texts: Why all negative ssRNA viruses have helical capsids?

texts:
You can always say it's a coincidence, but is there particular need to have a helical capsid? Do they need their RNA to be more protected than +ssRNA? Is it better for RdRp attachment?

This paper suggests it is mostly for RNA synthesis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993539/:

  For negative-strand RNA viruses (NSVs), eight families have been recognized by the International Committee on Taxonomy of Viruses (ICTV). The unique feature that distinguishes NSVs from the rest of the virosphere is that the nucleocapsid, instead of the naked genome, is used as the template for viral nucleotide synthesis. It is indubitable that the assembly of the NSV nucleocapsid is related to the unique mechanism of its viral RNA synthesis.

Also this one: https://www.sciencedirect.com/science/article/pii/S0042682215001543. But I don't know if anyone has tested inserting naked -ssRNA with RdRp and see if it does something.


texts: Book recommendation on the human muscle system

texts: I would like to learn more about the exact mechanism behind our movements, especially about what happens during intense training when anaerobic state arises.


texts: What is the biology behind a skin "mole"?

texts:
Are the dark marks aka "moles" on our skin a patch of dead cells? If so, why is it not cleared over time? In a (probably) similar vein, why do scar marks from injuries remain long after new cells replace the dead cells?

[Feel free to edit out the second question if the answers are unrelated]


texts:
Hi there,

For the first picture: can someone please explain in simple terms (I started learning biology a few days ago), why the answer to this osmosis question is no?

For the second picture: The answer is left because "the tension of the balloon can resist osmosis". Can someone explain what this means?


texts: How did the first life form on Earth reproduce without DNA?

texts:
How did the earliest life forms exist without DNA? The most likely scenario I can think of for life happening from nothing is that, over billions of years, with trillions of water molecules and dust particles and chemicals moving around, eventually a small clump of this murky stuff formed a pattern. Or maybe, under some lucky conditions, a whole mud pit of such a inorganic system started forming into structures which had a pattern of motion, and one of those structures became the first sub-cell, like a primitive ribosome or something. I remember learning some parts of cells were once separate entities, but there are massive gaps in that idea.

The primary gap being: How did reproduction occur in that incredibly lucky, freak incident of a tiny dust clump or whatever? How did reproduction occur without DNA? Do scientists have a theory on how the first reproduction occurred?


texts:
Given $N=5\times10^3$ and mutation rate is $\mu=10^{-5}$ per site, find the length of a DNA sequence so that the probability of mutation occuring M, is greater or equal than 0.95.

Is there a method or a formula for this type of calculation?


texts:
I am learning RNA-seq analysis. I always encounter this phase "poly(A)+ RNA". After searching, I got this: "Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection therefore enriches for messenger RNA. The technique has proved essential for construction of cDNA libraries."

Does it mean that when constructing the cDNA, we always use the ones with a A's tail? Then other RNAs like tRNA are filtered and not used to get their cDNA? I do find some RNAs records on UCSC where microRNAs are included.

When we say poly(A)+ RNA library, what is the difference between normal one? Or normal RNA library is a poly(A)+ RNA library? Thanks.


texts: What do blue cone cells add to visual function?

texts:
First of all, I saw this other question in the SE sites with a good answer, but I didn't find an explanation about the blue cones specifically.

So most human beings have 3 types of cones (cells specialized in color sensing : blue, green and red).
While it may seem obvious that the red and green-sensing cones are an evolutionary advantage (given our natural environment and how we ate for millenia), for instance to locate fruits and differentiate ripeness, I can't find a clear advantage in having the blue cones. Blue doesn't seem to relate to anything like food, predators, sexuality. Am I missing an obvious utility ?

Let's try to imagine what happens if we remove blue cones :

The sky would look gray. I don't see a survival issue there.
We wouldn't be able to make a difference between yellow and white (white = green + red in this case). Is it a big deal ?

I have the reflex to think "if a character is widespread, there must be a good reason". It seems I should rather say "there must be an explanation".

So I'm trying to think differently, and here are other possible approaches to address this question :

I read that dogs have only blue & yellow cones. Maybe our ancestors had only two cone types, including blue, then a third type appeared and blue stayed just because it wasn't a problem to keep it ?
What we call visible spectrum is in fact the only part of the spectrum that can go through air and water (in the eye) without being absorbed (link). Blue cones would be there just because "hey there's something to see" ?
For a long time we had only fires to look at, at night. No TV or screen with Q&A sites to consult. Is it possible that some of our ancestors stared for too long a hot fire, losing green and red cones ? Those with blue cones were not totally blind and managed to reproduce ! (this one is... almost a joke)

Sadly these approaches don't really convince me.

ADDITION : here is a visual example to see what happens if we remove blue information from an image (original image taken here). The image without any blue (middle) is confusing because it makes you think we could see yellow (while yellow wouldn't be different from white). That's why I added the image on the right, containing only information from red and green channels (the blue channel is replaced by min(Red,Green)). I think it illustrates well that blue isn't important, at least for vegetables and fruits !


texts:
Source: MY textbook-NCERT 12th Biology-Ch: Organisms and Population
(Pg 7 of pdf/Pg 223 of the book)

Is this graph for Partial regulators correct? Isn't it that animals tend to be regulators first and then when they can't maintain homeostasis anymore, they tend to conform aka adapt themselves to the surrounding for better survival?

So shouldn't the graph for Partial Regulators first be a straight-line parallel to the axis (signifying constant internal environment aka Homeostasis) upto certain External surroundings level and then be the inclined straight line when it behaves as conformer ?

I would like to know where I am wrong in my logic or Is it that The graph is wrong in my book ?


texts: What is the evolution metaphor about water flowing downhill?

texts:
As part of my biology undergrad degree, I took a course on the Origin of Species, where we read Darwin's book and also several other readings about the origins of evolution.
I recall that during this course we talked about a metaphor to the effect of "Like water flows downhill to fill every available lower spot, species evolve into every available niche," which really helped me understand Darwin's viewpoint on natural selection. But I cannot find this metaphor anywhere online.
What is the source for this metaphor? I don't recall it being in the Origin itself, but I could be wrong.


texts: The difference between the beta-sheets and the quaternary structure of proteins

texts:
My biochemistry book says that beta-pleated sheets is a form of secondary structure of proteins, and it is formed between two or more polypeptide chains.

I wonder why the sentence in bold doesn't belong to the quaternary structure instead?!


texts:
From numerical simulations I output a file that is input to STRUCTURE (Hubisz et al. 2009). I now realize that I would need to process my data with FSTAT (Goudet 1995). Both are text files.

Is there an extant algorithm that would reformat a file that is input to STRUCTURE into a .fstat format?


texts: How do neurons send electric pulses even though they are surrounded by liquid which is mostly water?

texts:
I just thought about the fact that people move through electrical pulses traveling through neurons in the brain and muscles through the body. Here is what i know: the body is full of 97 or more, percent of water. the thoughts we have and the moves we make are a result of electrical impulses within the neurons and cells.
  My question is why the water does not disperse the impulse and or make it completely ineffective. My personal guess would be that each neuron is made of or has an outer layer of electric resistance material that( is it conducts) electricity.


texts: Fungi in my Solarium - how do I stop it?

texts:
Noticed fungi growing in my solarium in a few spots - probably a few spots where moisture is getting in.  It is really tough, like rubber.  Can cut some of it out with a utility knife, but even that was not an easy process.  Couldn't dig all of it out as it has gotten into some little crevices.  How can I treat this?  Tea tree oil or Oil of Oregano, or ?

The type of flooring is Bamboo.

The spotty things you see on the floor are spider droppings.. how that critter got in there is a mystery - room is always closed, way up on the 3rd floor where I never see any spiders, room is hardly used, and no openings for little flies or anything to get in for its food...?  Anyways, I digress... my real concern is to stop this fungi growth!

Thanks in advance...


texts: Do people need nitrogen from air for health?

texts: Can people breath totally nitrogen-free atmosphere for a long time? I know, nitrogen is essential for life, and in big quantities, but maybe people can take it entirely from food, from proteins, etc?


texts: Role of microvilli in cell volume regulation

texts: Does the presence of microvilli on a cell's surface ensure that it's more resistant to cell swelling or lysis in a hypotonic solution, as compared to a normal cell?


texts:
In shotgun sequencing method or some related method that DNA is break up into random fragment. The fragment that have about 3kb in size is inserted into plasmid by enzyme ligase and then plasmid transform to E.coli using electroporator. As i understand, the goal is amplify the fragment to be sequencing.

At this time, i have a question :

After the e.coli growth up, we have too many different type of miscellaneous DNA strand with same size in a colony. How to purify a type of fragment to be sequencing ?

For example, i have 20.000 different DNA strand with the same 3kb in size after break up into random fragment :

-- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT -- (3kb fragment of chromosome 1)

-- GGGGXXXXXAAAAAAAAAAA...AAAAAAAAAAAAAAAAAAAAAAAA -- (3kb fragment of chromosome 2)

-- 19998 DNA fragment left ............................. -- (3kb fragment of random chromosome)

So after amplify them i have :

1000000x of -- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT --

1000000x of -- GGGGXXXXXAAAAAAAAAAA...AAAAAAAAAAAAAAAAAAAAAAAA --

1000000x of -- 19998 DNA fragment left........................ --

These DNA strand is mixed together in a colony. We cannot run sequencing them together as mixed, so how to have the only one for sequencing :

1000000x of -- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT --


texts: Is there an up-to-date database of known human proteins that is easily accessible using Python libraries?


texts: What happens when we know that there is something that we forgot but we can't remember what it was?

texts: I think it happens for everyone that sometimes we go to a room and forget why we went there. Is there any research or article on this?


texts: Iron deficiency anemia symptoms explanation

texts:
In my classes and on the internet, brittle nails and dry hair (or hair loss) are described as symptoms of iron deficiency anemia, but none explains the cause of such symptoms.

Does anyone have any clues or explanation of such symptoms?

http://en.wikipedia.org/wiki/Iron_deficiency_anemia#Signs_and_symptoms


texts:
I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose.

I've encountered a problem. This library interprets CD1 atom of ILE residue in the PDB file as AL_CD instead of AL_CD1*. Does it have a particular reason?

