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How does paracetamol interfere with immune system?
Paracetamol is used to reduce body temperature when it is to high. The high body temperature (fever) is known to be an indication that immune system fights against an infection.
In this context I have two related questions:

Is high body temperature one of the mechanisms of immune system to suppress an infection or it is just a side effect?
If it is just a side effect, does paracetamol remove it by decreasing the intensity with which immune system fights with an infection or not?

Your first question is a repeat of this one: http://biology.stackexchange.com/questions/7541/if-fever-is-a-natural-immune-defense-why-do-people-take-drugs-to-lower-it

First question: Yes. The immune system releases pyrogenic cytokines such as IL-1. Bacteria aren't typically used to 37C, they prefer working at under that temperature to function in the environment. Our body however can take a few degrees here or there however this severely compromises the bacterial enzyme activity. The same is true for other pathogen enzymes. The body also increases copper concentrations in the blood for similar reasons. Problem is of course if the body goes into overdrive and raises our temperature too much, this compromises our own ability to fight the infection so in that case antipyretics like paracetamol can reduce fever.
Second question. It isn't a side effect, however paracetamol works by blocking things like IL-1 that raise temperature. How IL-1 raises your temperature is quite interesting, it tells the hypothalamus (our thermostat) that it should be set higher. So we feel cold (so we try to keep ourselves warm) and the body thinks it's cold (so it increases the temperature by burning glucose mainly)


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What is the brightest color a light source that only emits blue frequency light can achieve?
Let's say there is a luminous light bulb that only emits blue light, and you (or a camera if you prefer) look at it from a close distance. Will the maximum brightness perceived not have any "white" to it? Because there is no white light if it's all blue. Probably the brightest it could be would be solid blue? Therefore, blue photons could produce a range of color of black to solid blue depending on the luminous or amount of photons hitting your eye per second? If that's the case then what happens if you raised the intensity of the bulb to an extreme? Is there a cut off point where even if you add more intensity to the bulb, you still see the same solid blue color?

'"white light" is perceived when there is a roughly equal mix of frequencies.' Not even that. White light is perceived when there is a roughly equal excitation of the three distinct types of color sensitive photocells in the eye, and they each have a broad sensitivity. Which is essentially the same information you need to answer all of these "How do humans see XXX?" questions. We've accepted them in the past because (1) there is some physics in them and (2) there was nowhere else for them to go, but at this time I would favor moving them out.

Generally, looking at the ray of a fairly powerful laser (3-4W) you still see it of whatever color it is (blue, red etc, but not white). NOTE: be careful if you try this, it may be very dangerous! Never look directly into the laser beam.

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Why it is so difficult to treat leukemia?
I want to ask what is the reason that T315I type CML leukemia is currently untreatable. I have read quite a few papers in this subject. Why the current genetic oriented engineering drugs failed to stop the leukemia stem cell's expansion but can only slow the secondary leukemia stem cell's expansion? I found it to be utterly hopeless for a patient to be in such a position, as chemical therapy does not work well and radiation therapy can only target specific area. There are experimental drugs in the developmental stage but from what I know they are mostly unreliable.

The T315l mutation of BCR/ABL gene produce the complete resistance of CML leukemia to all currently available BCR/ABL inhibitors.
There is a idea that is not yet tested for such patients - allogenic hematopoietic transplatation.
More information:
http://www.ncbi.nlm.nih.gov/pubmed/20657522
http://www.ingentaconnect.com/content/maney/hem/pre-prints/1607845412Y.0000000050

While this helps, it does not answer my question. But thanks.

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How to reduce edge effects in cell-based high-throughput experiments?
In high-throughput experiments where cells are cultured, treated, stained, and imaged in 384-well microplates, I frequently see significant edge effects. For instance, the following plot shows cell count (as measured by CellProfiler from images) for each well on such a plate:

How can I reduce these effects? I can try to correct for them statistically, but it would be so much nicer to reduce them at the wet-work stage.

Lundholt et al. describe a very simple trick: let the plates settle in air at room temperature for a couple of hours before placing it in the incubator. We tried it out, and although the color scales are different in the following plots, it is easy to see that it really does help:

(Thanks to Sigrun Gustafsdottir and Kate Madden for testing this.)
I have seen some people "pad" the plate by using only the 308 interior wells and filling the  76 edge wells with only liquid, but I have no data for how well that works.
Allison Tanner from Corning has collected a compendium of techniques to reduce the occurrence of irregular patterns of cell adhesion or “edge effect” in microplates. Brifly summarized:

Avoid bubble formation in the media when seeding cells.
Use cell harvesting methods that foster adequate mixing of the cells in the media and complete dissociation of the monolayer into single cells.
Seed cells at a density that will support attachment and growth.
Allow cell attachment to occur in media of the proper formulation for the particular cell type.
Dispense cells in an appropriate volume of media.
Follow strict aseptic techniques according to respected microbiological practices.
Cultures should be routinely monitored for mycoplasmal contamination.
Minimize entrance to incubators to help reduce fluctuations in the internal environment.
Allow cells to settle in the microplates while the microplates are on the benchtop.
Culture cells in an environment that reduces the formation of static electrical charges.


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Why are potassium channels slower than sodium channels?
I am relatively new in the subject of biology. I have a strong mathematical background and in order to get into the field of computational neuroscience, I am trying to get some biological background.
I am reading about the general mechanism of action potentials in neurons.
I understand that an action potential starts with a fast entrance of sodium into the postsynaptic cell. Since the potassium channels are slower than the sodium channels, potassium starts flowing out of the cell only around the peak of the action potential, thereby hyperpolarizing the cell's membrane potential.
What is the mechanism that causes the potassium channels to activate slower than the sodium channels? Does it involve differences in the behavior of the suitable neurotransmitters? Because I didn't manage to find transmitters or couples of transmitters and receptors which activate potassium channels, but not sodium channels (or sodium channels and not potassium channels).

Slower can mean two things: slower conduction or slower response.

Just a correction: the action potential does not begin with the entrance of sodium into the postsynaptic cell. This ionic flow changes the overall voltage potential of the cell, and the action potential begins at the axon hillock or just adjacent to the axon hillock, where the sum of all such inputs may start the depolarization known as the action potential.

You have to understand how the integral proteins work. $Na^+$ channels are fast while $K^+$ channels are slow and long lasting in terms of conductance. $Na^+$ channels are voltage gated, via the S4 domain which is blocked by $Mg^{2+}$, while $K^+$ conductance is not voltage gated most of the time.

Short answer
The activation kinetics of Na+ channels are faster than K+ channels.
Background
Voltage-dependent channel gating basically occurs through three possible states of the channel: open, closed and inactivated (Fig. 1).

Fig. 1. Gating of a voltage-activated sodium channel. Source: Balseiro Institute.
Basically, ion channels are protein pores in the membrane. Upon depolarization, the pore opens, which is a process with fast kinetics in Na+ channels and slower kinetics in K+ channels (Lacroix et al, 2013). K+ channel activation is in the order of 6 times slower than Na+ channel activation. The slower inactivation of K+ channels allows sufficient Na+ to flow in the cell for the depolarization phase of the action potential to develop (Fig. 2).

Fig. 2. Action potentials and underlying Na+ and K+ currents. Source: Dundee Med Student Notes.
After opening, the channel is inactivated, which can occurs through a physical "protein-plug" as shown in Fig. 1, or through conformational changes in the pore. This inactivation again is fast in Na+ channels leading to a transient spike in the action potential, and deactivation is slower for K+ channels (K+ channels do not inactivate, but rather deactivate). This inactivation step results in the refractory period of a neuron (silent period after firing). The channel is then de-inactivated and converted to the closed state, after which the channel is again ready to participate in another round of firing.
Note that neurotransmitters do not activate voltage-gated channels directly. Neurotransmitters can activate ion channels, but those are ligand-gated ion channels, such as the nicotinergic acetylcholine receptor, AMPA receptor or NMDA receptor (Purves et al., 2001).
References
- Lacroix et al, Neuron (2013); 79(4): 651-7
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)

What would be the difference between an "inactivated" and a "deactivated" channel?


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Are the antibodies developed by differing vaccines still the same?
If one person gets an mRNA vaccine that teaches their body to deal with a specific virus, and another person gets a similar but different mRNA vaccine, and another person gets a more "classic" vaccine with modified/weakened/dead virus cells, will there be any real difference in the antibodies developed by the three different people?
My gut instinct says that the antibodies/proteins developed by all of the people will be mostly identical, but I'm not a biologist.
I'm having difficulty finding articles/research on this. Full disclosure: this somewhat pertains to the SARS-CoV-2 and the varying vaccines, but it is also a more general question. I was hoping to find research on this, but it is proving difficult to google for such a verbose subject.

The mRNA may encode different antigenes, e.g. different parts of SARS-CoV-2's spike protein, or other parts of its membrane or hull. See https://www.nature.com/articles/s41422-020-00392-7. The immune response will/would differ accordingly even in the same individual. Obviously, inactivated viruses will expose several proteins, but not in isolation, and have a different response yet.

