 60 degrees Celsius?
Thanks a lot in advance!!

please clarify the experimental aim and procedure. And please expand the abbreviations at least once.

plus.. this question doesn't come under the domain of biology. try chemistry SE if your actual question doesn't involve any biological principle

The binding of proteins (and cells) to glass (or silicon) surfaces can be prevented by coating the glass with polyethylene glycol (PEG) groups. PEG-silane is a reagent used to create this coating.
PEG-silane (the image shows a methoxy- version) (image taken from here; no connection)  will coat glass surfaces because the silane portion (right hand end of the structure shown) will react with -OH groups on the glass surface.
I can't help with the part of the question about time and temperature of incubation, but it seems longer and hotter than protocols I have seen. Perhaps the indium tin oxide (ITO) coating on the slides has something to do with it?

Thanks a lot for your response Alan! What I do not understand yet from your answer is: where do the OH-groups on the glass surface come from?

Google Images: glass chemical structure

please go through the journal: S. Jo, K. Park, Biomaterials 21 (2000) 605-616.
The time and temperature probably helps to hydrolyze, formation of hydrogen bond and covalent bond formation. Hope this paper will help you.
Good luck!


text:
Why does Rigor Mortis occur after death?
After someone dies they become stiff, this is termed Rigor Mortis and happens because the cells run out of ATP (I think). But why do the cells need it to remain flexible?

It is not flexible cells but skeletal muscle function or flexibility.

You are right that ATP is needed in relation to Rigor Mortis: This for ion pumps to maintain concentration gradients in cells. Without a constant supply of ATP to the pumps, calcium starts to diffuse from the extracellular matrix (and other intracellular compartments with high concerntations of calcium) into the sarcomere where it binds to troponin, a regulatory protein in skeletal muscles. This holds myosin the actin filaments together creating the effect of rigor mortis.

you might add that ATP is required to release the myosin heads from the actin binding sites, meaning that without ATP the contractions don't stop


text:
Why is NAD used mainly for catabolic reactions and NADP used mainly for anabolic reactions?
NADH is used mainly in cellular respiration and the NAD+ to NADH ratio inside the cell is kept high, but NADPH is mainly used in photosynthesis and the NADPH to NADP+ ratio is kept low in animal cells.
Why is this?

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

Does this answer your question? NADH vs. NADPH: Where is each one used and why that instead of the other?. ——— Please note that one part of the expected prior research on this site is that you look for previous questions and answers..

[1] For a very interesting perspective on a slightly different question, "why are there two almost identical cofactors (NAD and NADP) anyway?" see Why NADP by B.T. Kaufman, who argues that phosphorylation on the 2'-position of the ribose may be protective "from the drastic
effects of the ribosylation reactions" and other non-redox reactions that NAD is involved in. ...

[2]  He points out that (only?) NADP and DNA are modified on the 2'-position of ribose, but Coenzyme-A, cyclic-AMP and PAPS are all modified at the 3'-position

NADPH is first generated in the light reactions of photosynthesis before it is used in the reductive synthesis of sugars. But this would seem irrelevant to mammalian systems. NADPH is used in mammalian cells for reductive synthetic reactions, e.g. fatty acid and steroid synthesis.
Although it is merely an opinion, it would seem to me advantageous to separate pools of reducing power for energy generation and synthesis so as to allow regulatory prioritization of the former over the latter. And, incidentally, the generation of NADPH in mammalian cells is independent of that of NADH, being primarily in the pentose phosphate shunt, a pathway found particularly in tissues like adipose tissue, mammary gland, liver and steroid-synthesizing tissues.
Although I now see that a similar question has been asked before the most voted answer repeats the somewhat unsatisfactory statement of the question (to be found in Albers et al.):
“The ratio of NAD+ to NADH inside the cell is high, while the ratio of NADP+ to NADPH is kept low.”
The reason I consider this unsatisfactory is, as just stated, some tissues are specialized for reductive synthesis of fatty acids and steroids, whereas others are not. Their need for NADPH will obviously differ, as will the redox ratio. Remarks about “the cell” are unfortunately typical of texts generalizing metabolism from bacteria.

@user338907 — Yes, of course you are right. I'm afraid I always tend to focus on the actual energy generation aspects of photosynthesis (the light reactions) — the dark reactions being of less fundamental interest to me. I'll correct my answer.


