text:
Why does strenous exercise cause vision of "lights"?
I had a hard climb a week ago. I got so tired then any time I closed my eyes I saw these lights inside my head. I see these lights almost every time that I run fast or some thing like that. What are they and where do they come from?

Here is a picture I drew using Photoshop ;)

I sometimes see similar “lights”, too. Although of somewhat different shapes.

interesting that you see hexagonal shapes. Hexagons often appear in 2D sensory processing due to its relation to sphere packing.

I have exactly the same, and have had for at least the last 40 years with no apparent ill effects.  They are in the middle of my foveal region and flash fast, maybe 30 Hz.  I get them during exercise but more noticeable immediately afterwards, until my heart rate slows.

I also get "seeing stars" but that's completely different.  For me seeing stars when I stand up suddenly involves multiple (10ish) tiny, bright white points of light randomly distributed across my entire visual field, that move rapidly (maybe 10% of the visual field) in semi-straight lines, for about 1-2 seconds, then suddenly stop, one by one, with a few persisting longer than the others.  It's a totally different visual phenomenon than the "centre flasher" the questioner describes.

This is a common phenomena which most of us come across. Seeing flashes of light, stars and other shapes in the eyes occur when the body goes through stressful activities. For example while you are climbing the blood flow will be more to other prominent parts like hands and lower waist so brain and eyes will get less supply of blood as well as nutrients. Hence those flashes or stars are visible to us. This phenomena is called "Phosphene" and a phosphene is a phenomenon characterized by the experience of seeing light without light actually entering the eye.
Wikipedia/Phosphene gives an explanation for occurrence of Phosphenes:

Phosphene is "seeing stars", from a sneeze, laughter, a heavy and deep cough, blowing of the nose, a blow on the head or low blood pressure (such as on standing up too quickly or prior to fainting). It is possible these involve some mechanical stimulation of the retina, but they may also involve mechanical and metabolic (such as from low oxygenation or lack of glucose) stimulation of neurons of the visual cortex or of other parts of the visual system.

So seeing flashes of light can be due to:

Blood shifting.
Low blood sugar(causes weakness).
Head trauma.
Headache.

So to summarize this thing, we should have enough nutrients, water supply to the body whenever we come across stressful activities. Phosphenes are temporary stuff which do not harm eyes.

One question, I also experience this pattern in my eye all the time I do workout. But in my case the pattern is always the same, meaning the "stars" are always at the same place, having always the same shape. Are those also phosphenes or are they normally 'random' in shape or position?

It could be posterior detachment of the vitreous humor. Stress on the optic nerve caused by motion of the vitreous humor inside the eye can lead to the sensation of lights. And since the nerve is circular, you see a pattern of circular light. Normally its not serious, and many people experience it as age progresses. If you are not hydrating well during your climbing that might also be aggravating it. To be safe you should have an eye doc check you out though since there is slight risk it could lead to retinal detachment.

This is very much like calling out "Zebra!" when you hear hoof beats (unless you happen to live on the grasslands of eastern and southern Africa. In that case, it's more like calling out "Caribou!"

@anongoodnurse I'm also a climber, a runner, experience dehydration and on occasion experience the same light sensations when I press my eyelids tight suddenly or turn my head suddenly left to right at night. And this is what my doctor diagnosed. So what are you suggesting might be the issue otherwise besides grassland animals?

What your doctor said doesn't carry much weight with me. They and I are of differing opinions. I don't think I could be any clearer expressing my opinion. If every time someone who exerted themselves saw lights it turned out to be a pulling on the retina, opthalmologists would be more common than dirt.


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Why are butterflies drinking blood?
According to this video, butterflies sometimes drink blood. Do they have the organs necessary to digest blood? I thought they eat only salts and nectar, which are easy to digest compared to proteins.
@aandreev
100mg/dL is the human blood sugar content (I assume it is similar in other animals). Afaik. sugar energy density is about 4kcal/g. A butterfly is about 1g of weight, which means 1mL if we count with water. So it can drink around 0.5mL of blood. That means 0.5mL×100mg/dL×4kcal/g = 0.002kcal = 8.4J. The top butterfly speed is about 12 mph, so I think we can count with 6mph by an average butterfly, which is about 2.7m/s. So it needs 1/2×1g×(2.7m/s)2 = 0.0036J kinetic energy to move and 1g×9.81m/s2×1m = 0.0098J potential energy to keep the 1m height of flight. I think we can guess that it loses this kind of energy in 2secs, which means it needs 0.0134J/2s = 0.0067W power to fly. So the 0.5mL blood means 8.4J/0.0067W = 24925s = 21min of flight time, which is not much compared to nectar (30g/dL$, $2500J$, $100h). Ofc. this is just a very rough estimation (the real flight time is probably much lower) based on data coming from non-scientific sources, but I think you can see the difference.

For salt content I think. Not sure enough to answer but blood is full of nice things besides calories.

calories in blood are glucose

@aandreev I edited the question.

what about salts though?

@aandreev Find evidence and send an answer. This is how science works. :-) http://scholar.google.com

check http://en.wikipedia.org/wiki/Hematophagy

I am quite sure blood contains far far more than just glucose. Most of the compounds in blood (proteins, lipids) can all be oxidised.

@MarchHo Ofc. they can be used to produce energy, but can a butterfly digest proteins and fats?

I didn't watch the video so I don't know if this was mentioned. Butterflies will exhibit a behavior called mud puddling which occurs mainly with male butterflies [1]. Puddling is when butterflies seek out moist surfaces in order to consume the fluid. Butterflies will puddle in soil, dung, carrion (rotting flesh/meat), etc. Boggs and Jackson claim that puddling falls into two categories which aren't mutually exclusive [1]:

scarce nutrients for example sodium
competitive exclusion of males or young individuals from flowers

But we can see blood isn't the only option for puddling. Basically anything that provides moisture and nutrients will do.

This competition for flowers is very new to me, I did not know that butterflies can fight each other. :-)

@in3rno I choose you Butterfree! Use Sleep Powder on the other Butterfree! Seriously though, I would assume they use the same tactics as birds...minus the beak stabbing, and vocalizations?

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why do some trees have trunks that branch out and others don't?
I've never seen a bald cypress that had a tree fork but oak trees have them all the time.
Any ideas as to why this is?
Bald Cypresses are usually found in very wet areas whereas oak trees tend to be found in more comparatively arid areas so maybe having lots of tree forks and a very wide crown helps catch precipitation in the leaves so that it might fall at a more controlled pace onto the soil below and be less likely to run off, away from the trees root system?

All conifers tend to have a primary leader , less pronounced in other trees . Although no rules- eg. pin oak will tend to be pyramidal with a primary leader.

There are apparently growth "rules" imbedded in the genome.  These determine branching patterns, among other things.  These rules can be quite simple, yet give rise to complex morphology.
You might look at L-systems, which are rules (or perhaps one might regard them as programs) that can be used to reproduce the growth patterns of plants on a computer.  The classic work, I think, is "The Algorithmic Beauty of Plants" by  Prusinkiewicz et. al.  It can easily be found as a free pdf.

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What does the 'y' mean in CHL1−/− / L1−/y double mutant mice?
I am reading a journal paper and I have come across the following statement:

To investigate this, $CHL1^{−/−}$ / $L1^{−/y}$ double mutant mice were generated
and analyzed for thalamocortical axon topography.

I know that -/- means knockout, +/- means heterozygous and +/+ means wild-type. But what does -/y mean? I have never seen this notation before.
Any insights are appreciated.

According to the introduction, human L1 is located at Xq28, in the q arm of the X chromosome. It is also on the mouse X chromosome. The $CHL1^{-/-}$ nomenclature you've already figured out: a homozygous knockout of the CHL1 gene. I haven't thoroughly read the whole paper, but there must be some undesirable phenotype when L1 is homozygously knocked out in female (X/X) mice, so the researchers in this paper are using male (X/Y) mice, with L1 knocked out on the single X chromosome. There is no corresponding allele on the Y chromosome, so the nomenclature is $L1^{-/y}$.
This is borne out in the Materials and Methods:

The L1 gene is located on the X chromosome, and its deletion results in poor breeding capability of males and thus female mice homozygous null for the CHL1 gene and heterozygous for L1 ($CHL1^{-/-}$/$L1^{+/-}$; C57BL/6/Sv129, ∼9:1) were crossed with $CHL1^{-/-}$/$L1^{+/y}$ males (C57BL/6) to produce $CHL1^{-/-}$/$L1^{-/y}$ double mutants.

From their methods as you've quoted it seems that the issue is that the male L1 knockouts don't breed well; that makes it difficult (perhaps impossible?) to produce a female with both copies knocked out, because one of those has to come from the male-that-doesn't-breed-well. There may not be an known undesirable phenotype for the female double knockouts, just that there's no way to produce them by breeding, and it's much easier to just genotype the male offspring.

I read that section from the M&Ms multiple times, and I still couldn't figure out exactly what the issue was. You finally broke through my brain fog, thanks :)

Took me a second too... my first thought was they were just using male mice for other convenience reasons; it's been fairly common in neuroscience to use only male rodents to reduce variance in measurements from sex differences and estrous cycle, though there's a bit of a push against that trend these days.

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In fluorescence microscopy images what is meant by the term "puncta"?
I am reading papers where confocal fluorescence microscopy images were analysed. In many of the papers I see the term "puncta" being used when researchers analyse the colocalisation between 2 proteins. For example, in the linked paper:

In addition, many C1q-positive puncta in the IPL were associated with
synaptic puncta identified by double immunostaining with synaptic
markers such as PSD-95

I am not sure what is meant by the term "puncta" in the context of immunocytochemistry. I have read that the general definition for puncta is a small, distinct point. However, I was wondering whether puncta is a synonym for clusters of a protein (e.g. in the example above, does synaptic puncta refer to clusters of the PSD-95 protein?)
Any insights are appreciated.

