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Any studies on the effects and/or benefits of oil pulling?
A friend recently recommended me a process called 'oil pulling' for my teeth as I am struggling with my dental health at the moment. The process involves using a tablespoon of some kind of vegetable oil (like coconut oil) and swilling it around in your mouth for 20 minutes without swallowing. This supposedly acts as an anti bacterial and pulls toxins out of the body and helps with dental hygiene.
Are there any studies demonstrating or refuting its validity? Any help would be much appreciated.

This is a classical pseudoscientific claim: It is supposed to help against everything, including AIDS, Diabetes, Bronchitis, Cancer and so on. See for example this table I found online:

First, there is no real mechanism, and it is rather implausible to have an universal cure-all drug for all these completely unrelated diseases. There seems to be some weak evidence for the dental hygiene claims, but as the first reference writes, study groups where too small, not effectively blinded, so there is no final clue if this is true:

Oil pulling’s positive effects are based entirely on anecdote and not
  at all on clinical research – because there’s been very little. Pubmed
  lists six clinical studies related to oil pulling, all performed in
  India, and their quality and results seem all over the map. Some do
  indicate mild improvement in gum health, comparable to mouthwash use.
  But they’re not well blinded, use very small sample sizes and involve
  oil pulling only as part of a proper oral hygiene regimen. So it’s
  impossible to tell what’s causing said improvement.

What clearly does not happen is the detoxification, as this is a pseudoscientific myth itself. Our detoxification is done pretty efficiently by liver and kidney, so there is no need to remove whatever toxin by a treatment.
See references 1-3 (especially 1) for background on the "oil pulling" and reference 4 for the detoxification.
References:

Oil Pulling: Miracle Treatment or Woo Mouthwash?
Oil Pulling Your Leg
Is Oil Pulling Effective for Curing Medical Ailments?
Fashionably toxic

In the scientific world, if there is an absence of good studies does this act as evidence against its validity? I would like to see a professional study done which forever refutes these kind of things so we know with surety that they are ineffective.That would put an end to 90% of alternative medicine.

@Charlie Believers never took care of facts. There are a lot of valid studies showing hemeopathy has no effect beyond placebo, still this idea is around. And you cannot proof the non-existance of a fact - so you can see if you find an effect or if your trials fail to show an effect. This is what happens to pseudomedicine over and over - but the believers still don'T care.

What do you think of the Wim Hof Method (if you've heard of it)? There have been some great studies on that so far and you wouldn't believe how that has quickly gained validity. I practice it myself and it is really powerful.

He gained quite some cold endurance - but the rest (active and willingfull control of the immune system) are pseudoscientific claims without any proof. You can read here about it. Controlling your breath and doing some sort of yoga is fine, but this will not make you immune to diseases.

Not true pal. He's worked with many reputable universities to prove his methods. I'll link them in. I can even explain how it work due to focused hyperventilation. Pseudoscience became science in Wim's case.

Have a read of this:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034215/

http://www.icemanwimhof.com/science

And to put it a biit more general: Every time I have seen a persons name followed by method or cure, this was not real. Another red flag should be the lacking of a specific and scientifically plausible mechanism as well as someone claiming to cure everything. This is not possible.

Wim Hof method doesn't claim to cure everything, however, it's being tested as a way of combating autoimmune disorders such as arthritis and Parkinson's Disease. Wim's body has also been proven to be producing an irregularly large quantity of opioids and cannabinoids.

You can have a look at this publication which looked specifically at the guy and his twin brother - one doing this breathing technique, the other not. Both have a comparable cold endurance - because they have a larger amount of brown fat tissue. Nothing too special here. Most of these "proofs" are either claims on fan (or his own) websites or a case study with only one participant. The other one has only 12 and 12. This is by far too low to draw valid conclucions from it.

Let us continue this discussion in chat.


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Why do bacteria eat enamel?
What causes tooth decay bacteria or acids?
I've been told that it is a combination of both but why would bacteria eat enamel?  There are much easier supplies of protein for bacteria to munch through (such as gums) and many of the elements within enamel are not needed for bacteria to respire. Is bacteria eating enamel a myth and if not why do they do it?

While I can't find any specific sources regarding bacteria eating enamel, I highly doubt this is what's happening in our mouths. I doubt this because your point is likely true - minerals in enamel provide no added benefit to the bacteria. I would ask a dentist about this to be sure though.
However, what is certainly true is that the acid produced by the bacteria in dental plaque is what causes tooth decay and gum disease. More specifically, S. mutans is the primary culprit behind dental plaque. Most notably is that S. mutans is an anaerobic organism and because it doesn't require oxygen to respirate, the pathway results in lactic acid as a by-product. This lactic acid is what makes enamel prone to demineralization and if untreated, can irritate your gums, causing gingivitis. It's also worth noting that not all bacteria will do this - not even all anaerobic bacteria that release lactic acid will do this. S. mutans is likely one of the few bacterial species that can survive in your mouth because of it's ability to withstand low pH environments in your mouth and form biofilms - able to nicely stick onto teeth.
S. mutans has no need to munch through enamel or gums. Much of what it breaks down for respiration can be easily obtained from the food and drinks that are left behind after a meal - mostly sugars such as sucrose.

Bacteria feed upon food particle left between n around the teeth and feed upon them. They also produce metabolic acid which corrodes tooth enamel.

Hi. Could you elaborate your entry and add references, like links to credible open sources? See help page for more information on how to write a good answer. I would also suggest to use standard English words to ensure readability. Here's a link to [edit].

The bacteria actually aren't eating the enamel, they eat the food attached to the enamel and excrete acids that wear down the enamel.
Over the decades there have been various experimental treatments for chronic tooth decay where S. mutans gets gene-edited for alcohol fermentation instead of lactic acid fermentation.

source: Stack Exchange

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sort: votes


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Why is the skin of European bog bodies brown?
What causes this? Is it to do with decay or is it to do with substances within the bog dying the skin?

The anaerobic decomposition of moss produces tannins in the peat.

The bog water interacts with the acids in the moss and produce tannin
  and other chemicals that preserve the bodies that fall or are cast
  into the bog; hence the numerous well-preserved bog bodies.
  http://www.digitalmedievalist.com/opinionated-celtic-faqs/bog-bodies/

The tannins tan the bodies just like tanning leather; the color of the bodies darken and the tanning action also preserves them.

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Does neural oscillation happen at the same frequency in all parts of the brain simultaneously?
Does neural oscillation happen at the same rate in all parts of the brain at a given time?
I'm trying to learn and understand about brainwaves, and I know about the various categories of brainwave. Therefore, my question is are all parts of the brain firing off at the same frequency at any given time or are some parts for example operating at a delta frequency and others operating at alpha frequency? Do different types of brainwave occur simultaneously or is always all of the brain operating at one frequency?

Neural oscillations occur on both a cellular level and on a macroscale level, the latter usually referred to as brain waves.
Looking at macroscale brain activity and particularly brain waves is often done via EEG, which has poor resolution and suffers from attenuation. EEG activation is really due to huge numbers of neurons. Hence, it represents a very coarse, averaged view of the current activity. So, even when the EEG shows nice smooth variation, the individual neurons are far from it! Of course, more recently, using other methods (e.g. fMRI) has become more common.

My question is are all parts of the brain firing off at the same frequency at any given time or are some parts for example operating at a delta frequency and others operating at alpha frequency? Do different types of brainwave occur simultaneously or is always all of the brain operating at one frequency?

No, as I said, most studies look at the cortical areas specifically. But even within the cortex, the brain activity is very complicated, and certainly not subscribing to any one frequency. (In fact, when this hyper-synchronization happens, it is called an epileptic seizure! e.g. see Garcia-Hernandez et al, Understanding synchronization and hyper-synchronization in the the septo-hippocampal system).
In any case, imagine brain activity being measured over time. We then look at the frequency components (e.g. via Fourier analysis). See e.g. Gross, Analytical methods and experimental approaches for electrophysiological studies of brain oscillations for details. Notice these methods usually give the "strength" of the activity across the frequency spectrum. When there are brain waves, we are merely saying that activity is concentrated in a specific frequency band. It is often smeared across the band, and activity usually exists throughout the spectrum.
It also depends on spatial resolution of the frequency analysis. Some studies look at, say, just the Hippocampus. So yes, it is quite possible for some of the brain to operate at one frequency, while others operate at another. Or one could average over the whole cortex. It depends on the study!
So pretty much in all cases, everything is more heterogeneous than you might think.
Some literature to read:

Breakspear, Dynamic Models of Large-Scale Brain Activity
Varela et al, The Brainweb: Phase Synchronization and Large-Scale Integration
Salinas et al, Correlated Neural Activity and the Flow of Neural Information

Top answer. Cheers :)

As the question mentioned "at any given time", I would like to add that activity in a certain frequency range for a specific region is not constant.