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What substances can selectively destroy certain cells?
Recently, I've watched a documentary about how, in the 1980s, people were buying and using drugs from the streets and then becoming paralyzed a few days afterwards. The drugs that they were using were contaminated with a substance called MPTP, which was able to selectively destroy dopamine-producing cells in the brain, essentially causing end-stage Parkinson's Disease, but leaving higher cognitive functions intact. Is MPTP unique in its ability to selectively destroy a certain type of cell, or are there other substances that can selectively destroy certain body cells while leaving the others intact? If yes, then by what mechanism do they work?


text:
What influences the timing of human bowel movements in the morning?
I'm trying to understand if the timing of human bowel movements in the morning is associated with the circadian rhythm, and can thus be used to make predictions about the circadian rhythm.
What influences the timing of bowel movements? Is it the timing of meals, caffeine intake or is it a biologically programmed time?
Thank you!

The bowel movements are influenced by a lot of factors. For example, when you eat a meal it induces a movement in your large intestines, to defecate and clear up space for new food.
Also, there is MMC, migrating motor complex, which is responsible for the bowel movements when you are fasting. It causes a flushing effect, which prevents bacteria to overproduce in intestines.
So, the daily bowel movements are mainly influenced by the timing and content of the food that you eat. But as I said there are many other factors. The gastrointestinal system has a very complex nervous system. Even psychological factors can effect the bowel movements greatly, for example extreme physical pain may induce the symphatetic system and cause constipation.
Also caffeine may affect it, like many drugs do.


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Why are interspecies hybrids so often larger than either parent species
Recently doing a little reading on interspecies hybrids I noticed that it seems interspecies hybrids are most often much larger than either parent.  Notably, Ligers, Dzo and Savannah Cats, but it seems like all or at least most.
Is there a reason for this genetic expression in hybrids?
If I am incorrectly inferring this to be the case let me know that instead.

While they do not necessarily constitute the majority, it is true that there is a large number of interspecies hybrids whose members are larger in size than the parent species, and there exist explanations that account for this phenomenon.
What you are describing is an example of positive heterosis, or hybrid vigor.  While the rationale for plants is more complex, it commonly arises between related species in mammals as a sort of heterozygote advantage in which the contrast in genetic contribution during conception spawns some phenotypic benefit.  The exact implementation of this varies from species to species, but this link here is a nice, concise explanation for why ligers might be so large.


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What would happen if one eats silica gel?
What happens if one actually does go about eating the beads in those "do-not-eat" packets?

did.... did you ask this question after ingesting a packet of silica gel?

@jamesmassey uhm...just asking for a friend-

Usually, nothing happens if you eat silica gel. In fact, you eat it all the time. Silica is added to improve flow in powdered foods. It occurs naturally in water, where it may help confer resistance against developing senility. Silica is just another name for silicon dioxide, the main component of sand.
Mayby you think if silica is harmless to eat, why do the packets carry the warning? The answer is that some silica contains toxic additives. For example, silica gel beads may contain toxic and potentially carcinogenic cobalt(II) chloride, which is added as a moisture indicator. You can recognize silica containing cobalt chloride because it will be colored blue (dry) or pink (hydrated). Another common moisture indicator is methyl violet, which is orange (dry) or green (hydrated). Methyl violet is a mutagen and mitotic poison. While you can expect most silica you encounter will be non-toxic, ingestion of a colored product warrants a call to Poison Control.

Also, even if no additives were added deliberately, the silica may contain traces of harmful substances left over from the production process. It's a legal/regulatory issue that silica meant for consumption is strictly controlled and of high purity, just like other food additives, while silica for technical uses is regulated differently. So the warning tells you that this particular silica is not licensed as food additive, but it's not necessarily poisonous.

I don't think it would harm you: apparently silica gel is a widely-used food additive. According to Wikipedia:

Silica gel, also referred to as silica aerogel or hydrated silica, has FDA GRAS (generally recognized as safe) status, meaning it can be added to food products without needing approval. Silica is allowed to be added to food in the US at up to 2% as permitted under 21 CFR 172.480. In the EU it can be in up to 5% concentrations.
Listed uses include: anticaking agent, defoaming agent, stabilizer, adsorbent, carrier, conditioning agent, chillproofing agent, filter aid, emulsifying agent, viscosity control agent, and anti-settling agent.