I have read that the general definition for puncta is a small, distinct point.

That's correct. From my understanding, puncta are dots.

However, I was wondering whether puncta is a synonym for clusters of a protein

In the context of fluorescence microscopy, a punctum (plural puncta) does not specifically refer to the aggregation of proteins. Any small, distinct points in the field of view may be called puncta. I like to think of puncta in contrast with foci, which I generally understand to be regions of interest, though, in practice, the two terms are often used interchangeably. Here are some examples from the literature:

The phosphorylation of H2AX at Ser139, resulting in the formation of γH2AX puncta in the nuclei, is an early event in the cellular response to DNA damage.

Chiu YH, Hsu SH, Hsu HW, Huang KC, Liu W, Wu CY, Huang WP, Chen JY, Chen BH, Chiu CC. Human non‑small cell lung cancer cells can be sensitized to camptothecin by modulating autophagy. Int J Oncol. 2018 Nov;53(5):1967-1979.

It is well known that histone H2AX becomes phosphorylated at Serine139 to γH2AX immediately after irradiation, and involves a large chromatin region of up to ~ 2 Mbp, thus forming distinct μm-sized foci at the sites of DSBs.

Memmel S, Sisario D, Zimmermann H, Sauer M, Sukhorukov VL, Djuzenova CS, Flentje M. FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy. BMC Bioinformatics. 2020 Jan 28;21(1):27.

My impression is that "puncta" is used in fluorescence microscopy (and autoradiography perhaps) when points are are indistinguishable from a single point source, but because it's plural they're talking about a bunch of dots from the perspective of the dots. When they write "foci" they're talking about a region that light emits from, without specifying whether they have observed individual puncta or not. You might get different descriptions of the same organization just because people think differently, or because of different imaging techniques. Or I might just be reading too much into it.

I agree with that. Puncta are dots. Foci may contain puncta, or foci may just be a diffuse but noticeable region of fluorescence.


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How to take professional SEM images of bacteria?
I am new to using SEM microscope I would like to take clear pictures of Bacillus subtilis. My sample is dropped on a piece of paper and carbon-coated. The picture is showing crumbs of something (maybe dust or burned bacteria). One of my images:

What is the problem here am I too using too much energy from the gun? or is it distance and magnification?

I'm no expert at all, but I don't think paper is normally part of the SEM sample prep...

Where did you find the protocol used for sample preparation? It's hard to troubleshoot without more details. SEM protocols for bacteria often include a fixative step to preserve structures and a dehydration step prior to sputter coating (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352184/). The one cell I can see in this image looks alright. Is it possible that you didn't apply enough sample, or didn't properly target the sample when collecting images?

The sample had a high optical density of bacteria. what do you mean by properly targeting the sample?

Loooooong ago, when I did some SEM, prep of a sample included fixating the specimen, removing the water by flushing the sample with acetone or ethanol, then liquid CO2, then letting the CO2 evaporate off, then putting the specimen on a stand in a vacuum chamber and bombarding it with electrons. I don't remember gold, but that was 40? years ago. It's not a simple process, and I'm surprised someone let you use their SEM without training you in its use.

Did you wash the cells before following the fixation procedure. I faced the same issues. Washing 3 to 4 times with PBS before and after fixation solved my problem and gave me crisp images of bacillus subtilis.
Let me know if that helps

I was introduced to SEM microscopy last year at school so I'm not the most reputable source. But here's what I think could be the reasons:

May need to coat in a more conductive heavy metal (like Gold) if you can access it
Smaller Aperture + Larger Distance (to increase the field of view)
Mount the sample on an aluminium stub with conductive sticky pads rather than paper
Adjust contrast

I have Mount the paper which is holding sample on an aluminium stub with conductive sticky pads. How about the gun power?


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How do Helper T cells activate Cytotoxic T cells?
Helper T  cells activate the Antigen-presenting Cells (APCs) through their secretions (the cytokines) (although the T cell in question gets activated in turn). This is typically achieved by cell-to-cell contact using  receptors on both the helper T
cell and APC.
Since Helper T cells also activate Cytotoxic T
cells, I am particularly interested in knowing whether cell-to-cell contact occurs between these two T cell subtypes (as is the case in helper T cell - APC communication).

So, are you asking about whether there's physical contact between CD4+ and CD8+ T cells?

@MattDMo Yes, that is exactly what I'm asking


text:
Can the sleep/wake cycle be influenced by non-visible spectrum electro-magnetic radiation?
I've been reading a few papers on Melanopsin and Suprachiasmatic Nucleus (SCN), and see that the sleep/wake transition is influenced and entrained by visible light, particularly in the blue spectrum that is registered by special cones in the eye and is transmitted to the SCN.
I've seen a fleeting hypothesis/mention in two of these articles, that electromagnetic radiation may also play a part in the sleep/wake transition and melatonin release, on top of the blue light. It was some time after I read those articles that it dawned on me to ask this question, and I'm unable to find the exact lines where the mention was made.
Has there been any modern studies on the connection between electro-magnetic radiation (non-visible spectrum) and the human's circadian rhythm entrainment?
Can humans be affected or feel the influence of electro magnetic radiation at all?
If there is a connection, what is the name of a process/organ/gland by which humans can be affected with electromagnetic radiation?
Thank you for your clarification!

Maybe this question can be better answered (or is already) at skeptics

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What is the timing of information assimilation within a human brain?
A little background: I'm an avid dreamer and have great dream recall, sometimes up to 5-7 per night.
In my experience, I can sometimes trace some elements of the dream to an event that occured within a 1-3 day window prior to the dream.
I've done similar experiments with the process of idea generation, where an idea that I have can be traced to experiences from the previous 1-3 days.
This makes me interested if there have been some kind of studies on how rapidly the brain absorbs and assimilates information from short term memory over to the long term memory. Has there been any studies on how long the brain keeps information before discarding or processing/assimilating it into dreams or new ideas?

I think this question is better suited for CogSci.SE where there are already questions similar to it

This question appears to be off-topic because it is belongs in  CogSci.SE

Try googling on "consciousness lag". I cannot cite any sources, but I have heard many times that working of consciousness happens in waves, and it is normal, when having some strong experience, for it to be experinced for some time, then come down, then rise again, say, in +1 minute, in +5 minutes, in +20 minutes, in +1 hour, in +1 day, in +3 days and so on... in some sense, the work of consciousness is similar to water surface with waves.. you can read much about that in eastern philosophy, and it plays well with electromagnetic nature of waves in the nervous system.


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Is human "sperm warfare" a concept supported by biology?
I've recently read the "Sperm wars" book by Robert Baker. It deals with human sexuality and infidelity. The main premise of the book is that  human male has different kinds of sperm:

Regular sperm for fertilization
Toxic sperm that kill competitor sperm (similar in concept to white blood cells)
Slow, inactive sperm to block channels in female cervical filter

According to the author, when a female engages in infidelity or group sex, the sperm actually "goes to war" killing competition and preventing passage through cervical filter.
Are there are indeed different kinds of functional sperm in humans, and are their functions involved in sperm competition / warfare? In other words, does human sperm not only fertilize the egg, but also to block passage of competitor sperm and even kill it?

This guy seems to have reasonable credentials. Next step would be to search academic journals for this research and see whether peer reviewed.

The logical conclusion to this claim seems to be that a woman could not get pregnant (or would be much less likely to do so) while engaging in "infidelity" or group sex.  I'm pretty sure that this is contradicted by experimental evidence.

Not in humans
Sperm competition is supported in humans (multiple sperm from multiple partners can be present in the same female)
Specialized sperm is not supported.
Specialized sperm is however confirmed in non-human non-vertebrate animals which was surprising, although what the different types of sperm do in these animals is not understood.


text:
Is there such thing as "biological cycles" of activity/performance/etc in mammals?
I'm looking for some information about the cycles of increased/decreased activity, mental performance or endurance that are related to a mammal's age and the time of a season.
First of all, I'm not sure what such cycles would be called. I know of circadian rhythm, which is an ~24 hour cycle. The other cycle I've heard about was circa-septan (7 days?). What keywords should I use to search for cycles that may have period of a month to several months?
The second question is - are there are episodes of increased activity/performance over a mammal's lifetime? I can think of two example - mating rituals may involve fighting and hibernation involves almost no movement at all.  Are there additional events that may last more than a month?
The final question is if the age comes into equation of increased/decreased activity. Lets say a younger rat an and older rat are put into the same maze, would their ability to "solve" the maze be related to age?
This question is rather broad. Maybe there are some keywords or a science branch that deals with these questions and I can refine my search?
I appreciate your input!

I think you have already answered your question of “are there such cycles?” – with that in mind, could you maybe make the question more directed to a single point that can be answered?

You could look for "seasonal rhythms" or "infradian rhythms"

This "might" be considered as an answer to at least on of your questions. http://en.wikipedia.org/wiki/Seasonal_affective_disorder. I don't have the time now, but will likely have a full answer later tonight.

With regard to episodes of increased activity/performance over a mammal's lifetime, I can add migration to breeding/mating and hibernation or torpor. Birds of course are better known for migration, but some mammals, notably in Africa migrate over an extended time.


text:
What is the species of this small bird in Germany?
I've recently (Steptember 2022) found this little guy in Frankfurt (Germany) in the morning. It could have fitted in my hand. It was staying very clam on the ground so I could go really close and take this photo with my smartphone.
I want to put it on Wikipedia. Can somebody help me to identify it?

