text:
What, other than genetic factors, influence which individual survives a parasite and which perishes?
What factors other than "good genes" are at play in determining whether one individual survives a parasite and another individual in the same species perishes as a result of the same parasite?  For example, is there variation in the amount of the parasite (not in the amount of parasite species but in the amount of one species) with which an individual is infected and how might this occur?  I'm mainly interested in this first example, but another example:  Might infection occur at different parts of life-history in which vulnerability varies? (I am asking generally about any parasite species and any host species.)  Thank you very much.

@David, thank you for the edit.  Wondering if you have an opinion on the question.  For just one example, take the 1918 influenza crisis that killed 40 million people.  Does it make sense to suggest that some individuals just happened to be exposed but exposed to some dosage that was sublethal?

I am neither a parasitologist nor an immunologist, so these suggestions are only provided as a starting point and may meet valid criticisms from others. However, as your comment mentions the 1918 flu epidemic, a couple of general suggestions.
Assuming that resistance to pathogenic organisms can involve the immune response, then at least two factors that might affect that — and hence resulting mortality or morbidity are:
Nutrition:
It is popular wisdom that undernourished individuals are more susceptible to disease. This might have diverse causes, but there would appear to be an extensive literature on the role of nutrition in the immune response, e.g. this article by  Chandra has been highly cited.
Previous immune challenges: There is, of course, the classic case of milk maids being resistant to smallpox because of immunity provided by the related cowpox. Thus exposure to previous strains of a virus may provide some protection. Speculating widely here, there may also be affects on the non-specific components of the immune response (macrophages and whatever).


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How do the antibodies in colostrum survive the infant’s digestive system?
What happens when the antibodies in colostrum reach the infant's stomach? Why aren’t they destroyed by digestive enzymes?

I have edited your title to make it reflect your question, and (I hope) clarified your question, which seems quite valid to me, although I haven't checked the reason for the close votes.

I think the close votes for this question on the basis that it is too broad should be reassesed. It seems a fair question to me and I don't know the answer to it (although I haven't searched for an answer myself).

There are two main differences between adults and newborn babies which allow the passage of antibodies (while maintaining the activity) through the stomach and the resorption in the gut.

The digestive activity of the stomach in newborns is still immature and needs to develop. This results in almost no production of hydrochloric acid (which is responsible for the very low pH in the stomach). It can take up to two years to until the pH in the stomach of children reaches the level of adults (see chapter 5 in reference 1).  Because of this higher pH much more proteins (and other components of the milk like anti-microbial proteins, carbohydrates and lipids) can pass the stomach unaltered.
The other really important feature of newborns is their much greater permeability of their intestine. This allows an efficient transport from the antibodies into the blood stream and where they provide protection. See references 2 and 3 for more details.

References:

Breastfeeding and Human Lactation
Antibodies in  Milk
Intestinal permeability in the newborn

Thanks Chris for your answer. I hope this lets the poster and others realize that a clearly expressed question with a carefully constructed title will increase the changes of someone who knows seeing it and answering it.

Another important factor that the previous answer missed is that the antibody secreted in breastmilk is IgA dimer. IgA dimer is two IgA molecules linked by a protein called the secretory component, which protects the antibodies from being degraded in the digestive system.

Welcome to bio.  Can you add sources?

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


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Consensus sequence for selection of initiation codon in eukaryotes
In bacteria the AUG (or other) codon at which translation of mRNA is initiated is preceded at a precise distance by a sequence known as the Shine and Dalgarno sequence, to which the 30S subunit initiation complex binds through base pairing of the 16S rRNA.
In eukaryotes, in contrast, the 40S initiation complex normally binds to the 5′-cap of the mRNA and scans until it reaches the appropriate AUG codon — usually the first. Marilyn Kozak, who originally proposed this model in 1978, updated it later to try to account for the approximately 10% of eukaryotic initiations that do not occur at the first AUG. She identified a consensus sequence surrounding initiating AUGs and suggested that this was important in their selection. (see Wikipedia article entitled Kozak Consensus Sequence).
What is the current status of this consensus sequence now that so much more sequence and transcript data are available? Is there any evidence as to how it might function, e.g. by interaction with 18S rRNA in a similar manner to the Shine and Dalgarno sequence?

What research have you done into this topic? You mention a Kozak sequence, but this is not a meaningful term or one in general use. Try searching for Kozak Model and you should find the answer to your own question. If not, repost explaining your problem.

@David, thanks for you comment. I was referring to Kozak consensus sequence, is this term still ambiguous? I saw many publications, characterising the Kozak consensus or highlighting its significance, but none providing a mechanism for its action. If you could refer me to any such paper, that would be very helpful.

I don't want to answer your question in a comment, and I suspect that this question may actually be a duplicate of another on this general topic, so I have rewritten it to illustrate how to formulate a question providing basic evidence of research. This is required, not only to prevent laziness on the part of posters, but to allow others interested to check the basis of the question. (In this case, for example, I might take issue with the second Wikipedia article.) I will withdraw my close vote and leave others to decide whether it is a duplicate of another question.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Translation of Poly-U in the Nirenberg and Matthaei experiment
In the Nirenberg and Matthaei experiment the artificial mRNA, polyU, was translated into polyphenylalanine in a cell-free system, establishing that UUU was the codon for Phe. How did this work as the artificial mRNA lacked an AUG initiation codon, which we now know is required for translation of cellular mRNAs?

I have modified your question, eliminating the question of whether there was AUG present. Obviously not — as this was the experiment that established the first codon and nothing was known about AUG and initiation. PolyU was PolyU was PolyU. I think I have clarified your question (as well as answering it below). If not, let me know.

This is an intelligent question that highlights the ‘sleight of hand’ simplifications employed in many text books to make experimental science appear cleaner and more logical than is in fact the case. From what we now know about the requirement for an AUG initiation codon in protein biosynthesis these experiments should not have worked.
The reason they did was that they were performed at an unphysiologically high concentration of Mg2+ which overcomes the need for specific initiation (and, incidentally, allows other reactions of protein synthesis to proceed in an abnormal manner, particularly the codon-directed tRNA binding reaction used to finish the deciphering of the genetic code). You should also bear in mind that the efficiency of the reaction was probably much less than that within the cell, but this was of no concern as all that was required was that a product be synthesised.
Reference
I worked in this area in the late 60s/early 70s and the importance of magnesium concentration was just common knowledge in the field, so it is difficult to cite a reference to support my assertion. However a brief search brought up a contemporay paper on the effect of magnesium on initiation of protein synthesis in phage RNA, illustrating its importance. There are, no doubt, others.


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Is it a valid generalization that kinases catalyse reactions involving energy transfer and utilization?
The Wikipedia entry for kinase states that "a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules [such as ATP] to specific substrates".
ATP is the energy currency of the cell, so, would it be accurate to say that a kinase catlayses reactions involving energy transfer and utilization within a cell?

I intuitively think of kinases as switches: they allow molecules to exist as either a or b, and one or both forms may be active.

Care to elaborate, maybe with an example or two?

@CMosychuk — please follow the instructions for comments and do not use them to answer questions. It breaks the SE model and encourages others to do likewise.

Does the Wikipedia page on kinases not answer your question? Can you expand on what actually is the doubt, since the Wiki page has examples with specific functions fulfilled by kinases.

I have put in a quotation from Wikipedia (Google is not a source) for kinase, and modified your definition of ATP to make it more acceptable. Kinase is the name of a a class of enzymes that catalyse certain types of reactions. I assume you are familiar with enzymes. I am not sure, however, how one thinks "intuitively" about them. One can generalize about the sort of reaction they catalyse. Is that what you are asking?

@David I think the OP's meaning is best described in the last sentence. OP knows that ATP is a form of energy, and knows that kinases convert ATP to ADP while they transfer a phosphate group to another molecule. OP wants to know, then: is it correct to think about a kinase as an enzyme that delivers stored energy within a cell? In my opinion, a good answer would explain that OP's description sounds a little more like what many ATPases do: they are using the energy from ATP to do some energetically unfavorable work. But also explaining that kinases have different functions...

...and that in some anabolic pathways, yes, kinases are helping to deliver stored energy in the form of phosphate groups onto 'building blocks' of other molecules. But when a kinase adds a phosphate to regulate the function of another molecule, I wouldn't really say that it is delivering energy, just that there is some energy cost to doing the business of flipping cellular light switches, and ATP is readily available as a source to do that.

@BryanKrause That sounds like an answer to me.

Wanted to add, it is Phosphoryl group that it is transferring and not Phosphate. Wikipedia is not a very good source for learning.

@Tytoalba Good point, although I'd add that many sources besides Wikipedia talk about "transfering a phosphate" as the outcome of phosphorylation (I paged through some google scholar results for search terms like "kinase phosphorylation review" and confirmed this). I think it's intended as a bit of a shorthand, because the outcome is a phosphate group on the target, but it could also be a misstatement. For the biology (besides the specifics of the biochemistry) it doesn't really matter.

@Tytoalba Also I mostly blame the chemists who decided a phosphate+phosphoryl group would be called a "diphosphate", etc. ;)

I prefer the other term Pyrophosphate. @BryanKrause Yes it is Anidosinediphosphate again.