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If alcohol is a depressant, why does it makes certain people more hyperactive?
Alcohol is by traditional definition a depressant from what I have been taught, ergo it shows down CNS responses.
However, why does alcohol then make some people act out and be more energetic than when they don't drink?

These types of reactions in pharmacology in general are called paradoxical effects.
The main effect of alcohol on the CNS is the potentiation of GABA receptors. GABA receptors are (mostly) inhibitory receptors in the CNS, so potentiation of GABA receptors mostly decreases brain activity by increasing inhibition.
However, you can distinguish between neural inhibition and behavioral inhibition. Some brain regions, like the prefrontal cortex, seem to primarily have inhibitory effects on behavior. That is, usually prefrontal cortex is active when suppressing actions. If you were to suppress the prefrontal cortex, you would get the opposite effect on behavior. When there is "inhibition of inhibition" the term often used is "disinhibition."
It isn't yet clear why exactly alcohol leads to behavioral disinhibition at lower doses, but this is one possible mechanism. In general, U-shaped dose-response curves are quite common in neuroscience, so alcohol isn't all that unusual in that sense.

Most people experience some stimulating effects from alcohol in small doses. Drinking alcohol, often a person finds increased talkatively, feelings of energy, and desire for action. In small to moderate doses of alcohol, the initial effects of alcohol act like a stimulant. However, alcohol is actually in the depressant class of drug types. Alcohol, like sedatives and tranquilizers, actually slows down activity in the central nervous system. To be more specific, it slows down the activity in the GABA receptors of our brains. The slowing of these systems is responsible for the relaxing quality produced by alcohol. The slowing of the central nervous system is also responsible for the lowered reaction time and dissociation.
Look at this wikipedia article: https://en.wikipedia.org/wiki/Short-term_effects_of_alcohol_consumption

" slows down the activity in the GABA receptors of our brains" - ehhh... that statement is misleading at best, completely wrong at worst. Ethanol potentiates GABA-A receptors through multiple kinetic effects; the only thing you could describe it as 'slowing' possibly is the time to close, but that's not by an actual kinetic slowing.


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Can anyone id this flower
I took this photo on Madeira, in a botanical garden.

This is Kleinia, a genus from Asteraceae family. It is a succulent  native to  Africa.
I found a number of possible candidates, there may be more:

Kleinia abyssinica

Kleinia fulgens
Kleinia stapeliiformis
Kleinia pendula

P.S. There's not much free information from authoritative sources online about this genus. There are similarities in the blossoms' colour across  the Genus and also differences within a single species so to do a species level ID more information about the plant is needed.


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Effect on gene loss because of compartmentalisation of plastids/mitochondria/endosymbiont?
Considering the transfer of genes during endosymbiosis a gene transfer event (at least fundamentally, even if it's a special case), how does the fact that in this case the genes are inside a compartment, affect their gene loss, or incorporation into the host/recipient's genome (in context of gene transfer)?
I would imagine that the loss would be slower, recombination with other transferred genes less probable. But I can't find literature on the same. Any leads?

Could you clarify? What systems are you thinking of? Slower compared with what?

Slower compared to gene loss if the genes are in the nucleus.

Still don’t follow. Can you give some examples of the two?

I don't know if it's true or not. I am assuming that because of compartmentalisation there should be a significant difference in the rate of loss between the two compartments. But I may be very naive and maybe it's trivial that it's not true. What I am asking is for evidence or scientific literature on this topic (because i couldn't find much).

Here is an extreme example of rapid total loss of photosynthetic genes from a now parasitic organism. Compare that to the rate of loss (or lack of it) for photosynthetic genes in common photosynthetic plants. Now what I am thinking about is a comparison of this rate of loss in plastid genes, to that of genes incorporated into the nucleus. Think about a situation if those photosynthetic genes were incorporated into the nucleus somehow, directly, instead of being in a endosymbiotic compartment (giving rise to a plastid).

OK. I'm not helping. Perhaps it would be better for someone familiar with this sort of paratism to comment. My own observation is that gene loss is just loss. Gene transfer from organelle to nucleus would seem more complex, but the extent to which it has ocurred in different eukaryotes differs widely.

The parasite example was just to give an idea of how varied the rate of gene loss can be in general and to provide some context. But I need information on a more general perspective on gene loss. I'll even find it helpful if it's about pressures of natural selection acting differently (or not) on genes in nucleus vs other organelles, which would be something related to gene loss.
Thanks for the comments anyways.

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Hodgkin-Huxley Model and Propagation of Action Potential
I'm studying Hodgkin-Huxley model of action potential, and I have some confusion.
In the well-stated HH model, we have time constants for each ion currents, described as the reciprocal of the sum of forward rate and backward rate.
In the caple theory, there is another time constant that is defined as the multiple of cell resistance and cell capacitance.
Is there any relationship between the two time constants? Do we have to think the two processes, which means the 'generation' of action potential and the 'propagation' of it separately?
Thanks.

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GHK Equation and Action potential
Can GHK equation be used to predict the membrane potential even if the cell is not at resting state?
To say it again, can we use GHK equation at every moment during Action potential?
I'm confused because GHK equation is derived at the situation with total ionic current is zero, but is that true also during AP?

The GHK voltage equation also known as just "Goldman equation" is always valid for determining the voltage at which the net current is zero, given internal/external ion concentrations and their permeabilities. This includes times during the action potential, though the result you get from GHK will be changing faster than the actual membrane potential itself, since the change in membrane potential brings about changes in permeabilities.
It's still useful to think about this equation to determine in which direction the membrane potential is changing instantaneously: it will always be changing towards the equilibrium potential. You can also qualitatively estimate the relative rate of change: if the current voltage is very far away from the equilibrium potential, the voltage will change more rapidly than if it is close to equilibrium.
However, this equation is just a steady-state equation. It doesn't tell you how quickly you will get to the new voltage or exactly which ions will move. For this, you need some other equations and other parameters, namely the actual permeabilities (rather than relative permeabilities) of the ions and the membrane capacitance.
The GHK flux equation can help: this will give you the flux of each ion at a given membrane potential (Wikipedia shows how this equation is related algebraically to the Nernst equation, which in turn is equivalent to the Goldman/GHK voltage equation for a single ion). You can also think in terms of the Hodgkin-Huxley model and the simple differential equation for current.

In summary, with respect to your question:

Can GHK equation be used to predict the membrane potential even if the cell is not at resting state?

It can predict where the membrane potential is headed, but not what it actually is or how fast it's changing, and the voltage you get from GHK will itself change as membrane potential changes affect the parameters that go into the GHK equation itself.


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Is Thylakoid membrane continuous with the Inner membrane of Choloroplast?
This article mentions that thylakoid membrane is  continuous with the inner membrane of cholorplast

Thylakoid membrane encloses the innermost compartment or thylakoid
lumen. The inner membrane of chloroplast is sometimes continuous with
the thylakoid membrane. Thylakoid membrane is composed of
phospholipids and galactolipids. It is similar to the inner membrane
of chloroplast and also shares some characteristics with the
prokaryotic membranes such as cyanobacteria

but a answer on stack exchange on mentions that they are closed at the end

. Each , of these lamellae is composed of double membranes joined at
the ends & each membrane is 100-200 angstrom thick....

Accordind to me thylakoid membrane should be continuous with inner membrane because it has originated from the same membrane, but i am not sure about it??

key word, "sometimes" also what makes you think they originated from the same membrane, chloroplasts were likely one free living bacteria.


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Does Ethylene Triple response provide any advantage to the Arabidopsis thaliana Etiloated seedling,?
As ethylene has a triple response effect on  Arabidopsis thaliana Etiloated seedling-
1 Shortening and thickening of Hypocotyl
2 Exaggerated apical hook
3 Short root
According to this site

Ethylene mediates the triple response, which makes the shoots of
seedlings that are buried under debris grow short and wide as well as
bend horizontally. This makes it possible for the shoot to push
through the debris.

