text:
Opening probability of a voltage-dependent ion channel
Does the opening probability of a voltage-dependent ion channel depend on the unitary conductance?
I think so because of the equation:
but I am not sure.

Can you explain your thinking? Maybe mention what the variables in that equation represent and how it leads you to the question posed.

Now I realize that the equation is true for Squid giant axon. And the reason i think that the opening probability of a voltage dependent ion channel depend on the unitary conductance is because of the substates which depended in specific unitary conductance of this spesific state. AM i wrong?

I'm not following your comment, sorry. I think it would help to talk in terms of the variables in the equation if it's the equation that is motivating you.


text:
Understanding association kinetics
I would like to understand the classic kinetic model of association / dissociation that tries to describe the concentration of a compound $[\ce{AB}]$.
Let's say we have a model:
$\ce{A + B} \xrightleftharpoons[k_{\text{off}}]{k_{\text{on}}} \ce{AB}$
So $k_{\text{on}}$ is the rate of binding and $k_{\text{off}}$ is the rate of unbinding and the rate equation is:
$\frac{d[\ce{AB}]}{dt}=k_{\text{on}}[\ce{A}][\ce{B}]-k_{\text{off}}[\ce{AB}]$
I don't understand why texts say that if $k_{\text{on}}$ and $k_{\text{off}}$ are both constant then we reach a steady state, i.e., $k_{\text{on}}\ce{AB}=k_{\text{off}}[\ce{AB}]$ I mean: if, for example, the rate of binding, is greater then the rate of unbinding, shouldn't the concentration of the final compound increase up to infinity? What I have in mind is: we produce 4 proteins per second and degrade 2 proteins per second, then the net production is 2 proteins per second so, as time goes by, the concentration should increase and doesn't reach a plateau.
Why do we instead reach a plateau in the final concentration? I can understand the plateau in the plot of the reaction velocity but still, if the velocity is constant, still the concentration of the final compound should increase.

As @David said, this reaction has nothing to do with Michaelin-Menten model of enzyme catalysis. It looks like one reversible reaction (which can be physical or chemical).

I edited to remove the references to Michaelis-Menten, as we seem to all be in agreement that this is not that.

@MaximilianPress — That’s a lot better. However, unless either A or B are a protein — not stated — we are left with a question for SE Chemistry.

There is a misunderstanding here that is very common when first learning about chemical kinetics. First you say:

if $k_{\rm on}$ and $k_{\rm off}$ are both constant

but then:

if the velocity is constant

This is not one and the same!
$k$ is the rate constant of reaction.* The actual reaction rate (i.e., the change in concentration over time) is given in your example by:
$v_{\rm on} = k_{\rm on}[A][B]$ for the forward (binding) reaction, and
$v_{\rm off} = k_{\rm off}[AB]$ for the reverse (unbinding) reaction.
Suppose that $k_{\rm on} > k_{\rm off}$. Then at first $v_{\rm on} > v_{\rm off}$ and the product AB is produced faster than it degrades. Therefore the concentration of AB increases. On the other hand, A and B are consumed in the reaction, so their concentrations decrease.
Now look at the equations for reaction rates above! The rate of the forward reaction, $v_{\rm on}$, depends on concentrations of starting materials, $[A][B]$; and the rate of the reverse reaction, $v_{\rm off}$, depends on the concentration of product, $[AB]$. Therefore, as the reaction proceeds, $v_{\rm on}$ must decrease and $v_{\rm off}$ must increase until they reach equilibrium where both rates are equal.

* Note: As a convention, reaction rate constants are usually denoted by lowercase $k$. Uppercase $K$ is reserved for equilibrium constants, or the Michaelis constant $K_M$, or a number of other constants.

"Suppose that on>off." But kon is a second-order rate constant whereas koff is a first-order rate constant, and have very different units (M(-1).s(-1) versus s(-1), for example) and as such is it surely meaningless to compare them?

@user338907 Not necessarily. For example, the equilibrium constant is equal to the ratio of forward and reverse reaction rate constants, so here K = k_on/k_off. Then k_on > k_off means that K > 1, i.e., equilibrium favours the products.

You cannot directly compare the magnitude of a first order rate-constant with a second-order rate constant.  This IS a fundamental mistake in dealing with enzyme kinetics.  How can  something with dimensions of M(-1).s(-1) be greater or less than (or equal to) something with dimensions of s(-1)?  To take a more obvious example, how can pH 7 be considered greater than or less than 100 degrees celsius?  (Going back to MM, the steady-state dfn of Km is the sum of two first-order rate constants, divided by a second-order rate content, a good eg of the value of dimen. analysis)

This is probably a more relevant answer than mine.

Update: As noted by commenter, the example stated in the question is not actually Michaelis-Menten but is rather an example of binding kinetics. See also the other answer, which is likely more relevant.
I would suggest, if you would like to find the steady-state concentration of $[AB]$, that you can solve this yourself mathematically. Try differentiating and setting the $\Delta [AB]$ side of the equation to zero, and solving. You will find:
$ \Delta [AB] = (k_{on}[A][B] - k_{off}[AB])\Delta t$
$ 0 = (k_{on}[A][B] - k_{off}[AB])\Delta t$
Rearranging:
$k_{on}[A][B] = k_{off}[AB] $
And finally:
$\frac{[AB]}{[A][B]} = \frac{k_{on}}{k_{off}}$
Note that if the $k$ are constant, this amounts to the law of mass action.
You can also do a forward simulation (see R code):
# association/dissociation kinetics
kinetic_sim = function(k_on, k_off, a, b) {
  ab = 0
  ab_ts = c()
  a_ts = c()
  b_ts = c()
  for (i in 1:1000) {
    ab_old = ab
    ab = ab * (1 - k_off) + k_on * (a * b)
    a = a - a*b*k_on + ab_old * k_off
    b = b - a*b*k_on + ab_old * k_off
    #cat(i, a, b, ab, k_on*a*b, k_off*ab, "\n", sep=" ")
    ab_ts = append(ab_ts, ab)
    a_ts = append(a_ts, a)
    b_ts = append(b_ts, b)

  }
  return(list(ab_ts, a_ts, b_ts))
}
out = kinetic_sim(.1, .2, 1, 1)
plot(out[[1]] / (out[[2]] * out[[3]]), ylab="[AB] / ([A] * [B])", xlab="time step")
plot(out[[1]], ylab="[AB]", xlab="time step")

You can see that both the ratio and the final concentration equilibrate.

A few suggestions. 1. The reaction example shown by the OP does not depict an enzyme catalysis. So using the term "Michaelis-Menten" would be misleading. 2. The system has 3 variables but there are only two independent differential equations. The third equation should be the conservation of mass (a + b + ab = constant). Alternatively (deviating from OP's example), you can model the system as an open system with rates of synthesis and degradation of the different components.

@WYSIWYG thanks for the thoughtful comment. 1) You are absolutely correct that this is not michaelis-menten, my brain went immediately to the kinetic example shown without thinking about its name. 2) you are correct, the constant mass is implicitly modeled as shown in the simulation.

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text:
Why do some amino acids have more synonymous codons than others?

In the standard genetic code (above), tryptophan and methionine are coded for by a single codon, other amino acids such as phenylalanine by two codons, isoleucine by three codons, and some by four or even six codons.

Is there any explanation for this difference in number?

One possibility that occurred to me is whether, amino acids which are more crucial to a protein’s structure tend to have more synonymous codons? For example, Tryptophan is coded by a single codon, TGG, whereas Proline is coded for by the four codons, CCA, CCG, CCC, and CCT. A single mutation would always change tryptophan, but would have a 1 in 3 chance of leaving proline the same. Is this because a change in proline would be more likely to have a deleterious affect on a protein than a change in tryptophan, and for this reason there has been evolutionary selection to provide proline with more codons?
N.B. This is a different question from the previous general one on the evolution of the genetic code.

Welcome to SE Biology. We do expect people to do a little research before posting to try to answer questions themselves. Theoretical questions like this can only be approached by logical arguments, which anyone with basic biochemical knowledge can try. So ask yourself, would a change in methionine be unimportant? If you consider the mechanism of initiation of protein synthesis, I think you can reject that hypothesis. The fact that this hypothesis was not considered in the question you link to is also suggestive. A simpler idea is that the structurally simpler amino acids evolved first.

@David Yes, you are right that its status as a start codon makes ATG a bad example. I will change it to Tryptophan.

Could you clarify what you mean by “this would make sense”? Things only make sense in relation to a conceptual framework, and in this case you are presumably making some assumption about the way the genetic code evolved. I can guess what your assumption is, and if my guess is correct, almost certainly do not share it, but if you must ask questions like this and want an intelligent discussion you must spell your assumptions out. And changing met to trp doesn’t alter the fact that the situation with met is inconsistent with your proposition. How do you accommodate it?

@David I think I understand now that the unit that natural selection is operating on here is the boundaries between amino acids in codon space, rather than the codons themselves. It is different enough conceptually that I maybe should write another question.