@Tytoalba I am familiar with the existence of the term "pyrophosphate" but I have never seen it used in a biological context or to name a biological molecule. This question from chemistry suggests that the "bisphosphate" terminology is becoming more common in biochemistry for ortho-phosphates, whereas "pyrophosphate" is really only used for the inorganic anion. However I don't expect "ADP" and "ATP" to change for quite some time, if ever. Alas.

I have rewritten the question to make it generally more useful (before I answer it). It is best not to have subjective titles — in general we are not interested in you particularly — and a statement that talks about an enzyme ”metabolizing energy“ clearly will not do. Even though you can talk about energy metabolism, this actually means the metabolic reactions in which molecules with the potential to transfer free energy are generated. This may seem high-handed, but SE encourages improvement of both questions and answers.

No.

It is not possible to suggest a verbal or pictorial generalization of
the role of kinases.
It is futile to try to do so as it is incorrect to think that
kinases have a single general role of the type suggested, or that the
utilization of free energy from ATP is limited to reactions catalysed
by kinases.

Clarification
Kinase is a surviving trivial name for enzymes that have been classified by IUBMB as ATP phosophotransferases. The categorization solely reflects aspects the chemistry of the reaction catalysed, and the sub-categorization in terms of substrate relects a diversity of roles. Moreover such kinase reactions are only one way in which the free energy of hydrolysis of the phosopho-diester bond of ATP can be utilized — transfer of the phosphoryl group to another molecule. Other types of reaction (and enzyme) are just as, if not more, important.
The diversity of roles played by kinases
I list at random some examples of different types of kinase reactions:

Hexokinase transfers phosphate from ATP to glucose. One purpose is
to creaate a charged molecule, glucose 6-phosphate, that cannot
go back across the cell membrane.
Thymidine kinase converts thymidine to TMP. Like several other
    kinases it can be thought of as catalysing a synthetic reaction, the
    phosphate being a part of the structure of the TMP (and ultimately
    TPP) molecules.
Protein kinases transfer phosphate to serine, threonine or tyrosine
residues of proteins. This is not using ATP for an energetic process,
but to cause a change in the structure of the target protein that
modulates its activity.
Creatine kinase interconverts creatine and ATP with creatine
phosphate (a rapidly mobilizable energy store in muscle) and ADP. As
the reaction is reversible it can be thought as either catalysing
the formation of creatine phosphate or its mobilization.
Pyruvate kinase is a similar to 4 in that it produces ATP, and as the reaction it catalyses is essentially irreversible in the cell, the name is quite
misleading about its function.

Non-kinase enzymes involved in utilizing ATP
These include ATPases, as @BryanKrause remarks, but also some others. Again, some examples at random:

Sodium /Potassium ATPase catalyses active cation transport.
Firefly luciferase (an oxidase) hydroyses ATP to produce light.
Glutamine sythetase (glutamate-ammonia ligase) uses the free-energy
of hydrolysis of ATP to convert glutamate and ammonia to
glutamine.

Your (original) description:

a kinase helps chemically deliver or metabolize stored energy within a cell

sounds a little more like what many ATPases do: they are using the energy from ATP to do some energetically unfavorable work, such as moving molecules or ions against their concentration gradients. However, kinases have a broad range of different functions.
In some anabolic pathways, yes, kinases are helping to deliver stored energy in the form of phosphate groups onto 'building blocks' of other molecules, and this stored energy can be used for future reactions.
However, when a kinase phosphorylates another molecule (often a protein) to regulate its function, I wouldn't really say that it is delivering energy, just that there is some energy cost to doing the business of flipping cellular light switches, and ATP is readily available as a source to do that. One big advantage of using kinases in these sorts of reactions is that, because a fairly large energy input is required, such reactions don't occur easily by mistake or just due to thermal energy.


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Use of sunlight in biological processes
Sunlight is used by green plants in photosynthesis, but it is also used by animals in the synthesis of Vitamin D. Are there any similarities between the two processes and how is the light energy actually used?

It's synthesized from a type of cholesterol that is converted to vitamin D by uvb exposture. So nothing like photosynthesis really. See https://ods.od.nih.gov/factsheets/VitaminD-HealthProfessional/#h3 for more.

Radiation being the source of energy for photosynthesis and vitamin D synthesis seems a reasonable correlation to someone having obviously very limited knowledge about the most important biochemical reaction.

This source explains it really nicely if you have the science background to understand it. Basically, the ultraviolet light of a certain wavelength - or high energy photons - breaks a particular bond in a precursor normally made in the skin. From there, the body takes over.

We don't get it from the sun, it's synthesized.
Humans can get it...

via nutrition.
via synthesis in the skin, which depends on UV radiation. Sun is the major source of it (the radiation, not the vitamin), and synthesis in the skin the major source of the vitamin. However, it needs further modification in the liver or kidney to become bioactive. UV radiation is necessary and directly causing the opening of a cyclic molecule structure, changing a cholesterol to a previtamin D3.

For more details see chapter 'Biosynthesis' at https://en.wikipedia.org/wiki/Vitamin_D

What is the down vote about?

At a guess, it's because you start by saying we don't get vitamin D from the sun, then go on to explain how the body makes it.  Maybe it's just bad wording: of course vitamin D molecules aren't literally part of the solar wind :-)

@jamesqf I think it's legitimate to re-use the phrase from the question and to point out that things are different.

Similarities
Despite major overall differences, there are some basic similarities in the two processes:

Light energy excites an electron to a higher energy level.
A covalent bond is broken as the electron moves elsewhere. This
process is called ‘photolysis’ and is purely chemical.

Differences
The difference is in what happens to the excited electron and the extent of involvement of cellular proteins and lipids:

In Vitamin D synthesis the electron just moves ‘spontaneously’ to
another bond in the new molecule that is formed. That is the end of
the matter and enzymes are not involved in this reaction.
In photosynthesis the light is first captured by photoreceptors and
funnelled to the site of photolysis. After photolysis, the
co-operation of many proteins in a complex process within a
membrane-bond system ensures that the excited electron is transferred
to NAD+, forming NADH, the reducing power for then subsequent
conversion of carbon dioxide to phosphoglycerate. (An
electrochemical membrane potential is also generated, allowing ADP to
be converted to ATP, the hydrolysis of which is used for formation of
the C-C bonds of the phosphoglycerate.)

Vitamin D synthesis
The photolysis step in Vitamin D synthesis is shown below:

The precursor molecule is formed from cholesterol in a series of enzymic reactions and the Vitamin D3 produced (actually resulting from a spontaneous rearrangement of the initial product molecule) may be metabolized further in enzymic processes (see Berg et al. for more detail). However the photolysis of the bond indicated in red is purely chemical.
One may ask why no other electrons are raised to a higher energy level and the  corresponding bonds broken. Other electrons may conceivably be excited, but in the absence of a suitable reaction pathway to a compound of lower thermodynamic free energy the electron will fall back to its original energy level, liberating heat. In the case of 7-dehydrocholesterol the co-ordinated double-bond system provides a suitable reaction pathway to a product of lower free energy. One can think of light (of appropriate wavelength) providing the activation energy of the reaction (overcoming the energy barrier resulting from the higher free energy of the reaction intermediate).
Photosynthesis
The reactions of photosynthesis that utilize light energy (the so-called ‘light reactions’) involve two complex photosystems that are described in standard texts, e.g. Berg et al.. The simplified diagram deals only with the overall photolytic process.

The molecule undergoing photolysis here is water — the two H–O bonds are broken and oxygen is produced. However in this case the product is incidental to enabling the electron to reduce NAD+. (Chemically oxidation is removal of electrons, and reduction their addition.) As mentioned above, this complex series of reactions also results in an electrochemical gradient within the chloroplast. The movement of hydrogen ions through an ATP synthase in the thylakoid membrane of the chloroplast stroma converts ADP to ATP (in a similar manner to that of oxidative phosphorylation).
The result of the photolysis in this case is the provision of molecular reducing power and ‘energy’ that will be used to convert 1-C carbon dioxide to the 3-C reduced sugar in a separate series of reactions that do not themselves involve light energy (these are referred to as ‘dark reactions’, although they obviously do not have to take place in the dark).
Coda
Although one often hears loose reference to light energy being used to ‘make’ Vitamin D or sugars, this can be quite misleading. I would suggest that it is better to express what the light energy is achieving in chemical terms and then place this in the context of the relevant synthetic process.


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Nomenclature for mutations at specific nucleotide positions
I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of a nucleotide as location as  FGFR3:c.1843-35A>T. What does "1843-35" mean?

As 'c.' stands for 'coding' sequence (instead of 'g.' for 'genomic'), according the HGVS guidelines it denotes the A to T substitution at nucleotide -35 of an intron (in the coding DNA positioned between nucleotides 1842 and 1843).


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Violation of the law of energy conservation between photosynthesis and respiration?
For the production of one glucose molecule in the Calvin cycle a plant uses 18 molecules ATP, but when the same glucose molecule is oxidised — first in the cytoplasm and then in the mitochondrion — it can obtain approximately 36-38 molecules ATP. How is the theory of conservation of energy maintained here?

Please add references for the numbers you cite. Wikipedia or Berg et al. (NCBI Bookshelf online) would be suitable.