However, obviously, you shouldn't plan on eating lots of it.

it is the same as eating sand right?

The main problem is that small kids get hand on this and get it into the airways.


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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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Why are some chemical dangerous to aquatic environment only?
Recently I was changing the thermal grease on my PC. I have noticed on the back of box, that the grease is not dangerous when ingested or when touched. But there was specifically stated, that is dangerous to aquatic organisms.
What is so special about aquatic chemistry, that the grease is dangerous to them? I would guess that the chemistry of mammals, reptiles, and birds would be quite similar to that of fish.

just a guess, but dissolved in water it may coat the gills and prevent proper oxygen/CO2 exchange...

What type of thermal grease are you using? I think it depends on the ingredients.

From some of the MSDS (1, 2) I come across, a major component of thermal grease is aluminum oxide.
Risk Management for Hazardous Chemicals by Jeffrey Wayne Vincoli states in page 101 that aluminum oxide has both acute and chronic toxic effects to aquatic life; it also states that aluminum oxide has a half-life longer than 200 days in water; finally, it acknowledges that the short term toxicity data for non-aquatic animals are insufficient.
From this, the reason thermal greases have special notification regarding to fishes can be attributed to those following points:

The long half life makes fishes exposure to it longer and therefore makes them more susceptible.
We simply do not understand how aluminum oxide effect non-aquatic animals.

(According to Risk Management for Hazardous Chemicals, bioaccumulation in food chain might not be the concern.)

I have to admit, 'we don't know that it kills land creatures, but it definitely kills fish' is a scary reason to put an aquatic warning on it.


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What is the specific use of a capsule in E.coli?
In evolutionary terms, will the capsule cease to exist someday or will it improve ? Does it provide any boost to the organism in any way which harms us ? Can't we remove capsules or engineer E.coli without capsule ?

According to wikipedia, the capsule contains tightly packed polysaccharides that preform several functions including keeping bacteriophages out, blocking recognition by macrophages, and holding water during dessication. Given the wide diversity of bacteria with capsules, it's probably been around for a long time, which implies it isn't going away any time soon.
If the capsule prevents the E. coli from being taken up by macrophages, then yes, it could allow the bacteria to harm us more effectively. This is one form of a virulence factor.
With proper conditions we probably could develop a bacteria with little to no capsule. We have developed L-form bacteria, which don't have peptidoglycan cell walls. It would seem to me that the cell wall is more important than the capsule, but L-form bacteria are very fragile. I don't know what advantage would be gained by producing capsule free bacteria. There would probably be more to gain from making bacteria with different capsules, perhaps carrying proteins that recognize certain substances and produce a signal, allowing the bacteria to be used as a biosensor, or to accumulate toxic compounds for bioremediation.
references: http://en.wikipedia.org/wiki/Bacterial_capsule http://en.wikipedia.org/wiki/L-form_bacteria

Is there any other organic compound known to gain competency without capsule ?


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What is the smallest scale at which blood vessels, nerves and other structures are deterministic?
Super simple question, but I can't find the answer on the Internet (and I'm in a foreign country so the library is not English.) As the title says, what is the smallest scale at which blood vessels, nerves, lymphatic vessels, bronchi, renal structures, etc.. are deterministic (same for most of the population)? For example, I'd imagine capillaries are pretty much random, while (most?) people have an aorta, so where does the pattern break? Is there a scale at which an animal's body is probably similar to their siblings but dissimilar to a complete stranger? Or is it just a statistical distribution thing (the smaller you go the more standard deviation you get)?

Interesting question.. but I have no definitive answer.. All developmental structures arise because of some kind of morphogen gradient.. The smaller you go there are microgradients and there can be stochastic fluctuations there. It is not about capillaries being small.. Their branching results because of VEGF gradient in a very small area (I am guessing VEGF but there can be other morphogens too), which is not deterministic (or we can say the initial conditions are random). You can perhaps model it as each cell secreting some n VEGF molecules drawn from some distribution.

Even the major arteries and veins do not have a completely deterministic structure. They also have minor variability depending on the idiosyncrasies in the visceral structure. But yes their overall direction is more or less determined.