I tried google image search and I think it might be Regulus ignicapilla (image / other image) or Regulus regulus?
edit: In case somebody is curious:

https://commons.wikimedia.org/wiki/File:Regulus-ignicapilla-top.jpg
https://commons.wikimedia.org/wiki/File:Regulus-ignicapilla-side-left.jpg
https://commons.wikimedia.org/wiki/File:Regulus-ignicapilla-side-right.jpg

Smallest bird along with Goldcrest. Reckon thats Firecrest

This is a common firecrest (Regulus ignicapilla) because of it's "three" black lines* on the head, especially the one that is passing on the eyes and its pale (almost white) and well marked eyebrow.
*In french, we call it "Roitelet à triple bandeau" because of that. Its german name is Sommergoldhähnchen.

Facts
The Common Firecrest only occurs in the western Palaearctic. It is a lightweight like the Goldcrest which, however, unlike ist more robust twin species, mostly leaves Switzerland in the winter. It is less bound to spruce forests than the Goldcrest and in addition to coniferous trees also uses deciduous ones. Where forests are damaged, the birds soon have problems: The thinned out branches no longer provide sufficient shelter and the food supply is severely restricted.

Source: https://www.vogelwarte.ch/en/birds/birds-of-switzerland/common-firecrest
Also available in German:  https://www.vogelwarte.ch/de/voegel/voegel-der-schweiz/sommergoldhaehnchen

You can also try to differentiate his call from Regulus regulus; it's very subtle but there is one.
Both species appreciate the dark environment of coniferous. Because of their very small weight (5-7g!) they spent most of their time searching for food (mainly insects), especially in winter. It's also this characteristic which actually determines the maximum latitude they can reach; too far north, nights become too long and days too short for them to feed enough during the winter season. (oral communication, Museum of Natural History, city of Geneva).

European distribution of both regulus regulus and regulus ignicapilla.
Source: Le Guide ornitho, 2015. Ed. Delachaux et Niestlé. By Lars Svensson Killian, Mullarneym Dan, Zetterstrom. ISBN 9782603023938.
Meaning of the colors:

purple: all year presence,
light blue: winter presence,
orange: summer presence,
pale yellow: during migrations periods.

If you are searching for a nice guide, you can checkout this one: "Collins Bird Guide: The Most Complete Guide to the Birds of Britain and Europe".
By: Lars Svensson (Author), Killian Mullarney (Illustrator), Dan Zetterström (Illustrator), Peter J Grant (Contributor). ISBN: 9780008547455 Edition: 3, Hardback Nov 2022"


text:
Mushroom identification in in a balcony planter in Bavaria
I've seen the following mushroom pop up in a balkoney planter in Bavaria (Germany) in June. They were growing pretty quickly (just in a few days)
Description
So that others have a chance to find it via Google / text search:

Dimensions: The whole "body" is maybe 3cm high. The "cap" has probably a diameter of 1cm (I can measure it in the evening).
Stem: The stem is smooth and has a bright color.
Cap: Looks like a cocktail umbrella. It's beige on the top. On the bottom it has dark "stripes" going from the stem to the outside

Photos

A picture from the bottom:

My research
Google Reverse image search / https://tineye.com/: Parasola plicatilis - however, I think mushroom are pretty easy to confuse. As this is growing next to food plants I mainly want to know if they are poisonous / how careful one needs to be.
The cap is not transparent as What is this mushroom attached to the terrarium with transparent cap and black strips?


text:
Do neurons with dopamine inside only send signals to another neuron with dopamine?
A nerve cell with dopamine receptors gets an action potential and releases dopamine to other neurons. Does this nerve cell only release to cells with dopamine inside? Because what if a neuron has a dopamine receptor but serotonin as a transmitter?

If that was true, how would the rest of the brain ever communicate with dopaminergic cells and vice versa?

No, neurons with all sorts of neurotransmitters frequently synapse onto neurons that release other types of neurotransmitters. In fact, aside from the most common neurotransmitters like glutamate and GABA, this is the rule rather than the exception. You mention specifically dopamine, and this is a perfect example--the medium spiny neurons in the striatum that are the most "famous" dopamine-receiving cells are NOT dopaminergic themselves--they are all GABAergic. The other aminergic neurons are similar; the noradrenergic locus ceruleus neurons and the serotonergic neurons of the raphe nuclei project to much of the forebrain, which contains few noradrenergic or serotonergic neurons of its own.
Neurons frequently have receptors for neurotransmitters that they do not produce, and these are commonly known as heteroreceptors, as opposed to autoreceptors, which respond to the same transmitter that the cell possessing the receptor responds to. Autoreceptors commonly exist more for the purpose of negative feedback ("I've already released enough of my transmitter, therefore I need to stop so I don't overload the cells I synapse onto") than for neurons releasing the same transmitter to activate one another.


text:
How deep underwater could you breathe using a tube which breaks the surface until the water pressure makes it impossible to inhale air?
I'm struggling with a question asking how deep you can breathe underwater using a hollow reed before the water pressure makes it impossible to inhale. The question asked to use this data of maximal respiratory pressures:

The question also gave a hint that for every metre below the surface, hydrostatic pressure increases by 100 cm H2O.
I'm seriously lost on this question, from my research, all I could find was that a difference of approximately 50 cm H2O is needed in order to inhale, but I'm unsure if that is information I should deduce from the table instead of looking up. Even knowing that information, how would I then find out how deep that means you could breathe? Any help would be greatly appreciated.
Thanks

It shouldn't affect the question, but note that to get sufficient air past a certain point (depending on the tube volume), two tubes would be needed, one for inhalation and one for exhalation, otherwise you'd be rebreathing too much of your own exhaled air.

Different graph here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501025/table/T3/?report=objectonly your lungs and the different levels of the tube equalize to the surrounding water pressure, so the maths is simple, a male can fill their lungs till about 50% full at 75cm  although it would take your maximum force and it would require a tube with almost zero flow friction. To breathe comfortably at that depth, the tube body could be about 7cm diameter. Applying maximum force to achieve only 50% breaths would require training because it would be claustrophobic and cause heart acceleration.

I won't write an answer because I don't know the tube resistance relative to diameter, however the faster the breath the higher the tube resistance so the maths chart requires a tube with nearly zero friction, which is probably 4 inches or forearm sized.

First, a sanity check.  Snorkeling isn't generally done at much depth, and this question reflects some subjective sense of that.
My guess (after much confusion) is the table they're providing is apparently the pressures that the subjects were able to apply, when striving to breathe in or out at various levels of "Lung Volume".  But what is "Lung Volume"?  Not Total Lung Capacity - is it Tidal Volume, Expiratory Reserve Capacity, something else?
If I read it that the person, at 22-54% "Lung Volume", can apply only 53 cm H2O of pressure differential while inhaling, that implies that at this depth of external pressure, they can't inhale.  (Oddly, if they lose the battle and go to 1%, the data says their ability to inhale is reduced!) In theory the fluid pressure of water or air on the body should be similarly positioned.
Even so, there are two things that make me doubt this.  First, the inability to inhale should be coupled with a greater ability to exhale.  So I still wonder if sort of shallow breathing might still be possible at the limit of the expiratory reserve, or even in the range of "residual volume", as the external pressure is opposed by connective tissue.  Second, the diaphragm and the external intercostal muscles are, well, muscles, so it should be possible that someone could train those muscles well and resist more pressure.

It should not show greater ability to exhale as exhaling is controlled by inhalation, if you can't inhale your lungs are already at equilibrium pressure so you can't exhale either.

I'm a moderately-experienced scuba diver who's also done quite a bit of snorkeling, mostly no deeper than 10m.
I think the simple thing is to consider inhalation vs exhalation separately looking for the limiting factors. At best, the inhalation table suggests you can generate -53 cmH20 pressure.
Therefore the max breathable depth would be 53/100 x 1m = 0.53m.
That also roughly matches the assertion in the article of 1.5 to 2ft.
The link Mike Serfas used to a snorkeling site makes the same argument about CO2 remaining in the tube when you exhale as outas's comment.
That's a common mistake - yes with a normal snorkel you inhale and exhale through the same tube but that is not mandatory! If you were breathing through a long tube, assuming bubbles were allowed, you could exhale through your nose to avoid pushing CO2 back into the tube.


text:
What insect eggs are these?
There are only 3 eggs. A pink colour with stripes on it. Is it possible to identify the species? Found right below a window, on the wood.
I'm in Bangalore,
India.

These are caterpillar/butterfly eggs belonging to the Rounded Palm-Redeye (Erionota torus).
Here is an example of the eggs of a leaf:

The larvae / caterpillar form looks like this:

And fully formed butterfly looks like this:

All these pictures can be found on the iNaturalist page for this taxon:
https://inaturalist.ca/taxa/219475-Erionota-torus/browse_photos?quality_grade=any&photo_license=any&place_id=32239
And the geographical range of observations of this species includes your area:

Nice answer! +1. (Never thought I'd think, "Ugly butterfly...")

@anongoodnurse it used up all the pretty on its eggs.

@anongoodnurse Yes, I my first impression of the adult was that it was a moth

Wow! Thank you so much for the answer! I've seen these around the house!


text:
What happens to the excess immune cells or WBC in our body?
When we have an infection our immune system produces a large amount of white blood cells (WBCs) in our body to fight against the pathogen or parasite. My question is after the immune response has finished fighting the pathogens, what happens to the excess cells and antibodies that presumably are no longer needed? Will they disintegrate themselves, is there a final step in the immune response to dispose of these cells, or are excess of these cells and proteins present as if they are not in excess (they are filtered no more so than when at normal levels)?