In the COVID-19 pandemic, there has been some discussion on the effectiveness when people receive the first dose with one vaccine an the second dose with a different one.

"differing vaccines" - Do they differ? All Covid-19 vaccines seem to code for the same spike, in full length (m-RNA- and vector-vaccines only differ in their being based on either RNA or DNA), and differences if there are pertain to coding specific promoting oder stop codons only? And even protein vaccines do not differ in that respect. Don't they all use the same spike antigen with all its epitopes?

Due to the nature of the immune system, even people who receive the same vaccine will have a different set of antibodies.
Our immune systems generate a vast number of essentially random recognition combinations, unique to every individual. This leads to a polyclonal response to both infections and vaccines, involving multiple antibodies and the fine details of those antibodies differ based on the specific antibodies in the "library" that the person's body has generated.
Now, different antigens do result in different antibodies being selected for, so one might expect there to be additional differences due to getting an mRNA coding for a SARS-CoV-2 spike protein vs. getting a whole inactivated virus. There's a reason that the spike protein is the preferred target, however, in that its position on the outside of the virus leads it to be a focal point for the response to an inactivated virus.
Bottom line: the responses will differ, but will likely always have a varied set of antibodies targeting the spike protein in any case.

Great answer! I have a question. Won't all antibodies be targeted to antigens on the surface of the protein? Is it possible / useful for an antigen to bind to other types of proteins?

Antibodies do show up against non-structural proteins as well (e.g., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812099/).  I believe this is more significant for antigen presentation, whereas the surface proteins are more significant for neutralization of extracellular viruses.

Do the antibody tests just look at common antibodies that should be shared across almost almost individuals who have developed a resistance to the virus? Even when the tests work as desired, could they still miss resistance in a person who has different antibodies for Sars-Cov-2 than the ones being tested for? If so, is this a common issue?

@tparker Antibody tests don't actually check for specific antibodies. Instead, they present pieces of the antigen (in this case, various fragments of SARS-CoV-2 virus) and measure how many antibodies in a person's blood will bind to them.

Would be interesting to know about the role of the MHC which differs from person to person (does MHC type depend on the cell type, by the way? For instance, do B- and T-cells differ in their MHC?)

@PeterBernhard That sounds like a whole new question or two to ask...

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Why is proteinase K digestion performed at 50 °C?
Many DNA isolation protocols use a Proteinase K digestion to remove proteins. This is often performed at 50 °C. Why is this?

Proteinase K activity is greatly increased by addition of denaturing agents like SDS or urea (Hilz et al., 2008), indicating that the denaturation of the substrates helps Proteinase K to degrade them.
Increasing the temperature to 50°C will also unfold some proteins already, making it easier for the Proteinase K to degrade them. The proteinase K seems to be a pretty stable enzyme, and  can still work at this temperature.

In your linked wiki article: "An elevation of the reaction temperature from 37 °C to 50 - 60 °C may increase the activity (of Proteinase K) several times." The enzyme works faster at 50°C.

some proteins are deactivated at that temperature... they are all different, aren't they?

@shigeta yup, they are all different.


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What is the difference between added sugars and natural sugars in processed foods?
While buying juices, I came across two options, one with no added sugars, one with added sugars. The one with no added sugars had 11 grams of sugars, the one with added sugars had also 11 grams of sugar.
Hence my wonder, does it matter what is the source of your sugar intake, whether it is naturally occurring or artificially added?
I generally don't worry about how sweet something is as long as it’s natural, like mangoes are very sweet, but my mind tells me it’s a fruit hence healthy and I am neither diabetic nor fat, so mangoes are ok for me. But still I don't eat candies or other man-made sweet stuff because my mind says it’s artificial. Is my mind right or wrong?

One of the ways to measure the impacts of sugar in different foods is with the glycemic index, which is a measure of how quickly blood sugar rises after eating. Faster rises in blood sugar are thought to contribute to the development of diabetes and possibly contribute to weight gain, though as with most nutrition science the specifics are very difficult to study due to the difficulty of conducting true randomized trials over a long time period (people just won't stick to eating what a study assigns them to eat) and a vast array of potential individual differences in digestion and metabolism.
Generally, the glycemic index for a piece of fruit will be low despite containing sugars, because fruit also contains other things like fiber which slows the rate at which sugar is absorbed. Adding just sugar to any food will always increase the glycemic index, because added sugar isn't coming with anything to slow it down.
Sugar in juices are typically going to be absorbed quickly, whether the sugar came from the fruit (like an apple juice) or is added (like a lemonade), because you're typically removing the parts of the fruit that slow digestion (the fiber) when you make juice. If you have some hypothetical glass of juice, process it to magically remove just the sugar, and then add that much sugar back in, no, it won't matter that the sugar is now considered "added" versus not.
Labeling of added sugars is just intended to help you identify foods that have extra added sugars; it does not help you identify if the natural occurring sugars in something are going to contribute to a rapid increase in blood sugar or not. Manufacturers can use different tricks to avoid their sugars being considered "added", such as blending apple juice with a more sour fruit (the apple juice is mostly there to add sugar, yet isn't considered "added sugar" because it isn't added as sugar, it's added as sugary juice).

Sugar doesn't cause diabetes. However, being overweight is a risk factor for diabetes, and weight gain is caused by consuming to many calories. The biggest concern from added sugars should be consuming too many calories, since sugars are caloric, and manufacturers like to add a lot of sugar when they add sugar. If you're already diabetic, both added and natural sugars need to be regulated.

@Vaelus Ultimately diabetes is an insulin dysfunction; type 2 diabetes specifically is insulin insensitivity. Peaks in blood sugar result in peaks of insulin; not necessarily the same effect as total sugar in the diet. The cause and effect structure of weight gain and diabetes is not entirely clear.

Excess weight is not known to cause insulin resistance, but it's know to be a risk factor. None of the reputable health information websites I've searched (government health agencies, diabetic association's, etc.) even list sugar consumption as a risk factor. I do not regularly read literature on the topic, however, and perhaps you do. Are you saying you're aware of recent literature on the topic strongly indicating the possibilty of a causal link between sugar intake (binging, I suppose) and insulin resistance?

@Vaelus Like I said in the answer, it's hard to identify causality because of difficulty in doing experimental research and co-occurrence of potential risk factors. https://doi.org/10.2337%2Fdc10-1079 is an example paper that purports a link with sugar specifically beyond weight. I would not call this idea recent.

That particular study explicitly does not control for excess weight, and right in the conclusion, it says: "These data provide empirical evidence that intake of SSBs should be limited to reduce obesity-related risk of chronic metabolic diseases" (emphasis mine). To completely clear, I assert that government health agencies are competently communicating the best current scientifict concensus of risk factors for diabetes, and sugar intake independently from obesisty is not one of them. Therefore this answer would be improved by removing the focus on risk of diabetes.

@Vaelus: My comment on the question was inexplicably removed despite being relevant, and it also partially addresses your inquiry here. It linked to this study which of course some people wish to suppress. It is very well-known that there is a significant correlation between soft drink intake (e.g. coca cola) and diabetes, and also reason to believe that there is a causal relationship. Now we have evidence that sweeteners too are related.

@Vaelus: Indeed, I have searched hard too, yet nowhere could I find proper studies linking sugar intake and diabetes, when controlling for smoking, alcohol, and healthy diet excluding amount of sugar consumed.

The label is so you know how much sugar has been added, and juice just has issues with the label in the US.
It is put on the label so you can see how much sugar the companies are adding, compared to how much it contains normally. Most people would not have any idea how much sugar, say bread or juice, contains naturally, so it is important to know how many empty calories companies are adding.
Your mindset is the very issue. A loaf of bread or bottle of juice may have more than a candybar's worth of sugar added just to make it easier to sell. So you are eating lots of candy without knowing it. A bottle of juice may have just as much sugar as soda or other drinks we think of as "sugary". This is an issue in the US, because the US has little regulation on adding sugar (due to a powerful lobby), so many things are loaded with extra sugar. Your body does not care whether the added sugar is in a candy or or bread, or juice. This is one reason the US consumes 5 times the recommended amount of sugar.
From the FDA and CDC

The Dietary Guidelines for Americans recommends limiting calories from
added sugars to less than 10 percent of total calories per day. For
example, if you consume a 2,000 calorie daily diet, that would be 200
calories or 50 grams of added sugars per day. Consuming too much added
sugars can make it difficult to meet nutrient needs while staying
within calorie limits. Added sugars are listed on the Nutrition Facts
label so that you can make informed choices, based on your individual
needs and preferences.

If both juices had the same amount of sugar one was likely lying, again US crap regulation. They can put "no added sugar" on the label while still adding lots of sugar in forms like extra concentrate or honey, or agave nectar. Other countries are a lot more strict about what counts as added sugar. Added sugar is not bound in fiber or other things that slow the absorption.
To be accurate, the causes of diabetes are still being deeply studied because the complete mechanisms are not known. But one thing we have good evidence for is rapid absorption of sugar likely contributes to diabetes. Added sugar is essentially always rapidly absorbed and thus is a contributor to insulin resistance. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836142/#:~:text=Diets%20with%20high%20glycemic%20index,risk%20of%20type%202%20diabetes.
There are other factors as well. Excess sugar is basically always turned directly into fat and for actual diabetics, added sugar is an even bigger deal, so knowing how much added sugar is present is important for making knowledgeable choices.
A final consideration: Much of the sugar in candy is made from vegetables (beats, corn, or cane), so just because it comes from something healthy does not make it healthy.