Indeed a very good question. I'm afraid it might remain without a proper anatomy-based answer, but my intuition would tend towards agreeing with "the smaller you get, the more deviation you'll find".
Or rather, I would expect the same principle as in conservation of genetic patterns to apply here: the more central a tissue structure is to survival, i.e. the more downstream systems depend on it, the more likely it will grow in conserved patterns.
As an excellent example, the largest blood vessels including the aorta and its first- and second-degree branches are identical in branch number, approximate relative branch size and approximate branching location across probably all living humans (given that babies born with malformations on this scale would probably not survive without drastic surgery). Similarly, the largest-level nerves and nuclei are identical across the species. These are central systems that provide core functionality for survival.
On the other hand, teeth are quite important, but the odd tooth missing or additional doesn't harm terribly as no downstream systems depend on them. Indeed, it isn't uncommon for humans to be missing a permanent tooth and keep their primary (baby) tooth in that spot for decades; similarly, missing 8th teeth or additional 9th teeth also occur.

Just a small note on "the smaller you get, the more deviation you'll find".. Small is for the system size (absolute number of interacting entities and limits of diffusion etc) and not the size of the objects in consideration.

I agree with your answer in general, but I feel that humans are more uniform than they need to be, just for the sake of survival. I wonder why eye color is far more variable than nail color, even though they're equally trivial.

Nail colour is much less relevant for sexual attraction? I'm sure you'll find equally useful examples in other animal species to illustrate the principle I mention :)

The answer is... basically none. The variability is high, and can also happen in the macroscopic range. If you want a quick-and-dirty idea of the fraction of the population presenting a certain variability in humans, I would suggest a good anatomy atlas or manual. A good resource would be Gray's Anatomy (the book, not the soap ;-).
Apart from that, @Armatus is in my opinion correct in assuming that variability is inversely proportional to scale. However I would like to point out that even the largest blood vessels can derive from the classical structure in many ways, and are certainly not identical among all living humans.

Anatomy books wont answer this kind of a query.. Gray's anatomy has not included any new information since 50 years ago (that's an exaggeration but still)

@WYSIWYG Oh yeah... ? Well go tell that to all the anatomy researchers around the world, 'cause I am sure they will appreciate :-D Ok, I don't have Gray's at home, but I happen to have Sobotta's Atlas. Panel 86, tome 2: variable distribution of the coronary arteries; panel 116, tome 2: variability of the aortic arch. I'll admit there are just the clinically important variabilities in those books, though...

When looking at anatomical drawings, I've wondered if the fine details (ex. small blood vessels) are just a random sample of one individual, or do they only draw features that are common to "most" of the population. I had no idea until now that anatomical atlases include variability data.

@Misha Yes, they do for commonly encountered variabilities. The medical staff has to be aware of some of them to treat patients correctly. BTW, you might find more variability data (in the macroscopic range) in surgical technique atlases, since knowledge of anatomical variability is mostly useful to surgeons.

Biology is not deterministic. Traits like this have variable expressivity.
A phenotype with 100% expression in a population with an allele is said to have complete penetrance. There is no gene which could specify a single blood vessel pattern that could have complete penetrance. Variable expressivity means the same genes yield a spectrum of forms of the same phenotype.

A description of phenotype variability, penetrance and expressivity

Nothing is deterministic.. But deterministic approximation works well under certain condition. System size is definitely one factor. With expanding size, stochastic systems approach thermodynamic limit and deterministic approximations are valid.Depends on what you are looking at. Deterministic modeling is easier and less computationally intensive.

Logic is deterministic. Not sure what you mean by approximately deterministic. I know fuzzy logic lets booleans be approximate. But Idk that fuzzy logic is defined as deterministic. Sounds like a good question for someone who studies logic.


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Amino acid characteristics that determine their chemical properties?
What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order?

Sounds like a homework question to me.

What differences do the amino acids have from one another?  There is your answer.

Look up amino acid R groups.