The process you are asking about is called the termination of the immune response, and for a long time it was not studied very much for some reason, with scientists preferring to analyze initiation instead. However, this has changed in recent years, and while we still don't know a good deal, the picture is much clearer than it had been a decade or three ago.
Here is a special edition of Immunological Reviews focusing on termination of the immune response. While the site says you need to pay to access each article, they're actually available for free in PubMedCentral, so just look it up there for access. For a very brief overview, this section of the Wikipedia article on inflammation lists some of the mechanisms involved.
In regards to your question about immune cells and antibodies, a couple of things happen. First, the vast majority of responding cells are either "turned off" or directed to commit suicide (apoptosis) by a variety of signaling mechanisms, such as anti-inflammatory cytokines like IL-4, IL-10, IL-13, and IL-35, along with other molecules like TGFβ and IL1RA, soluble receptors to pro-inflammatory cytokines like TNFα and IL-6, or through "death receptors" like Fas/CD95 and others. However, some cells are prompted to turn into long-lived memory cells, which are able to be quickly activated upon re-exposure to antigen, in many cases completely clearing it without the need for a full-fledged immune response (such as one generating fever and sickness).
As for antibodies, like most circulating serum proteins, they are metabolized mainly in the liver and can be excreted via the kidneys. Their half-lives vary by isotype, but can be as long as three or more weeks. This is assisted by FcRn, the neonatal Fc receptor, which recycles antibodies back into circulation, protecting them from breakdown:

FcRn: the neonatal Fc receptor comes of age
Derry C. Roopenian & Shreeram Akilesh
Nature Reviews Immunology 7, 715-725 (September 2007)
doi:10.1038/nri2155

Good answer. The only thing I would point out, for others reading that may be less familiar with immunology is that you are basically referring to the adaptive response and aren't touching on innate WBCs.

@AMR which cells are you referring to as "innate WBCs"? Macs? DCs? Both are involved in antigen presentation and regulation of the "adaptive" response, especially in producing some of the cytokines I mentioned. As time goes on, the line between "innate" and "adaptive" immunity gets fuzzier and fuzzier, and some investigators I know don't even refer to them as such any more, there's so much overlap.

Neutrophils, eosinophils, basophils, and to a lesser degree natural killer cells.

There is however an article on granulocytes that you linked to. When I read your response the first time, the third paragraph sounded like it was focused on the end stages of the adaptive response, but apoptosis is kind of a catch all for the termination of most all the cells raised in an immune response.


text:
Is there a physiological difference between love and infatuation?
I find that people generally distinguish between love and infatuation. Is there a physiological difference between the two? Or are they biologically identical, and the difference is circumstantial?

Could you elaborate on what you feel the distinction between the 2 is? Infatuation could just mean obsession, whereas love could imply a more physical attraction?

I don't really know the difference. It's kind of what I'm asking.

My point was simply that the interpretation of the words is quite subjective, unless you define them in the question. E.g. dictionary.com definition #1 for infatuation is [to inspire or possess with a foolish or unreasoning passion, as of love], and love as [a profoundly tender, passionate affection for another person]. Is this how you interpret them? Or would you say they feelings are more divergent? In my opinion you could probably use either definition for each word, depending on the context.

I'm sure I don't know. I'm essentially asking about the biological definitions of those words, if there are any.

The distinction (if there even is one) is likely to be at the psychological level, rather than biological... but that's just my gut feeling - I've not read that anywhere!

Assuming that our emotions are the psychological manifestations of chemical changes in our bodies (an assumption I have no trouble with but one that others may take umbrage at), any emotion will be different.
If your brain can distinguish between two emotions, then the underlying chemistry through which these emotions are expressed will be different.
This is not to say that we, as scientists, can quantify this. Definitely not today at any rate. Simply that there will almost certainly be a physiological difference between any emotional state that can be differentiated by your brain. Otherwise the brain would not register different emotions.

UPDATE:
Human language has different words for different feelings. There is often a type of feeling "continuum" with different words representing different ranges on this scale. For example:
Adoration--->Love-->Infatuation-->Affection-->Indifference-->Dislike-->Hate
How you decide to qualify an emotion you are feeling is more a question of semantics than biology. The point I am making here is that each point on that scale (and every point in between that we haven't explicitly assigned a word to) will represent a slightly different mix of various chemical signals in your body.
If your question is more about the English language words love and infatuation, their definition and distinguishing between them, try posting on English.SE.

Okay, but I don't even know if the brain can differentiate between infatuation and love.

If  you can differentiate, your brain can.

I don't know that I can differentiate between the two.

@Avi, see my updated answer.

That answers my question (that answer being "no").

Using the Triarchic Theory of Love proposed by Robert Sternberg, love is divided into three components:

Intimacy
Passion
Commitment

Using the theory's particular Infatuation is just the passion portion of love which is lacking in intimacy and commitment required for Consummate Love or True Love.
Physiologically speaking, this is when a certain sense of dependency comes in and as we know from years of addiction research, there is a physiological difference between liking sex physically and liking sex with a particular person for non-physical reasons.

Psychologically infatuation is associated with a projection - attributing to a person the qualities of an idealized person. This is not the only example of projection - similar explanation is given to irrational hate or immediate dislike, which are usually based on projecting a certain stereotype, attributed to a person due to their physical characteristics, superficial elements of their behavior, social status, etc. This is how people come to immediately think of a black person as a criminal, beautiful woman as promiscuous, a bearded guy as a terrorist, rich as callous, poor as lazy, etc.
Being based on superficial characteristics, such projections disappear when we get to know the person better, which is why infatuation passes after a few weeks or months - one learns that the object of one's infatuation differs from the idealized image. Then love, as opposed to infatuation, is a lasting feeling of the attachment to a person, when one is no more ignorant of their faults.


text:
How do scientists decide which version of a polymorphism is the main one?
This in fact has bugged me for years, but now I finally remembered to ask.
I suppose that if one variation is more frequent, it can be labeled as the default, but what about variations that are equally as common?
The example that I just saw, it seems that the frequency of both variants is the same, and yet somebody claims that G is the default and C is the polymorphism:
Polymorphism with genotypes CC, CG and GG occuring in 30, 40 and 30% of the control group, respectively http://hell.org.pl/~kamyk/stackexchange/Zorena1.jpg
Maybe it is possible to determine which one was first, but how? Is there ancient data about polymorphism frequencies?

A DNA locus may have two (or more) variants (alleles), but there isn't one termed a main or default variant.  In the example you cite, Myśliwska 2009, the only asymmetric distinction between the G and C alleles that I could see was in this passage:

The polymorphic region −174G>C of IL-6 encoding gene is implicated in
  transcription of this cytokine. The G>C nucleotide substitution
  creates...

This passage uses "substitution" (and "G>C" in −174G>C), which suggests that "G" is what is termed the ancestral variant, and "C" a later variant. The ancestral variant was the form that is believed to have been essentially the only form in some ancestral population; the later variant is a mutation (substitution in this example) which became established in part of a later occurring population.
Not all polymorphisms have their variants characterized in this way.  Those that do usually have DNA sequence evidence showing that species other than humans have a homologous gene, and those genes appear to have only the "ancestral" variant.  For the locus in the example you cite, the human IL6 -174 locus, a early paper by Fishman et al. (1998) says this:

Considerable interethnic variation in the frequencies of these
  polymorphisms has been demonstrated (39), which is consistent with our
  data for the -174C allele, which is considerably rarer in Gujarati
  Indians and Afro-Caribbeans, compared with UK Caucasians. As all of
  the primates examined were GG homozygotes, it is likely that this
  allele is ancestral and that the C allele represents a relatively
  recent change in the IL-6 5' flanking sequence.

This assessment seems to have become generally accepted.  The rather even distribution of G and C variants in the table you show is likely due to the subjects being of European ancestry, as suggested by this from SNPedia:

It [IL6 -174] tends to be quite polymorphic in Caucasians, but Asian
  and African populations are almost monomorphic (for the (G) allele).

[..] G is the default and C is the polymorphism

An allele (or just a nucleotide variant) cannot be "the polymorphism". There is polymorphism, if a given locus (or just a given nucleotide position) is polymorphic, that is, if as this position, there are different variants existing in the population. Therefore, an allele cannot be called polymorphism, only a locus can be called to be polymorphic and if a locus is polymorphic, then there is some polymorphism in the population.
I have never of people talking about the main or default variant. Do they use this word in the article you link? If yes, can you please indicate where?
Commonly, people talk about the wildtype versus the mutant variants. In this case, the wildtype variant is just the most common variant. Rarely I have seen people referring to wildtype variant when talking about variants that are at low frequency because the mutant is increasing in frequency and slowly reaching fixation. In such case, the wildtype mutant would correspond to the original variant at an arbitrary time point in the past but would not depend on the frequencies observed today.

I am not sure whether I answered your question or whether I missed the point you were trying to make. Let me know!

In this case, G is the genotype used for comparison because that's what's in the reference sequence for humans. Of course, this raises the question of why that's the reference. The answer is that it's because that's the sequence from the sample used to create the BAC that was sequenced and used to create that portion of the reference sequence.
Of course, it's not always like that. For example, when we discovered KCNJ18 and I submitted it for inclusion in the genome, I specifically submitted a sequence that represented the most likely haplotype given all of the samples we had sequenced. Of course, "most likely" may be population dependent.
As an aside, this is actually a bigger issue with some regions of the genome, where polymorphisms describe whole regions rather than just single bases. In the reference genome, these are the _hap_ chromosomes, which will often contain things like common structural rearrangements. These present a problem currently because they lead to biased mapping and variant calling. The first program known to make proper use of these was only released within the last month, in fact. One of the goals for the next human reference genome is to come up with a convenient graph representation of the genome that can include common polymorphic regions. This should lead to better quality genotyping of patients and study subjects.


text:
How does a person get AIDS?
I am inquisitive to know about how a person contracts AIDS.
Among the common masses it's still the belief that having sex with multiple partners causes the disease but that is not the case when read online that it can come only from persons carrying the virus.
So, if a person (male or female) is carrying the virus (HIV positive) does it mean that he/she is suffering from the disease or the person may be carrying the HIV disease and still be free from AIDS. If so how did this chain reaction of spreading the virus start?
Also is it true that immune systems of some rare people in this world can fight with this disease.