I am not able to comprehend how this response of apical hook ,shortening can possibly help plant escape that condition? Does this response has some real benefit to plant or just a side effect of no importance to the plant, Although it was very helpful to the scientist


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Universal mathematical statements in biology similar to Price Equation
I just read about Price Equation and I thoroughly enjoyed the concept, as well as the elegance of the mathematical formulation. I especially enjoyed the fact that (to quote Wikipedia) it is "a purely mathematical relationship between various statistical descriptors of population dynamics".
I had no idea of even the existence of such elegant mathematics in biology. I have always thought biological systems or phenomena to be dealing with exceptions all the time. This on the other hand is close to a physical law, even if it is not exactly a law and merely (a severe understatement IMO) a mathematical relationship.
What are other similar mathematical relationships in biology that you could suggest? I'm especially interested in physiology, immunology, or similar topics.

I'd recommend searching this site, there are a lot of very closely related questions with worthwhile answers. See e.g. https://biology.stackexchange.com/questions/113997/examples-of-differential-equations-in-biology/113999#113999. I'll repeat what I wrote there, which is to say that you should go read Maynard Smith's book on mathematical biology. Population genetics and evolutionary theory are rife with examples. See also neuroscience (Hodgkin-Huxley), kinetics (michaelis-menten), population biology (Lotka-Volterra), ....

The books A Primer of Population Biology (Wilson & Bossert) and The Theory of  Island Biogeography (MacArthur & Wilson) are two very accessible sources of mathematical biology in evolution and ecology. I feel like any reasonably complete physiology text book at least has primers on mathematical relationships describing function like oxygen affinity (hemoglobin/myoglobin), blood circulation, action potentials, enzyme kinetics, membrane transport, gas exchange, and many others.

Thanks for the comments. Would you say that Hodgkin-Huxley or Michelis-Menten are comparable to Price Equation since the Price equation doesn't seem to make any strong assumptions unlike the other two? I liked the Price equation precisely because it doesn't depend on biological details and doesn't make any assumptions (except that the system is made of replicating elements). HH or MM models are, well, models trying to approximate a certain biological phenomenon to varying details (and there seem to be variations of the models themselves).


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Does our brain emit any kind of waves?
I am currently trying to start a research project, and this is the most important question that needs to be answered. I cant't move ahead without knowing the chemistry of the brain.

brain waves [as per title] and chemistry [as per question body] are related but not identical. Tip: google 'brain waves' and see what pops up. The first hit is likely to be very useful. As of now this question is too broad and unclear. I would advise editing it to make it fit the conventions of this site.

Cells in the brain communicate with each other through electrical (and chemical) signals. The electrical signals from millions of neurons add up, and can be detected from outside the skull. This is called electroencephalography.
The signals that are strongest when measured in this way are often periodic or oscillatory (i.e. wave-like), because similar electrical signals from many neurons support each other if they are active synchronously. In contrast, when neurons are firing in a disordered way, then their electrical signals can partially cancel each other out when measured from outside the skull.


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Will a person with two copies of the same set of chromosomes be normal?
Would a (theoretical) woman (because she must have two X's), that both sets of
her chromosomes were 100% identical, be "normal"?
Would she be healthy, or would she have genetic problems as a result of that?
Would all her egg cells contain the same copy, identical to all others in her
body?
Thanks very much for any answers!

It sounds like this person would be close to what you get with "pure lines", aka inbred strains in laboratory animals:

A population of identical homozygotes constitutes a pure line. Pure lines "breed true"; that is, they maintain their phenotype indefinitely if genetic crosses are restricted to members of the pure line (see True Breeding).

You get those by inbreeding for enough generations that the individuals become genetically identical, or monozygous for every allele at least.
And on the effect of being a homozygote for all genes:

Inbreeding in allogamic organisms bring the deleterious recessive alleles to homozygosity; the immediate consequence is an increase in the frequency of defective offspring, or, in another words, an increase in the genetic load of the population. This phenomenon is called inbreeding depression or inbreeding degeneration. As inbreeding continues, the deleterious alleles are selected out and eventually disappear.  The original heterozygous populations are often more fit than the resulting pure lines because they profit from heterosis and balanced polymorphisms; the main advantage of pure lines is the quick production of many individuals with the same well-adapted genotype

It sounds like she would only have genetic problems if she had problem genes; bad alleles are more likely to be harmful if you're monozygotic for them because there are no other alleles to compensate, but if you only have the good alleles to begin with there's no harm. You would have problems in cases where having two different alleles is itself superior to having a single one of any; for things like immunity for example that can be the case. Or being heterozygous for the sickle-cell allele in malaria country, for another standard example.
I don't know if any of those things would be harmful enough that we'd call that woman "unhealthy" or "suffering from genetic problems" though. I think if it did, it would be more a statement about how the human genomes contains these specific alleles that you have to be heterozygous for than about the intrinsic harm of being the combination of two identical haploid genomes.
As for whether her egg cells would all be identical, they should be since homologous recombination should be switching identical bits of DNA with each other, but that's ignoring mutations. Which shouldn't be ignored, because every human has on the order of 100 mutations that weren't in their parents. Still, compared to how much DNA there is in the eggs overall it would also be reasonable to call them identical.

She would be completely healthy (if no disease causing alleles are present). This is because only one of her X chromosomes will be active. https://en.m.wikipedia.org/wiki/X-inactivation

Last question is redundant... If no other X chromosomes are present then only one version exist and can be passed on

@JeppeNielsen I understood the question to be about all chromosomes, not just the X chromosome (the woman and X chromosome thing being specified because obviously a man cannot have all pairs of chromosomes be 100% identical). And the last question being redundant is irrelevant, all that matters is that the OP asked it, and also it isn't redundant if you take mutations and errors in recombination into account.


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Suggestion about head transplant
The success of the head transplant surgery depends on the acceptance of the immune cells of the body on which the head is going to be inserted. Can stem cells from thymus gland and bone marrow of the head donor be transplanted into the body on which the head is going to joined, then those stem cells will produce lymphocytes which will accept the transplanted head. Can this be a way to increase the probability of success of the head transplant operation?

Transplanting bone marrow is already done as a therapy for leukemia and is a transplantation with the risk of rejection itself. It is painful, risky and complicated. A person undergoing this would likely for a long time not be healthy enough to undergo yet another transplant.

I think that immune rejection is not the only major problem in head transplantation.
We are quite skilled at suturing vasculature, but it's not fully solved yet how can you make new and proper connections in the spine?
Concerning your questions, if you just took these naive lymphocytes, they would probably get destroyed by the acceptor's immune system pretty soon. If this wasn't the case, the approach would already probably be in use for other transplantations too.
What you possibly could do is a bone marrow transplantation, where you would replace the bone marrow of the acceptor with that one of a donor. However this would cause the opposite problem, the donor cells attacking the acceptors body.
For now, lifetime immunosuppresion is the only working way to go.
To get a better idea about how exactly the mechanism of rejection works and the prospective future therapies, see for example: http://emedicine.medscape.com/article/432209-overview#a8

"What you possibly could do is a bone marrow transplantation, where you would replace the bone marrow of the acceptor with that one of a donor. However this would cause the opposite problem, the donor cells attacking the acceptors body" : What do you think of this https://biology.stackexchange.com/questions/79881/could-bone-marrow-transplants-be-used-to-prevent-tissue-rejection-of-trans-speci as a fix for that, introduce both patient & body donors cells to the pig fetus then transplant it's bone marrow?


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Hepatitis Lab diagnosis based on serology
HBcAg which can't be detected in serum can be detected in hepatocytes , why is it so that they become detectable in hepatocytes?

HBcAg is capsuled by HBsAg and therefore can't be detected, while within the cells it's still free (before assembly of the virus).
The test checks for presence of antibodies (IgM) against HBcAg. It does not try to detect HBsAg anyways.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC154683/


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Function of the spermaceti organ
What is the use of the spermaceti organ of the sperm whale?
One possible theory considered is that it was used for floating and going underwater by heating/cooling the oil. However, it is a lot easier for this to be done mechanically.
Another possibility is that it is comparable to a helmet to safeguard it when it collides with another whale. However, other animals have much simpler structures to deal with this problem.
A third possibility is that it uses it to stun its prey like squid. However, research in inconclusive on whether squids can hear or not. The link below, says that it is probable that squids can only hear upto 500 Hz which is not the frequency used by whales, thus this theory is probably false as well.
https://www.treehugger.com/natural-sciences/what-can-squid-hear-and-why-does-it-matter.html

It would be better to link(cite) your first and second hypotheses by peer-reviewed articles.