@sreekara plant uses 18atp to fix light energy which is more than energy released during respiration.

@JM97 — When you open a comment box to a question you see the following: "Use comments to ask for more information or suggest improvements. Avoid answering questions in comments." Please do what it says, otherwise you are breaking the Stack Exchange system. In the present case your answer is contentious (I contend that it is incorrect), but unless it is formulated into an answer I cannot vote it down or comment on it (without compounding your behaviour). If the poster thinks it correct, he cannot accept it as an answer and the question would appear unanswered.

@David, I studied it in our text book and even our teachers taught the same.

@David: But if you put a simple & obvious answer into an actual 'answer', you will get numerous complaints about it not being supported by references &c.  As to 'breaking' the SE system, the only thing that breaks it are the over-officious moderators who insist on short-circuiting good discussions.

@jamesqf — Stack Exchange is not a discussion site. Please read http://biology.stackexchange.com/tour to  understand its philosophy and how it works. If you use this site you should abide by the rules. You have paid no subscription — someone else has covered the expenses of setting it up. If you don't like the rules, go elsewhere or build your own site.

The Fallacies in the argument
The question contains two main fallacies (some would say sleights of hand) in the energetic comparison of glucose synthesis from CO2 in the Calvin cycle and glucose oxidation via glycolysis, the tricarboxylic acid cycle and the electron transport chain:

The descriptions of the two reactions are incomplete — important co-substrates are ignored.
The formulation of the question seems to assume that the energetics of a biochemical reaction series is reflected solely in the
  interconversion of ATP and ADP, rather than the free energy changes
  that occur in all associated reactions.

Detailed explanation
To make a valid comparison of the thermodynamics of glucose oxidation to CO2 with its synthesis form CO2 we have to consider the single reversible reaction:

 (The ‘6H’ may appear rather odd, but it is accounted for in the reduction of cofactors etc.. We cannot include oxygen in the equation because it is not involved chemically in the synthesis of glucose. Therefore for this treatment the electron transport chain is not included, although it is discussed later.)
The reaction from left to right is associated with a certain decrease in Gibbs free energy (ΔG) and that from right to left in a corresponding increase of the same value. In a non-biological context this might involve the evolution and use of heat energy, but in the cell it involves the chemical energy of bonds between atoms. We therefore have to consider all the chemical reactions to which the reaction above is coupled, i.e. which receive or transfer free energy. The additional reactions and the free energy changes they involve can be found in the chapters on glycolysis, the tricarboxylic acid cycle and the Calvin cycle in Berg et al. and are (omitting water, hydrogen ions and inorganic phosphate):

From which it can be seen that the chemical energy input required for synthesis is greater than that obtained, contrary to what is asserted in the question
What about the ATP?
Yes, the cell oxidizes NADH and FADH2 and uses the free energy change to build an electrochemical gradient, the dissipation of which generates ATP (30 molecules per glucose molecule is the current estimate). However that is separate process, with no counterpart in the Calvin Cycle, where the NADPH is generated from photosynthetic reduction and not from ATP. However, if you perform a naive ‘currency conversion’ at the rate of 3ATP per NAD(P)H and 2ATP per FADH2, the balance is: input for synthesis 54 ATP, output from oxidation 38 ATP, i.e. the same general result as above.
Popularizing science is not easy, and those who make the effort can be excused for equating energy with ATP (often as clip-art lightening flashes). However if you wish to study metabolism you need to think scientifically about chemical thermodynamics and free energy. The fact that the hydrolysis of ATP to ADP is accompanied by a decrease in Gibbs free energy is not particularly chemically remarkable in the context of the free energy changes of other chemical conversions in the cell (including NAD(P) oxido-reductions). What is remarkable is that the cell has evolved enzyme that catalyse reactions in which the free energy change from this conversion is not lost as  heat, but can be used to offset the +ve ΔG of a reaction to which it is coupled. Reactions involving NAD(P)H do the same thing, but they are limited to reductions, and the free energy change is inconveniently large.
Why the accepted answer to this question is a red herring
The accepted answer addresses a different question to that posed. It cites a calculation of the photon energy required for converting carbon dioxide to glucose. This is irrelevant to the thermodynamics of the Calvin Cycle, which can occur in the dark. It is relevant only to the efficiency of the use of photon energy in phosphorylating ADP and reducing NADP+ (incidentally in an open system) — a distinct reaction. The thermodynamics of the reactions the question refers to — glucose / carbon dioxide interconversion processes — do not involve the generation of their co-substrates.

Thank you@David, I wasn't considering the NADPH if we consider them and then equate 12 NADPH produces approximately 12×3= 36 ATPs, and adding 18ATPs it gives 54 ATPs ,which are more than that produced in oxidising it that is 36ATPs.

@ David I have another doubt, the mechanism of ATP synthesis in mitochondria and chloroplast are almost the same, but there is a big difference in mitochondria the f1 particle uses 2 H+ ions to synthesis one ATP and whereas in chloroplast it uses 3H+ ions for the same, shall I post it as a separate question?

@sreekara — I'd definitely post that as a separate question. (And a small linguistic point. I realise that 'doubt' is used in Indian English to introduce a question. However in British and US English it is never used that way. 'Doubt' only conveys the idea of disbelief or uncertainty.)

I will post the question tomorrow because I have posted one today.

I have now revised my answer as I thought it important to address the misaprehensions about ATP and "energy" clearly with a table of free energy changes. The gist is the same as before.

Background: Law of conservation of energy states that energy in a  closed  system remains constant.
So the amount of energy in a molecule remains same when its annihilated( also consider law of energy mass equivalence).
Before answering this I would like to point that in the formation of glucose not only energy from ATP is utilised to fix carbon but also light energy is also utilised, which is about :

It takes eight (or perhaps 10 or more) photons to utilize one molecule of CO2. The Gibbs free energy for converting a mole of CO2 to glucose is 114 kcal, whereas eight moles of photons of wavelength 600 nm contains 381 kcal, giving a nominal efficiency of 30%. $^{(1)}$

So, how is the light energy utilised in Calvin cycle?
This light energy is used for formation of NADPH which used in Calvin cycle. Therefore not only ATP but also NADPH are required for generation of energy.
So after considering the above facts one can argue quantitatively that law conservation of energy is not violated in case of oxidation of glucose by mitochondria.

I do not think this answers the question posed, as it relates to the energetics of the generation of ATP and NADPH by light in a thermodynamically open system. The Calvin cycle does not involve light. I believe my own answer is correct in addressing the failure to consider the energetics of anything other than the hydrolysis of ATP.

@David  I never said that Calvin cycle directly utilises light energy. The OP asked broadly about violation of law of energy conservation between photosynthesis and respiration. My answer too says that the NADPH is the entity which the OP has forgotten. Just to have a broad perspective I highlighted the fact that a lot more of light energy is used to form glucose than the energy released on oxidation. How is my answer misleading?

I am sorry, but the poster did not ask broadly about the violation of energy conservation, he argued specifically from figures for ATP involvement in glucose synthesis and oxidation. By answering in terms of the energetics of a different reaction (the light reaction) you were implying that it was relevant to the thermodynamics of the dark reaction. It isn't.

I can't force OP to accept your answer as accepted.

That's not the point. The accepted answer need not be the best answer. It is valid to comment with diagreement, however. I am just copying the practice common of the original SE StackOverflow, which I was familiar with before joining this SE.


text:
What is the evidence that women experience a larger cortisol spike than men, when they see domestic clutter?
I'm reading a book "The Organized Mind: Thinking Straight in the Age of Information Overload" by Daniel Levitin.
At the beginning of chapter "Organizing our homes" he says that compared to men, women experience larger cortisol spike when they see mess. I googled that statement, and the source of that claim seems to come from https://doi.org/10.1177/0146167209352864
I don't have the access to the journal, but the abstract doesn't say much about how cluttered is the home. It just seems to correlate linguistic patterns with cortisol level.
But someone stressed for sure has different way of speaking than someone chill. No clutter scale is mentioned. The person might be stressed by something unaccounted in the research.
So please, can someone with journal access and proper qualifications tell me:

Was my googling attempt succesfull, or are there better sources?
If this is the most relevant paper... is it of quality? Or my remarks on it are valid?

The full test may be requested from the authors via ResearchGate.

To be fair, this question may be a better fit on [psychology.se]. You'd need to show your prior research there (as you should here too).

I don't pretend to understand the article, but I do have access. They compared usage  of "stressful" and "non-stressful" words used to describe their houses compared to words used to describe their gardens - the words were grouped into "clutter" "unfinished" and "restful"

I’m voting to close this question because, despite the title, this is a question about the contents of particular publication rather than one about biology.

There is a freely available version of the paper available here.