Consideration of the ‘importance’ argument
In some cases it is difficult to say whether changing one amino acid would have a more deleterious general effect than changing another, but one can put forward several examples in which the number of synonymous codons for different amino acids does not support any relationship to structural or functional importance in proteins.
• The fact that there is only one codon for methionine, which is of paramount ‘importance’ as it is essential for the initiation of protein synthesis.
• The difficulty in arguing that arginine (6 codons) is three times more ‘important’ than lysine (2 codons), when these amino acids are equally abundant in E.coli and lysine is involved in the catalytic function of numerous different types of enzyme.
• The difficulty in arguing that the non-catalytic leucine is ‘important’ enough to have 6 codons, when there are another 3 for the related isoleucine and a swathe of other amino acids with aliphatic side-chains, mutation to which may be allowable.
• The fact that unique indole ring of tryptophan (1 codon), as well as providing a large aromatic side-chain,  plays an essential catalytic role in a variety of enzymes such as oxidases.
Is selective pressure to minimize amino acid changes likely to have been important in the evolution of the genetic code?
The genetic code today is the same in almost all organisms, and the variations in the exceptional species are only minor. In the generally small and isolated mitochondrial genomes the selective pressure for variation would seem to have been to reduce the number of tRNAs needed to decode the mRNA. This is consistent with the “frozen accident” idea (originally proposed by Crick) — once the genetic code was to a certain stage it become frozen because changes would have been lethal. Remember changing the assignment in one codon would affect all proteins using that codon, in contrast to a mutation of a single codon in a single protein to a different amino acid. Further, any codon reassignment would affect the anticodon of the tRNA corresponding to that changed codon — often interacting with more than one codon and dependent on recognition by the amino acyl-tRNA synthetase for attachment of the correct amino acid.
An alternative explanation for the conundrum
Disclaimers:
We clearly cannot know how the genetic code evolved, so all we can hope for is to find the explanation with the fewest flaws in relation to scientific knowledge at that time. Some of this answer appears to have come subconsciously from the 1968 article by Crick on the Origin of the Genetic Code, which I re-discovered after having formulated it. Other aspects (no doubt the weaker ones) are my own, but must surely have been considered by others in the 60 odd years since the elucidation of the genetic code.
Summary of answer:
My suggestion for the difference in number of synonymous codons is that many of the amino acids with only two synonymous codons — and those with only a single codon — may have evolved later than those with three, four or six synonymous codons.
Answer
It is not unreasonable to suggest that the original genetic code specified fewer than the 20† contemporary encoded amino acids and the termination signal. This would have been because of the primitive stage of evolution of metabolic pathways for amino acid synthesis (presumably catalysed by ribozymes). There may even have been fewer than 16 amino acids, although with a triplet (rather than a duplet) codon length because of geometric and energetic considerations relating to the interaction with tRNAs (themselves ignoring or interacting promiscuously with the third codon position).
So the 16 blocks of codons would have been assigned to those initial amino acids, with some perhaps taking over two blocks (Leu?). As metabolism developed, new amino acids would be added, either occupying ‘empty’ blocks or taking over half of an existing block (Phe in the Leu block?). As new amino acids were added with more functional possibilities then simple aliphatics or aromatics, and more sophisticated proteins arose, it would have become increasingly difficult to change the genetic code because of the disruptive effect this would have had.
Any theory should clearly consider, as the OP did, the amino acid tryptophan with its single codon — but, likewise, also methionine. One can envisage a situation in which the code had developed to encompass the other 18 amino acids and perhaps four stop codons, but without a specific initiation codon. Others have argued that methionine emerged late as the initiating amino acid (an early role as another aliphatic is at odds with the high metabolic cost of its synthesis); suffice it to say here that Met is chemically similar to Ile, which one assumes it displaced in the AUN block, and such a change would therefore have been generally tolerated by proteins.
I think it likely that, because of its complex structure, Trp was added late (last?) and replaced a termination codon. This is because one can argue that it would have been less disruptive than replacing an amino acid codon. First, termination does not involve tRNA and aminoacyl tRNA synthetases — the codons are recognized by release (termination) factors. This would only require mutations in these factors, which show differences between eukaryotes and eubacteria. Second, the effect of a mutation in a stop codon is just a longer C-terminal segment to the protein: termination still occurs when one of the remaining stop codons is encountered by chance. Variation in the C-terminal segments in proteins are widespread between species, in different isoforms of a protein within a species, and in the strategies viruses use to expand their repertoire of proteins from a compact genome.
†The additional amino acids selenocysteine and pyrrolysine, although of interest, are not relevant to this argument.

That is a good point, but I am not sure that, at least before all 64 codons were assigned, all codons were frozen. With an unused codon available the genetic code can change by 1. assigning an amino acid to the codon, 2. switching all proteins to the new codon, then 3. assigning something else to the newly free codon. The fact that the code can't be changed without destroying almost every protein doesn't come in to play until the codons are all being used. That implies that natural selection may have influenced the choice of many codons, even if as you point out it can't change them today.

Having fewer codons makes an amino acid less likely to be mutated to, while having more codons makes an amino acid less likely to be mutated from. If a particular amino acid would drastically change protein expression if it either appeared or disappeared (for example fMet, the start codon in bacteria), it is not clear whether natural selection would prefer to guard against its appearance (by giving it fewer codons) or disappearance (by giving it more). If natural selection does determine the genetic code, it would have to do so by acting in a more subtle way that could differentiate between those two cases.

Your answer assumes that the consequences of mutation were key factors in determining codon assignments during evolution. I very much doubt this. The whole question is complex, but has been discussed repeatedly since the genetic code was deciphered. Before expressing an opinion on this it is wise to consider such previous arguments. I regret not having had time to do so, which is why I have been reluctant to get involved. However, I'll post an "answer" some time next week  explaining why I think your assumptions — and hence your answer — are invalid.

This answer ignores a whole bunch of interesting biology such as codon bias in different organisms etc. It is an interesting idea you have had, but you should back it up with some references that show this is actually the case.

@bob1 — Could you explain what codon bias in different organisms has to do with the evolution of the genetic code?

@David not off the top of my head, but I think it could play into the evolution somehow - energetic costs? availability of substrates for generation of bases?  Could simply be a founder effect.

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text:
Aminoacyl-tRNA synthetase and the degeneracy of the genetic code
Aminoacyl-tRNA synthetase catalyses the covalent linkage of amino acids to tRNA.  The aminoacylated tRNA is then bound to mRNA on the ribosome in a codon–anticodon hydrogen bonded interaction.
In order for several different codons to correspond to the same amino acid — according to the degeneracy of the genetic code — one or more of the following must be true:

Each amino acid is recognized by several different aminoacyl-tRNA  synthases, each one able to aminoacylate a tRNA specific for a different codon for that amino acid.

One aminoacyl-tRNA synthetase can aminocylate the several different tRNAs for a specific amino acid.

A single tRNA for a particular amino acid can bind to several different mRNA codons.

Which of these is true?

This topic is dealt with in most biochemical and molecular biological texts — there is a useful summary in Alberts et al.. However it may be useful to clarify this point as this is a fundamental question, the answer to which could not be anticipated.

Both 2 and 3 are correct, but 1 is incorrect.

As regards 2, it turns out that there is a single aminoacyl-tRNA synthetase for each amino acid and this recognizes all the different tRNAs for that amino acid. This is even true of initiator and elongator tRNAs for methionine. This implies that even though the anticodons of these tRNAs differ (or their conformations in the case of the two tRNAs for methionine) there is some common distinguishing feature of the tRNAs that the enzyme recognizes.
As regards 3, this relates to the phenomenon of wobble, the possibility of specific relaxed patterns of hydrogen bonding at the third position of the codon. This decreases the number of tRNAs required to decode the codons corresponding to a particular amino acid.
In principal neither of these features is neccesary for the degeneracy of the genetic code. They just reduce the number of molecular species (enzymes and tRNAs) required for decoding. One assumes that the practical advantage of this was sufficient to ensure its development and retention.
Coda
Nature is an anarchist, and although the above statements are generally true there are always exceptions. For example, some bacteria have developed ways of managing with fewer than the 20 expected aminoacyl-tRNA synthetases. But if one starts by understanding the general situation one is then in a position to accommodate the exceptions. A highly-cited review of aminoacyl-tRNA synthetases can be found in Ann. Rev. Biochem. for 2000.


text:
What is this snake
I took a picture of this snake in Switzerland (Geneva Area):

It looks to be an adder but cannot be sure about which species.
In Switzerland we have two kinds of adder:

Vipera berus
Vipera aspis

For me it looks like a Vipera berus, but all the images I saw from both species (and the variations) I cannot be sure.

amazing that you stood long enough to take a picture of an unknown snake.. I would be running my lungs out..

I was at reasonable distance and with a 70-200mm it helps. But yes I recognised an adder (lightly venomous) but I know they are quiet as long you don't go next to them.

An generally speaking, snakes in Europe tends to escape before attacking

I'm not an expert so don't feel qualified to answer, but a bit of reading suggests to me that it is Vipera aspis because the head looks rather broad and there is no clear dorsal zigzag.

I think it's an Vipera Aspis.
from wikipedia:

The dorsal markings vary strongly, but only rarely take the form of a
  clear zigzag, as in V. berus.

Your Snake in Maximum RGB Color (Broken ZigZag)

Vipera Aspis from Google Image

Thanks for your answer. After searching about the repartition of both snakes around Geneva, I found these maps that confirm vipera berus is not present in Geneva area as vipera aspis is

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text:
What species is this beetle (trichius family)
I took this picture in Jura region (Northern Switzerland, alt: ~700m) of that beetle (July 2018). It was taking food from a flower of a Morus nigra.

It seems to be part of the trichius genus but I want to report the exact species.
In Switzerland we have mainly:

Trichius fasciatus
Trichius rosaceus
Trichius sexualis

I think by the color of the hairs it would be a Trichius fasciatus.
Can someone confirm the species and what field marks I can use to make the distinction between those three species?


text:
What is this insect in India?
I found this insect today in front of my room.
I am just curious to know what kind of insect it is? And, is it poisonous?
Location: India

Where do you live? It may help narrow the possibilities

Its a black Cricket .
Crickets, (family Gryllidae) are related to the Grasshoppers Family.
It should have grasshopper like hind legs .
Crickets usually emit  noise from its body.