Sounds seriously like your homework, so it'd be better if you researched. However as a starting point amino acids can be polar and non-polar. These properties cause varying forces of attraction between amino acids and their surrounding environment. The location changes the way they can interact. Ask if you are unsure about something :)


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Is this a spider caught on video floating its web between trees?
I live in the US and have trail cameras on my property to capture wildlife, visitors, stray animals, etc.  Several are equipped with infrared and I have watched hundreds of hours of video. Many videos feature a large amount of insects flying so I know what a bug looks like on infrared.
What I captured yesterday is completely different. It is a perfectly round sphere floating from one side of my driveway to the other and back again. It appears to me to be on convection currents passing between the trees that line my driveway.
I uploaded this video to Youtube and would be very grateful if you could take a look and tell me if you think it is indeed a spider floating its web between trees. Additionally, are you aware if this phenomenon has ever been captured on video before?  I searched the web looking for other videos but am unable to find any.
The 'orb' appears at 10 seconds into this video.

If you're saying you think this is a spider riding air currents to travel from tree to tree, sorry, but I don't see it. If it's actually moving from one side of the drive to the other, it would have to be moving relatively quickly to cover that distance (about 20 feet according to the video) in only a second or so. If it's just being blown by the air, it seems to me like it would have to have been fairly windy to have moved that quickly, or be capable of directed flight.
It seems more likely to me that's it's just a particle of dust or similar material floating close to the camera. The reflection of the IR light causes it to appear much larger and causes the shape to appear more regular than it truly is. If it's actually a much closer to the camera, only light breeze would be required to show this behavior. There's a strand of web clearly visible near the camera, and perhaps this is indeed something caught in another strand web and dangling down in front of the camera—heck, it could actually be a small spider, but it appears dangling from a web near the camera rather than floating between trees.
I couldn't tell you exactly what it is, but it seems more likely to me that be a trick of light and perspective than a spider floating from one side of the drive to the other.
Disclaimer: I'm not an expert in arachnology or videography. These are just my thoughts on the video.

OK, so I posed the question in the wrong location.  This IS how spiders build webs between trees .. they DO float on convection currents that don't even have to be breezy but more made up of heat rising.  I submitted this to the international arachnid institute and they have verified that it is not only a spiders kiting bubble but at second 18 you can see the spider.

@user3037683 - Why posting a question where the answer is already given by a seemingly credible source?

@user3037683 To be clear, I'm sure that some spiders make their webs in this manner, I'm just skeptical that this is what's being shown here, given the speed at which the object would be moving. I've watched the video closely, and tried to look at each frame around the 18s mark as you suggest and I still can't see anything that can clearly be distinguished as something other than compression artifacts around the orb. You very well might have captured just what you say here, the video just isn't clear enough to say for certain.


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Is the 'fluttering feeling' when under stress neurological or physical?
I'm sure that everyone is familiar with the sensation commonly known as "butterflies in the stomach".  It is commonly experienced during periods of anxiety or stress (e.g. before high stakes job interviews or roller coaster rides) and apparently (after my web research) often felt in new romances without an obvious cause of tension.
However, whilst my googling did turn up an inordinate amount of rubbish regarding love-sicknesnes, I have been unable to find even a suggestion as to a mechanism as to the physiology behind this feeling.  Is it a sensation of physical change in the stomach (some sites vaguely mentioned the restriction of blood flow to critical organs but it was entirely unsupported) or is it neurological in nature?

apparently (after my web research) often felt in new romances without an obvious cause of tension. +1 sympathy vote.

@Poshpaws lol what can I say - I'm obviously just too smooth to get nervous ;-)

If you want to find out about the the relationship of this response to romance in particular, there's a pretty comprehensive research paper called Love is more than just a kiss: a neurobiological perspective on love and affection[1] which reviews a lot of the work done in this area. This is pretty good as it discusses all the different stages including breakup.
Essentially, there seems to be a lot factors at play which elicits various responses through different stages of love.
In terms of anxiety and stress, initially, there's a large increase in levels of cortisol[2] and a marked drop in serotonin. Depletion of serotonin is found in many psychiatric conditions such as depression, anxiety and panic disorder. There's even been evidence that these levels at early stages of love are similar to those suffering with OCD. Obviously, the 'symptoms' of early love are quite similar to these conditions so it's hypothesised that this, at least in part contributes to those feelings.[1]. It was found that these levels are back to normal in 12-24 months.
The elevated levels of cortisol contribute to the feelings of stress but this hormone has also been shown to promote attachment.[2].
There are also changes in activity of the amygdala. Responsible for regulating a lot of emotions such as fear and sexual drive, the amygdala can activate autonomic nervous system responses through the mechanisms which Kevin described.
There are a bunch of other things at play here including dopamine, oxytocin, vasopressin, nerve growth factor (NGF), testosterone, increased activity in the hypothalamic-pituitary-axis (HPA) and variations in activity in other areas of the brain.
Again, that first reference gives a pretty comprehensive overview of the mechanisms involved.
To answer the actual question about the fluttering feeling, as Kevin mentioned, it's hypothesised that this is caused by reduced peristalsis in the intestines as a result of sympathetic stimulation. I don't have an academic reference for this but there are plenty of non-academic sources that talk about it (a quick Google of butterflies in stomach and physiology will probably show them).
A lot of the mechanisms noted above can contribute to, sensitise for or cause sympathetic activation. For example, panic attacks and anxiety, mentioned earlier with the serotonin relationship, can cause the same feeling.