I linked to the paper above in a comment.
I'm not a behavioral scientist. So interpret with a grain of salt.
The study analyzes language used after tours of homes, to evaluate how stressful the homes appear to be. So it's an imperfect measurement probably, but in direct reference to their homes. It probably does reflect something about how stressful they feel their homes to be, but IDK.
Assuming that the slope of the diurnal cortisol curve is a meaningful measure (seems to be somewhat true based on my non-exhaustive search), and that the sample is adequately powered (n=30 couples, which is not too awful but not great either given the number of hypothesis tests). If you look at Tables 1 and 2, it does look like women are affected by a "stressful home" to a degree that men are not. Men also seem vaguely unhappy about stressful homes, though not as strongly as women. Granted, they only present regression tables, which is not always very helpful for understanding causal or statistical relationships.
Nonetheless, the paper seems well-cited in the literature (as might be expected if it made it into a book). A lot of the work citing it is saying things along the lines of "we need more work in this area to examine this effect". A small number of studies seem to confirm qualitatively that messy homes are stressful for women, see for example here or here. It is less clear that the same isn't true for men, but then the majority of housework and caregiving responsibility is concentrated on women.
Furthermore, it does seem like global cortisol differences in men and women are not surprising, and that cortisol-induced stress may affect women and men differently.
Generally, this study seems ok if not great. It fits into a broadly supportive narrative of (partially qualitative) research. The sum of the literature that I've skimmed very briefly cites this paper with approval, if perhaps making more of the results than is merited given the level of power for the study. No one has posted on pubpeer about it or found anything dodgy about the study, in spite of its relatively high profile, so it's not obviously awful. I don't love the linguistic analysis either, but clutter is itself subjective I guess.
There remains the issue that you raise that perhaps a person under stress will react more strongly than someone who is more relaxed. But it's a bit circular of course- in either case, it seems like women are more stressed, and they also get more stressed out about domestic clutter.
Interested to hear more from a real behavioral science professional. I hope that my answer doesn't discourage anyone with more credentials from posting.

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


text:
How to find a gene sequence?
So I need to learn how to find the sequence of a gene, polyphenoloxidase. Please do not do this for me. Tell me how to approach the problem.
I have found : https://www.ncbi.nlm.nih.gov/gene and searched for polyphenoloxidase and get a list of results.
Here is one PPO page:
https://www.ncbi.nlm.nih.gov/gene/107923401
There is a FASTA sequence there under " NC_030099.1 Reference ASM98774v1 Primary Assembly" but I am not sure if PPO gene is there.

You need a gene sequence. What're you trying to accomplish? The list you get from the NCBI search notes PPO in different isoforms/types from different species. Perhaps you should first lock down your target organism and gene isoform. And so I click the top result, LOC107923401 (aka PPO-3; PPO-6; PPO-8) from Cotton. Scroll down to Genomic regions, transcripts, and products and click on the FASTA link. There is the raw sequence. Your FASTA and FASTQ files will be the result of NGS on your organism's genome.

@CKM advocado is my target organism.

If you want to blast that sequence, remove the subquery range it provides for you beside the sequence box.

@CKM Tried doing a Blast search for a PPO gene: https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEFAULTS=on&BLAST_SPEC=OGP__3435__73885&DATABASE=GPIPE/3435/current
However there are no matches, which may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO.

It doesn't appear that anyone has sequenced it. See here.

You can find the sequence in the gene database, but it is perhaps easier to search the nucleotide database if you are only looking for the sequence of nucleotides.

I used the sequence you helped me find to do a Blast search of a genome here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEFAULTS=on&BLAST_SPEC=OGP__3435__73885&DATABASE=GPIPE/3435/current     However there are no matches, which is may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO as advocados do brown.

@Dale It doesn't appear as though there is a whole genome sequence for avocado, yet.

What about: https://www.ncbi.nlm.nih.gov/genome/?term=avocado

The existence of that page doesn't mean that the entire sequence is in the database.

@Dale There are a large number of ESTs for avocado and blasting against those (tblastn) with the tomato PPO protein sequence gave some hits.

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


text:
How to do a blast search for similar sequences?
Tried doing a Blast search for a PPO gene in an advocado genome: https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEFAULTS=on&BLAST_SPEC=OGP__3435__73885&DATABASE=GPIPE/3435/current
However there are no matches, which may be because it is a different species with a slightly different sequence? The genome I am searching is known to contain PPO.

Once again, RTFM!

As stated in the comments here, there is no complete genome sequence for avocado as of yet, though people appear to be working on it.
However, there are a large number of ESTs and doing a BLAST of their translations with the tomato PPO sequence (tblastn) gives some hits.
Here is a link to that BLAST.

However there are no matches, which may be because it is a different species with a slightly different sequence?

This is precisely the problem that BLAST was designed to solve.

how did you get that link to share your BLAST search?

@Dale There is a link on the page, near the top right, called "Bookmark".


text:
Markers for human genetic mapping
For human genetic mapping several different types of markers are used:

RFLPs (Restriction Fragment Length Polymorphisms)
VNTRs (Variable Number of Tandem Repeats) such as mini- and microsatellites
SNPs (Single Nucleotide Polymorphisms)

What are the pro's and con's of using each type?
Do any of these markers have a specific functionality in human genetic mapping, or can they all be used for the same purposes?

RFLP is a technique not a marker., thus i deleted this from your answer, but you can revert it if you wish.

But can't one use RFLP paired with Southern Blot as a genetic marker?

RFLP is not a sequence property it's a technique to compare sequences usually over a small segment of DNA. You take your samples, digest them, and run them on a gel, and compare the patterns. Its good for allele diagnosis etc.

The restriction sites are the sequence properties. Some people will have a different amount of them. Otherwise there wouldn't be patterns (the RFLPs) to compare.  Hence you can use the RFLPs/restriction sites as genetic markers.

Yes restrictions sites are sequence properties but they are 6-8 bases long, so there are waaay too many of them. You keep using RFLP the wrong way, that is the name of the technique / phenomenon noting more. It`s not like VNTR or SNP. You can identify SNPs with RFLP.

I have rolled back the edit to the original version. There are many cases in literature of RFLPs being referred to as markers, which they are.

SNPs are much denser than RFLPs and VNTRs therefore the DNA resolution is much greater with SNPs. VNTRs were historically used for linkage mapping while SNPs allowed for association studies (e.g. GWA studies). Therefore your question goes down to what are the differences between linkage mapping and association studies.
They are both forward genetic methods which aim to identify a genetic modification provoking a trait.
The two major differences between both approaches are 1) linkage mapping requires a pedigree but can be performed using a fairly small sample size while 2) association studies can be performed at the population level but usually require a much larger sample size.
Both approaches require markers but for different reasons. For linkage mapping, markers, such as microsatellites, are used to delimit the genomic region associated with the trait and take advantage of recombination events in the genome to pin down that region. This, of course, requires both 1) recombinant individuals in the pedigree and 2) at least one marker that is co-inherited with the trait. Linkage mapping allows to find virtually any genetic modifications, such as a genomic deletion, but only in the case of a genetic modification showing high penetrance.
For association studies, markers are the actual genomic modification themselves (usually SNPs) and are used directly in statistical tests (often a logistic or linear regression) for association with the trait. This means that either 1) the causal marker is available or 2) at least one marker is highly co-inherited with the causal mutation (i.e. in linkage disequilibrium). Association studies allows to find both low- or high-penetrance mutations, given a sufficiently big sample size. Also an association study can be conducted in the presence of a non-discrete (i.e. linear) phenotype which one cannot use in linkage mapping.
Another difference is that linkage mapping does not require any a priori knowledge of the genomic modification causing the trait while association studies do (as markers are statistically associated with the phenotype).
Usually both methods will highlight, with varying resolution based on the phenotype and markers used, the genomic region causing a trait but rarely the actual causal mutation will be found with 100% certainty.


text:
Common Metrics of Assessing DNA Sequence Quality
What are commonly accepted metrics for assessing DNA sequence quality (platform-specific answers are fine)? I am relatively new to this topic, and I want to either find or code (in Python or C++) algorithms for checking sequencing data quality before getting into analysis.

if you are talking about Sanger sequencing, look here: http://en.wikipedia.org/wiki/Phred_quality_score

as @aandreev pointed out Phred score is a universal metric used for denoting the quality of a sequence read. Phred is basically log transformed error probability. However, the error probabilities and their calculation procedure differs between platforms.

As mention in the comments Phred scores are the quality scores for most sequencing platforms. This value expresses the probability of a base is being called wrongly. You can find more information here. This values can be found in a fastq file coded by symbols.
For example, a phred score of 30 means that there is a probability of 1 base being wrong every 1,000 (that is 99.9% accuracy). In general values around 30 are considered good enough, but it depends on your analysis whether you want to be more more or less restrictive.
Biopython has some examples on how to plot and filter phred scores. There exits lots of other software to do QA checks, for example this one.
You can also check length and distribution of the reads, duplication levels, etc.
In case you need to trim sequences from Illumina there are several stand-alone software like this that you can use.


text:
What contributes to the variation of protein sequence across different species?
What contribute to the variation of protein sequence across different species (e.g. phenotype, environment, evolutionary pressure) and how do those factors contribute to the variation?
I have tried to search using google + google scholar but they generally show papers discussing why and how the protein conserved across species rather than why/how the protein diverged across species. Please help me on this and references/sources are very important and highly appreciated. Thank you!
An example to clarify my question. The gene CD81 is not identical among human, chimp, rat, chicken based on this identity matrix from ClustalW2. Why is CD81 not identical in all species? What factors cause the different in CD81s? How do those factors cause that (e.g. evolutionary pressure)?
#
#
Percent Identity  Matrix - created by Clustal2.1
#
#
 1: sp|P60033|CD81_HUMAN    100.00  100.00   93.22   82.55
 2: sp|P60034|CD81_PANTR    100.00  100.00   93.22   82.55
 3: sp|Q62745|CD81_RAT       93.22   93.22  100.00   82.55
 4: tr|F1NW06|F1NW06_CHICK   82.55   82.55   82.55  100.00

Welcome to Biology.SE. What contribute to the variation [..]. The maintenance of genetic (and therefore protein and phenotypic) variation is one of the main question of evolutionary biology. It is extremely studied and there are a lot of processes that either retain or remove genetic variation. The question is too broad. [..] and how do they influence? How do they influence what? (I am not sure what they stands for either) It is unclear.