The principal function of spermaceti and the associated structures in a sperm whale head, is echolocation. The composition of spermaceti suggests that it functions as an acoustical transducer, helping to focus the powerful sound waves used for echolocation. These sound waves likely do not actually stun squids, but they do help sperm whales to find and pursue squids in deep, dark waters.
An echolocation click is formed at the tip of sperm whale's nose, where it is directed backwards, through the spermaceti, toward the sperm whales brain. It then is reflected off an air sac on the sperm whale skull, and redirected forward through a series of lenses before it moves into the water. Check out an illustration of this in the Møhl et al 2003 paper: https://pdfs.semanticscholar.org/88d4/271e9f7490c1173234a2445cf8ddf92fd51f.pdf
The complicated anatomy in a sperm whale's head seems to be directly evolved for echolocation.
Sources:
Karol, R., Litchfield, C., Caldwell, D.K. et al. Mar. Biol. (1978) 47: 115. https://doi.org/10.1007/BF00395632
Møhl, B., Wahlberg, M., Madsen, P. T., Heerfordt, A., & Lund, A. (2003). The monopulsed nature of sperm whale clicks. The Journal of the Acoustical Society of America, 114(2), 1143-1154.


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Why does yeast react the way it does to water combined with sugar?
I almost wanted to ask this in Cooking SE, but thought it would be better fit here.
So I understand than when you mix yeast with sugar and warm water, you get CO2. When using baking powder, it's a standard redox reaction, but what is it with yeast? Is the yeast still present after whatever reaction happens there? I don't think so, because that would mean that the reaction would go on forever. But what evolutionary sense is there for yeast to evaporate into CO2 when confronted with sugar and warm water?

When you take in sugar and use it, you give off CO2; similar deal as with yeast.  Yeast, however, are tiny and fit better in a dough or batter than you do.

Yeasts are living organisms, they do not evaporate. However it is true that in most fermented food we eat, yeast are no longer there. So why is it so?
It is not the reaction with sugar and warm water that makes them disappear. Most of the time they get killed later in the food making process. For instance, if you consider yeasts in bread, like french baguette for instance, after the dough raised, it goes to the oven where yeasts cells get heat killed.
For other processes, like brewering, yeasts used to stay in the final product. But then you had to drink it before it got spoiled by yeasts that were consuming all the sugar. So nowadays, industrially produced beers are filtered or pasteurized, or both, in order to get rid of the yeasts. Only artisanal beers are still "alive", with living yeasts in it.

EDIT:
As for the question "why/how do yeasts react with sugar?", sugar is actually fuel for yeasts. Yeasts oxidize sugar into CO2 in order to gain energy for their metabolism.

A good start, but it doesn't really answer the question --- where does the CO2 come from? You might add that CO2 is derives from the sugar, and is a byproduct of cellular respiration to obtain energy.

@Roland thanks for the feedback. I edited my post and added a brief explanation


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Can a human being live without any carbohydrates?
Nowadays low-carb is in fashion, but what I recently wondered is whether a human can live without any carbohydrates at all?
Of course this would be hard to do in reality, as most food will contain proteins as well as carbohydrates, but let's assume it would be possible to circumvent any carbohydrates.

No, humans cannot live without carbohydrates. Low-carb diets seem to work well in some people for short-term weight loss, but they can be rather damaging long-term. While a diet consisting of meat and meat may sound good to some people, you would not be very healthy for very long on it.

see this previous question and answer... amino acids are all ketogenic or glucogenic and can be broken down into all Krebs Cycle intermediates... http://biology.stackexchange.com/a/41255/16299

Have a look at: https://en.wikipedia.org/wiki/No-carbohydrate_diet It should answer most of your question and give you some good references.

The Atkins diet is based on that. Without carb intake, however, the citric acid cycle (CAC) eventually basically stops and proteins will be utilized to be converted to carb intermediates to feed the CAC. Progressive and strict use of the Atkins diet will eventually kill you as the CAC is essential to life.
The idea behind Atkins is that fats will be used to feed the CAC, and that will happen until the carbohydrates that keep the cycle running are depleted. At that point one will develop ketosis and the CAC stops, and with it the production of ATP. Note that fatty acids can be fed into the CAC, but are not sufficient to keep it running; fats burn on a fire of carbs.


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Why does hair know when it needs to stop to grow
I'm still not quite sure if head hair grows endlessly, or if it stops at some point, but that's not the question.
When the hair on my leg grows, it obviously doesn't grow endlessly, but it also stops at some point. I learnt that hair is dead matter, so why does the body know that my hair reached maximum length, and realizes I cut it when I did?

That's an awesome question! Let me help you rephrase, as I don't have a direct answer; why does hair stop growing at certain lengths, and differentially at various locations on the body?
There are three stages to hair growth:

Anagen phase- growth
Catagen phase- transition
Telogen phase- rest
(then falls out!)

You're asking why and how the anagen phase stops, or more concisely, what processes cause anagen phase to cease and proceed to transition to a degenerated rest.
The indirect answer I have for you is this: there doesn't exist a definitive mechanism for how the the telogen phase is induced- that is to say that the process by which the hair-producing follicle "turns off" it's cycle to come to a halt has not yet been fully elucidated in the literature and remains a discovery to be made.
I hope I've helped you understand your targeted question


text:
What can saliva tell about ones health?
I was wondering if I d want to analyze something related to my current health based on my saliva. What could it be?
I mean e.g. by putting a thermometer in your mouth you can know your body temperature and know whether your immune system is eventually fighting some disease. But as you already have that apparatus in your mouth I think it would be usefull to prelevate some saliva (hit two birds withone stone) or other stuff in order to eventually easily investigate ones health.

If there was broadly relevant information about one's health available by sampling saliva, tests would already have been developed. There are some specific assays that can be performed by analyzing saliva, such as looking for the presence of certain pathogens and proteins, but you won't be able to get anywhere near the broad-spectrum indicator of health (or disease) as you would be able to from a carefully-chosen panel of blood tests.

@MattDMo: Sex hormones analysis, for hormonal disorders specific to females and males by saliva tests. Correct?

there do exist tests for that, yes. And I mentioned that some clinical salivary tests exist in my above comment, but the point remains that the broad range of assays available for blood isn't even distantly approached by how many and what kind are available for saliva.

Well, saliva (or the rate of production of saliva in your mouth) can tell you a lot about health, but the information you acquire is extremely general, so it won't really give you an entire health analysis in terms of diseases, sugar levels, body temperature, likewise.
As for what saliva does tell about your health, here is an extract from a source:

"Dr. Stuart Froum, president of the American Academy of Periodontists, says: “If the eye is the window to the soul, the mouth is the window to the body.” Saliva in the mouth is one of the best indicators of health. If something is off, there is a good chance your saliva will change as a direct reflection.
Saliva is produced around the clock and is affected not only by every bite of food you take, but also every other thing you put in your mouth. If you notice your saliva is too stringy or thick, your body might be having a hard time producing saliva. This could be because of the prescription and over-the-counter medication you are taking.
Studies indicate that an imbalance of the ‘stress hormone’ cortisol in saliva points to emotional sensitivity to stressful situations...the measurement of cortisol in saliva is becoming increasingly acceptable as a screening test for hypercortisolism, such as depression, hypertension and diabetes.