Your last sentence goes the other way too. Just because a sugar source is a fruit or vegetable (e.g. sugar cane) does not imply it is healthy to eat much of it!

@user21820 of course, as I said, the body does not care where the sugar comes from but how fast it makes it into the blood stream.

@John by that logic it seems that I could come up with a balanced diet that consisted of candy (or raw sugar) combined with various nutrients and fiber.  Regarding excess sugar "always" being turned directly into fat I'm wondering if that is "always" true - have there been any studies done on people who eat an excess of calories (even considering activity) but never seem to gain weight to see if they may be eliminating some of the calories unprocessed?

@Michael sure if you added the other macronutrients, and mixed it to get the benefit of the fiber, artificial compiled food sources similar to that exist. Also such people don't exist outside a few fatal cases, some people just burn more calories through higher basal metabolic rates. often through less efficient mitochondria. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786199/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535334/

Natural sugars are mostly glucose, fructose, and saccarose. Added sugars can be anything, from glucose to a variety of syrups. There isn't much difference, although caramelized sugars (brown syrups) also contain longer carbohydrates, and if the caramelization process is not good, other complex molecules can form. Industrial sugars also contain extra additives, colorants, and stabilizers (https://en.wikipedia.org/wiki/Anticaking_agent , https://infinitabiotech.com/blog/sugar-processing-chemicals , https://en.wikipedia.org/wiki/Corn_syrup , https://hummingbirdmarket.com/blogs/news/what-are-the-chemicals-in-white-sugar). In theory, all safe substances. In practice, only time will tell... The calories are the same.

Can you please add some references for stabilizers in industrial sugar? The plain sugar you buy in the store is something like 99.9% saccharose. It is of biological origin, so not, there is not difference.

@Chris I have added a few links

@alec_djinn: All those links seem to be about agents added to table sugar not to sugars added in industrial sugar production.

@JackAidley, it is a general overview of sugar production. Not only table sugar, but in general powder sugar and syrups.

If you live in the E.U., a beverage labeled "juice" may not contain added sugar. If both beverages you compare are 100% juice from the same fruit, adding sugar to one would lead to it having a higher overall sugar content than the unaltered one. So let's assume that the drinks are from the same fruit, but the one with added sugar is diluted.
It is typical that the taste of diluted juices is improved with added sugars. The resulting overall sugar contents may add up to be the same as for the original juice, but obviously only half of the more desirable fruit components are present together with it.
Thus, the added sugar is not a bad thing in itself but rather an indicator for a bad thing: It indicates that the beverage contains less of the more desirable constituents; it is an inferior product.
That can be the case with many processed foods: Ketchup with more added sugar was made from inferior tomatoes, a ready-made meal with a lot of added sugar wouldn't have much flavor without it etc.

The FDA explains the nutrition label requirements.
https://www.fda.gov/food/nutrition-facts-label/added-sugars-nutrition-facts-label

Total Sugars include sugars naturally present in many nutritious foods and beverages, such as sugar in milk and fruits as well as any added sugars that may be present in the product. There is no Daily Value* for total sugars because no recommendation has been made for the total amount to eat in a day.
Added sugars include sugars that are added during the processing of foods (such as sucrose or dextrose), foods packaged as sweeteners (such as table sugar), sugars from syrups and honey, and sugars from concentrated fruit or vegetable juices. They do not include naturally occurring sugars that are found in milk, fruits, and vegetables. The Daily Value for added sugars is 50 grams per day based on a 2,000 calorie daily diet.
For most Americans, the main sources of added sugars are sugar-sweetened beverages, baked goods, desserts, and sweets.

Notice the order of ingredients (high to low) in Ocean Spray's Cran-Apple juice:

Water
Sugar
Cranberry juice
Apple juice

You can assume that the 23 (out of 26 total) added sugars are literal sugar added to the juice to make it more palatable. The other 3 are cranberry and apple sugars.

Aside from the Vitamin C, there is no reason for this food item to exist. It is literally an excess sugar beverage.

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Is there a reason why human eyesight and plants make use of the same wavelength of light?
The accepted range for the wavelengths of light that the human eye can detect is roughly between 400nm and 700nm.  Is it a co-incidence that these wavelengths are identical to those in the  Photosynthetically Active Radiation (PAR) range (the wavelength of light used for normal photosynthesis)?
Alternatively is there something special about photons with those energy levels that is leading to stabilising selection in multiple species as diverse as humans and plants?

The human species (and presumptive many of our close ancestors) have an extraordinary ability to detect shades of green and red. there is a theory behind this saying that we evolved this ability to better distinguish ripe fruits and thus optimizing the foraging. Most other mammals do not in fact have the ability to detect color. P.S. I have no direct reference to this theory, but I have most likely read about it in Campbell & Reece's biology textbook. D.S.

Good question.
If you look at the spectral energy distribution in the accepted answer here, we see that photons with wavelengths less than ~300 nm are absorbed by species such as ozone. Much beyond 750 infrared radiation is largely absorbed by species such as water and carbon dioxide. Therefore the vast majority of solar photons reaching the surface have wavelengths that lie between these two extremes.
Therefore, I would suggest that surface organisms will have adapted to use these wavelengths of light whether it be used in photoreceptors or in photosynthesis since these are the wavelengths available; i.e., organisms have adapted to use these wavelengths of light, rather than these wavelengths being special per se (although in the specific case of photosynthesis there is a photon energy sweet spot).
For example this study suggests that some fungi might actually be able to utilize ionizing radiation in metabolism. This suggests that hypothetical organisms on a world bathed in ionizing radiation may evolve mechanisms to utilize this energy.

For further reading, this review by Dartnell in 2011 discusses multiple roles cosmic and planetary ionizing radiation may have played in the origin of life.  http://online.liebertpub.com/doi/abs/10.1089/ast.2010.0528

The selection you refer in multiple species could be due to a mutual advantage.
If fruits absorb visible wavelengths, they can be spotted by other animals and eaten together with the seeds. Seeds can then mature inside the host and, once eliminated with the feces, grow up a new plant in a different place.
This is not only valid for light absorption, but for light emission also: for some fruits, the ripening causes a blue-UV luminescence that can be spotted by some insects.

If they absorb visible light, they don't reflect it, which would make them harder to see.

They preferentially absorb one or more colors, rendering the others easy to see. For instance, chlorophyl absorb more blue and red light, so you see leaves as green.

A rule of thumb in optics is that light interacts with materials that have features with  dimensions similar to the wavelength of light. For example, radio waves with large wavelengths interact with large objects like airplanes ,as in the case of radars, and really small wavelengths (x-rays & gamma rays) interact with really small objects like nuclei of atoms. If you take the visible spectrum, light interacts with materials with similar dimensions and/or energies like the C-C, C=O etc that constitute most of the organic compounds. Heck, light with the appropriate wavelength may even interact (or get diffracted in this case) with an organic material that possess many C=O-OH groups spaced with distances similar to the wavelength of light that is shone on it (provided they are regularly spaced and there are lots of them to produce an observable result). Since all organisms are carbon-based the C-C, C=O, C-O, C=_N etc dominate the constituents of the living matter from retina of the human eye to the photosensitive compounds in plants. Hence from the light-matter-interaction perspective all living beings are made up of more or less same materials and this is the reason why plants use the similar wavelength the human eye can detect for photosynthetic processes.
Source: just my intuition

This makes a lot of sense, and in combination with the "adaption based on wavelengths availability" answer provides the complete answer.

This question is related to the question: Why are some things transparent and others opaque?
Being able to see something requires that it is opaque and that sufficient light illuminates it.
UV and shorter wavelengths are not as prevalent as visible light on earth. The world would appear too dark to see if we used UV and shorter wavelengths. This is because our atmosphere absorbs most high energy light.
Infrared and longer wavelengths of light pass through many objects which would make vision difficult. There's less light here reaching the earth and even less being refracted.
Think about how much our vision relies on indirect light. The frequencies at which most objects are opaque makes those frequencies useful for vision due to the accumulation of refracted light.
Why are many objects opaque in the visible spectrum of light? Longer wavelengths of light have less energy than the valence electrons on most matter. Shorter wavelengths have too much energy, they cause chemical reactions, in addition to not being very prevalent on the surface of the earth.
Electrons are what absorb then remit light and have thresholds based on their chemistry for what they can absorb. No absorption = transparent. Too much energy and chemical reactions start to happen, which may be undesirable, or desirable in the synthesis of vitamin D by UV light.
Plants extract energy for chemical reactions from wavelengths shorter than infrared, which is too weak to drive photosynthesis, and not as abundant as visible light. But also absorb wavelengths longer than ionizing frequencies, which are not very prevalent, and usually cause damage.
Visible light is the spectrum of light which is prevalent enough on earth to see, but is not so energetic it would harm biological systems. The qualities for optimal light frequencies in sight and photosynthesis overlap because they have similar mechanisms for interacting with light. What is this mechanism? The chemistry of carbon based life.