Thanks Remi.b for your feedback! I have clarified my word and add an example.

I didn't like my answer so I deleted it. It is hard to answer such a broad question. However, there is one result you probably want to remember. If you can assume that both species and all of their ancestral lineages up to their Most Recent Common Ancestor, had the same mutation rate $\mu$, then, the substitution rate is $\mu$ as well.

It is indeed general so that's why I have such a hard time answering as well as finding literature. Anyway, I have found my answer related to the keyword "Neutral evolution" or "Molecular evolution".

I've edited the English in your title. Hope you don't mind.

I would dispute your conclusion that it is simply neutral evolution. Neutral change absolutely does occur but it is not a complete answer to your question. Similar proteins in different organisms are not in the same environment and rarely do exactly the same thing.
For example, your three mammals will have similar but not identical body temperatures while the chicken's body temperature will be slightly higher at 42 degrees. Enzyme efficiency is highly temperature dependent so it is likely that some of the difference is attributable to optimal function at different temperatures. I don't know anything about CD81 specifically but it is often the case that gene regulation pathways are similar, but not identical, between organisms so that you may find that it needs to interact with slightly different proteins in a slightly different way.

I have found an acceptable answer for my question. Just post here if any interest in it. Pardon my English.
Source:
Nei et. al. 2010. The Neutral Theory of Molecular Evolution in the Genomic Era. Annu. Rev. Genom. Human Genet.
Evolution and point mutation cause the sequence difference of the same functional protein across species. Neutral theory of molecular evolution shows that speciation level of evolution is an accumulation of molecular level of neutral evolution. In neutral evolution, the mutation only occur at a scope of point mutation in sequence in the manner that the function of the protein is retained. Overtime, speciation occurs yet the function carried out by that specific protein is still necessary and is conserved across species. Difference in protein sequence of the same functional protein is the residuals of random point mutation.


text:
Why is a magnesium ion essential for ATP activity in enzymic reactions?
The Wikipedia entry on Magnesium in Biology includes the following:

ATP (adenosine triphosphate), the main source of energy in cells, must be bound to a magnesium ion in order to be biologically active. What is called ATP is often actually Mg-ATP.

I don't understand why magnesium is essential for breaking the high energy bond in ATP?

One of the key reasons is that Mg covers the negative charge of the triphosphate and therby allowing Mg-ATP to bind to hydrophobic clefts in the active site

wouldn't the presence of mg hinder release of phosphate?

I will add that to my answer @JM97

As far as I know there are two main reasons for this:

promoting a nucleophilic attack

In general, Mg2+ interacts with substrates through inner sphere
  coordination, stabilising anions or reactive intermediates, also
  including binding to ATP and activating the molecule to nucleophilic
  attack (wiki)

 - assists in the leaving a pyrophosphate group and may also facilitate the cleavage of the bond between the α- and β-phosphates by its electron-withdrawing effect. (source)

wouldn't the presence of mg hinder release of phosphate?

As with all reactions this is dependent of the concentration of the molecules
involved as stated here:

The Gibbs free energy change (ΔG) due to ATP hydrolysis depends upon
  the concentrations of the various participants in the reaction. When
  the concentrations are farther from their equilibrium values, the
  absolute value of ΔG is greater. Under “standard” conditions (i.e.
  concentrations of 1M for all reactants except water which is taken at
  its characteristic concentration of 55M) the Gibbs free energy of ATP
  hydrolysis varies from -28 to -34 kJ/mol (i.e. ≈12 kBT, BNID 101989)
  depending on the concentration of the cation Mg2+. The dependence on
  Mg ions occurs because the positively-charged magnesium ions help to
  stabilize the ATP molecule. However, in the cell the conditions are
  never even close to the standard state values. (source)

The answer by Rick Beelo discusses the role of magnesium ions in relation to catalytic mechanism, but does not include a more general and long-accepted role of the ion. This is to hold the triphosphate ‘chain’ of ATP in a specific conformation and in this and other ways to enhance the binding to the enzyme, an essential initial step in the catalysis of any reaction involving ATP. Thus, in a section of the standard undergraduate text book, Berg et al. one finds the following:

How does the binding of the magnesium ion to the nucleotide affect catalysis? There are a number of related consequences, but all serve to enhance the specificity of the enzyme–substrate interactions by enhancing binding energy.
First, the magnesium ion neutralizes some of the negative charges present on the polyphosphate chain, reducing nonspecific ionic interactions between the enzyme and the polyphosphate group of the nucleotide.
Second, the interactions between the magnesium ion and the oxygen atoms in the phosphoryl group hold the nucleotide in well-defined conformations that can be specifically bound by the enzyme…
…Third, the magnesium ion provides additional points of interaction between the ATP-Mg2+ complex and the enzyme, thus increasing the binding energy.

This latter point can be seen in the 3D structures of ATP bound to enzymes, illustrated in Figure 9.50 of that edition, where the ATP interacts with an Asp residue through two water molecules bound to the magnesium ion:


text:
Are two eyes necessary for 3D vision?
It has always been my understanding that humans have two eyes so that we can have 3D vision: the left eye sees more of the left side of an object than the right eye and vice versa. This helps us to estimate depth among other things.
Now when I close one eye, I still am able to perceive depth. I assume this is because my brain fills in the blanks For how long does this work? Do people eventually lose the depth perception (or at least it diminishes significantly) when they lose a single eye?
If so, how low does it take? If not, clearly we are capable of perceiving everything with one eye. Why do we then have two (besides redundancy and a larger field of view)? What is considering the evolution of man better in having two eyes as opposed to one or three, or four,..?

Here's an open-access article on monocular stereopsis that might be interesting: https://www.researchgate.net/publication/253334388_Seeing_in_3-D_With_Just_One_Eye_Stereopsis_Without_Binocular_Vision .. Being said this may very well be more suited on cognitive science SE.

@Kendall +1 for neat article. But I disagree about migrating the question.

I guess distance can be perceived with information from lens focal length, but that is not sufficient for 3D vision.

It seems like you suffer from a misconception. "The left eye sees more of the left side of an object..." is not how distance perception works. Otherwise we wouldn't be able to estimate the distance from flat objects, such as traffic signs and shooting targets.
The actual mechanism is parallax estimation, or Binocular disparity. In a nutshell, the closer an object is to your eyes, the bigger the difference of its position on the left and right eye's retina will be.
You may perform a simple experiment: find a place where several parallel wires hang in the air: a train line or aerial phone/power line. Look at the wires normally, and they will appear just as black lines in the sky, with no distance perception. Now tilt your head to the side, and you will instantly gain a feeling which one is closer, and which one is further away. Why the difference? Because any shift of a horizontal wire gives the same picture, meanwhile for vertical wires the difference is obvious.
When you close one eye, your brain loses the ability to estimate parallax. However, it is left with several options:

Visual cues. If one object overlaps another, it's obviously closer. If two objects look the same but one is smaller, it's probably further away (or a child). If you know the expected size of an object (a mountain/a horse/a fly), you may get the feeling of distance as well.
Focusing distance. When you focus your eye on a near and far object, the feelings are different.
Memories. You remember what you've seen with two eyes.

Of these, only (3) depends on previous binocular vision. (1) and (2) are available even to those who were born with one eye. However, parallax estimation is much faster and more precise. With a single eye you will be able to hit a fly on the wall, but catching it in the air will be extremely difficult.

Actually, there is 4. moving your head (or the whole body) in order to get different viewpoints. Human brain is perfectly adapted for this approach and computer graphics frequently "abuse" it, because the 2D screen cancels any binocular vision or focusing distance cues. That's why 3D object are frequently presented slowly rotating.

As someone who is blind on one eye I can confirm an option 1 works pretty well under most circumstances and option 2 covers a lot of the others. they don't work well on quickly moving objects though.

Edit01 (here and scattered throughout)

[Not meaning to be antagonistic… but admittedly somewhat defensive.]
Insofar as the following is a citation of an existing work, it is the below Martin and Foley item, pp165-185 (with a noted exception) — noting again that I read this years ago, and did not consult it (nor anything else) when writing the below… and (again) that I consider that, although this can be studied as a science, most of the root knowledge is innate (of course) and implicit and could be rendered explicit by any adult who did not already have it so (as in the following example).  (It is of course theoretically possible that I have read other sources on the same material.  As far as I am concerned, most modern adults would consider almost everything here neither insightful nor controversial, with the exception of brightness (for which I have no source), height cues (which I did not mention) and kinetic depth effect (which I did not mention and which is not obviously and certainly relevant to the question).)
Atmospheric colouring is an exception in that one can use this to work out that air is blue (as opposed to needing to know that air is blue to make sense of an apparent phenomenon).
Brightness is an exception in the case of which indeed I should have supplied a reference… except that, as noted, I can not see it in the noted text book, and thus have no idea where I heard it (noting that I do have a memory of the excitement of learning this (or possibly working it out)).
More citation anomaly and disparity as noted.
End — Main Body of  Edit01.