I can't tell what its legs look like from that image, it's kind of blurry. But I think it's either a type of cricket or cockroach. If those are wings at the bottom of the insect I'd lean towards cockroach. And I swear I remember crickets and cockroaches as both being orthoptera, but now cockroaches are grouped with termites? When did that happen?

@user137 crickets were never grouped with cockroaches as far as I'm aware. Some scientists used to group together mantises, orthopterans, cockroaches, and stick insects together.

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text:
Who are these biologists?

I know the third one in the front row is James Watson.
Does anyone recognize the others?

This has no relevance in biology

Should we put the species-identification tag?

While not being an ideal question (where and when was the photo taken? why do you want to know?), I still think these kinds of questions should be allowed here. We have the history tag, which is relevant for this Q (history of biology), the Q has a definite answer, and BioSE should be as good a place as any to ask about the identification of prominent biologists.

I agree with fileunderwater. I vote to reopen

Without the context of where (geographical location + setting) and when this photo was taken - I vote to leave closed on the basis of being unclear what you are asking -slash - homework (no effort whatsoever / poorly researched)

Sitting next to Jim Watson is another Nobel Laureate, Wally Gilbert (on the right in the photo) but actually on Watson's left.

Plus there is a History of Science and Mathematics SE site, so wouldn't it be best to keep this question there?

Front row, left to right; Victor McKusick, Maurice Wilkins, James Watson, Walter Gilbert and John Kendrew.

Great! +1 Do you know where/when the picture was taken? Seems to have a high density of Nobel laureates.

Unfortunately I was unable to find any context for this photo, I just recognized the scientists. It appears to be a relatively formal meeting and most of them are molecular biologists/geneticists, but I'm not sure why they would be holding papers if it was anything but an experiment (though I can't imagine what experiment they would attend that involved molecular biology) my only other guess would be perhaps some sort of a conference because they all seem to be taking notes and looking in the same direction. Again, I'm not sure. I apologize for not being able to find anything on it.


text:
What species is this? Seashell from Indonesia

Anyone know exactly what species this is?  I gather it may be an auger (family) or cerith (family) of some sort.
This particular one is native to Indonesia's black beaches.
I would like to know what is the genus and species of this specimen.

That is a piece broken off of a sea urchin shell.

Without it's spines, it's not possible for me to say which species it is.

Good eye anongoodnurse +1

WOW!  Holy cow anongoodnurse, I am impressed.  You are totally right.


text:
Binding BSA to silver surface via large difference in isoelectric points of the two materials
I would like to bind BSA to a silver surface so that I can utilize plasmonic sensing to detect the BSA. There seems to be two methods of doing this: 1) to rely on electrostatic forces or 2) to form a covalent bond. The former seems to be the easier route, especially for someone like me who does not have a background in chemistry/biology.
So I found a paper (https://doi.org/10.1016/0021-9797(91)90121-N), which has been cited 54 times, that determined a silver (oxide) surface has an isoelectric point (iP) of ~10 pH. So this should mean that it has a positive charge when a neutral pH solution covers the surface. In other literature BSA has been shown to have an iP of pH 4-5, so it should become negatively charged in a neutral pH solution. So the BSA should bond to the silver surface in a neutral solution, correct?
The reason I ask is two-fold. First, I found a more recent paper (https://doi.org/10.1021/am400909g) that has a conflicting value for the iP of a silver film (~3 pH). Second, I found a paper (https://doi.org/10.1016/j.vibspec.2003.09.003) were the authors adsorbed BSA onto silver films, but with the intermediate step of applying 2-mercaptoethanesulphonate to the silver surface. Why the need for this if the silver should attract the BSA electrostatically?
In addition, if BSA bonding to silver were to work in this way, am I correct in thinking that a neutral solvent such as phosphate buffered saline would hinder the electrostatic bonding process because the positive and negative ions from the salt solution would bond to the respectively charged molecules and neutralize the charge?

Concerning the apparent discrepancy between your first and second citations, the difference in values is addressed by the authors in the more recent work:

Perusal of the literature yields few IEP values for silver metal. Chau and Porter reported an IEP of 10.4 for an evaporated silver film as determined by contact angle titration.(6) The method employed in their investigation used only neutral and basic liquids, and the maximum contact angle achieved on the silver films was ∼35°, in contrast to the maximum we observe of 52° at pH 3.2 (Figure 1d). This dichotomy may be indicative of the amphoteric behavior of the native oxide at the surface.

Concerning your third citation where the authors bound BSA to silver via a 2-mercaptoethanesulphonate linkage monolayer, the authors give their reasoning in the abstract:

The direct adsorption of proteins on metal surfaces usually leads to loss of their enzymatic activity

So, to answer one of your questions

Why the need for this if the silver should attract the BSA electrostatically?

BSA here is a proxy for other proteins.  The purpose of the research was to examine how the structure of the linkage monolayer changed in response to protein adsorption, not how BSA specifically binds a silver substrate.

Oh I see now. So although both papers claim to have an oxide layer on their silver, paper #2 is claiming that Chau and porter did not use a sufficient number of pH solutions over the whole range, and therefore did not have enough data points to extract the iP value (Fig 1 of paper #2). But that value of 10 has been cited after paper #2 was published. Maybe I should just choose a different metal such as copper.
What exactly is loss of enzymatic activity?

"Loss of enzymatic activity" means that the adsorption of an enzyme to the substrate leads to changes in conformation that reduce or eliminate enzyme function.

Ok. So I think if I am only interested in binding BSA to silver for the sake of sensing BSA, then loss of enzymatic activity should be irrelevant.

Probably, but I'd suggest editing your question to better address what it is you are actually trying to accomplish. By your comment, this question smells of an XY problem.

I wanted to have reassurance before I possibly wasted money buying the products.


text:
Could you identify which species of ant is this queen?
could you identify which species of ant is this queen. I caught it in Bangalore, India. I caught it after a rain at around five to six.
]2

You should probably add more information, such as the time and place where it was caught (including ecological context).

I caught it at around five to six. I also caught it directly after a rain storm. I live in a relatively warm place which is not to humid. Oh and I caught it just outside my house.

Oh I also caught it in Bangalore, India which is where I live.

@DarkGuardian2006 please [edit] your question to add the details. Do not reply in comments.

Although absolutely no formal criteria are visible on your photo, the general shape of the ant, especially the wide elongated head and low thorax, is typical of the ant genus Camponotus.
See ref below:

Bolton, B., Alpert, G., Ward, P. S., & Naskrecki, P. (2006). Bolton’s
  Catalogue of Ants of the World. Massachusetts, Harvard University
  Press (CD-ROM).


text:
Can you explain the behavior of this snake?
I just saw this video in which a snake is swallowing grapes.
 ("Whip snake eating grapes").
In the video, the snake just doesn't eat but goes on to swallow 2-3 grapes.
I did some research on the internet and in "bio stack exchange" but only to find that "snakes are obligate carnivores", which simply means they don't have the body mechanism to digest a vegetarian diet.
My guess is that it mistook the grapes for a prey due to the smell coming from the grapes, which may be left there by a rodent or any other organism the snake feeds on.
Can you provide a possible explanation for this snake's behavior? Regards

Hi, and welcome to the site!  Please don't just include links; they break with time.  Describe the behaviour, including pictures & figures as needful, with the link for reference.  Please [edit] so that this question would make sense even if the link were to break.  Thanks!

@rotaredom Hello, I didn't know about that. Made the changes.

Maybe that's an egg-eating snake that confused the fruits with eggs?

@Roland : Maybe, but my guess is that its something to do with the smell/odor of the grapes. Either the pray (like a small mouse) left its smell on the grapes or certain smell released by the grapes caught the attention of this snake. But I'm not sure..

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular, the title of your question should be clear and as specific as possible — the current title unhelpful since you've already provide clear evidence that yes they can. ——— We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

@tyersome Hello, thanks for the info. I made the changes to the post. I hope they are in alignment with the Biology.SE format. I also hope that the title and the content are more comprehensive to the reader.

You can convert up to 30 sec of a youtube video to a GIF file using gifs.com. If the resulting gif is > 2mb in size, then I recommend using ezgif.com to "optimize" it (e.g., cropping, reducing quality or size, etc.). In any event, it'd be best to have some stable evidence of your video on Bio.SE, which you can do by uploading the gif in the question editor. You can sill link to your original video, but inclusion of the animation on our site ensures that even if your youtube link dies, this post will still be "complete" and useful to someone in the future. Please [edit] accordingly. Thanks!

You're right, snakes rely on scent to capture their prey. The fact that snakes are carnivores may be the one constant among all snake species; absolutely none feed even partially on plant matter. So if plant matter is found in their feces, it must have gotten there accidentally.
Here, check out this post, which answers your question perfectly:

In most instances, these have been attributed to accidental ingestion, perhaps eaten with a prey item or mistaken for prey by scent...One interesting case was discovered by Harvey Lillywhite in a study published in the journal BioScience in 2008. Studying the scavenging behavior of pitvipers in the intertidal zone, Lillywhite observed cottomouth droppings that were composed almost entirely of seaweed. This was too much plant material to have been eaten secondarily or by accident, and he suspected that there was some other cause for the snakes to be eating it (it certainly wasn't for energy as the seaweed was passing through completely undigested. Lillywhite wondered if it was possible the snakes were feeding on seaweed simply because it smelled like fish. An interesting laboratory experiment proved their hypothesis correct; they offered various plants to cottonmouths, some with fish and others without. The plants without fish were investigated by the snakes, but ultimately left uneaten. Those that did contain fish were quickly devoured. Even when the fish was removed, the snakes ate the remaining seaweed simply because it smelled like their prey!

Thanks. The blog post, as well as the research (mentioned in the blog) conducted on such behaviors of snakes, answered my question very well. Thanks again.