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


text:
What are the major evolutionary pressures for Bioluminescence?
What are the major evolutionary pressures for Bioluminescence?

Sorry for not being specific. I was mostly curious about deep sea. Should I break this up into separate questions?

This question is close to my heart since I saw the Phosphorescent Bay in SW Puerto Rico. Its interesting to contrast the deep ocean with fresh water caves, where the fish become blind / eyeless.  The difference might simply be a lack of phosphorescent microorganisms to provide the light for the fish, or maybe the distant connection to the surface allowed the phosphorescent algae to influence the sunless deep parts of the ocean.

In many cases, and in particular in marine invertebrates, the bioluminescence is in fact produced by symbiotic bacteria of the Vibrionaceae family. In most cases the bacteria can sense when they are being hosted by the animal through quorum sensing mechanisms, and start producing light.
The evolutionary pressure for the bacteria to produce light is to be in the protected environment of the animal which often feeds them. On the animal side, there can be several reasons to host the luminescent bacteria. In many cases, the evolutionary pressure is linked to reproduction. In order to successfully reproduce in the immensity of oceans, marine animals need to know that they are among their kind before they release their gametes.
Another example is the one of some deep see fish like the anglerfish which have developed a special "flash light" organ to host bio-luminescent bacteria. Fish can use the bacteria to emit a light to aid in camouflage, hunting, and attracting mates. See http://microbewiki.kenyon.edu/index.php/Deep_sea_fish

Whilst it's not exactly academic, the BBC documentary "Blue Planet" had an excellent episode on deep-sea creatures, containing a large section about bioluminescence. Well worth a watch.

No matter the reason the "Blue Planet" is always worth watching.

@Polynomial In fact, the II came out about three years ago, but I haven't been able to see it yet.

Bioluminescence, in particular in marine organisms, has also been linked to way to get rid of reactive oxygen species (ROS). In fact, luciferases catalyse the photogenic oxydation of luciferins. In [1], the authors propose that this system's function was primarily for antioxydation, while in deep seas, where the water is oxygen-poor, the lower selective pressure toward antioxydation would have given rise to light emitting functions in specialized organs.
THE ORIGINS OF MARINE BIOLUMINESCENCE: TURNING OXYGEN DEFENCE
MECHANISMS INTO DEEP-SEA COMMUNICATION TOOLS
Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity


text:
Are single-celled organisms capable of learning?
I've read that the amoeba is capable of learning.  Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the evolutionary distance.
How does this species learn?  I would presume that there is a complicated chain of receptor mediated transcription regulation, but what are the specifics?  What types of receptors does an amoeba have to sense its environs?

Amoebas are not animals, this term means wide range of similar, but not related unicellular organisms. Do you mean something like the learning behaviour of Physarum slime molde link?

Just a note: qualifying a species of "lower organism" could make some purist cringe ...
I dont have a straight answer, but you might be interested in this paper which describes a model of event memory in amoeba

@MartaCz-C Yes, I had written "animal" in and taken it out for a better substitute and ended up leaving it in.  You are absolutely correct about its misuse.  I have not encountered the study in your link, but I will take a look at it.

I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for  "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system.
In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter.  E. coli in the digestive tracts of mammals will typically be exposed to initially a lactose, and then later to a maltose environment as the bacteria pass down through the animal tract. This suggests that upon encountering a lactose environment, maltose operons are induced. I.e., upon encountering lactose, maltose is anticipated. This suggests a "genetic memory" of the sequence of sugar types where lactose is always encountered before maltose.
Further cultures (500 generations) of E. coli in the absence of maltose but in the presence of lactose reduced the maltose operon activity to negligible levels, suggesting that this is an adaptive prediction of environmental changes.
Mitchell, A et al., Adaptive Prediction of environmental changes by microorganisms, 2009, 460, 1038

That’s more like adaptation through evolution though. I don’t know about the OP, but when I’m thinking about “learning”, I usually think in terms of a single lifetime.

In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory.
It is possible to design various bistable switches using protein pathways, RNAi, or other means that will latch a particular state. In that way, an organism could effectively "remember" one bit of data by querying the state of the toggle.
For a specific example, see the Gardner 2000 paper [1]. It's a transcription-level circuit, that in response to a certain stimulus can latch either high or low. While the synthetic version itself is not terribly robust, one could see how in nature a highly evolved / refined circuit could maintain state and effectively serve as "memory" for a single-celled organism.
[1] Gardner, et. al 2000 "Construction of a genetic toggle switch in Escherichia coli."

This is an interesting point. A big issue with the toggle switch is that the network topology from Gardner's paper is rarely if ever seen in biology. However, there remains plenty of examples where hysteresis may occur in naturally relevant systems.

The authors of The omnistat: A flexible continuous‐culture system for prolonged experimental evolution report on an experiment where they evolved Lactococcus lactis to have an anticipatory response to their environment. A culture was set up in their bioreactor, and periodically one of two weak bases was introduced: either lactate or acetate, and then, depending on the base, fresh media of fructose or galactose was introduced. The simple idea is depicted below:
1. randomly choose either:
  dose with dilute acetate -> fructose comes next
  dose with dilute lactate -> galactose comes next
2. go back to step 1.

The culture is continually exposed to this treatment over many days or weeks (it's not clear from their paper), during which, there is an evolutionary pressure for the bacteria to engineer a response between the weak base and future energy source. That is, a bacterium that can shift its metabolism slightly towards processing fructose faster when acetate is present will have higher fitness, and likewise of lactate/galactose.
In the end, after many rounds, the bacteria have encoded the relationship into their genes - a type of "learning" that the other answers to this question also give examples of.


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What are the clotting factors' effect on avascular necrosis development?
Do clotting factors tpa and pai-1 lead to degenerative osteoarthritis in the same way that lupus anticoagulant and prothrombin might? Is one of these pathways particularly detrimental during formation of osteoarthritis or avascular necrosis (if these factors are inhibited or modified in some way)?

First of all we should distinguish between the physiological clotting factors that are parts of the normal clotting pathways, and those that might affect clotting pathways but are not observed under healthy conditions.
TPA (tissue plasminogen activation), PAI-1 (plasminogen activator inhibitor) and prothrombin are normal clotting factors that are essential for blood clotting. Any deficiency (congenital or acquired) might cause certain pathologic conditions, including the osteoarthritis and avascular bone necrosis.
Lupus anticoagulant, however, is an antibody against cell membrane that is common for Lupus. This antibody can intervene into the process of clotting and increase the prothrombine time (the common lab method to test blood clotting properties), hence the name "anticoagulant". But this effect is just a sort of "side-effect" of this antibody, that leads to certain symptoms in case of auto-immune attack against different target organs.
So, after this introduction I can rephrase your first question as: "Does the deficiency of clotting factors TPA and PAI-1 lead to degenerative arthritis in the same way that lupus anticoagulant and prothrombin deficiency might?"
The part of the answer is already in this question: yes, the deficiency of these factors might and under certain conditions, leads to the development of osteoarhritis and avascular necrosis.
I must confess, I found no evidence whether the underlying mechanism is different or not. Papers just prove that these factors are discovered in the affected joins, and see the correlation in mice models between the factors and the articifially induced arthritis. But I found no study which would try to address the mechanisms of these actions or to show, whether these are different.


text:
What factors affect the rate of transpiration in plant leaves?
I'm trying to get my head around factors which affect transpiration in leaves.
For example, how would applying petroleum jelly to the surface of plant leaves affect their rate of transpiration?
I get that it's basically going to decrease the trasnpiration rate because the stomata will be covered, but I'm not sure about these parts:

How would it affect the rate of transpiration if only the top surface was covered?
How would it affect the rate of transpiration if only the bottom surface was covered?

Also, I think I'm right in saying that increasing wind / applying a fan to plant leaves will increase the transpiration rate, but why?

The rate of transpiration is very closely linked with the rate of evaporation from the leaf surface.  Increased air movement across the surface of the leaf (e.g. from a fan) increases the rate of evaporation of water from the leaf surface. This happens because water saturated air is moved away; making the osmotic gradient more pronounced.
As for the relative changes from adding an impermeable substance like petroleum jelly to the top and bottom surfaces of leaves, it's a question of plant-anatomy.  In the majority of plants, stomata are only located on the bottom surface of the leaf.  This is to prevent them getting 'clogged' during rainfall and to keep them out of the sun to minimise water loss (again more sunlight on the stomata would increase the rate of evaporation).  Therefore a plant with the underside covered would have a much slower rate of transpiration than one with the top surface of the leaf covered.
Other factors that would affect the rate of transpiration:

Temperature (Positive Correlation)
Humidity (Negative Correlation)
Light Availability Excluding CAM photosynthesis pathway plants (Positive Correlation - the stomata are in the main only open when photosynthesis is occurring, so transpiration is less at night or on a cloudy day in addition to light  heating the leaf surface)
Water content of soil (Positive Correlation)

amount of salt in soil (negative correlation)


text:
Why is it that cats can jump so high for their size, compared with humans?
My cat is about 1' high at the shoulder, and I am a little over 6', but my cat can easily jump onto something as high as I am. That is 6x it's height. If a cat can do this, then Why can't I jump up onto my barn roof? That is a little less than 36' up. I have a hard time jumping onto even a 4' platform. Now if my cat had trouble jumping onto an 8" platform, I would think that pathetic. Do cats have muscles 20x stronger than humans, for their mass?
Is it just their skeleton providing leverage?