It's maybe helpful that within the source code, in Residue_data.cc, there is a mapping between atom lebels:

Atom_fallback_data atom_fallback_data_[]=
      {{Residue::AL_CD1, Residue::AL_CD},
       {Residue::AL_1HA, Residue::AL_HA},
       {Residue::AL_1HB, Residue::AL_HB},
       {Residue::AL_1HD, Residue::AL_HD},
       {Residue::AL_1HE, Residue::AL_HE},
       {Residue::AL_1HZ, Residue::AL_HZ},
       //{Residue::AL_1HH, Residue::AL_HH},
       {Residue::AL_1HD1, Residue::AL_1HD},
       {Residue::AL_2HD1, Residue::AL_2HD},
       {Residue::AL_3HD1, Residue::AL_3HD},
       {Residue::AL_INVALID, Residue::AL_INVALID}};

It means that AL_CD1 is deliberately converted to AL_CD or for example AL_1HA to AL_HA.

Thanks.

In general, in dsr-pdb library, AL_X is the atom label of atom X.


texts: Two brown-haired people have two children, P and Q. P has blond hair. Q has brown hair. What is the probability that Q is heterozygous?

texts:
Two brown-haired people have two children, P and Q. P has blond hair. We therefore believe that each parent is heterozygous and that blond hair is a recessive trait.
Q has brown hair. What is the probability that Q is heterozygous?

My answer:  2/3.  There are four possibilities Bb, bB, BB,and bb. Before observing the color of Q's hair, we assign equal chance to each.  We eliminate bb as a possibility.  The chance that it is bB or Bb and not BB is 2/3.

A Biology PhD disagrees with me and says that the probability is 1/2. Who is right?


texts: Why can AB people receive blood from A, B or O?

texts: AB people don't have agglutinins anti A or anti B so it might seem they can receive any type of blood. But if the donator is A for example, it's own blood will have agglutinins anti B that will agglutinate the AB blood. So why can AB people receive blood from non AB people?


texts: Air purifier agains bacteria and viruses?

texts:
We would buy a mobile air purifier in our home.

Against the smoke of the city, etc.

It would have a HEPA + activated carbon filter. They are marketing it as:

  "filtration process captures 99.97% of airborne particles down to 0.1
  micron in size."

and having also:

  "encapsulated ion particle charging chamber"

But the question:

Would the mentioned filter+ion charger also help cleaning the air from bacteria and viruses?

Ex.: "Coronavirus/2019-nCoV" is about "Coronavirus virions are spherical with diameters of approximately 125 nm" - but I just Googled it, not from an official source. And 0.1 micron is 100 nm.

UPDATE: would it be more effective, if it would have UV-C light in the air purifier?


texts:
I am reading about growth stages in Maize and found this image.

I downloaded a brochure of a maize variety grown in Brazil.

On the right column, it says male flowering 63 days after planting (947 degree days) and female flowering 63.5 days after planting (955 degree days).

When stage does the male and female flowering happens in the first image?


texts: What are the minimum conditions required for "open-ended evolution"?

texts:
According to a paper about artificial life systems, the following four conditions have to be fulfilled for "open-ended evolution":

  Condition 1: A rule should be enforced that individuals must meet some minimal criterion (MC) before they can reproduce, and that
  criterion must be nontrivial
  Condition 2: The evolution of new individuals should create novel opportunities for satisfying the MC
  Condition 3: Decisions about how and where individuals interact with the world should be made by the individuals themselves
  Condition 4: The potential size and complexity of the individuals’ phenotypes should be (in principle) unbounded

My question
Must these conditions be met for open-ended evolution to occur? If so, do we have evidence that all of these conditions fulfilled in nature? If not, could you give examples where one or more conditions are violated?


texts: Why is pericardium muscle repolarizated earlier than endocardium?

texts:
I was reading about heat muscle contraction and I read:

  The endocardium depolarization happens earlier than pericardium , but
  pericarduim repolarization happens earlier, therefore the T wave in
  healthy people is always positive.

I have two questions:

What's the reason?
Why doesn't it happen in atrium and atrial repolarization(T wave)?


texts: Definitions of robustness and canalization

texts:
The concepts of robustness and canalization are fashionable today in the biology literature. However, I am not sure of their definitions and I am not sure either that all authors actually use the same definition.

I am therefore asking here for a the definitions of these terms or for a short review of the common definitions of robustness and canalization. How do different authors define these words? I am particularly interested in...

The differences between robustness and canalization (canalization seems to apply more in developmental biology than robustness who seems to be a more general concepts)
At what level do these concepts apply? To populations, to genotypes, to both, ..?
How does the concept of adaptation link to these definitions.
How does the concept of plasticity fits in opposition of the concepts of robustness and canalization?


texts: Plant anatomy, what are these stem like filaments growing under the flower

texts: The picture below shows what I am talking about. Each flower has one and I am just wondering what they are?


texts: Gene configuration : Divergent vs convergent

texts:
I start reading a paper where they discuss the effect of the divergent promoter/gene and the convergent promoter/gene on the genetic expression of an organism.

So I want to know what is the difference between the two of them ?


texts: Is "Cloning" exact or almost similar to parent?

texts:
I was studying "Reproduction in Organism" as an interest of my own and there was a line

  offspring produced through single parent are exact copies of their parent. Also, they are genetically identical.

So, in here, it says, "genetically identical" (I assume that identical here implies exactly same) but then the next line quite confused me.....

  The term clone is used to describe such morphologically and genetically similar individuals.

Here, the term "genetically similar" is used.

So, clones (offspring produced through asexual reproduction- involvement of one parent) are "genetically exact" to their parents or genetically similar?

If "genetically exact", Then how is it possible since, there is 'No 100% efficient DNA Replication' that can be achieved?


texts: What are the typical values of probabilities for nonspecific binding to an antibody?

texts:
I'm physicist by training, so please excuse me if I don't use the proper terminology.

I think there is a way to make a sensor that detects if a single antibody has caught something from the flow. So I'm trying to figure out if this would be a useful sensor, but this depends on how specific the antibodies really are.

When I ask biologists "How specific are antibodies?", they reply: "Very-very specific", but provide no values that I understand on microscopic level. But I am trying to make a quantitative estimation, e.g. for the following thought experiment:

Suppose I have attached an antibody to inorganic surface. It's an antibody for catching object X. And I flow blood over the surface, slowly. Suppose there's no X in this blood at all. But there are lots (maybe 1017, or some crazy number like that) of other stray particles flowing by this antibody every second, right? So, when one of these particles bumps into this one antibody, what is the probability that it would stick to this antibody? Is it really 10-17 ? Is it really so small?

And, in any case, how do I estimate this probability at least to 1-2 orders of magnitude?

Also, how do I estimate the "collision cross section area" through which an object has to fly to make an attempt to bind to an antibody? In other words, does it only have to touch it slightly, or bump into antibody in a hard and messy collision?

Does the probability of successful bind depend on the flow speed?

How would the values change if I take serum instead of blood?

Could you please point to some relevant papers, books or just keywords? I would very much appreciate any help.


texts: Are there fungi that are directly beneficial for humans?

texts:
It is well known that the human body benefits from a lot of different bacteria - and indeed wouldn't be able to survive without them.

Are there fungi that are beneficial to humans, or even needed directly for surviving?


texts: Biological modeling languages - some basic issues

texts:
I am trying to get used to with couple of modeling languages in biological context like SBML, BioPAX, Kappa and BEL. Some basic issues came up to my mind that are unclear to me even after a lot of related studies I read.

Are there any causal reasoning algorithms available for SBML? If yes please give me the reference.
Which "framework" supports modeling and mining (e.g. candidate mechanism identification / identification of upstream controllers) in Kappa?

Anyone has any idea about these?

Thanks in advance!


texts: What buffer should I choose for IEX chromatography for purifying IgY

texts:
I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this step to just change buffer system?

The pI of IgY is 5.6-7.6, and so, what buffer should I use for the chromatography? I know I want the IgY to be negative, so I would want pH in start buffer to be higher than pI?

I bought a column but it has not arrived yet. Does it come with recommendations on preferred buffer system for the chromatography or can I use any one I want? And also, what buffer should I use to elute my protein?
Do you have any recommendations?

In previous steps, prior to dialysis, I used phosphate buffered saline with pH 7.

Thanks in advance


texts: How to measure metabolic rates of microscopically small animals?

texts:
I want to measure metabolism rates in Tardigrades

Metabolic rates will be assessed immediately following their exit from cryptobiosis (an animal dormant state).

I know that oxygen levels is the usual way to measure metabolism, but tardigrades are extremely small and hence oxygen level differences will be minute. Is there any other way to characterize metabolic rates, or is there a way to make the oxygen method viable?


texts: How much do urban pigeons move around cities?

texts:
Do they tend to live their lives in one area of the city or do they move around? For example, do pigeons born on London's Trafalgar Square live their whole lives centered around Trafalgar Square or can they move and become Marble Arch based pigeons?

What is the typical range of a city pigeon? Have Trafalgar Square pigeons ever made the trip to Buckingham palace just down the road from them, or do they hang out in the square all the time?

How different are these behaviors from their wild behaviors and how effected by humans actions in the city are they? For example, do pigeons learn that a particular city square will become busy with tourists in the summer and travel there at these times of the year seeking food?


texts: percentage of animal diseases caused by bacteria?

texts: I know this is a long shot, but what is the approximate percentage out of all the animal diseases that are caused by bacteria? One of the Q&A websites answer it as 90, but is there any conclusive scientific evidence?


texts:
Let's take a quote from Wikipedia about zebroids.

  Donkeys are closely related to zebras and both animals belong to the horse family. These zebra donkey hybrids are very rare. In South Africa, they occur where zebras and donkeys are found in proximity to each other. Like mules, however, they are generally genetically unable to breed, due to an odd number of chromosomes disrupting meiosis.

First, if I understand meiosis, the resulting cells don't actually end up with half the number of chromosomes, but closer to a full set of halves of chromosomes. How is the meiotic process disrupted?

Then,

  A donkey has 62 chromosomes; the zebra has between 32 and 46 chromosomes.