I've seen a deer eating a live bird so a snake eating grapes doesn't surprise me.
My philosophy is that animals know better than us what they are doing, so if someone is mistaking it's probably us.
Anyway, my answer would be that this snake needs a substance (perhaps the acid since it's unrip) contained in those grapes, if it's not for feeding then it's for healing.

Welcome to Biology.SE! Please take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. In particular, answers are expected to be based on facts rather than speculations. You are also more likely to get a positive response to an answer if you include supporting references to reputable sources. Without this your answer is indistinguishable from opinion. Thank you!

an herbivore eating meat and a carnivore eating plants are very different, all herbivores can digest meat, meat is just far easier for an animal to digest.


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Relationship between membrane current and voltage in neurons
Depolarization of neurons leads currents of different magnitudes flow in or out of the cell, and the Sodium and Potassium currents can be separately plotted (Purves):

Caption: Relationship between current amplitude and membrane potential,
taken from experiments such as the one shown in Figure 3.2. Whereas the late outward
current increases steeply with increasing depolarization, the early inward current
first increases in magnitude, but then decreases and reverses to outward current
at about +55 mV (the sodium equilibrium potential). (After Hodgkin et al.,
1952.)
Here we see the dependency of the currents (early: Sodium, late: Potassium) on membrane potential.
What I was wondering was this: It looks like the dependency of the Sodium current on the membrane potential is very non-linear.
However, experiments which assess the amplitude of injected current on excitatory postsynaptic potentials (EPSP) state that the amplitude of EPSPs are proportional to the injected current. How is this consistent with the non-linear current/permeability changes of Sodium? Is the Sodium current linearly dependent on voltage (and vice versa) before the action potential threshold is reached?

I don't have Purves in front of me, can you add the caption there? And careful with the axes: the x-axis is voltage, not time, so saying "a dependency on time would have the "early" function shifted to the left" does not make sense.

I have added the caption. Yes exactly, here the x-axis is voltage. If it would be time, as the name says, the early function would be left-shifted wrt to the late function. I removed that comment now though.

This is a bit of a strange way to plot out these data, I think Figure 3.2 is easier to understand, but basically these are data plotted from early voltage-clamp experiments trying to walk you through how the Hodgkin-Huxley model was developed.
They step the voltage to a particular point and look at the current. There are two phases to this current: an early transient and a later plateau.

The shape of the "early" component ultimately results from the multiplication of two functions: the gating curve of the voltage-gated sodium channels and the reversal potential for sodium around 50 mV. If the voltage gated channels were simply open all the time, you would just have a straight line through +50mV, it would follow the right-side shape of the curve. The left-side of the curve is due to more channels opening as you depolarize more.
For the late component, which comes from voltage-gated potassium channels, all of the dependence is on voltage, because the plateau is at a point where all the potassium channels are open. You will also notice, however, that the slope changes a bit in time: it's steeper at the higher voltages, because the potassium channels open more quickly (and also sodium channels inactivate; the combination of the two would make it hard to separate them here).
Your picture is a bit different from these traces plotted in time: figure 3.3 is showing the peak of each component as a function of the voltage step. I think it would be better to present 3.3 as a series of data points rather than a smooth curve to make this more obvious.
Note that the actual numbers here are a bit different than one would see in a mammalian cell, because these original experiments used the squid giant axon which has some differences in voltage dependence, gating, and ion concentrations.
The reason sodium and potassium can be seen separately in these voltage clamp experiments is because:
A) Sodium channels open really fast early on, and then inactivate
B) Therefore, in the long term the potassium current dominates the sodium current.
If you blocked the potassium current and VG sodium channels didn't inactivate, the "early" part would look like a mirror image of the "late" part of the voltage-clamp traces. As-is, the early component is mostly sodium but also includes some voltage-gated potassium current as well that cancels it out and makes it appear smaller than it would otherwise be.
If you look at the late curve in your original figure, it's mostly straight from the point that all the K channels are open. For the late component, the K permeability is at max by -30mV so after that it's all linear from driving force. The little curve at the bottom up to about -30mV is the range at which not all the K channels are open, otherwise it would be a completely straight line, and it would reverse at the K reversal potential instead of asymptoting around zero. But it's not exactly zero because there is also some leak which is mostly potassium, and that does reverse around the K reversal.

Many thanks for the answer - I think I understand these points, also that in my plot we have max(current) for each point on the x-axis (mV). But my question is this: (1) If I understand correctly, the non-linearity of Na+ follows from the non-linear permeability changes and the time-dependent inactivation of Na+, correct? (2) Does this then also mean that K+ permeability is constant over mV (hence the somewhat linear function in the plot I have used)? But in particular: (3) If Na+ permeability changes are non-linear, how can EPSPs be a linear function of injected current amplitude?

@Pugl I don't follow what you are asking about EPSPs and injected current. EPSPs are caused by activating ligand-gated ion channels. In that case, the amplitude corresponds to how many ligand-gated channels are bound and opened (aka, the permeability). If you open enough of them to also open voltage-gated sodium channels, then you get a nonlinear response, including possibly an action potential if the EPSP is large enough to reach threshold. One could also inject current to mimic an EPSP, and you'd have the same result. However these experiments are in voltage clamp, not IC.

@Pugl I'd also add that the difference between sodium and potassium here is largely because sodium channels inactivate and because the potassium current dominates the sodium current at a long time. If you blocked the potassium current and VG sodium channels didn't inactivate, the "early" part would look like a mirror image of the "late" part of the voltage-clamp traces. As-is, the early component is mostly sodium but also includes some voltage-gated potassium current as well that cancels it out.

Ok that is important to understand, thanks for the addition: Hence the non-linear part in the functions is time-dependent inactivation of Na+ channels. The only thing that still confuses me is this: I often read that higher mV also means more K+ channels are open (and not only that they open more quickly). Would this in contrast not mean that the mv/mA plot would be non-linear (as permeability is the proportionality constant in Ohm's law, and we would have different slopes for different mV)?

(2/2) ...or, I guess the linearity is a result of the permeability x driving force interaction?

@Pugl Both inactivation and activation, yes. If you look at the late curve in your original figure, it's mostly straight from the point that all the K channels are open. The little curve at the bottom up to about -30mV is the range at which not all the K channels are open, otherwise it would be a completely straight line, and it would reverse at the K reversal potential instead of asymptoting around zero. But it's not exactly zero because there is also some leak which is mostly potassium, and that does reverse around the K reversal.

Yes permeability x driving force. For the late component, the K permeability is at max by -30mV so after that it's all linear from driving force.


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What is the DNA sequences between two Inverted Repeats called?
I would like to know some rules about the nomenclature of Inverted Repeats DNA sequences. More in detail, I want to know what is the name of sequences between two inverted repeats.
For example, I have two genes A and B in this order: A, B, -A. The gene A is inverted duplicated and forms an inverted repeat with gene B in the middle. What do I call this gene B?
Here below are some names I found or that I thought, however, I don't consider them a good choice. Could you suggest some other names?
"intervening sequence", "in-between", "inserted", "separating", "spacer", "non-palindromic spacer", "loop", "gap".
In Wikipedia, they used the name "intervening sequence".
https://en.wikipedia.org/wiki/Inverted_repeat

Welecome to SE Biology. Come si chiama, como se llama, Wie heißt, comment s'appelle. But in English is is What, not How.

There is no "rule" or even convention, as you found from Wikipedia. Such sequences are not sufficiently important (and have no general function) to have been given a name. Intervening sequence is a description, but as it is the long form of intron, I wouldn't use it. For suggestions on how to describe it (there are problems with all of yours), SE English Language & Usage would seem more appropriate. However you will need to give an example sentence there, which should relate to the specific circumstances.

To add to David's points, "inverted repeats" typically described very short sequences. Even so-called "long inverted repeats" are just tens of bp long. Since you have designated sequences A and B to be genes, it would be better to described your system as "gene B flanked by inverted copies of gene A", or something like that.

Thank you David and acvill, both comments were very useful. Yes, unfortunately, I have some long Inverted repeats with many genes and kilobases long which are not common and not well described (named).
I want to name them to describe a property that I think these sequences might have. I think I will use the term "internal sequences" or "sequences flanked by internal repeats" as acvill suggested.

I'll add that most green-plant chloroplast genomes contain a large inverted repeat (~10-76 kb). The chloroplast genome is circular, and the two intervening regions are creatively named the Large Single Copy and the Small Single Copy.


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Endosymbiosis Probability
What is the probability of endosymbiosis occurring? I remember seeing it in my AP Biology textbook but haven't been able to find it anywhere after forgetting it. I want to say I remember it being something like 1e-40 but can't say for sure. Also, I'm not a biology student so I'm not sure if endosymbiosis is the proper term for it but I think what I'm referring to is the successful absorption of a prokaryote by an organism to become a eukaryotic organism with mitochondrion.

According to endosymbiotic theory, the probability on Earth is 1. It's not really meaningful or useful to estimate probabilities of one seemingly unlikely thing that you have evidence has occurred. What do you hope to do with this probability?

You are going to want to look up endosymbiosis and algae for lots of examples of the spectrum of endosymbiosis .

I’m voting to close this question because it is unclear (or unanswerable due to not making sense), and lacks the expected level of prior research. Please note these are both sufficient reasons for downvoting and closure. Please [edit] your question and tell us: what your question is, 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.


text:
Species identification: what kind of fungus is this?
Found in a cave
Location: Israel
The white tentacles appear to be sticky. When they touch something, they stick to it and detach from the main body

Welcome to Biology.SE! Please [edit] your post to include the size of these structures, where they were located in the cave (e.g. on the walls near the entrance), and why you concluded they were fungi. ——— If possible clear, closeup photos of the structures from multiple angles would also be helpful. Thanks!