Why are Cheetahs so fast?

Cheetahs are strong.

Square-cube law. In fact it predicts that jump height (absolute height, not in terms of size) is the same for all animals. In reality it varies of course, but it isn't a simple rule.

Cats have different body structure than human beings. Its body-kinetics are quite different from us. Yes, muscles are quite strong, but this not the only reason. To know in-depth about the reasons behind the cats’ extreme jumping abilities, you can just refer this online article - "The Glory of the Cat – adidarwinian" at http://adidarwinian.com/the-glory-of-the-cat  Along with the flexible spine, strong muscles, flexible joints, they have a peculiar trait known as righting reflex. The same article has information on this peculiar trait. Due to the righting reflex instinct, cats can even survive falls from the high rise buildings.

There is not a linear relationship between the size of a muscle and its power. The cat weighs significantly less, but the decline in muscle power is not identical. If he weighs 20x less than you, but his muscle generate 1/5 as much force, he will still be able to jump way higher than you.

Here is another answer talking about this non-linear relationship between size and muscle strength.

Both the mass of an animal and the amount of energy their muscle can release rapidly are proportional to their volume. The height to which they can jump is proportional to the ratio of the two, so most animals can jump as high as any other to within a small factor. The remaining difference between those who can who can jump about 6' such as your cat or Javier Sotomayor, and yourself, is practice.

Shortwinded answer:
Cats are not exceptional jumpers.
Their mystique fits a pattern defined by physics and illusion.
Medium-winded answer for cat lovers:
I care for cats who began feral
and now come and go as they please.
My territory-marked (tattered) curtains show exactly
how high these cats can reach without jumping.
They are amazing, with marvelous agility, senses, personalities and wits.
These acrobats cannot, however, jump as high as it looks.
Longwinded . . .
To compare the jumping abilities of humans and cats,
and countless other animals,
requires more than measuring the altitude of a platform.
Two pertinent factors easy to overlook are:
 A. How much did the center of mass rise?
B. Did the maneuver include climbing as well as jumping?
A misleading factor is:
C. How does jump height compare to body size?
Considered in reverse order,
comparing a human who can reach 7 feet without jumping
to a cat who can reach 3 feet:

C.   How does jump height compare to body size?
              This is surprisingly irrelevant.
Physics alone determines that
jump height is generally independent of body size,
down to smaller than a mouse,
where limiting factors become
the fluid properties of air resistance and viscosity,
not the
kinetic factors
of gravity and musculoskeletal physiology.
Under the neutral assumptions of
power laws,
a 7/3-as-long human is expected to produce roughly
49/9 ≈ 5.4 times the jumping force
of a 3/7-as-long cat.
This force acts over a muscle contraction
approximately 7/3 as long,
delivering ∼343/27 ≈ 13 times the jumping energy.
The weights of this human and cat
likewise have somewhere near a 13 :1 ratio,
which happens to cancel out the difference in energy,
and that is not a coincidence.
It is physics.
[Somewhat ugly mathematical formulas to be added if requested.]

B.   Did the maneuver include climbing as well as jumping?
              The cat is quicker than the eye.
A human’s jumping onto a meter-tall platform
typically ends with a footed landing.
No climbing involved.
When a human gains a three-meters-above-ground tree branch, though,
that branch is first grabbed by the hands,
followed by a lot of pulling and climbing
before the feat is complete.
When a cat bounds upon a two-meter-tall fence,
the same sequence of pulling and scrambling occurs, only quicker.
Here are two slow-motion videos.
One shows a cat climbing more than jumping.
The other shows a cat reaching a high target purely by springing.
https://www.youtube.com/watch?v=705OzYq7cXU
https://www.youtube.com/watch?v=UYEeJEYMDwI
Beautiful!
And note that the highest leap
reaches perhaps 7 feet.
Which leads to . . .

A.   How much did the center of mass rise?
              Cats have an edge on humans, but not by much.
Cats who can reach
3 feet
without jumping and
7 feet on the fly
raise their centers of mass by
7−3 = 4 feet.
This is impressively comparable to the best human athletes,
but this does not reach a separate realm of ability.

Ps. Yes every feral cat who comes close enough receives a veterinary visit. Cheers to county funding! (Nonetheless these wondercats still exhibit territorial behavior and occasionally receive patch-up visits. Perhaps material for a future question.)

I mean, I've had my cats clear jump over 6'. Assuming a cat is 2 1/2 feet tall, like you said, if it was standing like a human, that's jumping over twice it's height. I've seen them do this without 'climbing', but even if we say that the cat scrambled up the last foot, that's still at least a 5 foot jump. Now I am 6' 3" tall. I've never come close to jumping twice my height (around 12 feet). And then if you're going to look at weight, a cougar would be close to me (I'm 205 lbs). Cougars have been measured at 18' vertical jumps in one bound (some say well over 20').

I love this question, @J.Musser. If a cougar can raise its center of mass 10 feet or more, that is beyond astounding!  That you have leapt upon a platform 4 feet tall is believably impressive. Not easy, coming from someone who has tried. Nonetheless, our familiar felines are amazing in other ways.

I have done a 52" box jump, max. My original question was why cats (specifically house cats, but I guess any cat) can jump so much higher compared to their size than humans can

Size is an attractive diversion. I'm still looking for the right question at this site to go on and on about that.

I wouldn't mind reading if you have something to write... yeah I was into fitness. 640lb deadlift, 350lb bench, 80lb curl, 160lb weighted squats... I've gone somewhat softer in recent years would be interesting to see how I can jump now

There is no way to lift that much without developing a fast twitch.

I don't have a twitch other than normal random twitches. I failed to land a 25 foot jump while (trying to) demonstrate tuck and roll techniques, suffered a lot of damage, and never really came back from that. Loose skin now

We humans have overgrown our safe performance boundaries. Another answer in search of a question.

Sorry to have deleted the comment that rejoiced an over-4-foot-and-then-some spring, J. Musser. By "fast twitch," I referred to muscle fibre and you probably understood that, but saying so now just for the record . . .

There's also a scale effect.  For instance, my 70 lb (~30 kg) dog can easily jump the 4 ft (~1.2 m) panels around the corral.  I can vault them too, using hands to go over,  My 1200 lb (~500 kg) horses either can't or don't want to jump that fence.

@jamesqf a horse is not a cat. I talked about scale earlier, going up to human size (cougar). They can clear 18 feet in one bound.

@homnid  I wasn't familiar with the term. Hahaha.


text:
Why is a lack of oxygen fatal to cells?
In animals temporary anaerobic respiration leads to the breakdown of the pyruvate formed by glycolysis into lactate.  The buildup of lactate in the bloodstream is accompanied by a large number of protons causing lactic acidosis, which is detrimental to the health of the organism.  This is one of the main suggestions I have come across for why a lack of oxygen is fatal to cells, however the LD50 for lactic acid as referenced by the COSHH MSDS seem awfully high (even if the route is by ingestion rather than directly into the bloodstream) for this to be a cause of cell death:

Toxicological Data on Ingredients:
  ORAL (LD50): Acute:
3543 mg/kg [Rat (Lactic Acid (CAS no. 50-21-5))].
4875 mg/kg [Mouse (Lactic Acid (CAS no. 50-21-5))].

I also wonder if this is a larger problem for an organism as a whole rather than on a cellular level.
The alternative, I suppose, is that glycolysis alone does not provide sufficient ATP for vital cellular processes to occur.  If this is the case, which ATP requiring processes are most vital for the short term survival for a cell?

You're being a bit anthropocentric, plenty of organisms get on fine without, some are even harmed by free oxygen. :P

As a corollary, perhaps, oxygen toxicity occurs at the other end of the scale http://en.wikipedia.org/wiki/Oxygen_toxicity

Here's an illustrated example in neurons:
ATP, of course, is generated by aerobic respiration. The critical biochemical reaction in the brain that is halted due to lack of ATP (and therefore O2) is the glutmaine synthetase reaction, which is very important for the metabolism and excretion of nitrogenous wastes:

The body uses this reaction to dump excess ammonia (which is a metabolic waste product) on glutamate to make glutamine. The glutamine is then transported via the circulatory system to the kidney, where the terminal amino group is hydrolyzed by glutaminase, and the free ammonium ion is excreted in the urine.