Apparently this difference doesn't obstruct producing (infertile) offspring. How comes the process of recombination of such vastly different number of chromosomes in gametes is viable? What happens to chromosomes that don't find their 'pair'?

And then,

  Horses have 64 chromosomes, while most zebroids end up with 54 chromosomes.

54 is an even number. How comes zebroids can't just normally produce fertile offspring with other zebroids of the same number of chromosomes?


texts: What is the right definition of 'Sex Linkage'?

texts:
I am confused about definition of "sex linkage". I have found different definitions but they do no match.

From P.S Verma, V.K Agarwal cell biology, genetics, molecular biology, evolution and ecology:

  If the genes are situated in the same chromosome and are fairly close to each other, they tend to be inherited together. This type of coexistence of two or more gene in the same chromosome is known as linkage.

From: Anthony J.F Griffith "Introduction to genetic analysis

  In general, genes in the differential regions are said to show inheritance patterns called sex linkage.

From: Wikipedia

  Sex linkage is phenotypic expression of an allele related to the allosome (sex chromosome) of the individual.


texts: If massive animals live longer, why do humans with gigantism die younger?

texts:
What I mean is humans suffering from gigantism (type 1 neurofibromatosis, Marfan syndrome, X-linked dominant acro-gigantism, et cetera) rarely live more than 5 decades (50 years).
The same can be said to wolves: wild ones rarely live more than 9 years, and domesticated wolves (dogs) can live up to 20 years if they are small like chihuahuas, beagles, and toy poodles, and no more than 7 years if they are massive like great Danes, mastiffs, and Rottweilers.
But, at the same time, horses can live 3 decades (30 years), but hamsters only live 4 years.


texts: What are the biochemical interactions between human body and Polyethylene?

texts:
Our waterways and oceans are showing increased levels of plastic contamination. These plastics are breaking down into smaller pieces. When one goes to the beach and plays in the surf they often swallow some seawater and thus some amounts of plastics, including Polyethylene.

What are the biochemical pathways or effects of plastic, specifically Polyethylene, in the human body? I am looking for toxicity of both a large amount scenario (plastic bag milkshake) and a small amount (some in ocean water).


texts: I photographed this flower in Central Europe. I looked in online databases but can't really identify the actual flower, since there are so many that look quite similar. Can you help me? What's the name of this flower?


texts:
There was a recent incident at Yellowstone National Park in which tourists placed a bison calf in their vehicle, and that eventually led to the calf being euthanized.

The National Park Service issued a statement in which they said:

  In addition, interference by people can cause mothers to reject their offspring. In this case, park rangers tried repeatedly to reunite the newborn bison calf with the herd. These efforts failed.

Why would a mother reject her offspring if it has been "interfered" with by humans?


texts: Why is 450 nm monochromatic light perceived as blue or violet depending on its intensity?

texts:
Trying to do some color matching I purchased a 450 nm laser. I expected monochromatic light of this laser to have similar properties to those of all others I've already played with — 808, 640, 520, 405 nm — in that they all cause an unambiguous color sensation.

But when I shined it onto my wall (having removed the lens), I was surprised to see something unusual. In the center, where the intensity is high, it looks as "very blue" — much like those 465 nm blue indicator LEDs we can see everywhere today, only more saturated. But on the sides, where the intensity falls off, the color looks like violet! When I shine this laser on a ceiling obscured by a wall, I see its reflected light as violet. When I move the spot so that the reflected light becomes more intense, I begin to see it as blue again in the intense areas, and still violet in dimmer ones.

I've checked with a spectrometer, and there doesn't appear to be any fluorescence in the light spot to confuse me.

Interestingly, if I increase amount of ambient lighting (white LED lamps + CCFL ones), sensation of blue once again transforms to violet. Also, the "very blue" intense spot looks violet in bright sunlight, although I can make it blue again by focusing into a smaller spot to make it brighter. In a fully dark (apart from the laser) room I still do notice the violet areas on the sides of the spot.

405 nm light also seems a bit silvery-whitish when its intensity is high, unlike at low intensity. Maybe it's the same phenomenon, which I simply didn't notice before because the tint is not that blue in this case.

In both cases of 450 nm and 405 nm the additional color on high intensities is still "shiny" due to the speckles specific to high monochromaticity, so this indeed doesn't look like the result of fluorescence of the objects I shine the light to.

I've asked several people whether they see it the same, and they answered affirmative.

I suppose it's not related to color balance, because I only changed the intensity of ambient light, not the tint to observe the changes in color. Especially it shouldn't be due to color balance since I can simultaneously see different colors in the areas with different intensities.

Interestingly, while I thought the "very blue" color to be the main color of 450 nm, CIE 1931 XYZ value for it, converted to sRGB, appears to be (if we desaturate and normalize to fit in sRGB range) (0.43,0,1), which is purple, not blue.

So, what is going on here? Is it a well-known phenomenon? Could it be due to some fluorescence of the retina itself rather than the objects lit by the laser?


texts: Can humans perceive sounds above 20 kHz?

texts:
In the never-ending debate raging in the audiophile community about sound quality and what humans can or cannot hear, it is very very very very incredibly often cited that the upper-limit of the audible range of human hearing is 20 kHz, give or take. Some indicate that this is a conservative estimate, and that the actual upper-limit is actually lower than that (~18 kHz). While others suggest that sounds could be heard or otherwise perceived up to about 25 kHz-30 kHz:

  Sampling rates higher than about 50 kHz to 60 kHz cannot supply more usable information for human listeners.

And some others suggest that there is substantial variation between individuals around the upper limit:

  The human range is commonly given as 20 to 20,000 Hz, though there is considerable variation between individuals, especially at high frequencies

So is there any biological evidence whatsoever that young, healthy humans can hear or otherwise perceive (or sense) sound waves above 20 kHz? And what would be a conservative estimate of the absolute upper limit of the audible spectrum for humans (i.e. usable sound information for human ears and senses)?


texts: I took this picture a few days ago in Val Rendena, in the dolomitic Brenta group (2000 m). The whole plant was 15 cm tall at most, and it had a single leaf on the stem. What flower is it?


texts: Why do people in the scientific community use terminology such as renal, hepatic, cardiac instead of kidney, liver and heart?

texts: Are there differences between renal, hepatic, cardiac and kidney, liver and heart? Is the "jargon" used more commonly because of tradition, or is there some definitive biological basis to it?


texts: Affinity Column of membrane bound receptors

texts: I understand affinity columns can be used to study the ligand/enzyme affinity. But is an affinity column able to be used for membrane bound receptors? I


texts: Why is there only adrenoreceptors and no active adrenergic innervation in bronchus and uterus?

texts: Our bronchus and uterus has beta adrenoreceptors, but they have no active sympathetic nervous system innervation in these organs. Was there a sympathetic innervation in trachea and uterus, earlier, that we lost it during the course of evolution, if no, why did nature gives us only adrenergic receptors and no adrenergic nerves in trachea and uterus?


texts: Could inhibition of progerin formation slow the rate at which a body ages?

texts:
According to wikipedia, progerin is activated in senescent cells. The protein itself is known to be the cause of a rare affliction 'progeria' - a disease marked by accelerated aging of the body. This disease is not accompanied by neurodegeneration.

Is progerin the key factor in the aging process?
If yes, could inhibition of progerin formation control the rate at which a body ages?


texts: Is mucus significantly affected by the presence of ions?

texts: In mucus, there is besides water and the mucins (Proteins for mucus), there are Ions like $Ca^{2+},Na^{+}$, etc. I have read that These Ions can Control the mucus swelling, i.e. the volume that the mucus occupies. Moreover, I have heard that some polymers can be affected by the presence of Ions, These are called "electroactive polymers". Is mucus a substance that changes ist consistence dramatically, when Ions are added or removed (equivalently, if pH value is changed due to $H^+$ ions)?


texts: What is the water content of avian blood?

texts: I'm doing a work about heavy metal contamination in seabirds. I have found that the toxic threshold for Cu in blood is 1,15 μg/g wet weight. That number refers to an average between some seabirds. I need to convert that value from wet weight to dry weight.


texts: Is it possible to use two forward primer and one reverse primer?

texts: I have eGFP and the gene fragment i assembled by pcr.The next step is that i have to join my fragment fragment into 3'p end of the eGFP.I have three primers FP1 is forward primer for eGFP, FP2 has overlapping between eGFP and my fragment. RP1 is just revcom of my fragment 3 prime sequence. How can I assemble this by pcr. is it possible to mix all the three primers together with GFP and my fragment.


texts: Is it more likely to develop a throat-ache at night?

texts: I have noticed that I rarely develop phlemmy throat-aches in the daytime, but often notice them after I have been sleeping.  Is this a recognised phenomenon?  Could it be because viruses or bacteria aren't being flushed out by food, water and vibration of the throat from speaking or that one's immune system is lower at night? If it is the latter, why is this?


texts: Does all of life on Earth use the same DNA compounds for all species?

texts: If an organism on Earth has got DNA, would it always have C,T,G,A?


texts: What kind of shiny bronze beetle is this?

texts:
Lots of these on my rosemary bush

About 7mm long


texts:
What type of Caterpillar is this?

My hand brushed against this last night and it burned and itched immediately. Today it's starting to blister, is red, and itches all around the bumps. I was camping at the John Knox Ranch in Fischer, Texas. It was dark and I reached to grab the chair when I suddenly felt pain. It was about two inches long. This is the reaction I initially got. I didn't even feel when i brushed against it until i started feeling pain.
These were the best pictures I could get.
Any help is appreciated!!


texts: Leaf formation on unknown tree: cocoon or something else?

texts:
A small tree in my yard has leaves which appears to double over themselves. The first two pictures show this phenomena, and the third is the same tree to maybe aid identification.

I can't absolutely guarantee when this first appeared, but I believe it was this growing season, and I know it's been there at least a month (unless it's reoccurring, I am not tracking the individual leaves).

My first thought is cocoons or some other insect behavior. Can anyone tell me what it is?