I think these are parasitized insects.
Fungi of various types can infect insects.  The end stage produces these fruiting bodies.  Here is an example I found on the excellent site WhatsThatBug.

Here is another example.

http://www.anura.it/the-parasites-parasite-everyone-has-a-bad-day/clasp04/
The second site notes

Entomopathogenic fungus (Clavicipitaceae sp.) killed a troglophile
  moth, Veins cave (Grotta delle Vene), Italy

I would guess something similar for what you found.
I must say your images are incredible.  The long fungal tendrils on the second image are the most amazing example of this I have ever seen.


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Mutations, Death and the theory of Evolution
Evolution always made sense to me and I still find it to be true. However, I quite recently found a comment online that gave me some doubts and made me curious on the subject. Although a student of biology, I don't really know genetics all that much (I'm more of an ecology type), so I'm asking here - I hope there's somebody who can help. Without further ado, how would you respond to this comment (fyi the original post was on the subject of a woman denying evolution, then talking about her new short-eared dog breed):
"The woman was probably demonstrating that changes that we see in dogs (variation within one kind) is NOT Evolution because it cannot create new genetic info (so it cannot explain the origin of organs). It causes CHANGE with what is already there, and these changes are only NEGATIVE or NEUTRAL (but often negative, that's why our dogs are degenerate from wolves). I used to make a living out of Selective Breeding so I know that you can only change a fish's color and size but you can never add feathers or wings or limbs to it since the codes for those doesn't exist in a fish, nor can we create one just by random mutation. That's like trying to create Windows10 OS by relying on random bit-rot/data corruption -- death of program is ensured. The word "engineering" in Genetic Engineering isn't there for no reason. Coding genetic programs requires more intellect than coding binaries. Literally, we're all digital programs (but very intelligently coded). Welcome to modern science.
Having said that, you do realize that the reason why you grow old is because of mutations, right? I will be neutral here (neither Evolutionist nor Creationist) but let's be realistic. If mutations can improve us, why do we grow old and die from it even though our body undergoes "selection" too? And you do know that our genome as a population is also getting older, right? Let's math this out: Let's say you're Adam with no mutations yet. Your offspring will inherit an average of 50 mutations from you (you generated this mutations as you grow old). Let's say that we die when reaching 10,000 mutations (Natural Selection). Your offspring started his life on earth a little bit older than you. And he shall add your 50 mutation, plus his own 50 mutation to his offspring. The 3rd generation will now start his life with 100 mutations. Some may mutate faster, but since ALL organism mutates and pass it down, it's easy to see where all of us will end up. Think of your last PC. :)"

Welcome to Biology.SE. I read only the first paragraph which can be summarized into "Consider the following claim:". I am too lazy to read what follows. You should try to drastically shorten your post if you want the attention of people who can answer. Also, I am sure you can make a title that at least specify a little bit the subfield within the field of evolutionary biology.

Also if you have a quotation, please indicate the link and use the quote format (start the line with >)

I've changed your title to demonstrate that the length of your question does not preclude a short indicative title. You should do this yourself next time — it's an important part of the analytical process.

This question rambles a lot, has lots of misconceptions, and I don't see what exactly it is that is being asked. VTC.

@MarchHo What does VTC stand for? non-native english speaker here : )

@Remi.b Vote to close, I would guess.

It's very sad to see an "ecology" fellow that knows so little biology to ask such a question.

"The woman was probably demonstrating that changes that we see in dogs (variation within one kind) is NOT Evolution because it cannot create new genetic info (so it cannot explain the origin of organs)." ...  Simple answer, the woman is an idiot.

@Eli Korvigo Not everyone had the luck to be born in a country where evolution isn't taught for only one day in primary school and high school, where teaching evolution isn't almost a taboo and where you're not ridiculed by the general public if you accept evolution as true, while religious education is mandatory in both primary and highschool. I live with people who think that rain and thunder are the sign of God (whatever your stance on his existence might be, you understand how ridiculous that argument is).

Introduction
Welcome to Biology.SE. Please see my comment for issues relating the form of your question. Below my answers are very short as it would take too long to give complete answer. I just redirect you toward a source of information.
Questions

Having said that, you do realize that the reason why you grow old is because of mutations, right?

No, that's wrong!

I will be neutral here (neither Evolutionist nor Creationist) but let's be realistic. If mutations can improve us, why do we grow old and die from it even though our body undergoes "selection" too?

Nope, our body does not undergo "selection". (At least not in any way you may have meant it!)

And you do know that our genome as a population is also getting older, right?

No, that's wrong!

Let's math this out: Let's say you're Adam with no mutations yet.

There was no such thing as a first human and no perfect human free of any deleterious mutations. Adam and Eve are characters from the christian mythology (kind like the equivalent of the first unnamed man Epimetheus and Prometheus created and Pandora (first woman) that Zeus created to punish men).

Your offspring will inherit an average of 50 mutations from you (you generated this mutations as you grow old).

Good job, this is a relatively realistic number (although a bit too high) of new mutations a human baby inherits. Note that these new mutations occur in the ovaries and in the testis either during mitosis or during the meiosis (mutation rate is much higher during meiosis).

Let's say that we die when reaching 10,000 mutations (Natural Selection). Your offspring started his life on earth a little bit older than you. And he shall add your 50 mutation, plus his own 50 mutation to his offspring. The 3rd generation will now start his life with 100 mutations. Some may mutate faster, but since ALL organism mutates and pass it down, it's easy to see where all of us will end up. Think of your last PC. :)"

Most mutations are neutral. Those that are deleterious are (most often) washed out by selection and therefore do not accumulate in the way you describe.
Source of information
I cannot provide complete answers as it would unfortunately be too much for a single post. Instead I redirect you to an online source of information.
There are great (free) online courses. Consider for example having a look at Understanding Evolution (by UC Berkeley). It is a very introductory source of information on evolutionary biology. It is quite short and you will quickly learn a lot!

In addition, the "change" argument of OP could be addressed by Glassford et al. 2015 http://www.ncbi.nlm.nih.gov/pubmed/26343453 and the "engineering" for circuits by the existence and results of a full research field (dedicated to evolvable hardware)

I like that you gave the OP a heads up with the "Good job". However, the approx. 50 mutations in a newborn are not really introduced in the aging process of the parents, but rather emerge due to error prone DNA replication. The actual number of mutations might be higher in case of older parents (increasing replication error with age), but that is not what the OP is suggesting.

Yes, you are right. I added a small comment. I did not want to go too technical. I had to use the terms mitosis and meiosis that the OP likely don't know though. Feel free to edit if you can avoid that the OP misunderstand the answer while remaining short. Thanks

Interesting, but growing old and mutation has nothing to do I guess. it's a common sense. but the starting arguments are quite convincing. What do evolutionists says to the argument that 'genetic engineering' can only turn switch on or off the current DNA and cannot make something new? This 'genetic engineering' is a form of what natural selection can do the creatures I guess.

Thank you a lot for answering! The part of the post in quotation marks was not actually mine, I just saw that comment on a site and wanted someone with better knowledge than I have to explain what might be wrong with it. I decided to copy-paste it because I thought I might leave out something important otherwise.
Also, please forgive my lack of knowledge, when my teachers got to the subject of evolution they (I guess?) were required to keep it very neutral while teaching, supporting neither side. I hope to learn more in uni now :)

You don't have to apologize for your lack of knowledge :) I understand how religious extremism (probably christian extremism given your reference to Adam and Eve) can try to restrict access to knowledge when the reality does not match their preconception. I hope you won't take any downvote and close vote as an offense. It was quite impossible to answer such question but you did well to ask and you are very welcome to come to this site to keep learning. If you come back for evolutionary biology, then I would recommend first having a look at Understanding Evolution (or other online resource).


text:
What is the scientific name of this evergreen plant?
This plant is found in India. It is an evergreen plant. Would love to know the scientific name.

In which country did you make this images?

@Chris India - it says at the top ;) ... where in India might be useful too though, it's a big country

@rg255 You're right and  I should get another coffee :-)

If you could say which part of India you found the plant in, that would be helpful. I would guess that it is a conifer, but not a pine because the needles to not seem to be clustered into fascicles.

The tree in question belongs to the Araucariaceae family,
There are multiple species of Genus Araucaria,
I'd place Araucaria araucana on the first place, but there are multiple others:
Araucaria araucana

Araucaria luxurians

Araucaria columnaris

Araucaria subulata

Just FTR, the tree in question is not A. auraucana (Molina) K. Koch. A quick image search will show you that A. auracana has much larger, robust leaves.


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How to determine the direction of regulation of a gene by comparing gene expressions?
I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease.
I am confused about how people can determine whether a gene is down-regulated or up-regulated by its gene expression.
Assume we have a few samples of a gene: some of the samples are normal patients samples and rest of them are disease-infected samples. Do we determine the direction of regulation of a gene by the ratio of gene expression of normal/disease-infected samples?
For example, if the ratio of expressions is a negative value, do we say that the gene is a down-regulated gene, otherwise, it is a up-regulated gene ?

If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated.
Gene expression values are usually measured genome-wide and then normalized before computing the ratios. So you rarely deal with individual raw expression values.


text:
Are there fishes with a double circulatory system?
Our courseware materials say there are such fishes, but my Internet searches suggests fishes only have a single circulatory system.

Can you please put a little more effort into your question?

It seems that lungfish display the beginnings of a double circulatory system:


text:
What kinds of light attract moths best?
On average, do we know what kind of lights attract moths best?
LED, filament bulb, candle...?
And what about colour? Does that matter?


text:
What is the nesting period of the European Turtle Dove in middle to southern Italy?
While the breeding period to the north, in Switzerland, seems to be early May until early July, and I have not found any information for the Naples area.
Also, are they likely to nest a second time?