Therefore, as you'd expect, under hypoxic conditions in the brain, excess ammonia builds up which is very toxic to the cells. Neurons are also highly metabolically active, which means they generate more waste products. A buildup of nitrogenous waste products in the cell (and bloodstream) can be potentially fatal due to it's effects on pH (screws up enzymes and a whole slew of biochemical reactions).
In addition, the buildup of ammonia will cause glutamate dehydrogenase to convert ammonia + aKG to glutamate, which depletes the brain of alpha-ketoglutarate (key intermediate in TCA cycle). This basically creates a logjam in the central metabolic cycle which further depletes the cell of energy.
This is just one example of many. Of course, there are many, many other critical metabolic processes that require ATP (i.e. the Na+/K+ ATPase pump that regulates neuronal firing and osmotic pressure), but nitrogen metabolism was the first that came to mind :)

Energy production starts with glycolysis, which generates NADH and pyruvate.  Pyruvate goes to the mitochondria to make more NADH (or FADH2, which is similar to NADH) in the Krebs Cycle.  NADH is used to power the electron transport chain, which gives most of the energy the cell uses.  The last step of the electron transport chain consumes oxygen (Complex IV reduces oxygen to water).
If you do not have oxygen, the electron transport chain will not work.  If that doesn't work, the Krebs Cycle slows.  If that's not consuming pyruvate, glycolysis slows.  The cell dies from lack of energy.  It has less to do with the acid buildup as a consequence of lactate as it does with buildup of NADH and the consequent slowing of the central metabolism.
The issue is most pronounced in multicellular organisms  because it's much more difficult to get oxygen to all your tissues, so "think" tissues have cells that are already close to hypoxia already.


text:
Why is the Patellar reflex not triggered when the tendon is extended slowly?
I have been previously told that the Patellar reflex (knee-jerk-reaction) exists to prevent the hyper-extension of the patellar tendon.  Yet if the impact to the tendon is delivered slowly - i.e. by pressing down on it rather than striking it - there is no reflex response.  Why is this, as surely the tendon is being extended by the same amount?

This effect you are observing has to do with the nature of the afferent neurons (Ia fibers), which carry a signal into the spinal cord and synapse onto motor neurons directly.  See this text (scroll down to section 1.10) for a diagram.  At their other end, these Ia fibers penetrate into the muscle and wrap themselves around the body of the muscle spindles, "[which] are specialized receptors that signal (a) the length and (b) the rate of change of length (velocity) of the muscle."
Because the main role of these spindles is to monitor the muscles for very rapid changes in length, the neurons have a static range which is optimized for these quick jerks (rather than firing over a wide range of velocities).  When you are stretching the muscle slowly, the Ia fiber is not building up a sufficient depolarization to fire off an action potential.

+1 this explains the mechanism nicely, but it makes me wonder: if the neurons are capable of measuring the length, then why isn't there a need for a reflex based on length? To bring in some teleology: why would the system be optimized only to automatically respond to (b) and not also to (a)?

Presumably because (a) is handled by higher, slower, functions. If nothing is happening particularly quickly the spinal cord can 'wait for instructions' from the brain. Reflexes exist because when things are happening very quickly it's too slow to contact the brain and wait for a reply. If they're happening slowly, that's not an issue.


text:
How can flies sense mirrors?
I've noted that flies in my house have no problem landing on even perfectly clean mirrors. Why don't they fly straight into them? Can they sense that there is a surface there, even though they can't see it?

@casey Yes, but flies will often fly into a window, while the same fly will land on a mirror.

Maybe fly vision isn't very good, but good enough to see the outside through the window, while a mirror reflects the wall across from it, so it looks like a wall. Try to put a mirror across from a window and see if flies treat it like a window.

@user137 Hmm, interesting theory, but if the fly has any depth perception, wouldn't it see the wall (if it can) as far away? It has no reason that I can see to know there is a surface at that point

@J.Musser, That's why it's an experiment, I don't know anything about the visual acuity of flies. Maybe the mirror reflects more glare from the lights around it, while a window appears to have less reflection because any reflection would have to compete with sunlight behind it.

IDK what is your mirror, but flies definitely bump into my room's mirror constantly.

It might be pretty straightforward. Common window/mirror glass is opaque to UV, so as far as the fly is concerned mirrors are just translucent surfaces.
This of course leads to the question of why flies can't see window glass. Maybe the large amount of light passing through at visible frequencies makes it look like a tinted fog to the housefly? Maybe they're trying to fly through mirrors too, but land on their feet and just roll with it?

First link doesn't appear useful anymore.


text:
Do flies actually take off backwards?
I've been told that flies take off backwards, but I haven't really been able to prove it to myself. The closest I've gotten was noticing that they fly into window glass back-first, with their heads pointing up. Is that how they take off?

A 2008 study on fruit flies found that when faced with an immediate threat, flies would tend to launch themselves into the air in the opposite direction to the threat.  So when confronted by a threat from directly ahead, the flies would jump backwards.
Interestingly, "in response to stimuli approaching from the side, however, flies jumped at an angle that was approximately halfway between directly away and directly forward."  In other words, the response was biased toward taking off in the forward direction.
The study's authors note that "voluntary takeoffs elicited by either attractive odors or internal cues are almost always in the forward direction".
To summarize, fruit flies will take off in a forward direction when possible, but can take off backwards or at an angle when faced with an immediate threat.
Source:

Card, Gwyneth; Dickinson, Michael H. (September 9, 2008). "Visually mediated motor planning in the escape response of Drosophila". Current Biology 18: 1300–1307. doi:10.1016/j.cub.2008.07.094.

From this video demonstration in caltech, you can clearly see that Drosophila can fly forwards as well as backwards using high fps video image capture and it even does unexpected behaviours in times of perceived danger/threat.


text:
Genetic variation and sensitivity of wild cabbage

1: Is it true that the genetic variation of kale plants is smaller
  than wild cabbage?

I think so, because of human selection of the kale plants.

2: Are broccoli and cauliflower more sensitive to changing
  environmental conditions than wild cabbage?

I think so, because domesticated crops have a lower genetic diversity than wild varieties. Genetic diversity is useful for adaptation

3: Is it a good recommendation to grow new Sprout plants from the
  seed of wild cabbage plants?

I don't think this is the best idea, because genetically engineered Sprout plants could be much better.

sounds like homework - could you provide a little of the background please?

I am going to assume that Kale is a plant derived from wild cabbage and has been selected upon for certain attributes by humans for 1000's of generations.
1 There are two principle reasons why genetic (allelic) diversity might be lower in the kale subgroup than in the wild cabbage. Firstly, strong selection imposed by humans may have diminished allelic diversity. Strong selection can drive alleles to fixation. Secondly, if the kale has come from a small sub-population of the wild cabbage it may have been through a genetic bottleneck, this is likely to reduce allelic diversity because, unless all alleles from the original population are captured in the founder populations, some alleles will be lost by genetic drift.
2 Generally allelic diversity is a "good" thing in an unstable environment. It allows different trait combinations and variation in traits to occur. If the environment changes drastically then it could impose severe selective forces on the population, those with high allelic diversity are likely to come up with a combination of alleles that survives.
E.g. Humans only allow the cabbages over 18cm in diameter to reproduce in to the next generation. 5 loci affect cabbage size, each having a "large cabbage" (C) allele and a "small cabbage" (c) allele. Having 5 c alleles gives a cabbage size of 15cm. Each C allele adds 1cm. If a population has fixed the c allele at 3 loci (i.e. there is low genetic diversity) then none of the cabbages will be >18cm. If a population has both the C and c allele at all loci then some of the population will be over 18cm.
3 The final question is difficult to answer, it depends on what you define as "a good recommendation,"  that is very subjective. If the aim is to maximize allelic diversity then yes, if it is to maximize cabbage size it is probably no (because the "genetically engineered" plants have been selected upon for large cabbages - they might have the C alleles fixed in the populations!)

Could you be a bit more clear on which parts of your answer are responses to which subquestions?

@user4847 there you go


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What is the difference between osmotic potential and osmotic pressure?
Which term is used to calculate water potential? Does osmotic potential mean the same as solute potential?

Welcome on biology.stackexhchange. This is a pretty broad question, so it would be nice if you could start on these topics yourself (either with a good biology book or the Wikipedia) and then ask specific questions.

Please donot comment if u cannot help me .I know about these term but I need deeper explanation not your criticism .

Then you need to edit your question so people can answer specific questions. There are certain rules about questions, if you choose to not pay attention to them, questions can be closed, as this has already happened here. You can still edit the question and it can be nominated for reopening.