(What kind of tree it is will also be valuable, in case we can't find the answer to the leaf question here)

EDIT: Location is outside Boston, MA (USA).


texts: I've heard of a bunch of finger lime hybrids, and as the pomelo is among the 4 big citrus ancestors, there are a ton of hybrids there, but is there any known finger lime/pomelo hybrids? Currently the closest one is the asutralian blood lime, a cross of red finger lime, mandarine and swett orange, which itself is a pomelo/mandarine hybrid.


texts: How do tea, coffee, and beer dehydrate you?

texts:
For the long time I am trying to find out if the following is truth: They say that some beverages dehydrates. I heard that about tea (sometimes green, sometimes black, sometimes both), coffee, beer and more (for example coke).

How does hydration from these sorts of drinks compare to others (e.g. water)? Why do these drinks less efficiently hydrate?


texts: Which part of the genome are the developmental sequences of embryogenesis located?

texts: Which part or parts of the the genome are the sequences located. Are they spread across the chromosomes? If so how are they accessed sequentially with precision during embrygenesis?


texts: Loss of antibiotic resistance due to long term storage

texts: How possible is it for antibiotic resistant bacteria stored for a long time to lose such resistance?


texts: Why analyse transcriptome instead of proteome?

texts:
Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (functional analyses, GO etc) to infer biological cellular consequences. RNAs are really only the middle-man. Presence of an mRNA doesn't necessarily mean that it will become a protein. It could be degraded by microRNAs etc. before translation. It is eventually the protein that are actually causal to a biological change.

So, my question is why not just go directly to the proteins. Why not just extract the proteins and sequence them, quantify them, analyse and draw conclusions? What are the compelling arguments to study the transcriptome to understand biological processes?


texts: Why was Darwin's Finch argument valid considering Weismann's argument?

texts:
According to Darwin, there was only 1 species of Finch bird in Galapagos. Then Darwin argued that due to diet adaptation and natural selection, their beak changes causing new species--which is confirmed by John Gauld at the Geological Society of London.

In contrast, Weismann's and his mouse proofed that environment factor won't effect next generations.

Don't Weismann's argument contradicts Darwin? Ok, say that the Finch bird adapts (and killing the one who don't) with their diet. Their beak changes. But when these Finch bird breeds, their new generation's beak should reset to normal beak again.

The reason I asked this reason is because one article said that our teeth are changing due to overbites using utensils(1). However, not everyone use eating utensils. Indian mostly used finger. Indonesian don't really care whether we use our hand or spoon. If this trend keeps happening in the future, won't human evolve into two species? Homo sapien and Homo spoon (pun intended.)

Or am I mixing Darwin with Lamarck?

(1):http://www.theatlantic.com/health/archive/2013/01/how-forks-gave-us-overbites-and-pots-saved-the-toothless/267252/


texts: Interpretation of faint band for Linear Array HPV Genotyping Test

texts: After having used the test for research it would appear as if it is very specific. What is one to make of bands that are there but faint? Or what if there are two bands and one is big and bold and the other is faint? Intuitively, I would believe that the starting concentration of the type represented by the bold band is way higher than the type represented by the faint band. Is my intuition correct? Any insights into what that means? Are both HPV types driving the disease process (eg papillomas) or is it just the bold one? Any data? Any intuitions? Any references?


texts: Non-coding DNA correlation with rate of evolution

texts:
Non-coding DNA can be helpful in generating useful mutations that can go on to become new features/functionality of an organism.
Non-coding DNA also indirectly reduces chances of mutation of useful/functional genes.

So if an organism has a larger proportion of non coding DNA it'll be safer from mutation. Humans have 80%-90% non-coding DNA. But this number is far lesser in many other species especially plants. Some plants have as few as only 3% non-coding DNA.

My question is, do these species with less non-coding DNA undergo evolution faster? Because their functional genes are more susceptible to mutations (which would be disadvantageous on average I guess). Would it be fair to say that evolution tries to keep expanding this proportion of buffer DNA? Lastly, is my question related to C-value paradox?

My assumption that non-coding DNA indirectly offers adaptive advantage (evolutionarily speaking) seems to be questioned. Let's consider the following case:

Let A and B be two genomes of equal size. Let A have 80 % non-coding DNA and 20% coding DNA. And let B have the opposite i.e., 20% non-coding DNA and 80% coding DNA. Let both A and B be exposed to the same amount of UV radiation for the same amount of time. All conditions being the same, let's assume that this causes the same amount of mutation in both A and B, say 10%. Now what is the probability that this mutation happened in non-coding DNA (which means it doesn't harm the organism) in each of A and B? Evidently, the probability is higher in A meaning it's safer from mutation caused due to UV radiation. So A has an advantage of surviving over B.


texts:
It might be a dumb question to ask, but I find it confusing.
Is the perception of taste additive?

Or to be more precise, can two tasty food items combine to give a more delicious product?

For me, this sounds logical. I believe that the sense of taste is due to some chemical reactions in our mouths, which in turn fire up our taste receptors to give some specific signals to the brain. So when two tasty foods combine, there would be more signals that are identified as 'Tasty' by the brain. That should give the food combination a stronger taste than its constituents.

But I found some contradicting examples.

I like to drink tea and coffee. But once, when I accidentally mixed a cup of tea with coffee, it wasn't tasty at all.
I have seen some specific 'COMBINATIONS' of foods that taste better than their constituents.

What does this mean? More likely, my understanding of taste perception is flawed.  If it is, then what is the real working mechanism of taste?


texts: What kind of viruses can be found in sperm?

texts:
It is well known that the HIV virus can contaminate other people via sperm. But is this the only virus that sperm successfully could contain, or could for example rhinoviruses also be part of sperm?

What causes the difference if there is one?


texts:
We found this in our UK garden! Any ideas? Not sure if it had/has wings.

It has a segmented tail and 6 legs. It’s about 2 inches/ 8cm long.


texts:
If we had a hypotheical gene called gene exampleGene and this gene had 5 exons, labeled A, B, C, D, and E in that order on the chromosome, could it be the case that the stop codon for this gene be on exon D and the exon E still being a exon that would be transcribed in? I can not see this to be true, since If I  remember correctly, transcription stops BEFORE the stop codon, and when stopped, the pre-mRNA is then further processed, but everything after that stop would not be a part of the exampleGene ?

My lazy diagram of how I think of the supposed exampleGene to be:

---A-----B---C---------D(stop codon)-------E---

After transcription via RNA polymerase:

A-----B---C---------D


texts: What is this 5"-across spider found in my bedroom in France?

texts: As the subject-line says, what is s/he? I've removed more spiders than I remember over the years, but one that almost fills a pint-glass was approached with some trepidation!


texts: What do the names of Immunoglobulin subtypes mean?

texts: What is the exact meaning and full form of  IgM, IgG, IgA, etc? What is the rationale behind the names of the isotypes, if there is one? For example, what does "M" mean in IgM?


texts: Why did multicellular organisms evolve when a single cell can survive on its own?

texts: Since unicellular organisms can survive, why would there be evolution of multicellular organisms?


texts: How to determine the primary Uniprot accession number from a list of accession numbers?

texts:
Given a list of UniProt IDs that are linked to an Ensembl ID, is there a way to systematically determine which is the primary accession number with no other information?

According to ExPasy

  Researchers who wish to cite entries in their publications should always cite the first accession number. This is commonly referred to as the 'primary accession number'. 'Secondary accession numbers' are sorted alphanumerically.

But what if the order has been jumbled or compiled from a different source and resorted.

For example:

Ensembl:

ENSMUSG00000035642

Uniprot:

Q8R0P4, Q8CF11, D6RJK8, D6RJJ4, D3Z442, D3Z1Q3, D3YZD8, D3YY39, D3YX09, D3YWY5

This question is cross listed on the Bioinformatics stack-exchange.


texts: Are all dead plant cells (that die to do a job), have secondary wall?

texts: Can we say that all plant cells that die to do a job (they are dead now), like the outer cell surface of the root cap, have secondary cell wall?


texts: What is the top speed of muscle contraction?

texts:
Currently I am looking into what muscles groups are most used during a football kick. I have a hypothesis that the quadriceps are not as used as most people think because the momentum the swing creates makes the knee extend to fast for the quadriceps to contract.

To prove this I need to know the speed the knee extends during a football kick and the time it takes for the quadriceps to contract. I know how fast the knee extends through my own research.

Does anyone have any information on the speed of muscle contraction?
Quadriceps contraction time would be optimal, but any information relevant would be very helpful


texts: Which contributes more to cancer clearance, T cells or NK cells?

texts: Both T cells and NK cells have cytotoxicity. However, most immunotherapy targets T cells rather than NK cells, such as CAR T and PD-1 inhibitor. Is it because T cells kills more cancer cells than NK cells?


texts: How to know if your breathing is normal?

texts: Is it possible for a device to measure how much air we breathe in and out over the entire day and at what rate? I think if we have access to this data we can compare it across people.


texts:
Does it possible to create any custom gene or protein we want with current technology?
I have a protein sequence or a gene sequence about 4000 bp write down on my computer, is there anyway to "print" it to real gene molecule or protein molecule (for example use chemistry and enzyme and automatic machine..) ? What is the challenge ?


texts: Can radiation exposure cause cancer later in life even if no traces of radioactive material are present in the body anymore?

texts:
I had a long-lasting debate with a friend of mine about the Fukushima incident.

The question that we tried to solve was if radiation or toxin exposure can cause cancer later in life even if no traces of radioactive material or toxins are present in the body anymore.


texts: Animals spend a good portion of every day doing nothing, and it seems like that time could be better spent hunting, searching for mates, etc. Also, animals are not aware during sleep, so it would be easier for a predator to attack them. Why is sleep required for animals?


texts:
TL;DR
What's the relationship between the following?

Mutation rates (expressed as "mutations per year" for a virus like e.g. COVID-19 (SARS-CoV-2). E.g. this article mentions "The rate looks to be about 24 mutations per year"
Actual virion replication error rates in a single host cell, measured as e.g. error rates per released virion from the infected cell, i.e. (# of mutated released virions) per infected cell.

Assumptions
I would assume that mutations happen at a single virion-cell level because there are differences in e.g. nucleotides in RNA  between:

the virion infecting a cell (e.g. ACE2 for SARS-CoV-2)
the released virions from that same single cell

If so, wouldn't one argue that:

replication errors (at the nucleotide and thus released virion level) can easily happen, potentially billions of times during the infection of a single host organism
there is no "single successful" mutation or RNA variant within a host, rather, we have a distribution of RNAs, many of which could be simultaneously transmitted to another host organism?