Original, with references in “[]” added.

Going from memory, since no one else has covered this… .
This is more a psychology question (as below).
3D vision utilises about seven different mechanisms.  Binocular vision accounts for only two of these.
• Occlusion — each eye sees slightly different areas of a partly occluded object.  [(“Occlusion” suggests also the monocular topic “interposition”, below.)  As a binocular phenomenon, Martin and Foley (p183) label this “binocular disparity”, which is [from a quick look] actually about the image from the same object falling on “different” — I would say “non-corresponding” — areas of the retina (as a function of being closer to, on, or further from, the focal distance).  [From a quick look] they do not seem to cover the fact that one eye will actually see more of a partly occluded object (which means I have no idea where I heard it (and I am thinking that I might well have worked it out myself)).
• Focus — you have to focus both of your eyes on an object to see it not-fuzzy; your system knows about (relative) eye positions and subject distance.  This includes both focusing the lens in the eye [“accommodation” [p167] is lens shape] and pointing both eyes at the object [“convergence” [p182] is the eyes turning towards each other].
Binocular occlusion information only works out to about (from memory) 2m [“10 feet” Martin and Foley p183].  This would be increased by having the eyes further apart.  (Focus works out to a much greater distance; I am not sure which of the above two aspects is more useful, but I am guessing it is lens shape (and that they are of roughly similar usefulness).  [Martin and Foley mention “10 feet” (p167), citing Hochberg (1971) for accommodation (lens shape)… but appear to have chosen this as immediately arbitrary.  Their point is that it yields “rather weak” distance information.]
Other (monocular) 3D vision cues include the following.
• Object size — many objects have a standard size [“familiar size” p167], and almost all objects have different proportions (such as leg thickness) according to how big and heavy they are [which Martin and Foley do not cover; the source is me]… and an object that is further away will have a smaller image size.  [pp167-169 “size cues”, “relative size”.]
• Brightness — any given object will reflect less light into the eye from further away (because the eye is a smaller target further away).  (This is more useful and important than one realises.)  [From a quick check, this one does not appear to be in the noted text.  I do not think (particularly) that I worked this out for myself, but if it is not in that text, then I have no idea where I heard it.]
• Perspective — many types of object (e.g. road, path, wall, river) have a stable width, or similar or analogous, and this will have a progressively smaller image size with greater distance.  [“linear perspective” p170.]
• Texture — many objects have a known texture (or (assumptively) a regular texture), and the image size of the detail of the texture will decrease with distance.  This works for groups of animals, and leaves, and the like, as well.  [pp169-170.]
• Air tinting — the further away an object is, the more it is tinted blue by the interposing nitrogen.  [“atmospheric perspective” p170.  Martin and Foley also say that more distant objects appear “blurr/y/”.  I would say that that is largely because we have less visual acuity for an object that is further away (because the image size is smaller); Martin and Foley put it down to interference by air particles.]
• The physics of movement — speed and acceleration can be informative.  [Martin and Foley treat this area on pp174-176.  I was thinking of… what I said.  M&F mention “motion cues” (the class), “motion parallax” (which involves the subject moving laterally, and multiple stationary objects), “motion perspective” (which involves the subject moving towards or away, in any environment) and “kinetic depth effect” (which is about apparent 3D-ness in rotating objects, and is ostensibly not about distance).]
[Other monocular items that Martin and Foley mention… .  • Shading [p170] — objects can cast shadows on other objects.  I would say that this is primarily not about distance perception.  • Interposition [p167] — the nearer object obscures part of the further object (or not).  • Height cues [pp173-174] — my take on this is that, on flat ground (and because the viewer is above the ground), an object that is further away will have its base closer to the horizon and thus visually higher… and, for objects in the air, I would say here only that it is more complicated.]
Focus is very valuable for (for instance) catching a ball, whereas a task like driving [with one eye] has much more 3D information available.  [Source:  I worked this out using thinking.  …So it’s me.]
As for having more than 2 eyes… having eyes spaced apart vertically (as well as having the existing horizontal spacing) would give additional occlusion information, but the gain would be minimal.  [Source:  I worked this out using thinking.  …So it’s me.]
Source

The source is a custom book — that is, “Custom Book”, which is, “a compilation of chapters from… [existing] Pearson Education Australia titles.”  The publisher logo “Prentice Hall” appears, but only as a logo, and not on the cover.
The Custom Book is “PSYC236 Cognition and Perception”, ©2001, Pearson Education Australia Pty Ltd.  It is “Sourced from:  Sensation and Perception 4th Edition”, ©2001, Martin and Foley.
The cited material is from a chapter numbered 6, which appears to be its number in the original/source book; ditto for the page numbers.

But the question is based on a misconception or reversal of causality. "humans have 2 eyes so that we can have 3D vision" is backwards.  We have 3D vision because we have two eyes.  We have two eyes because, like all vertebrates (and insects &c), we are bilaterally symmetric and have two (or pairs) of just about everything.  But starfish, for instance, with 5-fold symmetry, have 5 eyes.

Welcome to Biology.SE! While this could be part of a good answer, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion and thus not appropriate for this site. This is a good example of how to format references. ——— You may also want to take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site. Thank you!

@jamesqf Eh, I do think the OP has a bit of confusion about that, but I think their question is more along the lines of "why can I still perceive depth with only one eye". "We have 3D vision because we have two eyes" isn't true - there are several monocular depth cues that give us 3D vision as well. People physically missing an eye or with amblyopia still see in 3D. Additionally, many other mammals have poor stereoscopic vision despite having 2 eyes, our quality of stereo vision is an adaptive trait shared with other mammals like other primates and carnivores (and non-mammals like raptors).

In summary, I think this answer perfectly answers the question that was asked, it's just missing references as noted in the banner and pointed out by tyersome.

@Bryan Krause: True, and also binocular stereopsis only works for relatively close objects.  For instance, ever noticed the exaggerated 3D effect of viewing a fairly close subject with good binoculars?

That the following 3D vision cues are available is necessarily true (given gravity et al.):  occlusion, lens focusing, eye focusing, object size, brightness, perspective, texture, air tinting, acceleration physics (which is, of course, all of them).  Any text book on the psychology of vision will mention these.  (I can dig mine up if this would actually help?)  I do not think I ever read any attempt at explaining how the human vision system utilises this information.

Theoretically, I could do a huge search for mention of experiments that show that we use them?  However, I think a reasonable person could accept {the fact that the items in the list belong there necessarily} as sufficient.  …So I am taking this as yet another personal slight.

The ability of seeing in 3-D is an emergent quality of the brain. Yes; at a certain level, all perception is based on emergent qualities of our brains.
That being said, when I was sleep deprived for almost three full days, I began to see in 3-D using only one eye. Somehow, my brain ‘unlocked’ an ability that had previously been limited to seeing with both eyes. Even more astonishing 2-D printed photos and 2-D computer images appeared in 3-D as well.
Anecdotal? Yes. But genuine and real to my perception as anything else I experience. Go figure!
See definition of ‘neural reality’. I believe this allows a sneak peak behind the curtain of human perception.


text:
Is every protein encoded by just one gene?
Beadle and Tatum proposed the “one gene, one enzyme” hypothesis in the 1940s, and this was later modified to “one gene, one protein”, i.e. that one gene codes for one protein.
Have any exceptions to this emerged subsequently? Are there single proteins, parts of which are encoded by separate genes?

don't forget that one gene can can code for multiple proteins... splice variants https://en.wikipedia.org/wiki/Alternative_splicing

@VanceLAlbaugh But are there proteins that emerge from more than one gene instead of parts of one?

@VanceLAlbaugh Is it possible that two adjacent genes melt together and are expressed if as they are óne gene?

The short answer to your initial question is yes. There are many examples of proteins that are the result of the expression of multiple genes. Hemoglobin, immunoglobulins, microtubules made of different tubulin subunits, etc. As for the other question, that is less prevalent in eukaryotes. It is not unheard of for bacteria to express operons as a single RNA, though ribosomes usually translate individual proteins. Viruses are known to do this. HIV's genome is translated from a long RNA that contains multiple genes into a single polypeptide which is then cleaved post-translationally.

@AMR There is a single gene that codes for a polyprotein, not multiple genes. After proteolytic cleavage multiple proteins arise. This is an example of one gene, many proteins and not the vice-versa.

@WYSIWYG "During viral maturation, the virally encoded protease cleaves the Pol polypeptide away from Gag and further digests it to separate the protease (p10), RT (p50), RNase H (p15), and integrase (p31) activities. These cleavages do not all occur efficiently, for example, roughly 50% of the RT protein remains linked to RNase H as a single polypeptide (p65)." http://hivinsite.ucsf.edu/InSite?page=kb-02-01-02#S2.1.2X

@AMR I didn't deny. But this essentially means that they are encoded by a single gene. There is no dispute there, I believe.