Yes they are likely to breed a second time, and sometimes three times. It mostly depends on the complex graph of nourishment that they can come by to breed up to three times in a year.
They have higher chances of breeding 2-3 times in Naples than in Switzerland according to this document: http://www.birds.kz/v2taxon.php?l=en&s=289
The mean first egg date is May the 18th in the UK, and if you compare the average temperature for London and Naples at that time, spring is about 30 days earlier in Naples, and the birds can migrate there from Africa first, so the mean first egg date in Naples is between the 18th of April and 18th May. They probably start nesting very soon after they arrive.
It depends how good the harvests are and how disruptive the industrial farming is on their migratory path that year, while the nesting time was measured for may in the UK one year, a satellite tracking of a turtle dove placed it's arrival in the UK in June another year.
The result is an erratic timing from April to June in Italy.
http://www.avibirds.com/migration/Turtle-Dove.jpg

That Kazakhstan link is interesting because it shows they CAN breed multiple times, but of course it doesn't tell us if it happens in Italy. The climate differs to much between those.

And secondly, bird migration doesn't have to work like that. That the temperature is 30 days earlier in Naples, doesn't mean they arrive there 30 days earlier. They might all start together. Flying from Italy to the UK takes only a day or perhaps a few.

Italy's springtime and fall are 2-3 months longer and more verdant than the UK's I expect they can breed 2 times at least there on a good year.

Oh, I expect they can, but that doesn't mean they DO. Streptopelia decaocto, a close relative, breeds 6 times or more and even in winter in Holland and the UK.

I was reading references that say " The most important ultimate
factor affecting on the timing of the breeding season of most
birds is the food supply, either for the laying female, or for
feeding the young" so I'm just saying that winter dormancy is much earlier and later southern Europe, because I used to check birds eggs in the woods in mid May, which is a lot colder and stiller than italy and france are in mid April. one month earlier, like april 18th, is a very coherent assumption, and more than one brood is a very likely possibility.

I think it would be difficult to answer except people living around or visiting frequently the Naples region as the bird distribution covers the whole central Europe during summer time.
Then my answer will focus more on the italian part.
One interesting reading would be this document from the European Commission.
Disclaimer: this document refers to biological aspects of the turtle dove, but the main topic is the pressure of the hunt on that bird.
In page 10 they mention that:

Stable populations are found in central Europe: Italy, Austria, The Czech Republic and Slovenia (BirdLife International 2004a).

Page 14 table shows the period of migration and breeding countries (EU 25 only).
And in page 17, they shows that probably between 200'000 to 400'000 breedings pairs are present in the whole Italy (Estimation by Birdlife International)
Here are some refrences:

Breeding and distribution at IUCN
Distribution at avibase

As you can see the distribution os quite large and the figures of estimated breeding pairs very large.
You can also check the observations (not only breeding) with that avibase link.
For the probability to nest the same place, I would say it's possible as in general the birds can go to the same place as the previous year but I cannot say more if the European Turtle Dove have a different behaviour or not. If they have a quiet place where there are no disturbance (Hunting, human activities) or predators, they would probably come back to the same place.

Although you have gathered a lot of info, you have not answered the question: what is the breeding period in Italy and do they nest more than once (in a single year).


text:
Can you identify this bird?
Can somebody please identify this bird for me?
I spotted this in July 2012 while birding in Ranganthittu Bird Sanctuary.

A snowy egret that got "into" some fermented canteloupe, then slept it off.

This is a Cattle Egret (Bubulcus ibis), which is a heron in its breeding plumage. When not breeding, the bird is white. See the images for comparision:

Breeding cattle egret with colored feathers.

Nonbreeding cattle egret, completely white.

Just an addition, this is the bird's breeding plumage. Non-breeding individuals are just white.

Good point, I added it to the answer.


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Trying To Identify this Fish

My 4 year old fell in love with this fish at the aquarium.
I'm trying to find out what species it is so we can learn more about it.

Welcome to Bio.SE. Please can u add the location and size of the fish. A clearer image would be appreciated.

You can also go to the aquarium's website (if it was commercial) and look up their fish.

It looks like a unicornfish (genus Naso), maybe Naso vlamingii, the Bignose Unicornfish. They're Acanthurids, related to surgeonfishes and tangs.
These are mainly found in Indo-Pacific ocean around the depth of 50 mts from surface. Coral reefs are their main habitat and destruction of coral reefs is their current biggest threat alongside trading by fisheries. A good source of information for this species is available here.
A copy of this fish.

Picture credits: UM Rosenstiel School

Yes, this is the right fish! There were other unicorn fish in the tank that actually had the "horn." I didn't realize there were other variations. Thank you so much!


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Spider identification Delaware
It looks like a wolf spider, but I've not seen these exact markings.

It could help if you gave indications of the size and environment.

That's a nice female Dolomedes tenebrosus - the upland Fishing Spider that lives in similar habitat to Wolf Spiders, and eats the same sort of foods.
The way it holds its long, stripey legs together (the front pair, anyway) is pretty standard for the Pisauridae, and the pattern on the body (while a bit variable in this species) is pretty distinctive.
https://bugguide.net/node/view/2011


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How straightforward is in vitro compartmentalization?
in vitro compartmentalization (IVC) is one of those technologies that everyone knows about, talks about, but never actual does due to the rather technical difficulties in setting the system up. I was wonder if anyone not named Tawfik, Griffiths or someone who did a post-doc with them have been successful in making IVC work? Details in how stable emulsions and a homogeneous mixture of cell-free components in the droplet are made would be wonderful.

one of those technologies that everyone knows about. Everyone but me! Nice link, always good to learn something new.

You might want to look up synthesis techniques  artificial cells, like artificial red blood cells.  A resource that has led me to believe this stuff isn't impossible to set up is at www.artcell.mcgill.ca

@ThomasIngalls, while certainly neat, the dimensions of artificial cells are completely different from the dimensions of IVC which prevents the concepts learned in this body of work from being translated to smaller emulsions. This will still be interesting reading material.

Thanks for pointing that out, it'll save me some reading, too.  Sequencing technologies like 454, SOLiD, IonTorrent use emulsion PCR on a large scale.  The SOLiD system even has an sample prep machine that automates the creation of these emulsions.  I think these emulsions end up a bit smaller, but they're at least in the right ballpark.

@ThomasIngalls i think you should expand into an answer, eh?

It is actually surprisingly easy and reproducible to make emulsions with defined components. We do it routinely in our lab:
http://www.sciencemag.org/content/332/6026/209.full - CBT protocols
http://www.sciencemag.org/content/336/6079/341.full - CST protocols

Thanks! Since it has been awhile since I've asked this question, I now get the impression that certain reactions like transcription and smPCR work well. When concentrations and size become more important or translation is important things go south.


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Comparing angles between population vectors of neural activity
I am reading this paper on fear conditioning, where the following is given:

The n-dimensional population vector (activity of n neurons) evoked by the conditioned stimulus (CS+, auditory tone) before conditioning
The n-dimensional population vector (activity of n neurons) for the CS+ after conditioning

The authors write that: "[After conditioning] the CS+ population vector rotated out of the plane defined by the US [unconditioned stimulus] and the initial CS+". They conclude that this out-of-plane rotation corresponds to "new learning".
My question: Why is out-of-plane-rotation of neural activity vectors equated with a new representation/new learning?

They are not writing about "after conditioning" as you write, but, importantly, after extinction.
What they observe is that, during learning, the response to the conditioned stimulus (CS+) becomes more similar to the response to the US. In the n-dimensional space in which a population response lives, you can describe this as the population vector evoked by CS+ pointing closer to same direction as the population vector from the US.
We expect that during extinction, the CS+ vector will become different from the US compared to at the peak of conditioning. There are two general possibilities for how that could happen. The first possibility (perhaps the simplest one to expect) is that with extinction the CS+ vector returns to where it was initially, before the conditioned stimulus was paired with the US. You could describe this as merely forgetting what has been learned: responses to the US and CS go back to how they were before conditioning and it's as if nothing was ever learned.
However, that's not what these authors observe:

During within-session extinction, the CS+ representation did not revert and gained no more similarity to its initial representation before learning

Although they do observe that with extinction the CS+ vector moves away from the US, it doesn't move back towards the old response, it points in a new direction that is further both from the US response and from the original CS response. That can be described as an "out of plane" rotation, not towards either of the other vectors.
In case it's hard to think about these things in N-dimensional space, we can think of a more familiar situation in our own 3-dimensional world.
Let's say the US causes a response corresponding to "12 o'clock". The conditioned stimulus causes a response corresponding to "3 o'clock" before any training. As you do some conditioning training, pairing the US and CS, the CS response moves towards "1 o'clock", beginning to resemble the US response. During extinction, we might expect the CS response to move back towards "3 o'clock", maybe we'll find it at "2 o'clock". This would represent rotation in the "plane of the CS and US" made by the clock. Instead, the hand points out away from the wall, so it is further from both the original US at 12 and original CS at 3. That's the "new learning".

Thanks for the fast response! Right - extinction in particular. I think my point is a bit deeper: I understand that extinction is considered new learning, and hence the representation of the CS+ should not convert to its original form. I still don't see, however, why out-of-plane-rotation is "new learning". My understanding would be that previously inactive neurons would display activity now, as you describe the rotation would be into a new plane not defined by the original orthonormal vectors. Right? This seems to me a mathematical property, however, and very removed from behavioral learning?

..2/2 like, how do we know this mathematical out-of-plane-rotation is in any way physiologically meaningfull? What is the typical argument made for such an interpretation?