Further context
I quote from e.g. this paper:

On a per-site level, DNA viruses typically have mutation rates on the order of 10E-8 to 10E-6 substitutions per nucleotide site per cell infection (s/n/c). RNA viruses, however, have higher mutation rates that range between 10E−6 and 10E−4 s/n/c

Again, wouldn't that mean that a single host could 1) easily generate many mutations of the same virus and 2) pass most of those uniquely generated mutations to another host? If so, how come we can simply say "24 mutations (over time) per year"?


texts: What happens to blood pressure when we exercise? Does it increase, decrease, or remain the same? If it does increase, why are patients with high blood pressure recommended to exercise?


texts: Why does touch the face make more likely to be infected?

texts:
Why is it risky to touch the face although there is no direct contact with into the nose, eyes and mouth?
Is there any possibility that pathogens infect us from our facial skin?
Suppose we have viruses or bacteria on our hands and we touch the side of our nose with our hands.
Can these bacteria reach our noses by their own?


texts: What in the brain has gone awry during sleep paralysis?

texts:
I experience episodes of what I assume is sleep paralysis (lasting ~ 10-30 seconds) a few times a year, where I'm conscious of being somewhat awake but unable to move.  I can hear, but not see, and am quite focused on my breathing which feels labored and uncomfortable (can be accompanied by a feeling my face is covered by a sheet).  Sometimes, I've even been able to "jolt" myself awake if somehow muscle control is regained. Otherwise, I assume I drift off back to sleep.

Do we know yet what has gone wrong (if it can be assumed to be aberrant) and which neural circuits are involved? What i'm looking for is a specific explanation at the neural circuit level of how it can occur.

Is anyone aware of anyone conducting research into this or how it could be studied as it doesn't occur frequently and likely difficult to induce on demand?


texts: Why do physicians try to match HLA complexes for organ transplant?

texts:
My understanding of acute transplant rejection is that donor dendritic cells present donor antigens on MHC1 to host naive CD8+ T-cells resulting in an immune response against the graft. If you match MHC1 complexes between donor and host, wouldn't t-cell activation actually be more likely than the case where MHC1 complexes between donor and host are different?

Reasoning: I imagine in the case where MHC1 complexes between donor and host are different that the  t-cell receptor is unable to bind the MHC1 complex in the first place..making the transplant essentially invisible. In the case where MHC1 complex between donor and host are the same, the t-cell receptor would bind the MHC1 complex, and increase the likelihood of an immune response. Given that HLA mismatch is a major cause of transplant rejection, something is wrong with my reasoning. Thoughts?


texts:
My attempt: This site says that it is due to flight or fight mechanism, which results in more amount of blood being passed to face causing red face.

But isn't it wasteful for our body to send more blood to face than to our muscles for efficient action?

Also an answer to this question says quite opposite.

So, I think that first site maybe wrong.

So, what exactly is the reason for red face during rage(anger)?

Evidence for my claim:

  Several physiological studies have demonstrated that human facial color also varies with emotional states. The face often flushes during anger, or pleasure, and sometimes goes pale when experiencing fear or fear mixed with anger.

Source:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259783/


texts: What is an simple way to burn glucose for visible effect?

texts:
I want to make a partially working model of the digestive system that could digest complex carbohydrates. My ultimate goal is to be able to cut up some bread, put it into the model, operate it, and eventually see some effect equivelent to glucose being used in a muscle. I obviously have a very limited buget. How could I simulate glucose being burned in some way that has a visible effect?

Edit: I'm specifically looking for some way glucose can be used to achieve some visible effect that makes sense as a metaphor for combustion, without dangerous/expensive chemicals.


texts: Number of different clones of B lymphocytes

texts:
My professor told us that there are about a million different B cells based on their surface receptor.

I have read that we have about 30000 genes in all. Since receptors are proteins how do these 30000 genes make such a large number of receptors?
I read about something called alternative splicing. Is this the mechanism behind this?


texts: Why doesn't T5 exonuclease have endonuclease activity in Gibson assembly?

texts: Gibson assembly uses T5 exonuclease to chew back the 5' end of dsDNA to generate overhangs. However, T5 exonuclease, in contrast to lambda exonuclease, is reported to have ssDNA endonuclease activity (https://www.neb.com/products/m0363-t5-exonuclease#tabselect0). Why doesn't his cause problems during gibson assembly? Is it just because these don't yield viable assemblies? Or is it because this activity is inhibited somehow, such as the T5 concentration is too low?


texts: An online tree of life with extinct species present?

texts:
There are awesome online phylogenetic trees such as OneZoom.

But they all only list living species.

I want to see dinosaurs between birds and crocodiles.

I wanna see that humans are reptiliomorphs and eupelycosaurs.

species.wikimedia.org seems to contain this info, but it's not presented in a navigable tree structure.


texts: Do all +ssRNA viruses have similar structures and life cycles?

texts:
Take HCV for example. HCV doesn't package any enzymes in it's virions. When it infects a cell, it first translates its RNA genome. It's RdRp is synthesized with other non-structural proteins. Then its RdRp began replicating the RNA genome. Newly synthesized RNA are served as either translation templates or genomes of new virions. Finally new virions are assembled and released.

So do all +ssRNA viruses have the same pattern? There's no enzyme in the virions, and all the enzymes are synthesized after entry into the cells. They have the same life cycles: entry→translation(non-structural)→replication→translation(structural)→assembly→release.


texts: I had recently read an article that the possibility of having natural blue rose is extremely rare because of the absence of delphinidin in most roses. Are all blue roses just a product of cross-breeding?


texts: Allergies - congenital situations or created and developed over the years?

texts:
This is probably an easy question, but I've yet to find an answer.

Recently I felt under the weather more and more often, especially at the time I was waking up. I assumed this was an allergy-related thing so I did an allergy test and found out that I am allergic to dust-mites. This does explain my condition after waking up, as these mites mostly reside in the mattress and thus affect you during sleep. However, it doesn't explain why this allergy hadn't affected me at all until now and why it suddently appeared after 20+ years. So the question is, is this (and more generally other allergies) a congenital situation, or was it developed due to my way of life, (non) cleaning habits etc.?


texts: Chiral (a)symmetry of curly hair (and fur)

texts:
Some people have curly hair, as well as fur of some animals can be curly.
However, shapes which are curly are not mirror symmetric, much alike screws or chiral molecules.

The question is whether curly hair in a given species (say, humans, but I don't stick to this example) are in the same proportion left-handed and right-handed?

One can easily imagine that chirality of molecules (e.g. keratin) gives rise to macroscopic chirality of curly hair. However, it is far from obvious whether this effect is strong enough.

EDIT:

I am interested mostly in data. It might be easy (yet misleading) to convince oneself that there should (or there shouldn't) be relation of microscopic to macroscopic mirror symmetry (or lack of it).

(E.g. in some other cases there is such effect - e.g. with left/right orientation of body organs like heart, or asymmetry of left and right brain.)


texts:
Do red blood cells have no MHC? (I have often heard that they do not.)

If so why are they not destroyed by immune cells?


texts: How much force is required to cut off the blood circulation of, lets say the average human arm? I'm asking because i'm bored and want to try it on myself. I know that in just a couple of seconds with lack of blood flow you will lose complete use of your arm. I'm only going to do this for a second or two with people watching so please do not worry about safety!


texts: Why do humans not have a powerful sense of smell?

texts: It seems like a useful ability to be able to detect many different things about, say, another organism. A lot of mammals have this ability. Why not humans? Did we evolve it out or never develop it?


texts:
While talking about the evolution and conservation of dingoes in Australia, someone asked an interesting question:

  Can I define the dingo as an endemic species?

That question, despite apparently simple, deals with some terminological conflicts and I must confess that I was not able to say yes or no at the moment.

The context:

As everybody knows, the dingoes (Canis lupus, but for some people Canis dingo1) were introduced in Australia by human beings, between 4,000 and 12,000 YBP. That being said, it's acceptable to define the dingo as an invasive, exotic species. Using Campbell's2 definition:

  Invasive species: a species, often introduced by humans, that takes hold outside its native range.

However, some researchers argue that the dingoes, being isolated in Australia for a relatively long time, have a unique genetic profile. As this is controversial, let's suppose, just for the sake of the argument, that they do have a unique, distinctive genetic profile (and that they became a distinct species).

That being the case, the dingoes may be defined as endemic. Quoting Campbell again:

  Endemic: referring to a species that is confined to a specific, relatively small geographic area.

I have taught biology for many years and I must confess that, for me, endemic and exotic were always opposite, mutually exclusive terms. However, in this case (and many others), it makes sense to say that the dingoes are exotic and endemic.

Maybe one can say that, from the moment the population became a distinct species on, it stopped to be exotic and started to be endemic, which would keep the two terms mutually exclusive.

My question

So, my question is: can a given species (or population) be defined as exotic  and endemic simultaneously?

PS: I'm not asking for opinions, which would make this question off topic  for SE Biology. I'm asking for rules and guidelines in the use of the terms, preferably with references.


texts:
What makes synapses not move or pre- and postsynaptic cells neither touch nor move away from each other? I mean the synaptic cleft is a gap between the pre- and postsynaptic cells that is about 20 nm wide (according to Wikipedia), so what makes it of that width? Are there some protein fibers anchored in both pre- and postsynaptic cells? Or do the glial cells keep them at that (often temporarily) fixed position? What prevents them from being displaced by the slightest movement of the body? I'm talking obviously about the chemical synapses.

Thanks in advance for the answer.


texts: Why is phagocytosis not included as a type of receptor-mediated endocytosis?

texts:
A common classification of endocytotic processes groups them into Phagocytosis, Pinocytosis, and receptor-mediated endocytosis (1) & (2). But Phagocytosis involves the use of specific receptors like opsonin receptors, toll-like receptors, etc (3). Why then does this classification still hold?
(1) https://courses.lumenlearning.com/boundless-biology/chapter/bulk-transport/
(2) Essentials of Medical Physiology 6th edition by K. Sembulingam and Preya Sembulingam (page 34)
(3) Histology_A text_and_an_atlas_with_correlated_cell_and_molecular_biology 6th Edition (page 32)


texts: How does CpG island methylation lead to gene silencing?

texts:
I see often the blanket statement that CpG island methylation can lead to gene silencing.  However, I have been unable to find a straightforward explanation of the mechanism by this.