@WYSIWYG  you are mistaken. gag and pol are considered to be distinct and independent genes from one another. Both are genes that encode for polyprotiens. They are expressed together as they are transcribed in a single RNA, are translated as a single polypeptide chain, and then are post-translation ally cleaved by HIV proteases. Not my definition, just what virologists and geneticist shave characterized.

@AMR that's what I said. gag is a gene that codes for a polyprotein that gives rise to multiple proteins. That is one gene many proteins. Are you saying that gag and pol are transcribed together as a single RNA and so they should be considered one gene? That's more like a polycistronic RNA. BTW, gag-pol is also a gene in itself and there is a gag-pol polyprotein. I haven't yet read HIV gene expression in detail but I know it is a bit complex.

@WYSIWYG it was only addressing the question in the third comment "@VanceLAlbaugh Is it possible that two adjacent genes melt together and are expressed if as they are óne gene?" And I answered initial that you would not find it in Eukaryotes, but can see it in viruses. I am not saying they are one gene, but would fit the description of two genes being expressed as if they were one gene and then the translated product of those to genes, itself a single polypeptide chain is posttranslationally cleaved into the relevant gene products.

As this has come up again I have edited the question and provided an original reference to the idea.

You may be interested in trans-splicing.

There are proteins encoded by more than one gene.
It would be a heterodimer protein of quaternary structure. One famous example would be haemaglobin, which is assembled from alpha and beta sub-units.
Also, one gene is capable of coding for multiple proteins!
https://en.wikipedia.org/wiki/Protein_dimer
https://en.wikipedia.org/wiki/Protein_quaternary_structure
https://en.wikipedia.org/wiki/Hemoglobin

Though hemoglobin is not a dimer as your answer seems to imply.

As I had modified the question I had to clarify the "yes" in your answer.

I'm surprised that one gene is capable of coding multiple genes, which brings to mind a question I'm gonna ask now.

Generally speaking the answer would seem to be:

“No, a single polypeptide chain is encoded by a single mRNA from a
  single transcript of a single gene.”

Obviously if one uses the epithet, protein, for a hetero-multimer like haemoglobin, one could say yes instead.
So far, nothing new since the question was posed two years ago. But, at the risk of being shot down in flames, let me suggest two possibilities.
1. Immunoglobulins
The vast diversity of antibodies arises not from the fact that there are a vast number of immunoglobulin genes in the genome, but that there is a repertoire corresponding to different sections of each antibodody chain, the recombination of which in individual B-cells gives rise to different genes. See, for example, this section of Alberts et al. As far as the precursor cell is concerned, the mature immunoglobulin chains are the products of different genes. As far as the mature individual B cells are concerned, each chain of their gene products arise from a single recombined gene.
You pays your money and you takes your choice.
2. Metalloproteins
Let us consider the metalloprotein like urease. This enzyme, which breaks down urea to ammonia and carbon dioxide, requires Nickel to function. One can adopt the standpoint that the protein is not complete without the metal cofactor. The genetics of urease has been well studied in certain pathogentic bacteria like Helicobacter pylori, where it is part of a gene cluster. Other components of this gene cluster encode proteins required to deliver nickel ions to the inactive enzyme.
One could argue that without Nickel the protein is incomplete, so that functional urease is encoded by multiple genes of that cluster.
Depends what rules we are playing.

There are protein complexes which are made up of multiple subunits.  Whether you call that one protein or a multi-protein complex might depend on whether you have a gene-centric or protein-centric point of view.

Not really. A protein is a single polypeptide chain. There are many proteins that exist (sometimes solely) as a part of multi-member complexes, but those complexes are never referred to as proteins. They're called protein complexes, even by very "protein-centric" (your phrase) biochemists.

Now, there have been cases where a complex was initially thought to be a single protein, and named as such, but further research showed it contained multiple subunits. But after the new knowledge is disseminated, one wouldn't keep referring to the complex as a protein.

@MattDMo What is meant by subunits? Doesn´t every protein contain them?

@descheleschilder - ask a question as a question post, not a comment.

@MattDMo You are kidding, right? from Lehninger Principles of Biochemistry; protein: A macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by polypeptide bonds. quaternary  structure: The three-dimensional structure of a multisubunit protein, particularly in the manner in which the subunits fit together. Hemoglobin is a protein... and its subunits come from distinctly different genes that encode the polypeptides that make up the subunits of the protein.

I would say the distinction is functional and structural. A polymerase holoenzyme has subunits that perform different functions and could be considered a protein complex. A nuclear pore complex is structural and provides a substrate for interactions with other proteins that creates a selective barrier into and out of the nucleus as well as creating directionality in nuclear transport. The subunits of hemoglobin or the light and heavy chains of immunoglobulins work together to produce a particular function so those would be considered more proteins than true protein complexes.


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Was there originally a non-ribosomal way of synthesizing proteins?
Proteins are synthesized on ribosomes from mRNA copies of regions of the DNA. But ribosomes themselves are made up of proteins (and RNA). So how could the first ribosomes have arisen? Was there previously some other way of making proteins other than by ribosomes and mRNA?

most of a ribosome is RNA including most of the functional surfaces, ribosomes are made of protein is about as true is saying you are made of bone. They are certainly important but they are by no means the bulk of its functional systems.

Although I am of the same opinion as fpdx and the majority of scientists — that there was an RNA world in which the genetic material and the catalytic molecules were RNA (rather than DNA and protein, respectively) — there are some quite respectable scientists who hold a different view. As there is no proof for either viewpoint (and hence no correct answer to the question), it is important to present this alternative.
In brief, the alternative viewpoint is of a "proteins-first" world: i.e. the first proteins were made without ribosomes from chemical reactions in the "primeval soup". Only later did the contemporary and template-driven ribonucleoprotein machinery for making proteins evolve.
I do not know of an online source of arguments in favour of the protein-first viewpoint — an article by C. Kurland in Bioessays 32: 866–871,(2010) requires library access or purchase. However there is an on-line article discussing the objections to the RNA-world viewpoint, which, even though it argues against these objections, gives one an idea why the question cannot be considered settled. This is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495036/#B57.

(A quick answer to a question that will be likely closed being not well focused on the physics of all this)
First: the ribosome translates mRNA into the chain of amino acids that eventually will become a protein. The ribosome is a huge complex, made of both proteins and RNA. RNA can have enzymatic activity like a protein: the ribosome is a Ribozyme.
This chicken or the egg problem has puzzled biologists, chemists and biophysicists for a while. The structure itself of the ribosome was the "smocking gun" for the model we have today: the RNA world. In few words: because RNA can act as a protein and it is so similar to DNA, probably our DNA-world (i.e. information stored on the DNA, work done by proteins, RNA between the two) emerged from a fully RNA-world, where RNA was responsible for both protein activity and information storage.
How in detail all this happened by evolution, is probably the subject of several nobel prizes to come.


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Epistasis when interacting loci are codons within a single gene
There is epistasis when the effect on the phenotype of one gene is influenced by one or more other genes (called modifiers). Is there a similar concept when the effect on the phenotype of one site within a gene is influenced by one or more other sites within the same gene?
For example: Think about an opsin (a light sensitive protein) that gets activited when hit by a wavelength of, say 500nm.  If the mutation A124S (at position 124 the aminoacid A is replaced by the amino acid S) exists, then the protein is activated when it gets hit by a wavelength of 560nm but this shift occurs only if there is a V (instead of a I) at position 95. Hope you get the idea! Are there specific words to describe such phenomena?

The Wikipedia article on epistasis has a section on epistasis within genes, which it terms intragenic complementation:

Just as mutations in two separate genes can be non-additive if those genes interact, mutations in two codons within a gene can be non-additive. In genetics this is sometimes called intragenic complementation when one deleterious mutation can be compensated for by a second mutation within that gene.

It appears that many interesting examples of this phenomenon occur when the protein forms multimeric complexes. A multimer consisting of monomers with different mutations may function where a homogenous multimer of monomers of only one of the mutations might be inactive. See Turner et al., (1997) PNAS 94:9063-9068. The Wikipedia article mentions some examples of this under the term interallelic complementation or heterozygotic epistasis.
This reminded me of the phenomenon of protein coevolution that is currently being used to try to leverage evolutionary information to solve protein structures. When the homologous sequences of a protein are known in many different species, then a reasonable assumption is that mutations in protein residues that are in close spatial proximity will correlate, e.g. if a lysine is switched to an glutamate, then other nearby residues may mutate to accommodate the change in ambient electric charge. For more information on this effect, two very interesting papers are Hopf TA, Colwell LJ et al., (2012) Cell 149(7):1607-1621, where the sequences of a family of membrane proteins are used to predict their structure, and Skerker et al (2008) Cell 133:1043-1054, where the covariation between residues in a complex of two proteins is used to re-wire the specificity of one protein for another.