@Pugl Maybe you're thinking about it too deeply. It's just a geometric interpretation for the extincted CS+ response not returning to the original CS+ response. "New learning" just means that the CS, post-extinction, produces a response that is similar neither to the US nor to the original CS. That's it. It's evidence against a hypothesis that extinction means the response returns to how it was originally before learning.

@Pugl Another way to say it (sorry if I'm getting exhaustive) is that during learning of the CS-US association, the population response stays in the plane of the clock. It moves really just in one dimension defined by the plane of the initial CS and US responses, like the minute hand on a clock. Extinction moves the response in a different direction to that plane, into new territory not observed during the initial learning process.

Not at all. I appreciate all input. I actually would like to understand that better: Previously, they described in-plane rotation based on newly active cells. How is cell activity different between in-plane and out-of-plane rotations?

@Pugl Not sure what you mean by "they described in-plane rotation based on newly active cells". Might be worth another question. Also important that you have some grasp on what these vectors and planes are. Easiest to think about is with just 3 neurons, the population vector would be given by the activity of those three neurons on the X, Y, and Z dimensions. So if only X is active, you'd have a vector right along the X-axis. If only X and Y are active, you'd have vector pointing somewhere along the XY plane, but with no magnitude in the Z direction. Etc.


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What are "inactive" cells during Ca2+ imaging of neurons?
I am reading this paper, and have found the following Figure (Extended Data Figure 5) where they show maps of active cells in the amygdala as imaged with a miniscope and GCaMP6m:

Legend:

Using the spatial filters provided for each neuron by the automated
cell sorting algorithm7,44, maps of all active cells detected in the
BLA on each day of the study were made. Standard methods of image
alignment43 were used to register these maps across the different
days. Approximately 50% of all neurons observed across the entire
experiment were detected as active on individual days. a, Example maps
of active BLA cells from three mice on the first (left), third
(middle), and last (right) day of the 6-day experimental protocol
(Fig. 1c). Circles indicate cells that were active in only one of the
three recordings (grey), on two of the three days (blue), or on all
three days (red). Scale bars, 30 μm. The maximum number of active
cells seen in one session was 192

As can be seen not all cells are active every day.
My questions:

What are "inactive" cells? I am asking as I assume that cells always do have some baseline spontaneous activity which could be recorded with Ca2 imaging. I guess my confusion is that if we define cells as inactive which only have baseline activity, I wonder how we quantify "spontaneous" activity where an animal is for instance just exploring the environment without an experimental stimulus being present (periods of time which would be used typically to determine baseline activity)?

Are "inactive" cells not visible at all during Ca2 imaging (is it not possible to even see the cell's morphology/shape when there is no GcaMP signal)?

They mention how they define active cells on the first page: "P≤0.01, evoked signals
versus baseline, rank-sum test". Then from the Methods (section "Identification of neuronal sub-classes"): "To compute the
baseline activity level of each cell, we averaged its fluorescence signal over the
complete imaging session excluding all stimulus presentations". Inactive cells are those that did not pass this test.

@vkehayas Thank you! I think that these would be the stimulus irresponsive cells (Ext Data Fig 2). I just read one of their older papers, and inactive is described as "inactive: no detection of a transient within the recording session". This to me seems stricter than the P<=0.01 threshold - in particular also because even when failing the P<=0.01 threshold the cell might be above baseline and hence still detectable (and not invisible as shown above). Also, how they could distinguish spontaneous activity from baseline (spontaneous activity being e.g. exploring the environment)?


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Would this disprove the theory of evolution?
I did my philosophical homework today in which I answered the question of whether evolution could be disproved.
I basically argued that one way it could be disproved was if one could prove that humans are somehow "perfect" (see below for definition) and for which the probability of evolving by natural selection was 0. This would mean that evolution could not explain the existence of humans in nature, and so natural selection would be disproved. While this is philosophical, the reason I posted it on here is because I am not a biologist, and am rather interested in what biologists would make of this idea, and whether it is just complete nonsense (which, not being a biologist, I do not deny).
My definition of "perfect" was that it would have to be mathematically proved perfection. It would be no good to just say humans can do mathematics while other animals can't, therefore humans are perfect. This is too vague. So I defined something as being "perfect" if it was proved mathematically as being perfect. I defined this as being done by a new "mathematics of consciousness" which would then be applied to different animals, and only humans would come out as being perfect according to this (as yet undiscovered) mathematical theory. And then one would have to show that the probability of this occurring via natural selection was 0.
Edit: a more precise example explaining how evolution could be disproved (to avoid ambiguity):

Describe consciousness mathematically
Show that, for humans, this shows up as something similar to the Riemann Hypothesis, where all the zeros lie on one line.
Show that this cannot occur via natural selection, either due to the infinite amount of time needed, or because of corruptive influences in nature, etc. The point is that the probability would be 0.
This would imply that natural selection is inadequate for explaining humans.

This proposal doesn't really make any sense scientifically especially because you are starting from a premise that doesn't make any scientific sense: "mathemetically proven perfection"

@BryanKrause: Thank you for your response. Could you please elaborate what is wrong with there being developed a mathematics of consciousness, which somehow shows that humans are "perfect"? As I said, I am not using "perfect" vaguely, but rather in the sense that when this mathematics is applied to humans, it would show that the probability of this occurring via natural selection was 0. This could be something like showing that all their "zeros" (which would have a definite meaning in this new mathematics) lied on the same line kind of like in the Riemann Hypothesis for example.

@Raghib: This fails because 1) There is no universal definition of "perfect"; 2) Why should consciousness be an aspect of your ill-defined perfection.  Tardigrades and cockroaches are superior to humans in many respects, and are probably not conscious; 3) The fact that humans are imperfect is practically demonstrated by the vertebrae of my lower back, among many other things.

I'm voting to close this question as off-topic because it is not a question about Biology in terms of SE. This is a clear discussion question about, as the poster admits, philosophy. That falls clearly into the sort of questions one should avoid asking.

I agree that it's off-topic.  Still, I'm a bit curious to know which individual human might be considered perfect, since no two of us are identical.

Humans are far from perfect by any definition, the human body and mind are full of recognizable flaws, everything from poorly designed eyes, anuses, and backs to minds that see faces and minds where they don't exist.

Your revised question contains a fundamental paradox.  If your #3 is true, then #4 follows, but the logical consequence of that is that consciousness can't exist.  That is, either humans became conscious through natural processes, or they were created by some entity that supplied consciousness.  But that entity must have attained consciousness through some natural processes, which by #3 can't happen.

What do you mean by "Darwinian evolution"?
The theory of evolution (aka. modern evolutionary synthesis) is much more than what Darwin said in his books. Calling it "Darwinian evolution" is misleading (and is very rarely used in the scientific literature).
What is the theory of evolution?
The theory of evolution represents a large set of tested hypotheses. It does not mean much to disprove the theory of evolution, as much as it would mean something to disprove specific elements of this theory.
Would "showing that humans are perfect" disprove an element of this theory?
I don't really understand the hypothesis that you are willing to be testing. It is unclear how you define "perfect" and what you mean by "mathematics of consciousness". All these concepts are very undefined. If they are clear to you, please define them and please suggest a clear experimental set up and we could talk about it. You also seem to phrase your hypothesis upon an explicitly undefined mathematical tool (according to this (as yet undiscovered) mathematical theory). That makes your hypothesis very unclear.
In any case, stating that it would be the only way to "disprove the theory of evolution" would be extremely wrong.
How to disprove specific elements of the theory of evolution?
There are millions of ways to disprove elements of the theory of evolution! There are maybe ten thousands (maybe more, maybe less, I don't know) papers published every year in the field of evolutionary biology. Many of them, to some extend, are opportunities to test falsifiable hypotheses about the modern evolution synthesis. For examples

show that a beneficial mutation that sweeps to high frequency does not reduce polymorphism and heterozygosity at linked sites.
show that new living organisms are being created spontaneously
show that fossil age estimates through carbon 14 and other methods do not match estimates with molecular clock.
show that mutations don't happen.
show that any functional (such as beneficial mutations) or structural (such as gene duplications) subcategory of mutations do not happen.
show that the probability of fixation (fixation = reaching a frequency of 1 in the population) of a mutation associated with a given selection coefficient does not depend upon the effective population size.
show that a lineage cannot evolve reproductive isolation
show that there is no genetic variance in populations
show that coalescence times don't differ among independently segregating sequences.
show that allele frequency do not change in experimental evolution experiments
show that population selection does not work in experimental evolution experiments
show that fitness heritability is zero
etc...

Your essay
It is funny that such question is being asked to you in a philosophy class. One can only suggest falsifiable hypotheses if (s)he understand the underlying set of claims to be challenged. I understand that the purpose of the essay is likely to get you more familiar with the concepts of falsifiability but the students might miss the science skills required to investigate the question on a given specific scientific theory. I suppose that if you were asked the same question about the theory of strings, you might realize better that it does not take a philosopher to produce such hypotheses but a physicist. At the end of the day, addressing the question in this essay would require you to learn a bit more about evolutionary biology.
About your edit

Edit: a more precise example explaining how evolution could be disproved (to avoid ambiguity):

Describe consciousness mathematically

This remains to be done. One cannot ask whether a test makes sense without defining the concepts being tested. It is like asking I would like to test if schmilblik equals 3. First, we'll need to define schmilblik. Would this disprove Newton's theory of gravitation?. One cannot tell whether it would disprove Newton's theory of gravitation without knowing what the schmilblik is! Whether it disproves anything depends upon the definition of schmilblik.

Show that, for humans, this shows up as something similar to the Riemann Hypothesis, where all the zeros lie on one line.