Source: http://healthtoday.com/5-things-your-saliva-can-tell-you-about-your-health/
http://www.medicaldaily.com


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How to calculate apparent diffusion coefficient (ADC) with example?
Can someone give an example calculation for the apparent diffusion coefficient (ADC)?
There appears to be multiple ways that this can be calculated, e.g. as discussed here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166577/

Do you like R ? if so, look at this package "dcemriS4"  and its example http://www.inside-r.org/packages/cran/dcemriS4/docs/adc.lm
install.packages("dcemriS4")
install.packages("minpack.lm")
library(dcemriS4)
library(dcemriS4)

S0 <- 10
b <- c(0, 50, 400, 800)  # units?
D <- 0.7e-3              # mm^2 / sec (normal white matter)

## Signal intensities based on the (simplified) Bloch-Torry equation
dwi <- function(S0, b, D) {
  S0 * exp(-b*D)
}

set.seed(1234) # this is just to make the example reproducible
signal <- array(dwi(S0, b, D) + rnorm(length(b), sd=0.15),
                c(rep(1,3), length(b)))
ADC <- ADC.fast(signal, b, array(TRUE, rep(1,3)))
unlist(ADC) # text output
par(mfrow=c(1,1)) # graphical output
plot(b, signal, xlab="b-value", ylab="Signal intensity")
lines(seq(0,800,10), dwi(S0, seq(0,800,10), D), lwd=2, col=1)
lines(seq(0,800,10), dwi(ADC$S0, seq(0,800,10), ADC$D), lwd=2, col=2)
legend("topright", c("True","Estimated"), lwd=2, col=1:2)

Here you can see an example of the steps used for mir http://rsl.stanford.edu/moseley/tensorcalc/tensorcalc/Steps/ADCmaps/adc.html
here is to understand the math behind of its calculation
http://www.ajronline.org/doi/full/10.2214/AJR.12.9231
if you don't like R but you like Matlab, here you can use this code to calculate it in Matlab http://www.mathworks.com/matlabcentral/fileexchange/21130-dti-and-fiber-tracking/content/DTI.m one of the output is ADC for mir data

I think you should explain the principle behind the calculation rather than posting a code. The code is of little value in this site and if the OP is actually interested in coding then this is not the site for such questions. I guess that is not the case here.


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Does hormone participate in metabolic activites?
strong text
My take on question-

All hormone are not water soluble, some are fat soluble also so this option is definiely wrong.

Thyroxine Hormone is do stored in the body in Follicle of thyroid gland, All is not mentioned so we can say this option is not wrong.

Hormones are destroyed after use, and that's a fact, so this option is also correct.

Now here comes the tough part

Hormone do not participate in the metabolic activities, well signaling is not participating as far as I think, Hormones do not act as A Substrate or as A enzyme, so this option seems correct to me, but I am not sure, Does Signalling means Participating??

The molecules of most of the hormones are small. I don't know what to make of it, well if compare simple one molecule Hormones like Epinephrine and Melatonin to Peptide hormone, Peptide hormone seems large,this options is so Ambiguous I need help in this

Ah, good old bad exam questions. Invoking subjective, arbitrary and ambiguous adjectives and verbs. My very rough and blunt appraisal would be that many hormones are indeed widely and relatively small -ish. They are often 're-usable' after binding since their binding to receptors is often reversible. Some endocrine cells store hormones, while other hormones are entirely in flux. Some hormones are soluble, others aren't, yet others are not but are emulsified by things like micelles (e.g. casein). Some hormones certainly participate in metabolism; think insulin's role in glucose metabolism.
First, let's just acknowledge the lax definition of hormone before we go into each one-by-one.

Most hormones are small molecules

Generally correct. I think most biologists would be okay with saying this is generally true. They are necessarily small in many cases because they function in long-range endocrine or paracrine signaling and must satisfy preconditions for such functions. Consequently, it's easier to make a long list with small molecular weight hormones than it is to make a list of large molecular weight hormones.

Hormones are destroyed after use

Generally incorrect. That depends what destroyed and use mean. If by use one means binding to a receptor to transduce a cascade, then a single hormone molecule typically can be re-bound to the same receptor on one cell, and/or can be received by different cells. Some hormones are 'destroyed' by endocytosis and subsequent lysis within the endomembrane system, others have to be inactivated by proteases or filtered from bodily fluids by, say, kidneys.

Hormones are stored in the body

Some are, others are not. Steroid hormones, being lipophilic, cannot be stored in vesicles, and so are synthesized in mitochondria and smooth endoplasmic reticulum as precursors. I would be cautious to claim that precursors are hormones, so let's say with confidence that these cannot be stored. However, many other hormones that are usually not lipophilic, such as amino-acid based hormones, are typically stored in secretory granules. See here or here.

All hormones are soluble in water

False. Counterexample: steroid hormones are insoluble in water, which is why they are carried by transport proteins in the aqueous medium of the blood.

Hormones do not participate in metabolic activities

False. Counterexample: insulin.

Hormones do not participate in metabolic activities
False. Counterexample: insulin     , Isnt the participation means, being the substrate or enzyme, Insulin does signal transduction by kinases , which ultimately leads to GLUT 4 to insert in cell membrane, this is isn't metabolism , anbolic or catabolic, as the signal transduction only lead to influx of glucose, not in metabolism of glucose, in short i am not able to digest that signal transduction is also a paraticpitation in metabolism, it is facilitating metabolism

You are right that insulin does not directly participate in chemical pathways. It is a central player in the metabolism of glucose. It directly influences the availability of glucose for glycolysis! ATP is catabolically consumed to begin glycolysis. How about the case of adrenaline? Does adrenaline not increase the availability of oxygen? This is semantic confusion that the question leaves open to interpretation, hence the preface. But certainly one can reason that metabolism, defined as the total set of life-sustaining chemical reactions in organisms, excludes insulin as a participant!


text:
What is role of centriole in the formation of microtubule during cell divison?
I was learning about the centriole from different sources , and a common misconception I had was that centriole forms spindle fibres but the reality is very different.

Gamma Tubulin protein found in pericentriolar material serves as a
anchor for formation of Microtubule,

So my question is
What is the function of centrioles( two barrel shaped structure perpendicular to each other) in the formation of microtubule? Is it gives support to the pericentriolar material thoughts its appendages? As we can see it is not involved in microtubule formation
photo

What is the function of centrioles( two barrel-shaped structure perpendicular to each other) in the formation of microtubules?
Let's clear your basics first, Centrioles have no function in the formation of microtubules. Why ??
Because, Structurally, centrioles are made up of microtubules.
Even this paper states

At the core of most centrioles is a microtubule scaffold formed from a radial array of nine triplet microtubules.
The triplet microtubules define the cylindrical barrel of centrioles and basal bodies. The triplets are at a small angle off the
circumference giving the centrioles the look of a turbine.

Eukaryotic centrioles consist of 9 triplet microtubules arranged in a particular spatial arrangement. Each microtubule has 3 tubules ie., A-, B- & C-tubules. That's even visible in the image you provided in the question.

Each tubule is a protofilament ie, a chain of 13-16 tubulin subunits. Each subunit is a heterodimer of α-tubulin and β-tubulin molecules. The overall tubulin structure can differ from species to species based on the tubulin genes they encode for. Many species also have γ-, δ-, and ε-tubulin encoding genes.
The same tubulin proteins are also found in structures of cilia, flagella, and basal bodies.

REFERENCES

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113101/pdf/rstb20130457.pdf
https://www.ncbi.nlm.nih.gov/books/NBK21580/
Molecular Cell Biology (Lodish et.al), Eighth Edition

So centriole is just a scaffold of centrosome nothing more???

Apart from centriole, centrosome also contains pericentrin, ninein and gamma tubulin molecules as pericentriolar material. So I won't say, centriole is just a scaffold of centrosome.


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T-vector creation
I'm working on TA cloning for the first time and I need to turn some existing plasmid backbones into T-vectors. I'm using a Klenow fragment (3' -> 5' exo-) to dA-tail my inserts. Is there any reason why I couldn't use this Klenow fragment to dT-tail my vectors with a similar reaction set up? Thanks in advance for any insight!

Personally I would use Taq DNA polymerase to A overhang my inserts, especially if you are PCR amplifying the insert. It leaves an A overhang on the end of all amplicons natively. All you have to do here is add some Taq at the end of the reaction and incubate for 15 min at 72 $^\circ$C, it'll work in pretty much any PCR buffer and many restriction enzyme buffers too.
Generally it is the vectors that have a T overhang, but this is a legacy of when Taq was pretty much the only polymerase around, so there is no reason you can't have an insert with a T and the vector with the A.
As a general note, often these days it is easier (and cheaper (when you factor in the cost of your time etc) + quicker) to buy a suitable TA cloning vector pre-made, they are highly reliable and should work every time, which is not necessarily something you can say about home-made ones.
Another option, if it fits your workflow, is to add restriction sites to your primers and amplify the insert by PCR. You can then digest the amplified insert and vector with the restriction enzyme of choice and get directional cloning (where your insert always goes in in the same orientation, particularly useful for protein expression). This also allows you to do things like insert short tags (e.g. FLAG, HA, V5), make frame adjustments and even modify the ends of the sequence.


text:
Which method of gene amplification for toehold switches?
My team and I are from a high school and are planning to carry out some research investigating some toehold switch riboregulators which we have designed in silico. However, we have little experience in wet lab work. We plan to order 3 genes containing an arabinose inducible promoter, a riboswitch, a leuciferase CDS and a terminator. These genes are each ~3kb in length.
We plan to order our genes from IDT, but we're not quite sure which strategy to deploy to amplify these genes before adding them to a cell free extract for characterisation.
The four methods we have narrowed it down to are as follows:

Order the genes in plasmids, linearise, PCR,  ligate, add to cell
free extract for characterisation.
Order genes in plasmids, transform straight into E. coli, culture, mini prep, add to cell free extract for characterisation.
Order genes in plasmids, linearise, PCR, ligate, transform into E. coli, culture, mini prep, add to cell free extract for characterisation.
Order genes as gBlocks (not in plasmids), amplify with PCR, ligate into plasmid backbone, transform, culture, mini prep, add to cell free extract for characterisation.