You read right: it can only come from people already infected through:

sexual contact
contact with an infected person's body fluids (blood transfusions), although not all fluids carry HIV (saliva, tears)
from mother to child (pregnancy, breast feeding)

Having unprotected sex with multiple partners statistically increases the risk of stumbling upon someone infected.
A person carrying the HIV virus may not show symptoms of AIDS, because the HIV infection passes through a stage of clinical and symptomatic latency (the asymptomatic HIV or chronic HIV) which can last up 20 years (average of 8 years) when only uncommon symptoms like fever and weight loss show up.
Where it started? It is believed that HIV originated in non-human primates in West-central Africa and were transferred to humans in the early 20th century. The virus adapted and became strong, because the virus from primates is typically suppressed by the human immune system within weeks of infection.
HIV is a retrovirus that primarily infects components of the human immune system such as CD4+ T cells, macrophages and dendritic cells. It directly and indirectly destroys CD4+ T cells.
So it destroys the cells reponsible of its removal from the human body. Hard to believe that there are people whose immune can really destroy the virus. A virus lives inside the cell it parasite, so the immune cells must destroy one the other. Also the virus infects and kills them (the good ones). However, as MattDMo suggested an infected person may take antiretroviral drugs and the disease progression can be slowed down.
Source: Wikipedia - HIV, AIDS

It is not entirely correct that a "person carrying the HIV virus is suffering from AIDS." HIV (Human Immunodeficiency Virus Type 1) is the virus that causes the disease known as AIDS (Acquired Immune Deficiency Syndrome). People can be carrying the virus and yet not displaying any of the symptoms of AIDS, at various timepoints from the point of infection, not just in the very beginning. It is much more scientifically/medically correct to refer to one's status as HIV-positive or HIV-negative, thanks to the amazing anti-viral drugs now on the market.

Being HIV+ and having AIDS are slightly different terminologies:
If the virus is detectable in an individual by existing medical techniques he/she is called HIV+.
A HIV+ person is said to have progressed to AIDS only when the CD4+ T-lymphocyte count drops below 200 cells per ml of blood.
Cornelius has nicely summarized the infection routes so I wont touch on that.

Also is it true that immune systems of some rare people in this world
  can fight with this disease.

Yes. In some people the progression from HIV+ to AIDS is very slow and they practically lead a normal life. Such individuals are called long term non progressors (LTNP). Some genetic reasons for having an LTNP phenotype is summarized in the link, however, this topic is still under active research.
Some individuals just don't acquire HIV. This is because they lack the CCR5 chemokine receptor which is essential for HIV entry into the cells. Deleting this receptor is also being considered to cure AIDS via a stem cell therapy.

Simple transplants wont work because the virus may infect the transplanted cells. In case of transplant from a CCR5-$\Delta$ individual there is a risk of immune complications such as GVHD. Transplanting CCR5-$\Delta$ HSC (either obtained from bone marrow or iPSC and then engineered) would be a solution but it is also quite difficult.

Agreed it does work when you transplant a CCR5-$\Delta$ HSC to a patient but there may be risk of GVHD. Plus you may not find suitable donors every time.

what about if it is done by CRISPR as done by chinese scientist "https://www.bbc.com/news/world-asia-china-46368731"

Cornelius covers Primary Infection and some of Dissemination.
Wysiwyg covers some reasons when HIV cannot proceeds to AIDS.
Little however is discussed yet exactly about the Pathogenesis - how HIV proceeds into AIDS.
There are many stages:

Primary infection
Dissemination of virus to lymphoid organs
Latency
Increased HIV expression
Constitutional symptoms
AIDS
opportunistic diseases (etc pneumocystis pneumonia - P. jirovecii for human; HIV-induced thrombocytopenia; ...)
death

Cornelius nicely mentions that HIV infects CD4+ T lymphocytes, macrophages and dendritic cells.
In other words, HIV infects CD4+ T lymphocytes and the major Antigen Presenting Cells (APC).
Also monocytes are infected.
These infected cells play a major role in dissemination and pathogenesis of HIV infection.
Antigen presentation couples innate and adaptive immune system.
Any attack on those cells will be difficult to control:

where I left NK cells only to innate immunity because they do not participate in antigen presentation.
Innate and adaptive immune systems are visualised on the plane.
You have then humoral immunity working around that plane as circles.
I emphasize with that the local nature of humoral immune system and how it extends the cell-mediated immune system.
Any attack on the heart of this system i.e. antigen presentation will also risk the humoral immunity and thus cause fast progression of the disease.
These APCs act as reservoirs for HIV virus in the body during latent period and after the latent period.
However, there is very active replication of the virus also during the latent period in these reservoirs.
The virus replicates actively in lymphatic system.
This is why you see steady level of HIV virus in blood during first eight years, see Figure below [Fitzpatrick's Color Atlas and Synopsis of Clinical Dermatology, 7e > Section 27. Viral Diseases of Skin and Mucosa].

The structure of lymph nodes is disrupted eventually.
There is a degeneration and loss of virus holding function.
Virus leaks into the blood which can be seen as increased viral load at about 7-8 years after infection when constitutional symptoms start.
This amount of virus is very large that is released into circulation.
There is a rise in viremia.
Now the infection becomes T-tropic (proliferates and replicates actively on CD4+ T lymphocytes), while it was M-tropic (proliferates and replicates actively on APCs in lymphatic circulation) until the start of AIDS.
Actually, these APCs play a major role in trapping the virus, until their architecture changes.
Some antiviral drugs work on these CD4+ cells i.e. at least macrophages coupled with MHC II complexes.
There is still much unknown in the pathogenesis of HIV:

role of dendritic cells in M-tropic phase
role of dendritic cells in T-tropic phase and restricting the functioning of HAART (Highly Active Antiretroviral Therapy) therapy.

and there exist no antiretroviral drug which can target the major antigen presenting cells or use another way - to stop viral replication completely.
Cornelius writes HIV virus kills CD4+ cells.
It is better to say HIV virus decreases CD4+ cell count.
Killing is just one mechanism.
The mechanisms are

HIV can induce apoptosis of CD4+ cells
lysis of CD4+ cells
killing (natural killers, macrophages)
networks (CD4+ cells will bind to other CD4+ cells so cells cannot work)
gp120 antigenic - which attach to CD4+ antibodies

which decreases CD4+ cell count.
Sources

Thomas, C. F, et al. Pneumocystis Pneumonia. The New England Journal of Medicine. 2004.
Fitzpatrick's Color Atlas and Synopsis of Clinical Dermatology, 7e > Section 27. Viral Diseases of Skin and Mucosa.
My class notes 2014-2016.


text:
What does hemozoin do?
My bio book refers to HEMOZOIN that is responsible for the shiver during malaria. How does hemozoin work to raise the body heat?

That is correct. When plasmodium infects red blood cells, it consumes the hemoglobin in the cell, leaving the heme behind, which they can not metabolize (heme is a heterocyclic porphyrine ring with an iron atom coordinated in the center). Since the heme (or $\alpha$-hematin) causes the production of reactive oxygen species and thus oxidative stress, it has to be removed from the cell. This is done by the conversion into the insoluble and inactive hemozoin (or $\beta$-hematin). This crystalizes in the cell and is not causing any harm to the parasite. See here for more details.
When the parasite finishes this development step, the cells burst and set their interior free into the blood stream. Among the substances released in this step are hemozoin and also glucose phosphate isomerase which stimulate macrophages to secrete cytokines and other factors which then cause the fever and the shivering observed in malaria.
See here for more details:

Hemozoin Induces Macrophage Chemokine Expression through Oxidative
Stress-Dependent and -Independent Mechanisms
Malarial pigment hemozoin and the innate inflammatory response.
Effect of malaria components on blood mononuclear cells involved in
immune response.


text:
What is the thinnest spot on the ilium called?
Is there a specific name for the spot on the human iliac fossa where the bone is the thinnest? (Or, is there a name for the thickness measurement of that spot, e.g. the left/right _________ is 2.1mm?)
Green arrow:

(image source: my own pelvis)
This point, for example (color maps thickness):

(image source: me)

The region is called iliac fossa. And it's basically the deepest part of the fossa. May be!!! I have never heard of a particular name of that thinnest part in my osteology books.

@A.N.Ψ it would just be called the thinnest or deepest part of the fossa, there is no special name for parts of a fossa you just use basic descriptive terms.


text:
Why do you retch when you see something disgusting?
Why do you retch when you see something disgusting?
I imagine it is some sort of evolutionary response, although I can't see the connection between receiving a signal that unhealthy conditions are in the current environment and wanting to empty the contents of one's stomach, which likely were eaten elsewhere. The response I would have expected to have developed would have been one of fleeing, rather than vomiting.
As a subquestion, why does the same reaction sometimes occur when imagining something disgusting, even if it is not real?
(I know "disgusting" is subjective; I'm referring to things humans may want to not be around for health reasons, e.g. rotting flesh, infestations of traditionally disease-carrying insects, etc.)

I wonder if this question isn't more appropriate on CogSci SE, as not all people are effected in this way, and there may be more of a psychosocial aspect to it than one that is strictly biological.

@AMR That's a good point. I'm going to give it a bit more time to marinate here to see what comes of it before moving it.

I am not very familiar with neurology, but I know that people can have sensitivities to things like blood draws etc. because of vasovagal response. Some may be more highly sensitive than others.