Does it meet the site rules now?

sometimes a question is just a question

Osmotic potential is the concentration of solute molecules in a solution while osmotic pressure is the pressure acting outward on the cell walls and internal membrane in plants

Osmotic pressure: pressure applied by a solution to prevent the inward flow of water across a semi-permeable membrane.
Osmotic potential: the potential of water molecules to move from a hypotonic solution to a hypertonic solution across a semi-permeable membrane.
Osmotic pressure can be calculated using the following formula:
$$Π = iMRT$$
where
$Π$ is the osmotic pressure in atm
$i$ = van 't Hoff factor of the solute.
$M$ = molar concentration in mol/L
$R$ = universal gas constant = 0.08206 L·atm/mol·K
$T$ = absolute temperature in K
The following page has a worked out example.
As for your question on solute potential vs osmotic potential, the answer is that they are indeed the same. You can compare the formula for $\Psi_{\pi}$ on the wikipedia page and the page of this pearson textbook. These formulas are the same:
$\Psi_{\pi} = -Π =-iMRT$
So there's a simple relationship between osmotic pressure and osmotic potential.


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Measuring reverse transcription yield?
Is there any measurement I could perform after RT that allows me to check the efficiency that the procedure had? Nanodrop cannot be used as remnants of RNA and poly T primers mask measure, or?

Nanodrop may be fine for the volumes but as you rightly guessed it is not so easy to distinguish DNA from RNA (and primers). Qubit (invitrogen) is a sensitive, dye based quantification assay. You can use that for estimating cDNA yield. The kit contains different dyes for DNA, RNA and protein estimation.

Treat with RNAse and spec at 260.
A spec can definitely be used. The extinction coefficient (Beers Lamberts Law) will not  be calculating measuring  NTPs, just intact dsDNA.


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Is there a specific mechanism for the delivery of pain medication?
For example, when one takes aspirin or ibuprofen does the chemical get dispersed to all pain receptor? My question really is, how does the chemical know where to target in the body? I figure wherever there is pain in the body that a certain signal is being produced; which possibly acts as a chaperone to direct the medication chemical where to bind and inhibit.

Short answer
No, orally taken painkillers act systemically.
Background
Taking a painkiller orally results in the drug being taken up into the bloodstream by the digestive system. From there it can potentially reach all tissues.
In other words, a pain response does not act as a chaperone. A hypothetical drug that would home in on tissues with a pain response, while avoiding unaffected tissues would be the ultimate painkiller, if it existed.
EDIT: To emphasize that painkillers act systemically I will elaborate on aspirine's pharmacokinetics. Notably, aspirine's actions are not restricted to the pain centers in the brain, and I quote the following excerpt from Wiley's interactive Concepts in Biochemistry]1:

Aspirin's analgesic and anti-inflammatory effects are due to the drug's ability to stop the production of prostaglandins that cause tissue swelling and pain.

Aspirin's antipyretic (fever-reducing) effect is due to its direct action on the hypothalamus gland, which results in vasodilation of peripheral blood vessels and sweating.
Prostaglandins are also the key mediators of platelet aggregation. By modifying the COX enzymes within platelets, aspirin causes platelets to lose the "stickiness" that is needed to stimulate blood clotting.
Hence, by these examples it can be seen that aspirine works in the periphery (wound swelling and pain), centrally (brain's hypothalamus) as well as in the bloodstream. Hence, aspirine (and other orally administered painkillers) do not target specific areas in the body, and most certainly not only the brain.
There are such targeted drugs, however. An interesting one is carbamezipine, an anti-epileptic that blocks Na+ channels. It blocks Na+ channels only when they are in an active conformation, however (i.e., engaged in action potential firing). Epileptic activity is basically paroxysmal (massive), synchronous over-activity in the brain that is accompanied by massive Na+ channel activity. Hence, epileptic activity will in effect trigger the drug into action.

Though these drugs enter systemic circulation, the pharmacokinetics for different body parts may be different.

Thanks for explaining. I always thought that it works by blocking the signals in brain i.e. at one place.

@WYSIWYG - agreed, but see edited answer. It is a systemic drug.

@jnovacho - no, your assumption is incorrect, I stressed that in the edited answer. If you ask a question in order to get your presumption verified just to dispute alternative (and in this case correct) answers, don't ask the question :)

See for a verification of a systemic mechanism of action @Corvus 'answer

Everything in the answer above is correct, but I think the OP wants to know about aspirin's action against pain specifically. Aspirin's action against inflammation is distributed throughout the body whereas its action again pain is distributed more locality (spinal nerves + perhaps brain). Even in the latter case I know of no evidence that it is targeted to specific neurons or brain regions; I believe the antipyretic effect on the hypothalamus is not to due to targeting but a consequence of whatever reduction in prostaglandins has occurred system-wide.

@Corvus, I doubt. OP is talking chaperones as if molecules are guided by something. They are not.

Most NSAIDs derive their analgesic effects from inhibit the cyclooxygenase (COX) enzymes that produce the prostaglandin-H2 precursor to the prostaglandins that sensitize neurons to pain.
Edit: With respect to where this takes place, the COX enzymes are expressed in inflamed tissues as well as constitutively in the stomach and kidney. The prostaglandins whose production they block act on the spinal nerves and can diffuse across the blood-brain barrier.

Can you add more information on distribution of COX2 in the body and if possible pharmacokinetics of any of these drugs to explain how they may affect different body parts differently.


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How does mass spectrometry detect histone methylation?
In this research paper they talk about the methylation of histone.  They use mass spectrometry to identify which peptide position is methylated. Does the number yielded by the spectrometer calculate the mass of the amino acid with and without the mass of methyl group? I wonder because I saw some introduction saying the number present the molecular mass of the molecular. I also would like to ask the mechanism of it and how you interpret this data? Thank you!

Can you provide link to that paper ?

The link is http://www.sciencedirect.com/science/article/pii/S1931312813001145 Thanks

It is not simple MS, it is tandem MS. They send the sample through multiple MS and they fragment it between them. So they can get info about the molecular structure as well, not just the mass/charge of the molecule.
A quote from your article:

MS/MS spectra of the methylated H3 protein (top down) and fragments
  upon electron transfer dissociation fragmentation. Fragments of the
  methylated H3 have a mass shift of 42 starting at C14, indicating a
  modification site at the K14 at the N terminus of the peptide.
  Normalized collision energy = 35%, activation Q = 0.250, activation
  time = 100 ms, accumulation time = 5 min.

A reference from your article:

Frese et al., 2011 C.K. Frese, A.F. Altelaar, M.L. Hennrich, D.
  Nolting, M. Zeller, J. Griep-Raming, A.J. Heck, S. Mohammed
Improved peptide identification by targeted fragmentation using CID,
  HCD and ETD on an LTQ-Orbitrap Velos
J. Proteome Res., 10 (2011), pp. 2377–2388

The numbers yielded by any mass spectrometer are always the mass divided by charge (m/z).
Figure 2B in the paper shows the peaks from a peptide that was isolated and then fragmented inside the mass spectrometer. The ideal scenario is that each peak has an m/z that corresponds to a potential fragment of the peptide (or whatever is being analysed).
The fragment ions that indicate the methylation include the monoisotopic mass of three methyl groups (~42). These ions (C14 - C21) also carried two electrons. The machine provides m/z so add the monoisotopic mass of peptide + monoisotopic mass of three methyl groups + mass of two electrons and then divide by the charge (2).
The effect of the charge state can be seen when you look at C13(+;1360.79 m/z) and C14(++;766 m/z).
I didn't know how to address the "mechanism of it".


text:
What are the differences between insects and spiders?
I have always been told that a spider is not an insect, since the former has 8 legs and the latter 6 legs.
Is it just a matter of definition and spiders could have been defined as "8-legged insects"? Or are there more fundamental differences between the two kinds of animals and the distinction makes sense from the viewpoint of biology and evolution?

Spiders and Insects have been separate independent linages of animals for 500 million years. Spiders have two body parts (cephalothorax and abdomen), while insects have 3 (head, thorax and abdomen). Besides the differences in number of legs, spiders and insects have different forms of respiration, different mouthparts, and different exoskeletons. Insects have antennae, while spiders don't. In short, spiders and insects are more different from one another than mice are from sharks.


text:
Identification of these birds
We recently put up a bird house and put a camera in it. We appear to have two new neighbours, but what is the species?
We live in the south-western part of Norway.

This is very likely the great tit (Parvus major).

Photo by Walter Baxter.

this is probably the most common bird in norway,if i step outside my house in daylight i will see one in less than 5 min.


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Temperature to kill virus
Why do I see only high temperature advice to kill microorganism, and not low temperature?
Why isn't there any low temperature which kills virus? Are they more resistant to low temperature?

To re-create the spanish flu of 1918, they tried to collect it from graves from very cold countries like siberia, because cold temperatures stop most micro-organisms like pause on a TV, and when they wake up, they just keep going.

High temperatures means that lots of energy is available in the environment. This energy speeds up chemical reactions, and make possible some reactions that wouldn't happen at all at lower temperatures. In particular, proteins can adopt new shapes as temperatures get higher. It's the misshapen proteins rather than the temperature per se that kills the microorganisms.
Low temperatures mean there is relatively less energy available in the environment. This slows down or stops chemical reactions, including the ones that result in mis-shaped proteins. Extremely low temperatures may slow down a microorganism's metabolism and stop it from reproducing. That's why we keep perishable foods in refrigerators. However, if you warm the microorganisms back to a normal temperature, most of them will pick right where they left off. A few may be killed by the formation of ice crystals inside the cells that mechanically break the cell membrane.
If you walk into a microbiology lab you'll often see a wall of refrigerators, used to preserve microorganisms for later revival and use.


text:
Why doesn't our immune system react to infused antibodies produced in a horse?
Calmette tried injecting horses with snake venom and then taking out the serum which has produced antibodies against the venom and injecting in the snake-bitten human.
Shouldn't our immune system recognize this exogenous protein and try to eliminate it as it's a non-self protein?