Is it a purely physical block of binding for transcription factors?  Does the methylation create a tertiary structure that is compacting the DNA?  Does it recruit histone modification factors that compact the chromatin?

Please feel free to cite literature so I can go read the papers.


texts: After catching a bunch of mangrove snapper using live shrimp, my son caught this fish in about a foot of brackish saltwater water off a dock near a rock wall in  Vero Beach at around 10:00 AM  on July 5th. Fish was about 6 inches long and had a wide mouth with  small pointy teeth and what appeared to be two small horns/bumps that protruded from behind its eyes. Never encountered it before.


texts: Do ants actually stick better after "licking" their legs?

texts:
I found an uncommonly large black ant and put it in a glass cup to observe it. It initially had a lot of trouble climbing vertically by any amount. However, I noticed it paused and when I looked closely, it seemed to run its front legs quickly between its mandibles, and it looked as though it secreted some kind of orange liquid through its mouth. After it did this and climbed again, it climbed a little bit further up the cup, but fell down again.

Then, it repeated the process of pausing and running its front legs between its mandibles. After this, it tried to climb again and I saw it was able to climb a little bit further than it did after the first run before falling down, though I didn't think to measure the exact height on a drinking glass. I saw it repeat this process yet again, and it stuck to the cup even better and climbed even higher before inevitably falling, and I assumed it would continue this process indefinitely until it was able to climb out of the cup, so I threw it back outside.

I would hypothesize that the ant was coating its legs with its own saliva which has evolved to be sticky for situations like this, seeing as how it so quickly exhibited the mental aptitude for recognizing its climbing challenge. But, I'm not biology expert. Perhaps its legs already inherently possess all stickiness ability it needs, and it is only that its legs were dirty or covered with water.


texts: How many of the four meiotic daughter chromosomes of a homologous pair can be recombinant via crossover?

texts:
In graphics I've seen, crossing over occurs between the "inner" two chromatids in a side-by-side arrangement of two duplicated chromosomes:

This suggests that only two of the four meiotic daughter chromosomes of a homologous pair can be recombinant via crossingover. Is this true? Or can you have more complex patterns, like the one below, in which all four daughters are recombinant? Does the X-shaped geometry of the doubled chromosomes play a role in models of crossover phenomena?

ps. Sorry if my terminology is strange. I'm a beginner! Experts: Edits to improve clarity welcome!


texts:
I am trying to understand the current work on abiogenesis in biology, e.g. primordial soup, the Miller-Urey experiment, etc.

How has our understanding of abiogenesis been revised since the Miller-Urey 'primordial soup' hypothesis?


texts:
FRET only works for interactions between 1nm to 20nm.

How can you be sure that the interaction that you want to study isn't less than 1 nm/greater than 20nm apart?


texts: Since there are non-flying birds and secondary non-flying insects, it is reasonable to assume there were also non-flying pterosaurs.


texts: Did the Swedish cod fishery expand in the past years?

texts:
The Marine Stewardship Council states that the cod fishery in the Eastern Baltic sea recovered well and issued it's MSC certificate to the Swedish cod fishery in 2011 for that region. (MSC 2011)

Data downloaded from EUROSTAT shows that Portugal, a main importer of codfish and -products, imported less and less from Norway (besides Iceland and UK the main supplier) (FAO 2006); dropping from around 20,000 tons (2001) to < 1,000 tons (2011) and more and more from Sweden; < 5,000 tons until 2003 versus > 30,000 in 2010 and 2011.

This trade data does not necessarily show the origin of a product but rather the country that is selling the fish. I wonder if either the Swedish cod fishery expanded in the past few (~ five) years; Portugal changed it's main supplier from Norway to Sweden for whatever reason; or Sweden buys cod from Norway and distributes it.

Depending on this the answer may not be so closely related to biology but I hope to get an idea here.


texts:
I'm looking for a textbook in neuroscience for a rigorous introduction to the topic as an autodidact. I have no prior exposure to the field.

In particular, I'm interested in the chemical mechanisms of enzyme modulation, ideally something similar to Lehninger's Principles of Biochemistry where specific Protein Databank ID's are given, so I can load an enzyme in PyMOL and view where the inhibitors/activators bind, in conjunction with an explanation of the actual pathways involved from a molecular level.

I've read Wade: Organic Chemistry, and a good part of Clayden's Organic Chemistry, before self-studying biochemistry for 6 months, to give a little background of my knowledge.

I'm leaning towards Kandel's Principles of Neuroscience after reading some other suggestions here, but this seems like a gigantic text, and I'm unsure how detailed the biochemistry side of things is (which is my main interest)? Could anyone share some thoughts regarding that, or recommend an alternative smaller text with a specific focus on biochemistry?

I'm also concerned that a large amount of data and publications in the field of neuroscience fail replication (something as high as 60% I believe), so the book would need to contain only factual, widely accepted information and not cutting-edge speculative studies that haven't been replicated and widely accepted. Also, as little pharmaceutical-industry influenced as possible.

Ultimately, my interest lies in understanding how different medications and drugs cause different mental states, their exact pathways and mechanisms, and how they form tolerance. I'd like to one day conduct research in how to minimize said tolerance, eg: reverse receptor desensitization. Which book should I begin with to head towards this goal?

Thanks!


texts: Is there any animal database or website that classifies animals as wild / domestic?

texts:
Is there any animal database or website that classifies animals wild / domestic?

Or.. the site that I can get the wild / domestic information of animal list...


texts: Why do depleted blood veins seem to appear near the surface (or skin) more frequently than blood vessels and arteries?

texts:
I could be wrong, but it seems like blue veins generally exist closer to the surface of the body rather than red blood vessels and arteries. And I'm also wondering if this is evolutionary because during an injury, the outside gets damaged first, and I am just speculating that it's more important for muscle tissue to keep gaining blood from less damaged blood vessels than removing already depleted blood that simply bleeds anyway out due to the injury.

Or, if this is simply a trick of the color, that blue veins are just dramatically more noticeable and the first hypothesis is completely wrong.


texts: The evolution of dogs through domestication and artificial selection

texts:
I am currently reading Richard Dawkins's book 'The Greatest Show On Earth: The proof for evolution' and in the second chapter he talks very much about the evolution of dogs.

He says centuries ago there was only such dog-like creature as the wolf, but in a matter centuries the wolf has evolved into the many breeds of dog we have through artificial selection conducted by man.

This to me seemed very peculiar and quite frankly untrue, and I may be getting the wrong end of the stick and he is in fact being analogous, although I'm pretty sure he's not.

So, did wolves evolve into the many breeds of dog we have through artificial selection conducted by man?

If so, how many centuries did this take?

(Dawkins's point was that if the wolf can evolve into the vast amount of breeds of dog we have at the moment from artificial selection over a matter of centuries, then surely over many millions of years, the evolution we claim to know of through natural selection could definitely have happened).


texts: Catenation and decatenation by DNA Gyrase

texts: Decatenation is done for the replication of DNA and why is Catenation done and is it related to Crossing over


texts: Text Book Recommendation: Cell & Molecular Biology + Organic Chemistry

texts:
I am studying undergraduate biology course and I have cell biology and molecular biology in my next semester. Our college recommends three books : Cooper, Lodish & Bruce Alberts. It would be really helpful if you give me your opinion on which of these (or your own recommended book) would be the best to learn these subjects properly. The only thing I need is the book to be easy to understand because it will most probably be totally self taught because our instructors are not always helpful in explaining stuff properly.
We also have an organic chemistry class and the recommended books are Solomon's&Fryhle & LG Wade. It would be helpful if you help me choose between these as well, my requirement stays the same. Book should be easy for self learning.
If you know about online video lectures about organic chemistry and molecular biology do let me know. MIT OCW doesnt really have good bio videos. I cant seem to find video lectures anywhere for gre preparation. Thank you


texts: How do we determine a disease's incubation period?

texts:
There was a suspected case of Ebola in France, which was later dismissed, since the suspect lastly came into contact with a potentially contaminated person more than 21 days before, which is the maximum of Ebola's incubation period.

So, more generally speaking, how does one determine the period of incubation ? How do we know the day a person was contaminated ?


texts: What's the maximum pressure inside a bombardier beetle?

texts:
This question got me wondering about the pressure inside a bombardier beetle.

Lots of articles mention pressure, but don't specify the amount of it:

  One study records the velocity of the spray to be within a range of 325 to a stunning 1950 cm/s.
  [...]
  Once the muscles around the reservoir squeeze the first amount of
  reactants through the valve into the reaction chamber, the resulting
  explosion causes the pressure to rise rapidly in the reaction chamber,
  forcing shut the one-way valve. The products of the reaction then exit
  the chamber with a pop and a puff, and the pressure inside the
  reaction chamber lowers again, falling below the pressure of the
  collection reservoir, which is still being squeezed by the reservoir
  muscles.

Calculating from the spray characteristics is beyond me.


texts:
Whether it's snacking on chips, munching on salad, or simply chewing gum, when I hear someone do it within an earshot, it drives me completely bonkers!

It doesn't matter if it's my girlfriend, my mom, someone sitting next to me at the office, or random stranger on the train, it bothers me just as much. The "mouth open" chewing type makes me want to get violent, and I often find myself in a blind rage. I also notice the slower, and more "deliberate" the chewing/munching is, the more I get tense and more it bothers me.

Sometimes I feel like they are doing it on purpose, and completely fake, sort of like a commercial where they exaggerate the act of eating.

I want to know more about Misophonia or "Hatred of Sound"?


texts: Teens concerned about impregnation through clothes

texts:
Dry Humping, is:

  dry humping is the process of two people repeatedly moving up and down and back and forth on top of each other fully clothed( or missing various pieces, but the penis must not come in contact with the vagina with out some sort of fabric separating them ex: boxers,panties, or even sheets!!)

We all know that the basic rule for impregnation is that the sperm must come in contact with the egg, and even be able to fertilize it. While sperm can get through clothes, semen (but this is yet been proven or disproved) gets stuck, thus the sperm dies.