Seems to me your body telling you to stay away from something rather than it just being unpleasant to to look at is, is a stronger more reinforced manner of personal protection/preservation. Interesting ? Though curious to see what else era posted. I think it's fine here on bio SE By the way

Physiologically speaking, your body is reacting to something you have known associations learning. An extreme form of this phenomenon is seen in drug addiction.  After chronic use of a substance there are certain cues a person associates with the drug effects. Whether that be a certain group of people, a sound, a place, or an object the stimulant is eventually associated with the drug effect. After a certain amount of time a physiological reaction occurs with just the introduction to the stimulant without the drug. Often, if an addict receives a stimulation without a drug they are, at first, excited, calm, or feeling whatever the drug effects caused. But then, if no drug is received, the withdrawal effects come into play and makes the addict feel worse and crave the drug more intensely.
Anyway, so when you see something you associate with being gross or awful, your bodies physical reaction is essentially prepping you for the event.The biological and cellular effects of associative learning are regulated in the central nervous system (brain). The main theory is that the initial effect of the stimulus is regulated by dopaminergic channels, and the learning and associations are regulated by serotonergic channels. However, it is more like a complex network of synaptic channels at work in various parts of the brain. The regions known to be apart of associative learning are the emotional cortex of the brain are the amygdala, prefrontal cortex, and hippocampus.
For gastrointestinal upset the stimulus is most likely associated with an event that caused GI upset previously. For example, let's say you went out to a party and had too much to drink. You throw up everything you've eaten that day and you just generally feel awful and 'sick to your stomach.' Now, every time you see, smell, or taste that brand or flavor of alcohol you consumed, you immediately gag because your body is remembering the previous event and associates that stimulus with the vomiting and sick feeling. Does that make sense? Let me know if you would like more clarification.
Sources:

Drug Addiction Drug Habituation - Profiles in Science
Control of cocaine-seeking behavior by drug-associated stimuli in rats: Effects on recovery of extinguished operant-responding and extracellular dopamine levels in amygdala and nucleus accumbens
Neural and psychological mechanisms underlying appetitive learning: links to drug addiction
Physcopharmacology by: Meyer and Quenzer (ISBN 978-0-87893-510-9) (best source)

That sort of makes sense, except why vomiting / gagging? Not only are there other conceivable reactions to disgust (for example why not experience a sudden urge to wash one's self rather than purge stomach contents), but there are other conceivable reactions in general (for example, fear instead of disgust, that is an urge to flee rather than purge). Or, in other words, when you say "prepping you for the event", what event is being prepared for and why is vomiting preparation for it?

The association is usually something gastrointestinal based if you are gagging. Aka. usually the event associated with the stimulus is related to gastrointestinal upset, like eating bad food one time, or throwing up after drinking too much. I'll try to add that to my answer :)

So, the claim is, it's not an evolutionary response, but rather the remains of a learned response, specifically related to eating and now sometimes applied inappropriately, to stimuli encountered previously?

Essentially. It could be evolutionary, but it would be extremely difficult to prove and the less logical of the concepts. You would have to have a gag reflexes to stimuli you have never seen or have associations with, which most people don't. It is also pretty much impossible to research because babies are getting sensory overload and making learning associating from the second they are born, and we can't look at the animal lineage because there is no way to detect a gag in an animal.

I wonder if there is any studied and documented correlation between people who are more prone to having this response (such as those who gag at the site of blood) and some sort of specific eating-related events during childhood. I'm going to pursue that and see if I can find anything. I am also becoming more convinced that this may be a CogSci topic.

Hahaha, that depends upon the part of the question you are interested in pursuing. If you're interested in understanding the neurology of learning associations and blood-response cues, then it could stay on bio. But, if you are simply interested in the psychology of the event, then yes it is more a cogsci question.


text:
Why do my muscles move slowly when cold?
When my hands are cold, e.g. outside in the winter with no gloves for a while, their muscles begin to move slowly (assume I'm otherwise comfortably warm, e.g. dressed well but gloveless).
I don't seem to lose strength or endurance really, only maximum speed. Coordination is difficult and rapid repetitive movements are impossible, attempts instead lead to a continuous contraction (like normal, but the threshold is much slower). Of course normal function returns when the temperature is brought back to normal.
Why is this so? What is the correlation between lower temperatures and slower muscle response? Is it something with the neurons, something with the muscle tissue, or both? Is it related to blood flow (like when my hand "falls asleep" when circulation is cut off) or is it a property of the tissues themselves?

Both innervation and muscle activity are long chains of complicated biophysical transformations with thermodynamic kinetics -> that is your link to temperature. It's like the main perk (and the sole purpose) of being homeothermic.

@Eli Is the implication that this question is too broad?

This is that type of questions that have a two-word answer (i.e. thermodynamic kinetics). And as long as you understand that the processes involved happen to be complicated interactions between many molecular machines, those two words are sufficient. Yet, if you don't understand those things the question becomes too broad and you'd be better off reading some "Kinetics/Biophysics/Thermodynamics for dummies" textbook.

Damn. It's like that video of Feynman explaining magnetism. Guess I'm that guy.

This, while requiring some prior knowledge, will get you started. Refer to wiki for additional information while reading the paper.

As Feynman said, though, it is a great question. He wasn't disparaging the guy, he was teaching him. But yeah, the answers are looking and involved. For edification, you might want to scope out the freezing and thawing of frogs.

In fact, Feynman has inspired me to come up with an answer.

Sorry for the delay, I was low on time and didn't want to post a poor answer. Let's get into it step by step. The most important thing here is to understand that every single thing you do is a combination of many highly complicated biochemical and biophysical reactions/processes that slow down as temperature gets lower. Since any chemical reaction is a physical process I won't differentiate physics and chemistry any further. The speed of molecular processes is explained by thermodynamics. And in thermodynamics, all other things being equal, things slow down as the temperature gets lower, because temperature is a measure of thermal motion. Why? We will get to that later.
Now, what are those processes we are talking about? I'm not going to list every single molecular cascade in a eukaryotic cell that has something to do with muscle contraction (there are many, believe me). Instead, I'll give you a beautiful example that is directly related to movement. That is innervation. Everyone knows that neurones use axons for long-range transfer of electric impulses. Although people tend to portrait axons as wires, they really are nothing like metal wires, because the resistance is so high any biologically feasible electric signal won't travel for long. So how do axons work? Let's look at one:

Imagine a chain of Wi-Fi base-stations that retransmit a signal and you have a very good analogy. Any axon is mostly covered by glial cells, forming an isolation-coating (myelin sheath), but there are regular coating-free patches (Ranvier nodes). These nodes are the "base-stations". When a neurone sends a signal, it triggers the depolarisation of its cellular membrane by opening various ion-channels. The first Ranvier node senses the change in the electric potential and opens its own potential-sensitive ion channels, so the signal travels from node to node. In order the neurone to transmit a signal again, it has to recharge all the nodes (obviously, it takes time). The process is done by special active ion-pumps that use energy (ATP) to move ions against the concentration gradient. Now, let's list some thermodynamic processes:

Something senses the change in electric potential and changes its conformation. This is work.
The movement of ions along the concentration gradient. This is diffusion.
Something senses that the membrane is depolarised and triggers recharging. Once again, work.
The movement of ions against the gradient. This is done by molecular machines that require ATP. So here we have at least 2 reactions: 1. an ATPase transforms ATP to ADP; 2. an ion-pump works. Hey, what is work after all? ;)

In fact, a similar list of processes can be given for the actin-myosin system that actually performs the muscle contraction, when the cytoplasmic concentration of Ca ions increases after they are set loose from the intracellular Ca-storage facilities (the reticulum) in response to a neuronal or mechanical signal. It's just another charge-shoot-sharge cycle.
Now let's return to thermodynamics. First, consider diffusion. Diffusion depends on the speed of the molecules. The speed depends on temperature. So this is clear and simple (if you don't want to know, why it does). Now, let's consider reactions. Any reaction/process is probabilistic. We call reactions "fast" when the probability is so high there is no lag between individual events. Where does that probability come from? Although details, such as free energy distribution model (e.g. Maxwell distribution in ideal gases), depend on the medium you analyse, the basic idea of any reaction is to reduce the potential of a system. Aside from concentrations, there are 3 basic things to consider: 1. the starting free energy, 2. the activation energy, and 3. the resulting free energy. Let's look at a picture.

The higher the difference between 1 and 3, and the lesser the difference between 1 and 2, the higher the probability. Okay, this doesn't completely explain why this stuff is probabilistic. The thing is that the starting free energy of reagents forms a distribution, hence only a fraction of molecules have the energy to break the activation barrier. Any time two molecules (that could possibly react) meet, you play a game called "can we make the jump or not". The game is clearly probabilistic. When you lower the temperature, you shift that distribution, reducing the fraction of molecules that can make the jump.
Now we can go further into details, but I feel like this is already enough to give a sense of why things slow down as you lower the temperature.

@m1clee although there is such thing a electromagnetic potential (four-potential), I do agree with you that I was supposed to write electric potential. I'm sorry for not double-checking the terminology.


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Can Ni-NTA-Atto Conjugates bind to single His-tag
Can I label a protein with a single His-tag with Ni-NTA-Atto conjugates?
Papers generally use this technique to label 6His-tag.

Please don't substantially change your question after it has been answered. The changes you made completely invalidated my answer. If you have a new question, ask it.

According to the unreferenced introduction to Wikipedia's article on poly-histidine tags, the number of His residues can vary from two to ten, with six being the most common. Since histidine is a naturally-occurring amino acid in many (most?) proteins, adding just a single one at either end likely won't do much of anything. In my work with His-Tags (20-something years ago), I seem to remember that 3-4XHis was about the minimum that produced any kind of differential binding in the purification system we were using (Ni2+-agarose, elution with imidazole). However, for our purposes (scaling up protein purification), the quality of the end product wasn't great, and there was a lot of our target protein in the flow-through, so we ended up going with either five or six His residues, I forget which one.
As always, your mileage may vary, so I strongly suggest testing out a range for your application, if for some reason using the full 6X-His isn't an option.

Thank you for your answer.
I am doing single molecule and I want to count how many 6His Tags I have in my molecular construct.
Do you think I will have one or multiple binding of Ni-NTA-Atto conjugates by 6His Tag ?

If you have a standard, and are able to reproducibly load exactly the same amount of protein in each lane, you should be able to. I haven't used this particular system before, so it'll be interesting to see how it turns out.