Our immune system does react to horse antibodies, but as with any adaptive immune response it takes some time for the response to develop. In the weeks before our immune response fully responds to the horse antibodies, the infused antibodies can have their effect.
If you then have a second infusion of horse antibodies, the immune response would not only prevent them from having their beneficial effect, but it might case serious adverse effects.  This serum sickness (Wikipedia link) has been known for over a century; here is a paper from 1918 discussing it as a well-known issue:

The injection of horse serum either in small or in large amounts in human beings is always followed sooner or later by the development of hypersensitiveness of the skin to subsequent injections of horse serum. For the development of this reaction serum disease is not essential.

--THE RELATION OF CIRCULATING ANTIBODIES TO SERUM DISEASE. J. Exp. Med. Published March 1, 1918
Although there aren't many modern situations in which horse (or other non-human species) serum is injected into humans, when it is (as with anti-venom, which is generally produced in non-human animals) serum sickness is still a concern.

Serum sickness is a delayed immune reaction resulting from the injection of foreign protein or serum. Antivenom is known to cause serum sickness but the incidence and characteristics are poorly defined. ... The primary outcome was the proportion with serum sickness, pre-defined as three or more of: fever, erythematous rash/urticaria, myalgia/arthralgia, headache, malaise, nausea/vomiting 5–20 days post-antivenom.

--Incidence of serum sickness after the administration of Australian snake antivenom (ASP-22). Clinical Toxicology. Published  2016

Human/mammalian immune system do not react to everything foreign that enters the body. This foreign substances are called "antigens". Instead, the host [i.e. body] reacts to "immunogens" - these are antigens, that CAN elicit immune reaction. Microbes are immunogens, for instance. They don't only consist of microbe proteins, but also of so-called PAMPs, pathogen-associated microbial particles. This can be a bacterial cell wall or "peculiar" DNA and double-stranded RNA, that are definitely cannot be found in mammalian tissue. And these PAMPs are recognized by PRRs, pattern recognition receptors, that are found on innate immune cells, such as dendritic cells and macrophages. WITHOUT activation of innate immune cells, without, basically, INFLAMMATION, the overall immune reaction is not possible. At least, this is a current concept.
So, horse antibodies are not sufficient to elicit immune reaction.
In order to induce immune reaction, these antibodies should be injected with something, that can activate PRRs or cause tissue damage, like aluminum dioxide. The latter substance is largely used in formulation of vaccines. Guess, why ;-)
Of course, there are immune reactions to proteins or harmless xeno-antibodies, but this is usually not physiological, if the manifested reaction is severe. Example: food allergy to egg protein, ovalbumin.
Hope, it helped.
Best,
S

Horse antibodies DO cause an immune reaction, it is just mild and therefore not perceptible as an adverse effect (just like our body reacts to and eliminates thousands of bugs every day).


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Can a bacterium infect another bacterium?
I researched about it by searching on Google and reading some bacteriological articles, but I did not get any answer. I also asked some of my teachers, and they were also a bit confused. Some said that it is possible and others said not. So the question remains:
Can a bacterium infect another bacterium? If so, how?

Not exactly what you asked but the YouTube channel Journey to the Microcosmos may be interesting along those lines, a recent video "Our Paramecia Are Infected" discusses some of this and has very pretty microscope video
https://www.youtube.com/watch?v=foKz81ElCjM

Bdellovibrio bacteriovorus (BV) “infects” other bacteria:

Similar to a virus, BV attacks bacteria such as Escherichia coli (E. coli) by attaching to and entering its prey, growing and replicating within the cell, and then suddenly bursting out, releasing its progeny into the surrounding environment. — How bacteria hunt other bacteria

Note that a lot of the answer to this question hinges on what you mean by "infect". Bdellovibrios (as Laurel has already established that this does happen) do something that does look a lot like infecting eukaryotic cells- but it is still spoken of as "hunting". Why? I am not sure.
There are lots of different ways that bacteria can have negative interactions with each other- though they often resemble "hunting" or "warfare" more than "infection".
Getting a bit more into the "how" of the question, a common mechanism for inter-bacterial negative interaction is the Type VI secretion system. This apparatus is often spoken of as a "weapon" that bacteria can use to kill each other, by adhering to the other cell and shooting toxins in through its membrane. They can use this to great ecological effect.
The type VI secretion system is also used in some contexts for infecting non-bacterial hosts, so by that logic you could argue that it resembles infection.
Update: for a short discussion of inter-bacterial killing (including Bdellovibrio + secretion systems) in the context of biotechnological applications, see here.


text:
Do antigens protrude through the capsule/slime layer in prokaryotic organisms where these features are present?
In prokaryotic organisms that have a slime layer or capsule, do intrinsic/extrinsic proteins and other molecules that could be used as antigens protrude through the capsule?

I assume that they must in order to maintain their function for the cell, yet am struggling to suggest another way in which the presence of a capsule/slime layer could serve as a defence against phagocytosis?  Unless the slime layer directly resists lysosomal activity after the pathogen has been recognised and engulfed?
On a related note, could the flagella of an organism (which must protrude through the capsule as above) trigger an immune response on its own?

Well that answers the question about flagella at least


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What is the contribution of viruses to the evolution of mankind?
I'm interested in horizontal gene transfer in bacteria, viruses, and organisms such as Bdelloid Rotifers. I've just read in Carl Zimmer's 'A Planet of Viruses' the following passage:

As a host cell manufactures new viruses, it sometimes accidentally adds some of its own genes to them. The new viruses carry the genes of their hosts as they swim through the ocean, and they insert them, along with their own, into the genomes of their new hosts. By one estimate, viruses transfer a trillion trillion genes between host genomes in the ocean every year.

It's interesting to consider the scale of DNA-swapping that has occurred given the frequency by which it happens and the evolutionary timescale.
Are there any examples of genes in the human genome that we know were deposited by viruses that would have given an evolving human a physical/mental advantage? Where did they come from? What benefit did they provide?
I'm interested in genetic additions from non-human-ancestor species, rather than the transfer of genes that occurred as mutations from other humans.

The number of candidates that help humans cognitively is hotter in comparing humans to other primates. Though it happens trillions of times a year, its much more common with bacteria and fungi than animals, so the catalog of human vertical transfers is small.

The processes that control the germline of metazoans (multicellular animals) are highly regulated compared to single cell bacteria and eukaryotes as well as plants.
At this point there are no clear stories of gene transfer into a complex animal, though there are some for plants:
"animals and fungi seem to be largely unaffected, with a few exceptions, while lateral gene transfer frequently occurs in protists with phagotrophic lifestyles, possibly with rates comparable to prokaryotic organisms."
Bacteria fungi and plants are more permissive and more susceptible to gene transfer and it probably is more important to their evolutionary path.
Its been estimated that as much as eight percent of the human genome has been affected by viral integration.  But viral genomes are highly selected against carrying non essential material - other genes rarely come along for the ride it seems.  What is probably more influential is that viral insertions could participate in rewiring the regulatory network of animal cells, not adding genes, but modifying the conditions under which they are active.

Human endogenous retroviruses (HERVs) have been an interesting (and expanding) topic of research in evolutionary biology and medicine. A retrovirus has an RNA genome in the virus particle, and integrates with the host cell's DNA upon infection to hijack the transcription/translation machinery and produce copies of itself. For this reason, it is not possible to "cure" a cell of a retroviral infection; instead all of the infected cells must be destroyed or commit suicide through apoptosis, also known as programmed cell death. Common examples of retroviruses include HIV (causative agent of AIDS), HTLV (human T-cell leukemia virus), and the Hepatitis B virus.
Viral infections are most common in somatic cells, where any change in the DNA sequence is not passed along to the next generation. However, any retroviral infection in germ cells (eggs, sperm, and the progenitor cells that make them) could be passed on to the next generation, and over time spread throughout a population. Some HERV fragments are apparently completely inactive (at least as far as we are able to tell currently), and are a possible source for some of the so-called "junk" or non-coding non-regulatory DNA that makes up a significant part of our genome - one estimate claims that 8% of our genetic material is of retroviral origin. Other HERVs have been implicated in various pathological conditions, including multiple sclerosis.
I'm not sure that any human genes have been found that were picked up by a virus, stayed with it for a time (and potentially mutated), then was reinserted back into the human genome, if that's what you're asking. There are certainly many cases of genes and gene fragments (coding regions, promotors, enhancers, etc.) being moved around as a result of viral integration/splicing. http://en.wikipedia.org/wiki/Endogenous_retrovirus#Genome_Evolution is a large, rather well-written section with numerous links to the primary literature showing how our genome has been altered over the years by HERVs.