What is your opinion about this? If two people are on top of each other, fully clothed, and the male comes to ejaculation, is there any chance that pregnancy can happen, in the realistic and biological look at it (and not some probability or statistical way)? What advice should be given to teens on the matter?

I am a computer scientist with no biology knowledge, and am very interested in getting the opinion of biologists.

But since I know that the stackexchange community likes to see work done before asking questions, I did my own research (I am used to googling code and algorithms):
Very few research has been done on the subject. There is one shining research that  concluded, as I recall, that:

  If the underwear is completely saturated with semen, and is in direct contact with the woman's vagina, pregnancy is possible statistically, but highly unlikely.


texts: What exactly happens to animals that fail mating rituals?

texts: Quite a few animals (usually males) participate in various mating rituals to showcase their fertility as mates. While presumably, the successful ones get a chance to mate with females, it occurred to me that I don't actually know what happens to the ones that fail. I would assume that not all the ones that fail don't mate, as that would result in roughly 50% of the male population being frustrated sexually. But I can't figure out an alternative, do they get another chance to fight other losers? Do they just mate anyway at a lower rate?


texts: What is the latency between paired neuronal responses in the brain?

texts:
Is there any data on how long it takes for signals to propagate from one neuron to its neighbors in complex networks, such as the brain (particularly the neo-cortex)?

If not, is there any reasonable way to estimate at least the order of magnitude (for example by considering synaptic delay, which is in the order of 0.5 ms and the firing delay)?


texts:
I am tasked with designing an in vivo experiment in humans that requires manipulating the gut flora in one sample group to gauge its effect. Please suggest ways of doing this besides administering antibiotics.

I am of the view that antibiotics may have unintended consequences and may be unethical; explain any opposing view.


texts: Is excessive hydration a risk factor for cancer in humans?

texts:
I was reading a book on radiation biology, and the book describes the process of "indirect action", where radiation can first ionize a water molecule forming a free radical, which then may interact with important cellular molecules, such as DNA.  This contrasts with "direct action" which involves direct ionization of a key cellular molecule.

The book states that as hydration increases, the probability of indirect action occurring increases.  Given that indirect action normally predominates over direct action in cells, could this mean that over-hydration could be a risk factor for developing cancer in humans? Has there been any research into this?

In addition, would larger humans, who obviously have a larger bodily water content, have an increased risk of developing cancer compared with smaller humans?


texts: what is the role of granulation tissue in bone fracture repair

texts:
When a bone fractures, let's say with a large enough gap that repair has to occur through secondary healing, vessel rupture will result in a hemorrhage that then coagulates, there's inflammation that removes tissue debris, and granulation tissue forms as capillaries and fibroblasts infiltrate, using the hematoma as scaffolding. Next is the formation of the soft callus. What is the composition of this soft callus?

I understand that chondroblast precursors are activated, and cartilage forms to bridge the fracture ends, but what happens to the granulation tissue from earlier? The fibroblasts that infiltrated the site of the fracture, do they lay down fibrous connective tissue or do they differentiate into cartilage cells and lay down cartilage matrix as well? I've been reading from multiple sources, and none of them really specify it well enough for the ambiguity to not remain.


texts:
How is breathing involuntary if the muscles that control it are skeletal?  Breathing is involuntary. However, the muscles that control it are skeletal: intercostal muscles and the diaphragm. Are there other muscles involved? Is it that these skeletal muscles are being controlled and/or acting involuntarily?

Humans can both continue to breathe while asleep, and they can also intentionally take a deep breath.

How is breathing be an involuntary act, that can also be controlled?


texts: Cytoplasmic determinants - protostomes and deuterostomes

texts:
Cytoplasmic determinants are spread unevenly in the egg, and so when embryo starts forming (cells start dividing), the determinants are also unequally divided between cell. This unequal distribution later plays a major role in differentiation and gene regulation.

Protostomes undergo determinate cleavage. Their cells' fates are determined very early in development, whereas deuterostomes undergo indeterminate cleavage. So, if you take away a cell at early stage of development, it can be replaced.

Now if we compare the division of cytoplasmic determinants in protostomes and deuterostomes, what I said in the first paragraph seems true (to some extent) for only protostomes.

My questions:

Do deuterostome oocytes have even distribution of cytoplasmic determinants initially and  divide unequally only after certain number of divisions?
Are there any studies showing correlation between the stage at which determination happens in deuterostome and beginning of unequal division of determinants?


texts:
I like this contradiction. But seems like my Biology teacher doesn't.

If oxygen oxidates us, why do we breath it? Why can't we evolve into a new kind of human being that breaths other component of air? Following the need of all species to survive longer.


texts: Are there seeds intended to feed eaters?

texts: Seeds are meant to survive digestive systems of the animals that disperse them. Are there seeds meant for a creature, who will digest most of the seeds for nutrition and disperse only a minority of intact seeds?


texts: Can we say that the source of the most circulatory regulation in the human is the nervous system?

texts: local regulation of blood flow and Baroreceptors, both stimulate the neurons and send messages to the brain. so can we say that the source of the most circulatory regulation in the human is the nervous system?


texts:
As I've learned, mRNA helps us to produce virus spikes proteins to induce learning of the immune system.
But then, I remember to have read that the coronavirus has some trick to pretend to be "food" to our cells, that is it has some lipid element. So it can entry the cell easily. But this was not same part as the spike protein, right? (otherwise it would have been contradictory with the mRNA approach?)


texts:
I need a way to calculate avocado ripeness rate in my experiment so I need a quantitative way, I'm not sure if calculating the cellular respiration for the avocado will result in ripeness rate for the fruit, if that's true I need references if you got.
And if you got another better quantitative ways to get the "rate" of the fruit ripeness.


texts: Are trees the only source of large amounts of oxygen?

texts:
Trees use carbon dioxide and produce oxygen in the presence of sunlight.

But is there any other source?

If yes, are trees the most important source of oxygen, or is there any other source which produce more than trees do?


texts: How long human can survive with just drinking water everyday

texts: Can humans live without eating food, just by drinking water?  How long can we survive just by drinking water everyday?


texts: What unicellular eukaryotes reproduce sexually?

texts:
By sexual reproduction I am referring to, at least, gametogenesis or mating bridges. I was previously under the impression that unicellular organisms did not reproduce sexually at all.

So far the sexually reproducing unicellular eukaryotes I am aware of are yeast, diatoms, malaria-causing Plasmodium and some diplomonads.


texts:
15-20mm long.
Brown legs, head, casing/wings (no flight witnessed).
Black body with protruding back part.
Long antennae.
Very fast running speed.
Seemingly keenly aware of surroundings.

Is this some sort of small cockroach?


texts: What is the meaning of "gap" in G1 phase?

texts: The full form of G1 phase is Gap one phase. G1 os also called first gap phase. Is there any specific meaning of " gap" here ?


texts: Does this procedure for extracting DNA from strawberries work?

texts:
I wanted to try out this experiment for extracting DNA from strawberries that can be done at home:

https://www.stevespanglerscience.com/lab/experiments/strawberry-dna/

However, while doing a bit of reading, I came across this article:

http://www.ncbe.reading.ac.uk/PRACTICALS/PDF/DNA_isolation.pdf

It states that, "Although these fruits [kiwi fruit, bananas and strawberries] seem to yield copious amounts of DNA, the substance produced is in fact little more than pectin."

Are they right? How could you tell that what you've extracted is actually DNA?


texts: Does DNA analysis allow determining amount of chromosomes?

texts:
Nowadays it is possible to sequence the DNA of extinct species, such as the Neanderthals, the Denisovans, and others.

Is it possible to determine, solely from the sequenced DNA or from known bone fragments, how many chromosomes the individual (or the species represented by the individual) had?


texts: Caterpillar(?) in Leaf Cocoon identification - Missouri

texts: A small chunk of leaves fell off of a potted tomato plant. We noticed our cats taking an interest in it once it started moving. Then a little caterpillar poked its head out. What kind of bug is this and should we worry about our plant?


texts:
A friend of mine found this bug in Germany. He sent the picture and asked if anyone knew what kind of bug it is. Since no one knew and I didn't find anything similar via google search, I decided to ask it here. Since he only sent me the image I can't really give good information regarding size.
So can anyone identify what type of bug this is?


texts: Standard recipes for yeast medium often include "bacto-peptone". Is this the same as bacteriological peptone? Is there an authoritative source that spells it out?


texts: Why lipophilic molecules can pass phospholipid bilayer, in spite of 2 hydrophilic layers?

texts:
It is commonly told that, hydrophobic/ lipophilic/ nonpolar molecules can quite easily pass phospholipid bilayer, and hydrophilic (polar or ionic) molecules can't pass (when no protein aid that); because hydrophobic nature of the lipid.

But in the same logic, hydrophobic molecules shouldn't pass through the bilayer. Because there are 2 hydrophilic layers in the membrane. i.e.

A and A' .

Then how the hydrophobic molecules can pass through A and A'?

I guess, it is due to thin diameter of A and A' . Is that?


texts: What portion of the electromagnetic spectrum do cats see?

texts:
I have seen numerous articles and various information about how cats and dogs see into the ultraviolet spectrum with interesting artistic renderings such as this:

http://www.livescience.com/40459-what-do-cats-see.html

But I have been unable to find any specific parameters of what wavelength boundaries actually exist for cats.

We know that humans see from around 750 to 400 nm, but what would a cat's range be?


texts:
Most day to day drugs such as caffeine and paracetamol require a dosage in milligrams to have the desired effect.

Why then, does it take many tens of grams of alcohol to have a tangible/noticeable physiological impact on the body? What is it about the composition of alcohol that makes it so weak, gram for gram, compared to other recreational and medicinal drugs? Are there any other psychoactive drugs that require similar dosages to alcohol to have an effect?