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Can plants grow healthily being watered in either deionized or distilled water?
I want to use deionized/distilled water to water plants from some. I have the choice whether to use tap water, deionized water or distilled water that come from a closed system that has a water cycle, with a preference of "the purer the water the better" for use in the system.
Can someone please provide me references to whether plants in general (most species) need the missing mineral and salt ions for healthy growth? And references to whether they need what's missing in distilled water for healthy growth (no mineral and salt ions and non-volatile organic compounds, to my understanding)? By references I mean scientific studies - papers or meta-analyses that were done on the topic
I can't provide more specifications on the plant species I'm asking about since I have no particular one I already selected to grow but I'm considering using Picea abies (Norway spruce) if I can get it to grow to a Bonsai form.

The question as-is shows no research - which we are expected to do here. (There's also the factor of pH, Picea Abies will prefer something more acidic than the  pH7 of distilled water being ericaceous). Can you edit in what you've looked at so far, and tell us where you got stuck.

I recommend you to start your googling journey by learning about plant macronutrients and micronutrients and compare plant needs with declared content in tap water from your area. Most likely you will find, that salts in drinking water are optimized for humans consumption and not really beneficial for plants. Consider including rain water + fertiliser in your list of options.


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VDJ sequencing in mice, DNA or RNA?
I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of radiation therapy on immune system of mice. Thanks

DNA is typically easier to work with. Just make sure the cells you're working with have actually matured enough and undergone VDJ recombination.

I agree with @MattDMo Colleagues next door have done this with single sorted cells which where sequenced afterwards.

@MattDMo @Chris♦ how do you suggest one makes sure T cells have matured and undergone VDJ recombination?? I have looked at literature and seen one study that looked at clonal expansion 22 days after radiation exposure but they did not say why. Also, I have read that RNA is better to use than DNA since DNA won’t give you the antigen specificity you can see with mRNA expression. I have also seen that DNA can only show you the possible combinations of VDJ you could get as mRNA shows you the ones you did get, in real time.

I suggest you spend some time looking at the details of somatic recombination. Early during maturation, the V, (D,) J, and C protogenes recombine in the DNA to form the first version of the recombined TCR $\alpha/\gamma$ and $\beta/\delta$ chains (different protogenes combine in different ways in the different chains). These recombined sequences are then transcribed as mRNA - to my knowledge the protogenes are never transcribed. So, mRNA sequences should match DNA sequences.

The reason I gave my caveat is because if you just take a whole thymus and do single-cell sequencing, you'll also get immature T cells that haven't undergone recombination. Instead, I would use either blood-derived cells, or sort thymocytes using a marker that is expressed after recombination. I would choose blood, because some of the recombined thymocytes will die during further maturation, and probably shouldn't be included in your measurements of TCR diversity.


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Why is living muscle tissue seemingly able to restore its shape under force, while dead tissue is not?
When I press my finger, even with relatively little force, into beef or chicken (say, at a grocery store), the indentation remains.
When I poke a cow with my finger, the indentation does not remain. When I squeeze my own arm, even with the same (or greater) amount of force used to alter the shape of meat with my finger, my arm remains the same shape afterwards.
What is the difference between dead and living muscle tissue, with respect to mechanisms that allow it to maintain its shape? Does living muscle tissue somehow actively maintain its shape while dead tissue cannot? Is it something more passive, such as a breakdown of something in dead muscle tissue that makes it more malleable (and if so, what)?

If you pounded your forearm with a baseball bat with time and force equivalent per ounce of muscle as using a tenderizing mallet, I guarantee you it would not spring back into shape at any time. Likely it would need to be amputated.  Likewise, punching a large cow as hard as you can doesn't mean you've done no permanent damage to any muscle fibers simply because it doesn't change shape perceptibly. You need to compare apples to apples. Active transport (of fluids, etc) doesn't occur in dead tissue. Your question needs to be reframed in different terms.

@anongoodnurse That's why I also gave the example of "poking". I can permanently alter the shape of meat with very little force (finger marks in meat at the grocery store from casual handling by customers are not uncommon), and applying that same force to my arm does not have the same effect. Does that cover the concern?

When you poke meat to indent it, a lot of what is being displaced by your finger is fluid (and it takes more that "just a very little force" or it would be unrecognizable after handling by several people) . There is no ability of dead tissue to redistribute that displaced fluid and remove the dent. It doesn't much matter the tissue - muscle or subcutaneous soft tissue in peripheral edema, for example. No active energy expenditure = no reactive movement.

@anongoodnurse It sounds like this active redistribution of fluid in living tissue that you mention is a possible answer to my question. Can you elaborate in an answer?

That's just one component. For muscle, myoglobin cross-linking also comes into play. It's a longer answer. Hence the comments.

Hence the question! :)

"Does living muscle tissue somehow actively maintain its shape while dead tissue cannot?" Yes. The answer can be boiled down to energy use and it's control. Dead tissue doesn't have it; living tissue does.

@anongoodnurse you should summarize that into an answer. Thanks.

Capillary refill time is defined as the time taken for the capillaries to refill after the blood in them has been squeezed out by pressure. It is widely used as a quick way to determine the effectiveness of the circulatory system in humans by doctors.
In a normal living organism, the capillaries will take time to refill after they have been emptied. Muscle volume consists of the cell volume (which is fixed in the absence of lysis), the blood, as well as lymph and other intracellular fluids (which will be displaced elsewhere when it is deformed by pressure).
When the organism is dead, there is no more circulation in both the blood and lymphatic systems, and therefore any fluids squeezed out by pressure will remain elsewhere, and the deformation is permanent without any regulatory effect by the circulatory system.

One difference between living and dead tissue, but specific to muscles is tonus.  In living skeletal muscle, random nerve impulses fire to keep muscles in a partially contracted, ready-to-use state.  Without this low-level tension sarcomeres, the basic units of skeletal muscle, would not recover from being poked and could more easily be pulled out of optimal position and damaged.

And yes, there are also structural changes unique to dead meat.  Rigor mortis happens when the sarcomeres exhaust all ATP after death and become trapped in a bound state.  Eventually putrefaction sets in and enzymes break off the mechanism and the muscle becomes permanently flaccid.


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How to align more than 2 sequences with Needleman-Wunsch?
I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-Wunsch does find them, however, I can only search/align the DNA protein sequence with 1 zinc finger at a time. Is there a way to do this simultaneous (serial or parallel, computational time is not a big problem) for all 1200 zinc fingers and have the result in a table as with BLAST?

Could you clarify please. 1. Do you want a multiple sequence alignment with your protein and 1200 zinc fingers all aligned, or do you want to find out which of the 1200 zinc fingers align? 2. Do you really mean zinc fingers? This term is usually employed for the protein motif that binds zinc through non-adjacent Cys and His residues. A 9bp sequence could only encode three amino acids.

Also: by "Needleman-Wunsch" what do you mean? Are you using a specific software tool?

Welcome to Biology.SE. I’m voting to close this question because it lacks clarity and doesn't seem to be about a biological mechanism or process. This question might be a better fit for [Bioinformatics.SE], but please do not crosspost, instead request migration after reading that sites help. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site for details.

@MaximilianPress — NW is a specific algorithm for global pairwise alignment and has an entry in Wikipedia, as I imagine you are aware. I therefore don’t understand what you are getting at in your comment, as the particular implementations wouldn’t seem relevant. And, of course, it is the wrong tool here — Smith-Waterman local alignment is more appropriate.

@David different software can have different parameters which control execution. Possibly a simple change of parameters would get the OP what they wanted out of "NW", depending on the tool, their inputs, etc. It does not seem to be an algorithmic problem as many algorithms might get them more or less the right answer (SW being another example that might work as you say, or my simple-minded suggestion below). Rather, they don't like the outputs and mode of execution of the tools they're using.

@MaximilianPress — I don't really follow you, but it hardly matters because it is not clear to me what the poster is asking, and as he has ignored requests for clarification I suggest the question is best ignored (and closed).

(I assume that by "DNA protein" you mean "coding DNA".)
"I can only search/align the sequence with 1 zinc finger at a time" - does this mean that you have not found out a way to do so, or that you desire to proceed in this fashion? I think that it is the first, based on the title of your question, but it is not at all clear what you are looking to do.
If you want to locate specific 9bp motifs in your sequence, then I can suggest this small piece of code that I wrote that looks for exact matches of specific sequences, that outputs a BLAST-like table. It is slow relative to BLASTN but it does not use the short-match-ignoring heuristics that BLASTN relies upon so it may be helpful.
The code was written in response to this bioinformatics SE question, which seems somewhat similar to your question here.
Note that you will have to input each expected 9bp query against the reference sequence in the form of a FASTA file.

So, I shot myself in the foot a bit by posting this question before the holidays. Sorry for not responding in a better fashion. Thank you for your answer, that will certainly help me further!


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What's the best way to purify my His tagged protein? Supernatant super viscous after first sonication?
I am trying to purify my his-tagged protein of interest, disulfide isomerase. It is about 40kDa and is cloned in pET28a vector, at XholI and NdelI, and expressed in BL21.
I'm having issues with my protein purification.
My current protocol:

1L culture incubated at 37°C for 6 hours until OD600 reaches 1.5-2.0.
IPTG is added to a final concentration of 1mM and is then further incubated for another 3-4 hours until OD600 reaches 2.2-2.7.
I then lyse the cells using 1X binding buffer with 1X Protease inhibitor, no urea, 0.1mg/ml lysozyme, and DNase1.
solubilize/sonicate with 1X binding buffer WITH 8M urea and 1X protease inhibitor.
purify my protein by doing affinity chromatography using a nickel column with 1mL of Ni-Nta resin.
I washed twice with 1XBB with 8M urea, 15-20mM imidazole, and 1X protease inhibitor.
elute with 1XBB with 8M urea, 250mM imidazole, and 1X protease inhibitor.