We'd ideally like to use the method which is most simple as we will not have a lot of time in the lab, and we don't have much experience.
Any advice on choosing between these strategies would be much appreciated!

The strategies you're thinking about seem fairly general, rather than specific to toehold switches. Can you clarify if there is something in particular that you're concerned about regarding toehold switches, or is this a more general question about assembly strategies?

@jakebeal There isn't anything really which toehold switches will affect. So this is more of a general question about assembly strategies, yes.

Welcome to the Biology Stackexchange! Are all three plasmids going to have the same Promoter, CDS and terminator, but a different riboswitch?

Option 2 is your simplest and easiest. It should give you unlimited plasmid to work from. Note that ordering pre-made sequences of this size isn't particularly cheap and might take a few weeks to get to your destination.
It may be easier (quicker + cheaper) to find a plasmid with the luciferase CDS and terminator already built in. You could then amplify this with primers incorporating your promoter and riboswitch sequences and some restriction enzyme sites to generate a product that looks like this:
RE1-ara-riboswitch-luciferase-RE2
You can then clone this into a(nother) plasmid cut with RE1 and RE2.
Another option is that if you have a plasmid with a luciferase gene in it already and a multiple cloning site (MCS) you can order complementary primers (note single-stranded DNA, anything less than about 150 bases is fine) containing the araC and riboswitch sequences flanked by two restriction sites, you then anneal the two primers, digest off the ends and ligate. You just have to be careful with making sure that everything is in-frame. I don't know anything about riboswitches though so frame may not matter so much.
As you have limited time I suggest buying chemically competent cells for heat-shock transformation (if you don't have some already); make sure you don't get electro-competent ones, as these will only work with an electroporator.  Also get a commercial mini-prep kit (e.g. Qiagen plasmid mini-prep). These are easy to use and reliable.
I think in option 1 you have something a bit odd going on - why would you digest your plasmid then re-ligate it, when it is already in the form that you are going to use?
I am not quite sure why in options 3 and 4 that you think that these are any different in terms of the end result to option 2.

I basically agree with Bob, but wanted to add a few more details.
Out of the options that you have available, option 4 is the most common way to do it. I wouldn't consider options 1 and 3. I don't think option 1 will really work to produce the amount of plasmid that you need, option 2 is a much easier way of amplifying it. As for option 3, you shouldn't need to amplify the plasmid before transforming it, on the IDT website they say:

All of our synthetic gene products are provided in an optimized
cloning vector that is ready to be transformed into E. coli.

Between options 2 and 4, it comes down to time and cost. Unless you have a deal for free synthesis from IDT, the cost of option 2 is going to be around £1100 vs £330 for the gBLOCK (although another consideration here is that the maximum gBlock length listed on the website is 3kb). In terms of timing, the website says it will take 5-8 business days before shipping a gBlock vs 25 business days for the plasmid. Someone who is an experienced cloner would definitely be able to clone the gBlock into a vector faster than that (might take as little as 1-2 days), but if you're first-timers you might find that it takes you months to get it to work (the first time I cloned it took me a long time).
Another factor for both options 2 and 4, depending on how you do it, is that if you're using different toehold switches then you'll either have to order 3 plasmids/gBlocks with essentially all the same stuff apart from the toehold switch, or replace the toehold switch using something like an inverse PCR.
Assuming you are an iGEM team, another option, although maybe not the best if you have free DNA synthesis from IDT, is that the iGEM distribution kit  will be distributed around the end of June. This kit should contain samples of the luciferase CDS which you can amplify using PCR with primers to assemble into a vector of your choice. I would only recommend this method if you're limited on synthesis capability/are having issues with amplifying your gBlocks. You also wouldn't have the promoter/terminator/toehold switch, so you'd need to include them.
To summarise:

The best way (if you have the funds) is option 2
A slightly cheaper way is to order the full plasmid for one toehold switch and then use PCR to replace the toehold switch for the two others
The 'normal' way that I in my experience is the way most people do it is option 4, this is also the quickest if you know what you're doing
The cheapest way to do it is using the iGEM distribution kit

In my experience none of the options are the most common, though 2 would be the closest. Generally most people I know would do just what I describe in my second paragraph - it's quick, cheap and easy. Should be able to get the primers for this for <$100.

That's interesting. Although everyone always talks about "getting rid of cloning", I haven't encountered a situation yet where an academic lab has used option 2, for the reasons that I outlined above. Any time I have done cloning it has been by amplifying a gBlock and either using Gibson assembly or restriction digestion to insert it into a vector of choice (option 4). Perhaps it varies from field to field.
I agree that already having the gene in a plasmid and amplifying it out is the easiest way, but as OP mentions they're at a high school they're unlikely to have it lying around.

My whole academic career (~20 y) I've been amplifying sequences from various genes and then inserting them into plasmids for gene/protein expression. Usually by including restriction sites on the primers. gBlocks etc are relatively recent, and still much much more expensive than a pair of primers, a couple of common REs and a PCR. Synthetic DNA of lengths over about 200 bp have only really become cheap enough to be feasible in the past 7-10 years. Smaller genes are cheaper in plasmids - I can easily get $0.19 per bp gene in plasmid for genes <8 kb = ~$600 (425 GBP) for 3 kb.


text:
How long will traces of mRNA vaccines stay in the cell?
Suppose a valid administration of an mRNA vaccine (e.g. Pfizer / Moderna), lipid nanoparticles with the mRNA instructions enter the cell, the lipid particles will merge with the endosome and the mRNA will release to the cytoplasm (do not enter the nucleus) before finding a ribosome.
How long will any of this stay in the cell? Is it a once off and after the production of the spike protein the mRNA evaporates from the cell? and what about the lipid nanoparticles?

Although specific time is not yet clear, the coronavirus mRNA vaccine is expected to be degraded within hours after translation, according to Rebecca Dutch, Ph.D., a virologist at the University of Kentucky.

"It’s unclear how long this degradation takes. With regular mRNA, it’s within hours. The special coating involved with mRNA coronavirus vaccines may make this take a bit longer, but how much longer is uncertain."

After entry into the cell, the LNP coated mRNA is taken to endosome, where mRNA undergoes endosomal escape and enters the cytoplasm. Eventually, LNP will be trafficked to and enzymatically degraded in lysosome, or secreted from the cell via exocytosis.
Resources

https://www.self.com/story/mrna-coronavirus-vaccine-questions

Pardi, N., Hogan, M., Porter, F. et al. mRNA vaccines — a new era in vaccinology. Nat Rev Drug Discov 17, 261–279 (2018). https://doi.org/10.1038/nrd.2017.243

Otegui, M. & Reyes, F. C. (2010) Endosomes in Plants. Nature Education 3(9):23


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Read neural activity only having access to the brain from the "outside"
Is it possible to read neural activity from the outside of the head and if you had an machine learning algorithm that could learn what the signals "mean" (for example moving the right arm)? Could that be achieved with having receptors at special places on the head? And what type of receptors that would need. I don't have any experience or knowledge with/from the brain. Sorry if this is a stupid question.