I am not really familiar with Riemann Hypothesis so I don't really understand what you mean here, sorry. Also, I am not sure what zero would mean on your scale of consciousness!

Show that this cannot occur via natural selection, either due to the infinite amount of time needed, or because of corruptive influences in nature, etc. The point is that the probability would be 0.

I am not sure what "this" is in your sentence because I did not understand what you meant above.

This would imply that natural selection is inadequate for explaining humans.

If A is impossible when B is true, then if you observe A, you can indeed conclude that B is false. I would happily agree with this logic. It remains to define what A and B are.

Thank you for your response. I edited the question to give an example of how "perfection" could be proved. Is it better now? Obviously, not being a biologist or even a scientist, I don't think I can give a precise experimental setup, but I don't see why the example I gave is not feasible. I have indeed read articles about "mathematics of consciousness" being at least a possibility within science. Edit: Also, I removed my claim that it would be the "only way" of disproving evolution, as well as "Darwinian".

@Raghib See my edit in response to your edit!

Even if all conditions required for point 4 were met, this would not disprove evolution (which could still apply to animals... or even mathematical functions themselves ...)

I basically argued that the only way it could be disproved was if one could prove that humans are somehow "perfect" (see below for definition) and for which the probability of evolving by natural selection was 0. This would mean that evolution could not explain the existence of humans in nature, and so natural selection would be disproved. While this is philosophical, the reason I posted it on here is because I am not a biologist, and am rather interested in what biologists would make of this idea, and whether it is just complete nonsense (which, not being a biologist, I do not deny)... My definition of "perfect" was that it would have to be mathematically proved perfection.

What you seem to be doing is asking us if a hypothetical, objective measurement of perfection was discovered and applied to humans, and whether or not Evolution would be "disproved" (obsolete as a Theory) by proving humans to be perfect.
If that's your premise; then no, proving human beings to be perfect does not disprove Evolution. Evolution is a process, a mechanism by which nature operates. That a perfect example exists of a thing does not invalidate the process by which it was made.

I also mentioned that the probability of this occuring naturally would be shown to be 0. I do not see how natural selection could still be true in that case, since it would clearly show that natural selection was inadequate for explaining humans.

@Raghib - So your suggestion appears to be that if humans were proven to be supernatural (or unnaturally perfect), then Evolution wouldn't apply to humans. Sure, that works -- but that's because scientific theories only apply to the natural world. Philosophically speaking, you're wrong because you're asking if the rules from Group A would apply to Group B when B is Mutually Exclusive from A. Or, for an analogy, you're asking if you can pitch a perfect game in football... It just doesn't make any sense.


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What is the source of the electrons generated in the Krebs cycle?
In the Krebs cycle, where do the hydrogens and electrons that NAD+ and FAD accept come from? It seems that citric acid only loses two hydrogens because it starts out with eight hydrogens and then becomes oxaloacetic acid, which has four hydrogens.

where have you looked for answers? have you tried google - this is a relatively straightforward question that should be easily found... try googling "where do electrons from krebs cycle come from"

Yes, I have googled this, discussed the question with friends, and thought about it myself and I have not found an answer. That's why I'm asking on stack exchange.

Nice, so electrons are coming from carbon and hydrogen bonds, and great information btw. But how is this happening. Is carbon double bonding where it wasn't previously, so that it can give up some electrons?

Very interesting question. Clearly this is far from obvious, with conflicting statements in the literature. I don't know if one should call it "splitting water", but the TCA cycle does take up 3 oxygen atoms from H2O (one via phosphate) which end up in CO2. Given that, it's not clear to me where the electrons of H2O end up, especially considering that electrons in the carboxyl groups are delocalized ... @TomD, were you able to find the missing references you mention in your other answer?

@TomD  Completely agree. Thanks for the reference! I think the summary equation of Herreos and Garcia-Sancho settles this question nicely, maybe you should turn that into an answer.

@user3163829 Citric acid has 8 Hs and not 6 Hs. If you consider the anion of this acid, the state usually found in body fluids then Citrate has 5 Hydrogens and Oxaloacetate 2 Hydrogens.

@TomD — I've thrashed out an answer from the references you gave. I felt the question was too interesting to be left without that in a formal answer. Do feel free to suggest changes.

The two electrons and a proton of NADH comes from a H$^-$ ion of a Krebs cycle intermediate during Isocitrate dehydrogenase reaction and Malate dehydrogenase reaction.
In the following reaction, Isocitrate is oxidised to Oxalosuccinate and in the process two Hydrogens are lost one as H$^-$ and the other as H+. This H$^-$ is accepted by NAD+ to form NADH.
Note: Oxalosuccinate is an intermediate formed during oxidative decarboxylation of Isocitrate.

Now coming to FADH$_2$ $-$
During oxidation of Succinate to Fumarate, Succinate looses a H$^-$ and a H+ ion which constitute the two protons and electrons of FADH$_2$  . Here's an image that illustrate the mechanism:

The alpha-ketoglutarate dehydrogenase complex reaction is similar to pyruvate dehydrogenase complex reaction(PDC).
PDC reaction is an oxidative decarboxylation reaction of Pyruvate in which the 2e$^-$ of NADH are derived from the electron shared between COO$^2-$ and C=O groups of Pyruvate.

The Hygrogen (H+) of NADH is either derived from the H+ of CoA-SH or from the medium. There's a series of complex reactions which need to be studied to fully understand the source of H of this NADH.
So you can understand that the 2 e$^-$ of NADH produced in Alpha-ketoglutarate dehydrogenase complex reaction are the electrons between COO$^2-$ and C=O groups of Alpha-ketoglutarate and the H is either from the medium or the H+ of CoA-SH.
Reference: Biochemistry by Berg

The malate dehydrogenase step is similar to ICD? Whats the intermediate there? But isn't the other reaction, the a-ketoglutarate step similar to pyruvate dehydrogenase? The former is a C-H bond, while the latter is a C-C bond. Correct me if wrong! Sanjukta Ghosh @TomD ?

H- ions? Do you have a real source for that?

@Chis I have deduced it from the diagram that I have shared from Biochemistry by Berg. They haven't mentioned H- ion, but that it what the picture says. Referring to the first diagram, H- and H+ must leave the Isocitrate to form Alpha-keto acid, oxalosuccinate.

@David I'd like to hear your views on the concept behind my answer. Do you find it correct?

@Polisetty Yes you are right MD step is similar to ICD step. Thanks for pointing out, I was in a hurry so I had messed up, but now I've corrected it. The PD step is also similar to AKD step.

@Chris This wiki page talks of the proton, hydride thing in NAD redox reactions https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide#Physical_and_chemical_properties

This is a question that has been a source of disagreement between some quite senior biochemists, so, although I am no angel, I waited a little to find an elusive volume of a journal before rushing in. At the outset it seemed to me that:

What was important in the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle was the source of electrons, not the
  source of hydrogen atoms. Oxidation is the removal of electrons.
The source of the electrons must be the carbohydrate being oxidized. It could not come from anywhere else (such as water).

This point was made in a comment (not an answer) by TomD, who pointed to his answer to a different but related SE Biology question. In that answer he refers to two ‘letters to the editor’ on the subject in TIBS vol.6, p.6 (1981), which unfortunately are not available in the online version of the journal. I recalled them from my own university library’s archives and have made them available here as a text pdf, although in the meantime TomD posted a scan himself. I recommend reading the letters carefully to consider their arguments, but quote extracts from each here to show why I personally tend towards their view.
D.E. Atkinson
Atkinson’s key point, as I understand it, is that although the H may come from water, this is only as a result of ionization — the water is not oxidized, so cannot provide electrons:

“Electrons cannot be tagged and traced, but the stoichiometry is clear:
  in the oxidation of an acetyl group to 2CO2, eight electrons are lost.
  Of these, six are used in the reduction of NAD+ to NADH and two in the
  reduction of the flavin of succinate dehydrogenase. Water is not
  oxidized; thus no electrons are supplied from water to be: ‘raised to
  the level of NADH2’ or for any other role. When water ionizes, the
  electrons all remain associated with the OH– ion; whatever the proton
  may do, it cannot reduce anything.”

B. Herreros  and J. Garcia-Sancho
These authors emphasize that it is the C–C and C–H bonds that are providing the electrons:

“As pointed out by Losada the carbon compounds themselves are the only
  source of reducing power in the TCA cycle, not water. The difficulty
  in realizing it arises from the contabilization of the reducing
  equivalents as pairs of H rather than as electron pairs. It is true
  that one molecule of glucose can not supply 12 pairs of H, but it can
  certainly supply 12 pairs of electrons…
… In the TCA cycle, the electrons shared in the C–C and the C–H bonds
  are the source of reducing power; they are transfered first to
  pyridine nucleotide (and flavin nucleotide) and then to the vicinity
  of oxygen through the respiratory chain.”

Towards the end of his letter, Atkinson writes “I have found it a useful pedagogical device to ask students to work through respiration (glycolysis plus the citrate cycle), keeping careful account of water and proton so that their equations will sum to the proper balanced overall equation.” I am afraid I haven’t provided that in this answer, limiting myself to surveying the wood rather than examining each tree.


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Length of base-pairing required in Argonautes
I've been reading a lot about Argonautes and its recognition mechanism and how there are some differences on how they match the target RNA.
I know that the (mi)RNA guides are quite longer than what is used to match the target.
The seed region is relatively conserved (nt g2–g7 or g2–g8), and there are some papers that define a supplementary region (g13–g16), but I did not find a consensus on that.
Are there resources about which nucleotides are really needed to pair with the target in different Argonautes? I am mostly interested in mammalian vs plant Argonautes.
I am not really interested in the dynamics, just the number of nucleotides needed to match the target (and how performance degrades with mismatches).