Boer, et al. Love is more than just a kiss: a neurobiological perspective on love and affection. Neuroscience. 2012. 201:114-124.
Marazziti, et al. Hormonal changes when falling in love.
Psychoneuroendocrinology. 2004. 29(7):931-936.
Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.

The review was really very interesting, but unfortunately didn't answer my main question :)

Oh, sorry! Do you mean the 'fluttering feeling'? I edited the post and added some more info. Does that help at all?

Hope it's useful!

Nervousness or excitement should cause an increase in activity in the sympathetic nervous system (the so-called "fight or flight" side of the autonomic system). Increased sympathetic activity will be associated with decreased parasympathetic activity (primarily digestion, but also crying and other "emittive" glandular activity).
I don't have a citation, but I suspect that the "butterflies" feeling is associated with the cessation of peristaltic activity in the gut, which puts the digestive and nervous systems in conflict. If you have just eaten, then there is a difference between what your gut wants to do (digest) and what your brain wants it to do (not digest) -- thus the frequently accompanying nausea.


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Why are restriction enzymes not frozen?
We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is so?

It's just so much more convenient to have the enzymes ready without having to thaw them. The main reason you freeze enzymes is to keep them active, if you figure out a buffer that keeps them unfrozen without compromising activity, that is a huge increase in convenience.
Not having to thaw the enzymes before use saves a lot of time, if you can manage to keep the enzymes active in those non-freezing conditions that is a clear advantage.
Glycerol also stabilizes proteins in solution, and multiple freeze and thaw cycles can negatively affect enzyme activity for some enzymes.

Just as an addition: you can do the same with antibodies. On reception, dilute them 1:2 in glycerol and you can avoid aliquoting them and don't have to worry about freezing cycles (remember to double the amount when you use them, though)!

Freeze-thaw cycles denature proteins through local pH change effects

A little brief? :)

It does get the point across.


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What is the biology behind a skin "mole"?
Are the dark marks aka "moles" on our skin a patch of dead cells? If so, why is it not cleared over time? In a (probably) similar vein, why do scar marks from injuries remain long after new cells replace the dead cells?
[Feel free to edit out the second question if the answers are unrelated]

A mole is simply a benign tumour, i.e. a proliferated cell growth that hasn’t become cancerous. So moles are not dead cells, they are very much alive. The colour is caused by a high concentration of the melanin, which is also responsible for normal darker skin.
Since moles are tumours, they can – but in most cases don’t – give rise to melanomas, malignant skin tumours, when they lose susceptibility to cell growth regulation and start invading surrounding tissue.
Scar tissue is entirely unrelated and due to regular regrowth of epithelial cells after injury forming a linear collagen structure (as opposed to the skin’s normal collagen structure, which resembles a “weaved“ structure).

A Mole may be a Hamartoma or a benign tumor. A congenital mole is usually a hamartoma, while acquired mole a benign tumor. In a few people mole very slowly grow in size.


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Why can't we breed watermelons without any remaining seeds in the flesh?
Watermelon is just starting to come in season in the northeastern U.S., and having a seedless watermelon is convenient.  The only downside is, the "seedless" almost always still have the immature, sterile white seeds in them.
What is the mechanism for breeding these watermelons so that only these white seeds remain?  What is the genotype that results?  Could the genetics be modified so that there are virtually no seeds (short of any minor aberrations) left in the flesh of the fruit?