It's not a stupid question in my opinion.
However, it is perhaps naive. Brain function is very complex and how the different parts of the brain exactly relate to memory and function is still being worked out.
We can monitor neural activity outside the brain by a number of methods. The most common one you might have come across is an electroencephalogram (EEG). This measures physiological electrical activity at the surface of the brain (remember, the brain is a 3D structure), so this can't measure activity within the folds of the brain. It is generally done with electrodes placed outside the skull, so non-invasive and produces no harm, even if used long-term. It's closely related to the electrocardiogram, which measures electrical function of the heart. You will have seen an ECG on TV or in a movie - it is often portrayed as a regularly beeping device that goes emits a long sustained beep when someone dies.
A similar system, though invasive is electrocorticography (ECoG), which uses electrodes implanted inside the skull. It requires surgery to be performed so it is much more risky to do. Like the EEG this measures physiological function and can not be used to read purpose into the signals.  I believe this system can be used as an interface/controllers for prosthetics such as hands/fingers, but I don't know how advanced this is and what is involved in getting it to work. I don't think, however, that this is a true reading of function as such, rather that the user is trained to set off a signal for the ECoG to read.
There are much more complex and functional  methods of actually reading brain function and applying it to precise signals within the brain. All of these methods require the use of large equipment such as Positron Emission Tomography (PET) or Magnetic Resonance Imaging (the particular application here is called functional MRI or fMRI). These all require the patient to lie very still inside a large noisy piece of equipment to measure some aspect of the brain interpretable by equipment/software in question. These methods can be quite specific and do show the interior of the brain.
I don't know much about these methods other than general principles. However, fMRI measures blood flow to a particular area of the brain and requires the person being scanned to concentrate on the topic at hand while the scan is being performed. PET and the related technique Single-Photon Emission Computed Tomography (SPECT) often require the use of an injectable material that the scanner can pick up - this is usually (always?) a mildly radioactive one, often conjugated to a specific biological molecule (see here for a list of radioactives and localizations) so that it is trafficked in the body to a specific location.
In conclusion, people are still working on brain function and assigning particular things to particular locations, so we are still a fairly long way from having methods that can be used to natively control devices via brain function.


text:
Is the respiratory substrate oxidised?

Cellular Respiration is a biochemical process in which food materials present in cell are oxidised slowly in presence of enzymes with the release of ATP and small amount of Heat.

I am not able to relate this to the process of Fermentation(more specifically Lactic acid formation)

$$C_6H_{12}O_6 \rightarrow 2CH_3CHOHCOOH + 36kcal$$

The average oxidation number of C in $C_6H_{12}O_6$ is $0$ and the average oxidation number of C in $CH_3CHOHCOOH$ is $0$. So, C is not oxidised according to oxidation number concept. So, can we say that all types of cellular respiration involve oxidative breakdown of substrate?

In lactate fermentation, there is no net oxidation or reduction: free energy is obtained from the "splitting of glucose" (glycolysis). But of course, there is an oxidation  step (GAPdh that generates NADH) AND a reduction step (pyruvate reduction by LDH to 'regenerate' NAD(+)), where the 'carbon skeleton' that is oxidized in the GAPdh reaction is reduced in the LDH reaction (so do no net ox/red).


text:
How are monosaccharides and amino acids absorbed in jejunum?

Duodenum receives bile from liver and Pancreatic juice from pancreas. Intestinal glands secrete Intestinal juice which acts at the ileum. Most of the absorption of food materials takes place in the jejunum, except for iron(duodenum) Vit $B_{12}$ and bile salts(terminal ileum).

I am learnt in high school text books that the succus entericus(intestinal juice) helps convert disaccharides to monosaccharides, dipeptides to amino acids and emulsified fat into fatty acids and glycerol. Then that implies that carbohydrates(monosaccharides) and proteins(amino acids) cannot be absorbed in the jejunum since they are not yet in the absorbable state(due to absence of succus entericus in jejunum). Then why only absorption of Vit $B_{12}$ and bile salts take place in ileum and not end products of digestion? How can they be absorbed in jejunum?


text:
Is it possible to put 100 live black ants and 100 live fire ants in a glass jar without them fighting each other immediately?
Background:
There is a claim falsely attributed to David Attemborough:

If you collect 100 black ants and 100 fire ants and put them in a
glass jar nothing will happen. But if you take the jar, shake it
violently and leave it on the table, the ants will start killing each
other.

The origin of this urban legend is possible this part in the novel Cat's Cradle of Kurt Vonnegut:

"What he was doing was spooning different kinds of bugs into the jar
and making them fight. "The bug fight was so interesting that I
stopped crying right away--forgot all about the old man. I can't
remember what all Frank had fighting in the jar that day, but I can
remember other bug fights we staged later on: one stag beetle against
a hundred red ants, one centipede against three spiders, red ants
against black ants. They won't fight unless you keep shaking the jar.
And that's what Frank was doing, shaking, shaking, the jar."

Since this is only a novel, not a scientific paper, we cannot be sure if it is possible or not in the real life. Some people argue that ants can identify each other by means of pheromones and automatically start to fight if an "enemy" is identified. But they are also not biologists. Is this argument correct?
I'm also not a biologist so please forgive me for the poor quality of my question.

This seems like it would be a very simple hypothesis to test, regardless of whether you're a biologist. Gently combine separate containers of the two kinds of ants, see if they start fighting within a minute or so. Then, combine another two separate containers and immediately shake it vigorously, then monitor for commencement of fighting.

I've found an article in Scientific American that states that newborn ants of different species mixed together do not harm each other.


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Bug Identification - Is this a bed bug?
What kind of bug is this? Side of a penny for size. Found on basement floor in a bedroom. Pleaase tell me this isn't a bed bug

Does this answer your question? Insect identification - Is this a bedbug?

No not a bedbug. ID is impossible without a location in the world (e.g. nearest big city, state). Likely a weevil of some sort.


text:
Why are there error bars for zero concentration in some cell viability graphs, if they are assumed to be 100%?
Take these for example:

As far as I know, the formula for cell viability is % Viability = (Treatment OD - Blank OD) / (Control OD - Blank OD) where each OD is the average of three wells (technical replicates). Say I want to check the cytotoxic effects of increasing concentrations of a drug. The treatment wells in this case contain the drug, the vehicle, and cell medium for the rest of the volume. The controls in my experiment contain the corresponding amount of vehicle and cell medium but no drug. So to check 5 different concentrations of a drug, I have five controls containing the corresponding volume of the vehicle for each drug concentration, each of which is used to normalize the treatment groups (or alternatively, if I serially dilute the drug stock beforehand, one control group to normalize all treatment groups since all treatment groups will contain the same amount of vehicle). However, when I plot such an experimental design, I naturally get no bars for a zero concentration because the group does not exist. I may assume 100% for such a group for each trial and add them to the graph, but it would have 0 SD (and SE) since every value is 100%.
I tried to make a table for a design to make everything clearer:

Three plates with cells from different passages, so n = 3, each group is applied to three wells (technical replicates but their average is counted as one biological replicate). As you can see, you still get 100% from every trial for controls and their SD when plotted is still 0.
How then, do the researchers of these experiments get error bars for zero drug groups while at the same time normalizing their treatment groups to obtain a % cell viability? What sort of design do they use?

They're probably (incorrectly) assuming equal variance among groups. If you want to know what method they used read the methods section: what do they say? If they say nothing then they're not doing science.

In the shown data analysis your are taken average and standard deviation after normalizing. So evidently you will have mean = 100%,  std = 0.
You can take average and standard deviation in the raw data (1.87, 1.808, 1.787, mean = 1.821, std = 0.0352). Then you will have a non zero std in the control group. Then you can normalized by the control average (mean = 100%, std = 1.93%).

I doubt they're doing this, they're almost certainly normalizing before doing any statistical analysis. I think they probably don't understand the analysis they performed and are just reporting the output of their statistical software blindly.


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Are these cassettes suitable for expressing PETase mutant in E. coli?
I created two potential gene expression cassettes (constitutive and inducible) for expression of a mutant PETase gene on PeptiCloud using the version tree feature, which allows users to create multiple versions for a biological sequence and organize it in a single location. Could you please check if the cassettes (nodes 3 and 5 in screenshot) are suitable for expression in E. coli K12? The original paper and plasmid sequence are attached in the files section. My project can be found in this link: https://www.pepticloud.com/public-project/PETase


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How to specify a promoter in de novo gene synthesis service?
I am trying to use a de novo gene synthesis service (Genscript) and one part confuses me:
Where do I pick the choice of promoter? Or is the promoter choice automatic based on my plasmid choice?
e.g. Say I want a regulable promoter (say lac induced by IPTG) how do I specify it? https://www.genscript.com/account/gene_services_gene_synthesis.html
I was given to understand in a related question that with a commercial gene you essentially just "pick the promoter you want"? Or must I somehow manually edit the gene sequence I have to incorporate the promoter I want?
How to put a gene under the control of a regulable promoter?
I can definitely email Genscript in case it is not a part of their default interface but I just wanted to verify my understanding of the matter before I do so.
PS. I even checked out Fischer's GeneArt service & even that interface has nowhere for me to select a specific promoter. Makes me wonder if I am getting the workflow wrong?