For clarification, as per the comments

For example, as a 90kg adult I can consume 30g of alcohol (3 UK units) before it has any noticeable impact, whereas a coffee containing just 100mg of caffeine (300 times less than alcohol) produces a noticeable reaction.


texts: Example of a virus becoming symbiotic with an organism

texts: The human gut has an indispensably beneficial ecosystem of bacteria. What are the examples of a virus that becomes symbiotic with an organism, or even incorporates beneficially into the genome of the organism?


texts: How would one go about isolating a specific mRNA out of a pool of others?

texts: I'm writing an essay about DNA recombinant techniques where the question asks to outline all the steps to arrive at having a colony of bacteria expressing a  gene of interest.The question makes you start with a pool of mRNAs, which I assume is for making cDNA. However, how do you go from having thousands of different mRNAs to just one kind?


texts: At which voltage will the conductance decrease due to the narrow pore in a voltage-gated potassium channel?

texts:
If you have a voltage-gated potassium channel that do not inactivate, at which voltage would you see decrease in ion conductance related to the narrow path in the pore?

With that said I know that in a solutions with other ions there is a possibility that the high driving force eventually will lead to blockage of the pore by other ions. This is more of a theoretical question.


texts: Math behind the Genetic Relationship Matrix

texts: The genetic relationship matrix (GRM) can estimate the genetic relationship between two individuals ($j$ and $k$) over $m$ SNPs and $i$ representing a specific SNP. What I don't understand from their equation is why we divide our summation by $m$ (the number of SNPs). $x_{ij}$ is the number of copies of the minor allele for the $j$-th individual in SNP $i$. $p_i$ is the frequency of the minor allele for SNP $i$.


texts: I have a dim recollection of having heard that when humans gain weight, adipose cells just get larger, rather than dividing.  True?


texts: Why is inhibition of inhibition (reciprocal inhibition) such a common motif in cell signalling?

texts: In transcriptional regulation, you often find that positive signals proceed by inhibiting or destroying a protein that is in turn inhibiting or destroying the effector protein. This can be seen in the retinoblastoma - E2F signalling pathway, and many others. I was wondering if there was any direct biological utility, and if so what this utility was.


texts: Does the use of UV light beam lead to poorer contrast in optical microscopy of cells than the higher wavelengths visible light?

texts:
I am reading about "diffraction-limited system" on Wikipedia, which mentioned

  "To increase the resolution, shorter wavelengths can be used, such as UV and X-ray microscopes. These techniques offer better resolution but are expensive, suffer from lack of contrast in biological samples and may damage the sample."

without giving a more detailed explanation for why the higher energy EM waves might lead to poor contrast. I have tried to search on Google, but still can't find a satisfying answer. Can anyone here kindly refer me to more detailed discussion on this question? Thank you.


texts: Is there are practical lower limit to gene length in E. coli?

texts:
Question is rather self-explanatory.

Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been transcribed in E. coli or other similar prokaryotic systems? Why couldn't this gene be any smaller?

Note that in the context of this question, I am disregarding factors like promoters, operators and terminators. Also note that this gene does not necessarily need to code for a protein.


texts: Lack of yolk in mammalian oocytes as compared to other vertebrates?

texts: Why do mammalian oocytes have little to no yolk? How does it compare to other vertebrates such as frogs, fish, and birds?


texts: Can we artificially produce a species that would be able to live on Antarctic ice sheet?

texts:
Can we artificially produce a multicellular species that would be able to live on Antarctic ice sheet?

By means of genetic engineering, selection etc.

UPDATE

There are organisms, called Watermelon snow or, scientifically Chlamydomonas nivalis, which do exactly that: populate snow. They are not multi-cellular, but eukaryotic (not bacterial), photosynthetic and form extensive colonies. They already populate both Arctica and Antarctica. They prefer snow to ice.


texts: Does all cancer cells come from a single clone of cells or are there evidences of polyclonal cancer cells too?


texts: Why do we sweat after drinking water and running?

texts:
Why do we sweat after running?
Also we sweat sometime after drinking lots of water. Why it is so?
Can someone please enlighten me in this regard?


texts: Potential immunization against airborn viruses

texts:
I have had an idea based on the principals of a virus and their properties and how they enter the cell by tricking it into believing it is a protein etc.

If we coated a copper particle (or another type of metal which should neutralize the atomic structure) and utilize the process they use to induct themself into our cells by mimicing the methods they connect by, would ejecting it in an aerosol steralize the earth from that specific airborn virus?

My ideology seems to fit that if we don't immunize the atmosphere against viruses that they will always naturally occur due to the Entropic nature of the universe. Does this fit into current medical science?


texts: Effect of high temperatures on plant stomata

texts:
My biology textbook states that stomatal closure occurs at high temperatures to avoid water loss. Another stackexchange thread I can find (What is the effect of temperature and carbon dioxide on the opening and closing of stomata?) agrees with this, however most actual studies on the subject I can find talk about stomatal opening occurring at higher temperatures, but say the effect if the plant is experiencing water stress.

Does anyone know why there is conflicting info on this, and which source is correct?


texts:
We know that the DNA copying mechanism that replicates DNA during cellular division is not 100% accurate and the resultant errors are the source of variation in the members of a population.

At the same time, we are also aware of the benefits of variation - how it is useful in ensuring the survival of a species over time and leading to evolution.

I would however like to know if 100% accurate DNA replication is possible (even if hypothetically) - because in my opinion, organisms can surely survive (atleast individually) without variation or evolution.

If it is so, is it possible that organisms with 100% accurate DNA replication did exist, but eventually their populations died out (due to natural selection) and we were left only with organisms that showed variation?

Putting in simpler terms, it is possible that evolution itself is the cause of variation that now causes further evolution?


texts:
In the common Calvin cycle diagram, it is commonly stated that "three cycles are combined to show the production of 1 molecule of G3P".
How does the G3P molecule escape from this cycle in one of these turns?
Is one carbon atom "released" from this cycle at each turn and the G3P forms in another reaction?
Or alternatively,
is the G3P released at the end of the three "turns"? If this is the case, then shouldn't this diagram represent only one "cycle" of the Calvin cycle?
[1]: https://i.stack.imgur.com/mzizw.jpg


texts: What makes us "tired" in the gym that forces us to rest?

texts:
If I'm doing push ups or any other of gym exercise, I can do 10 in a row, but each one I do I feel more "tired", but if I rest for 5 minutes, I'm much "full of energy". Please explain me exactly what is different in my muscles chemistry.

I read that lactic acid overproduction is possibly linked.


texts: The fundamental importance of R.E.M. Sleep. (Rapid Eye Movement)

texts:
Question:
I know that experiments have been conducted to determine the importance of R.E.M. sleep in our sleep cycle. It is particularly important for learning, information synthesis, and recovery from distress. Why else is R.E.M. sleep important? What experiments have been done/observations been made to determine the neurological mechanisms underlying R.E.M. sleep? I know that we exhibit high frequency $\alpha$ waves, similar to the waves we experience during wakefulness.
Wiki:
During REM sleep, high levels of acetylcholine in the hippocampus suppress feedback from hippocampus to the neocortex, and lower levels of acetylcholine and norepinephrine in the neocortex encourage the spread of associational activity within neocortical areas without control from the hippocampus. This is in contrast to waking consciousness, where higher levels of norepinephrine and acetylcholine inhibit recurrent connections in the neocortex. REM sleep through this process adds creativity by allowing "neocortical structures to reorganise associative hierarchies, in which information from the hippocampus would be reinterpreted in relation to previous semantic representations or nodes.
Do these reorganized neocortical hierarchies remain this way?
Just HOW integral is R.E.M. sleep to our brain development?


texts: What is the reason behind the subphylum name "Urochordata" for tunicates?

texts:
There are two major invertebrate subphyla of the chordates (phylum Chordata):

Cephalochordata (the lancelets)
Urochordata, aka Tunicata (the tunicates)

My understanding is that the cephalochordates are named as such (meaning “head chords”) because the notochord reaches into the head. From Wiktionary:

  Any of the primitive fishlike creatures, of the subphylum Cephalochordata, including the lancelets, that lack a true spine but have a notochord which, in the case of cephalochordates, reaches into the head, contrary to the Urochordata.

Urochordata, by contrast, means "tail chord", though I cannot find a reputable source (or any, really) that describes or details why this is the case.

I can surmise it's simply because the notochord doesn't reach the head of a tunicate embryo -- as is corroborated by an image from Lemaire 20111 copied below.

 Image D' shows notochord in red. Credit: Lemaire 2011

However, I would prefer a quotable, reputable source that indicates explicitly that the Urochordates are in fact named as such due to their notochord not reaching their head.

If this is not the case, then my question more broadly stands at: Why are the Urochordates named the way they are?

 1: Lemaire, P., 2011. Evolutionary crossroads in developmental biology: the tunicates. Development, 138(11), pp.2143-2152.


texts: same SNP rs# referenced to be found in two different genes

texts: Two GWAS papers have referenced the same SNP (rs7442295), but one states it's found in the gene GLUT9 and the other states it's found in SCL2A9. The ncbi dbSNP says it's in SCL2A9, and I thought that the rs number was unique to each SNP, so how can it be in two different genes? I'm really new to GWAS, so it might be a really stupid question, but any advice would be great!


texts:
I am not sure if this is the right place to ask this question, but I guess that ornithology enthusiasts (or ornithologists) will have the best knowledge about it.

I am wondering if there is a website which would identify birds by their looks. For example, I would specify that the bird is similar to a sparrow in size (just a little bigger), it has a gray back and yellow-ish-orange-ish belly and it would tell me the exact species.

Does such a website exist?


texts: How is a substance classified as a vitamin?

texts:
From wikipedia

  A vitamin is an organic compound and an essential nutrient that an organism requires in limited amounts.

There are many essential nutrients to an organism. Glucose for example. However, not all of them are classified as vitamins. Is there a clear, non-arbitrary definition of vitamin? If not, who decide what ought to be called a vitamin?


texts: Will the increase in atmospheric carbon dioxide lead to larger insects?

texts: From my understanding, the increase in atmospheric carbon dioxide will also increase oxygen levels. That makes me wonder if in the near future insects will grow larger than they are today, since their maximum size is limited by how deeply oxygen is able to diffuse into their body.


texts: How do you test soil for the nutrients present in it?

texts:
I recently noticed that my rose garden has been in a very terrible state. The roses keep dying. I tested the soil for its pH and that was fine.
Now I'm wondering how would I carry out a test to see what specific nutrients I should use to get my soil better.