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Is it possible for a prey to become its main predator's predator?
This is actually for a worldbuilding project, but I thought I'd just ask it here as it is solely about biology.
Anyway, would it be possible for a herbivore, let's call him X, that is predated by a predator, or Y, to evolve to become a specialized hunter of Y?
For example, wolves hunt deer. Imagine that in millions of years, the deer has evolved into the main predator of wolves.
If that's not possible, is it at least possible for X to evolve adaptations for fighting/killing Y (Not for food)?
If you require any further context or clarification, please let me know.

Humans, compared to everything ("Lions and tigers and bears, oh my!") that used to eat them.

@jamesqf Mine is a question more about evolutionary traits. Humans can hunt and wipe out those large predators because of their advanced tools.

Also it should be noted as you move from prey to predator, there is less energy to be had. This is why we often do not have a predator of a predator species. There simply isn't enough food at that level of a predator to support another predator above it.
That said, I am assuming you are thinking of an alien ecosystem. In which case you might be able to sustain such a system if there is a massive flux of bio-matter through the ecosystem. Ie plant food is extremely abundant and animals within it reproduce at an extremely fast pace. We can see such an environment at the bottom of a marine ecosystem in the polar regions during summer (near constant sunshine, and an up welling of minerals from the deep sea.

If that's not possible, is it at least possible for X to evolve
  adaptations for fighting/killing Y (Not for food)?

Happens all the time. While lions do hunt cape buffalo, cape buffalo can and do kill unwary lions.

I guess that the Cape buffalo can kill lions because it's just a dangerous animal in general. But if there was, for example, a rodent that was preyed on only by snakes, is it possible for that rodent to, say, become bipedal to have hands to grasp their serpentine predators? I don't mean "is it physically possible", that was just an example, but can anti-predator adaptations be that specialized?

Well the mongoose is immune to cobra neurotoxin because the molecular structures of acetylcholine receptors of the mongoose has an altered shape that prevent the neurotoxin. So yes, the anti-predator adaptation could become fairly specialized, especially if the prey has only a single predator.

As most prey are herbivores, becoming a predator requires large adaptions to the digestive system. I therefore think becoming a predator is unlikely.
However, some animals are able to defend themselves very well against their predators. The best example I know, is the African buffalo. This animal is capable of defending itself against all predators, including lions. I've once seen a documentatory where buffalo attack and kill young lion cubs.


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Stopping the Gag Reflex: How and why does it work?
I was talking to some friends over the weekend, and one of them made a comment about gagging. He said that he read or watched that clenching your thumb with your other fingers (making a tight fist with your thumb in the middle) stops your gag reflex. So, naturally, as a bunch of stupid teenagers, all 7 of us proceed to do this while shoving our fingers down our throats as far as possible. None of us had a gag reflex.
Why does this work? it seems totally random and weird.

It might work because it distracts you. When you have a gastroscopy (stomach investigation) in hospital, the nurses try to make you focus on other parts of your body ("try to relax your legs"). It helps.

OK, that's what I thought at first too. Just tried it while looking at my leg, and that also worked. Can you add that as an answer with some some source so I can mark it answered?

is this relatable to jendrassiks?


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Amino Acid requirement + intake in relation to diet + meat type
I was arguing with a friend:
I said: The Yulin festivals cannot be condemned by western culture, as we also kill animals in equally cruel ways.
She said: It isn't just that the killing is cruel, but it doesn't help us, as humans do not derive the same essential amino acids from consuming these less traditional meats (e.g. dogs, cats, etc) like they would from consuming more traditional meats (e.g. cow, pig, goat, etc) She cites her father, a geneticist, as her source.

Question one:
Are my friend and her father correct? Does the consumption of a less traditional meat (e.g. cats, dogs, etc) provide fewer essential amino acids than the consumption of traditional meats (e.g. cows, pigs, chickens, etc)?
Question two:
My friend also made a comment about veganism and vegetarianism (I am a vegetarian), stating that for the same reason as her and her father's above comment, people who exclude meat from their diet need to use supplements. Is this correct, or would it also be possible to just vary diet to obtain these essential amino acids?

There is a big difference between amino acid production and essential amino acids.

Edited. Sorry about the lack of clarity.

I don't see how there could be significant differences in amino acid composition between Cattle or Pigs and Cats or Dogs. They are all mammals, and therefore relatively closely related. The major proteins should all have similar sequences. This paper might have better information, but it's paywalled. Besides, if you only judge meat by whether or not it has the perfect mix of amino acids for human consumption, then humans would have the best meat because they already contain everything a human needs in the right proportions.

There is a difference between animals in their requirements for amino acids. For example, cats need high amounts of taurine (and can't make it) and when fed diets lacking enough can go blind. This is why vegans trying to feed vegan diets to their pets can be very bad for the pet. Animal proteins have sufficient taurine for the cat.
However, the meat of a cat or dog is just as a complete source of protein for humans as any other meat. All essential amino acids are there in sufficient ratios. Suggesting otherwise by her father suggests some confusion between the dietary needs of cat vs. the nutritional value of the cat to another predator.
Your second question is easily answered by looking up essential amino acids.  Wiki is plenty sufficient to get the gist Wiki Link. In short, most plants don't contain the full complement of amino acids that humans require (and can't make on their own). So to get this full complement, it requires eating multiple plant products that together contain the required amino acids.
From Harvard School of Public Health

Protein is built from building blocks called amino acids. Our bodies make amino acids in two different ways: Either from scratch, or by modifying others. A few amino acids (known as the essential amino acids) must come from food.
Animal sources of protein tend to deliver all the amino acids we need.
  Other protein sources, such as fruits, vegetables, grains, nuts and seeds, lack one or more essential amino acids.
Vegetarians need to be aware of this. People who don’t eat meat, fish, poultry, eggs, or dairy products need to eat a variety of protein-containing foods each day in order to get all the amino acids needed to make new protein.

Good info, but are there sources? Thanks

Animal meat is generally animal meat. I could find nothing about essential amino acid composition between different kinds of animal meat. You can find lots of differences in fat content and some differences in mineral content based on the species, but that isn't your question.

One more thought about her father. Cats do have a genetic difference that doesn't allow them to make taurine from other amino acids. This may be what he was thinking of, as humans and most animals do have this pathway.  However, as mentioned above, this has no bearing for the consumer of the cat as food.


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What does the gene name "lexA" stand for?
It is an important gene expressed in E. coli that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence the expression of repair genes and, if present, lambda phage genes. However I couldn't find a reference for its original name.

What does gene name X stand for? I think you might be expecting a little bit too much from the standard naming conventions...

What naming conventions?

I think there's some guessing going on here. I've looked pretty extensively and the information is not out there. Nothing conclusive. Lambda is a different depressor, worth noting. I would contact the person who discovered it: Miroslav Radman, Prof. Founder
tel:+385(0)21555601 fax:+385(0)21555605 e-mail:miroslav.radman@medils.hr

@Masih I linked a paper in my edited answer which I believe clears up some of the confusion in "Lambda Excision."

I'd go with Lambda Excision A. Terms like lex or rec often stand for what'd be termed a mnemonic, where for example rec may stand for recombination, or umu for UV mutator. The naming conventions can be difficult.
Edit: A 1981 study by Roger Brent and Mark Ptashne notes some data from initial studies that showed the lexA repressor downregulated a number of genes including himA, which they note to be required for integration of lambda phage.
http://www.pnas.org/content/78/7/4204.full.pdf

According to this website, it is a mnemonic for "lambda excision". I have also found this usage in scientific literature (eg. Harami et al., 2013). However, neither of these sources reference anything and I cannot find any defining paper. Almost all papers simply refer to it as lexA.
As far as I can find (it's difficult to dig up these old papers), this is how the locus (not necessarily gene) was originally described (Howard-Flanders and Boyce, 1966):

There is a ... locus, lex (locus for X-ray sensitivity), in E. coli K-12 ... [A] mutation at this locus increases the extent of UV-induced DNA breakdown. This effect is similar to, but less extreme than, that of the rec locus ...

It's possible that as this locus was better characterised, the name lex was retained for consistency with previous literature but redefined to reflect a better understanding of its function (although I don't think that "lambda excision" does this very well at all).

References
Harami GM, Gyimesi M, Kovacs M. 2013. From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins. Trends Biochem Sci 38(7):364-371
Howard-Flanders P, Boyce RP. 1966. DNA Repair and Genetic Recombination: Studies on Mutants of Escherichia coli Defective in These Processes. Radiat Res Supp 6:156-184

Lee Theriot's X-ray sensitive mutant https://thebradentontimes.com/lee-frances-theriot-p24426-154.htm I was a postdoc with Joseph Greenberg working in the same field at the time

This is well documented in Advances in Microbial Physiology, Volume 16, Moseley and Williams, pages 116-117 (searchable via Google Books).
Mattern et al. (1966) designated mutations that made E. coli Bs-1 sensitive to X-ray radiation as exr (X-ray sensitivity) mutations. That same year, Howard-Flanders and Boyce (1966) independently designated equivalent mutations in E. coli K-12 as lex (locus for X-ray sensitivity). In both strains these mutations were close to the malB locus (b4039; lexA is b4043). A year later, Greenberg was using a broader designation with the same causal root (Loci for Radiation Sensitivity) to designate these same mutations.
LexA is also known as umuA (UV-induction of mutations) and tsl (thermosensitive mutations).