During the solubilization step, I sonicate twice. After my first sonication and spinning down in the centrifuge for about 30min, my supernatant comes out super viscous and when I run it through my ni-nta column, it ends up clogging it and causing it to run super slow (1 drip = 5min). What can I do to fix this issue?
Should I try using 6M urea instead of 8M? Would that help with the viscosity?
Also, my elutions come out really dirty still with a lot of contaminant protein. How can I clean up my elutions?
My protocol for my wash calls for protease inhibitor, but I feel like that's a bit wasteful. Can I wash without using protease inhibitor first and then do another wash with the protease inhibitor? Or should I be using protease inhibitors in every wash?

Do you have DNAse in your buffers? This is most likely the chromosomal DNA which is causing problems here. Depending on how harsh you sonicate it should break down, but if you sonicate short and with low energy this must not happen.

It sounds like your protein is expressed in inclusion bodies. If that is the case, you shouldn’t need to worry about chromosomal DNA since it is rather trivial to wash away before solubilization. Be sure to centrifuge and filter your sample before applying it to the column to remove any insoluble debris.

As Chris said in the comments, make sure you have sufficient DNase in your lysis buffer. That combined with good sonication will definitely shear nucleic acids and make your solution less viscous. If you don't feel the lysate starting to warm up when you're sonicating, you might want to increase the power. To that end, keep the lysate on ice while sonicating so the heat doesn't denature your protein of interest irreversibly.
You may also want to increase the amount of lysis buffer you're using to dilute everything a little bit, as you'll be concentrating and eluting it later. Sometimes lysates can be so thick that even harsh sonication won't completely eliminate it, and you run the risk of damaging your protein.
As far as the dirty eluate is concerned, a couple tips. First, after binding, make sure you wash the column extensively before eluting. You may find with experience that washing with a little bit of imidazole helps clean up non-specific binding as well. If you have one available, use an automated fraction collector (or even collect small fractions by hand) instead of doing a bulk elution. This way you can test each fraction separately and get rid of the ones with the most contamination and least specific product. Keep in mind that very concentrated samples, even if they are quite pure, will look dirty if you load too much protein on the gel, so keep a protein quantitation kit that's compatible with your buffers handy.
Another option to doing a bulk, single-concentration imidazole elution (say, at 250 mM like you're doing currently) is to do what's called a gradient elution. Say you're using a 10 ml column. After washing with 10-20 column-volumes (CV), start eluting with 10 ml of perhaps 50 mM imidazole, let it run out (but not totally dry), then add 10 ml of 100 mM, and so on. This is obviously much easier if you have an FPLC or similar setup, but it can be done reproducibly by hand if you're careful. Collect 5 ml fractions, and test them individually before pooling the good ones.
Protease inhibitors aren't strictly necessary in the wash, but I'd include them at least in the first wash, as that's when proteases are most likely to be non-specifically associated with your column beads and acting on any available substrates. Keeping everything cold is helpful, as well.

I've done an awful lot of protein purification both in academic and industrial labs, with a lot of different types of equipment, so if you need more info just let me know.

I was told to try to use 6M Urea instead of 8M urea to help with the viscosity, but I'm not too sure about that. Should I change the urea to 6M? would it make a big difference? I don't want to do anything to ruin my chances of getting a lot of protein. Should I just stick with the 8M and use more DNase in my lysis buffer to see if it works before changing to 6M urea?

@Yoshokie I don't know if dropping the urea from 8M to 6M will make a huge difference. Sonicating more would be my first troubleshooting step - as long as you keep the lysate cool (i.e., not too hot to touch), you can't really denature it any more than you're already doing with the detergent (I'm assuming) in your lysis buffer and the urea, which is a chaotropic agent. Urea won't cleave DNA, no matter how much or little you have, so sonication and good quality DNase are your best bets.

Agree with all of the above. I have found benzonase a very good alternative to DNase. It is robust but it will lose activity in Urea above 7M. The added benefit of it removing DNA and RNA is improved solubility of most proteins. It is very stable so a small contamination in your final preparation may cause problems if you're wanting the protein to bind DNA or RNA.

@Michael_A that's actually one thing I didn't think of - the urea could be interfering with the DNase's activity. Another reason to reduce it...


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difference between "Petri dishes" and "Petri plates"?
In microbiology, we often hear "we use Petri dishes to prepare our cultural media".
Which is correct — "Petri dishes" or "Petri plates"?

Typically you'll hear either "petri dishes" or "plates", not usually "petri plates". Either way though people will understand what you're talking about.

I tried growing bacteria on paper plates once because the protocol just said plates.

@user137 That'll get you every time. Just leave some leftover food on the plate and it should grow just fine

@user137 lol. Seriously ?

@Dexter No not seriously, but it's generally a good idea to be as specific as you can in your methods section. You can say plates, but be sure to list size, material, manufacturer, etc. In the rest of the paper you can just say plates, but the reader needs to be able to look up how you did the procedure, and sometimes details about plates matter.

In my experience, a "Petri dish" or a "dish" refers to something like this:

From Wikimedia
i.e., a single-well container, made of either glass or, more commonly nowadays, plastic.
On the other hand, a "plate" (I've never heard the term "Petri plate" before) typically refers to a multi-well container, having anywhere from 6 to 1536 individual wells:

From pipette.com
Disclaimer: I work almost exclusively in the eukaryotic/mammalian world, so there may be different nomenclature among bacteriologists.


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How can I generate a random DNA sequence?
I've found this paper which involves the construction of 19-bp random DNA sequences, but I don't know enough biology to understand how this method works.  Could someone explain it to someone who is highly technical, but has knowledge of only introductory, undergraduate biology?  How do the authors know that their resultant sequence is truly random?

If you want to synthesize a specific DNA sequence chemically, you start by attaching your first nucleotide (one letter in your DNA) to a solid phase. You can then continue adding individual letters to it. Because it is bound to a solid support material, you can wash the whole thing without washing your growing DNA away.
So if you want to synthesize AGC, you would first only add A to your reaction and then wash away all the A that hasn't reacted. Then you'd add G, which binds to your previous A, and again wash away all the G that hasn't reacted. Then you'd add C, and do the whole thing again.
If you want to create a random or semi-random sequence, you simply add multiple letters at once. If you always add all four letters in each step, you'll get a completely random sequence. You can also randomize only specific positions, and only there add all letters.
The result is random, but I don't think it is as random as e.g. a cryptographically secure pseudorandom number generator. There are various factors that can affect the randomness, variations in the concentrations of your nucleotides, variations in the quality or composition of your reactants and probably a lot more.
See also Oligonucleotide synthesis on Wikipedia

They say that the maximum sequences is 4¹⁹ which means every permutation. So I am not sure if they really synthesized random bases per each position or just synthesized all possible variants by allowing equimolar mixture of nucleotides at every step. This is what you also describe but the result IMO cannot be called random. It is expected to yield all permutations.

@WYSIWYG I'll have to look at the paper again, I though I had read them indicating that they were using chemical synthesis like I described, but it looks like I read that into their description

This is what is written in the M&M: "Random sequences were synthesized with equimolar mixtures of phosphoramidites." This is exactly what you said but I am not sure if that can be called random, in the sense of RNG.

@WYSIWYG Each individual coupling is random, and if you get to a length of DNA where you don't have enough molecules for all permutations, it gets truly random as well.

Sure. In fact all chemical reactions are essentially stochastic. I would however interpret "random primers" as set of n primers generated using a random number toss for a nucleotide at each position for all n primers. At n→∞ all possible permutations can be obtained.

For practical purposes, IDT offers randomized oligos. Saves a lot of trouble.Other companies probably offer this too.

As far I know, the way that Mad Scientist describes it is how random oligos are generated. There may be more advanced methods that the synthetic DNA providers like IDT use these days, but in principle that was how it was done around the time of the publication date of the paper.

@AMR Fundamentally it's the same chemistry, but IDT has it very well optimized, at the chemistry and synthesizer level. I've seen their plant a couple times and it's amazing how they can turn out so many oligos in a day from some nondescript building next to the walmart. Their shipping department is probably the best nonviral DNA delivery group in the world.


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Genetic mutations and new alleles
Amongst silent, nonsense and missense genetic mutations, is the latter the only one that leads to the creation of new alleles?
If we define alleles as a specific form of a gene, and a gene as a heritable factor consisting of a length of DNA that influences a certain characteristic, since the missense mutation is the only one that leads to the physical creation of a new protein, is it not the only one that would lead to the creation of new alleles?
Or would nonsense also lead to new alleles as the lack of the protein may lead to the expression of a different characteristic?

Its a good question actually as allele concept confuses a lot of people. I am sure it will be helpful for lot of people in future Insha'Allah

So the term allele is a broad one, and simply refers to the different versions of any piece of DNA in circulation in the gene pool - it doesn't need to refer to a gene. I can talk about the alleles at a random place in the genome.
But if we proceed with your question and ask - 'do nonsense mutations within coding genes also lead to the creation of different proteins' - the answer is 'sometimes'. A nonsense mutation is just one that introduces a stop codon. The result is an mRNA that codes for a shortened protein. Sometimes, the mRNA will be recognized as faulty and degraded, and so little to no protein gets made. Sometimes, if made, that protein will be unstable, or the result will be as if no protein had been made. Sometimes though, the protein will be stable, and could hang around uselessly, or even do damage.

Allele is indeed a very broad term. Easily the term which confused me the most in the whole Molecular Biology. And +1 for the last part. I liked the explanation.

And sometimes the truncated protein can be useful for a different function. For example, apolipoprotein-B.

Allele is just a variant form of gene: independent of the final product of protein, so nonsense will also lead to new allele. I will quote Nature Scitable here:

Alleles can also refer to minor DNA sequence variations between
  alleles that do not necessarily influence the gene's phenotype.