Wouldn't their sales team be able to help out?

@James Sure. I will email them. I just wanted to confirm that my understanding of the workflow is right. i.e. That I ought to "pick a promoter" when ordering the plasmid rather than manually modify my gene sequence before I submit.

I'm not familiar with this service. I don't think it's a bad question to ask them if their site is unclear.

@James Thanks. I've emailed them. Are you familiar with any alternative gene synthesis services? Do you remember if they offer a option to select a promoter? In any case, thanks for confirming that my question isn't too silly or obvious to ask them!

If I am not mistaken, the promoter should be specified by the cloning plasmid.

Thanks @MarchHo. Do you mean that as soon as I indicate my choice of the pUC57 plasmid that automatically fixes my promoter? If so, what's the promoter for the pUC57 plasmid, any idea?

If you need to add a promoter in an unusual location, you can add it into the synthesized DNA sequence. But normally that's decided by the cloning plasmid. If you put in the right restriction sites you can put your synthesized DNA into any cloning plasmid you want.

@user137 Thanks. No, I don't think I need a promoter at an unusual location. All I need is a regulatable promoter. I was thinking of using the lac promoter & induction using IPTG but none of the gene synthesis sites I checked out seem to offer an option to let me indicate my promoter choice. That is what is confusing me.

@user137  Perhaps there is a default promoter for the pUC57 plasmid? But I am not sure which promoter that would be.

I would start with the pUC57 sequence. I would check with your manufacturer just in case their plasmid has a different sequence. If the promoter isn't one you like, plan to move your gene into a better plasmid.

@user137 Thanks that helped a lot. So the lacZ shows it is lac promoted & IPTG induction ought to work! http://www.genscript.com/gsfiles/techfiles/GenScript_pUC57-Simple_Plasmid_Map.pdf

Usually you should provide the entire sequence that you want to have (including promoter, polyA sites etc). They will clone this sequence in a plasmid and give it to you. They generally do not check for expression or any other function. That's your job. They just ensure that the sequence provided is correctly synthesized and cloned.

Just a comment about the PolyA sites, they are not the same as PolyA sequences. If you try to put 20 or more Adenosine in a row they will refuse to synthesize it. Our lab has made plasmids with "120", "240", or "360" adenosine PolyA tails built in, but these are our best estimates because producing these oligos is hard, and sequencing them is almost impossible.


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Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences
I want to compute the optimal alignment of two amino acid sequences as per the following definition from a patent:

"The percentage of identity between two peptidic or nucleotidic
  sequences is a function of the number of amino acids or nucleotide
  residues that are identical in the two sequences when an alignment of
  these two sequences has been generated. Identical residues are defined
  as residues that are the same in the two sequences in a given position
  of the alignment. The percentage of sequence identity, as used herein,
  is calculated from the optimal alignment by taking the number of
  residues identical between two sequences dividing it by the total
  number of residues in the shortest sequence and multiplying by 100.
  The optimal alignment is the alignment in which the percentage of
  identity is the highest possible. Gaps may be introduced into one or
  both sequences in one or more positions of the alignment to obtain the
  optimal alignment. These gaps are then taken into account as
  non-identical residues for the calculation of the percentage of
  sequence identity."

The Needleman and Wunsch implementation at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) mostly works but not exactly. Thanks to @David & @WYSIWIG from a related SE Thread that suggested this (Computing Percent Identity between DNA / Amino Acid Sequence)
I want to know if there is a way to fix the mismatch.
e.g. My test case is:
Seq1: ABDE
Seq2: AAAAAAAAAAABCDE

The NCBI implementation yields the following alignment which has only 3 identical residues:

But shouldn't an optimal alignment  with 4 identical residues be possible like so:
Seq1: ----------AB-DE
Seq2: AAAAAAAAAAABCDE

Thoughts? Any way to tweak the implementation to give the result I want? Alternatively any other algorithm that can be coerced into getting this alignment? BLAST or a variant?

Needleman-Wunsch does an end-to-end (global) alignment (BLAST uses Smith-Waterman). Needle from the EMBOSS toolkit performs Needleman-Wunsch alignment. It will report the highest scoring alignment. I am not sure which alignment it reports when there are two of them with equal scores (I don't think it is random).
I just tried your case: replaced B with W as the former does not denote any specific amino acid (it is ambiguous). It does give:
     1 ----------AW-DE      4
                 || ||
     1 AAAAAAAAAAAWCDE     15

Note that you can change this behaviour by altering the gap-open and gap-extend penalties. You can also change the end-gap penalties (gaps in the beginning or end of the alignment; not in the middle) in Needle.
In this case gap-open=10, gap-extend=0.5, end gap penalty=false and matrix=BLOSUM62
For performing a local alignment you can use Smith-Waterman. It just aligns the highest scoring region and does not do an end-to-end alignment. You can change gap-open and gap-extend penalties in Smith-Wateman and BLAST too, but these algorithms do not begin or end an alignment with a gap.
This is the output of Smith-Waterman with gap-open=1 and gap-extend=0.5 and BLOSUM62 as scoring matrix.
     1  AW-D  3
        || |
    11  AWCD 14

For more information see What is the difference between local and global sequence alignments?

Dang. What luck that I came across the wrong codes online at this link: http://www.fao.org/docrep/004/y2775e/y2775e0e.htm It says B denotes asparagine or aspartic acid. It is the top link at Google even. And the FAO seemed like an authoritative site. My bad!

@curious_cat Oh yes I didn't realize. Seems Needle accepts ambiguous codes like B and Z but many algorithms probably do not (though I am not too sure about this). Anyway, is your doubt clear?

Thanks. Yes, I think it is clear now. I am getting close to the patent optimal alignments by setting all penalties to zero. Maybe I will also provide a custom matrix now to make it a 1-0 alignment instead of the scoring function matrix that is natural propensity based like BLOSUM.

Your guess is made without knowing protein substitution probabilities.
Optimality of alignment in BLAST is a metrics of the scoring function. The scoring function depends on the word size (length of the seed that initiates an alignment), rewards and penalties for matches and mismatches - gap cost and substitution matrix. In general, BLAST uses BLOSUM and PAM-  these matrices are based on evolutionary data. More about scoring parameters you could read in the BLAST Help.
You could fine tune these parameters in "Algorithm parameters" in the very bottom of the analysis page. Knowing parameters you could decide does your wild guess alignment make sense or not.

That is a very bad test case.
The problem is that the sequences are too short and involve a long repetition. This means that the default gap penalties and the gap-length penalties are not applicable. They are designed to work with longer sequences, where the penalty of inserting a gap can be offset by an increase in matches. In any case you can get bad alignments at the ends of DNA sequences where the stretch of DNA that is aligned by introducing a gap is ‘off-screen’.
Even though the algorithm may be watertight, its implement in an alignment program makes certain assumptions where values for scores and penalties are involved. You have to know what these are and when they are applicable. There are even situations where you need to produce your own matrix to force alignment between pairs that you know from other information must align (active sites, regulatory motifs). This is quite valid because the program doesn't know about biology — you do.

An addition (on the same lines as providing your own matrix): PSI-BLAST does a calculation of a position specific scoring matrix using the homolog hits. With each iteration the hits are supposed to get better. This is a sort of machine learning; not really like putting your own matrix but it does take some biology into account.

As you say, this is a bit different. It's standard in MSA (multiple sequence alignment) — or at least Clustal does the same thing. But the key point is to think about the algorithm and the assumptions — difficult for a beginner obviously.


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a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis
Can the following oversimplified biochemical pathway for DNA synthesis serve as a model for evaluating the degree of the effect that the 3' to 5' exonuclease affinity for mismatched base pairs can have on the degree of the fidelity of dsDNA synthesis? Is this idea basically correct to model the relationship?

Thank you for your attention

What do you think, and where specifically are you stuck? Homework questions are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy. "Homework" is interpreted to mean any academic or other assignment, test preparation, or task given in relation to a class, educational setting, or self-learning.

@MattDMo — It doesn’t sound like homework to me, but neither does it sound like a question in terms of SE Biology. More like someone with a more numeric training starting out in Systems Biology and soliciting comment on his schema.

No, it is not a homework. I follow a course on DNA replication and had a lecture on the role of the 3' to 5' endonuclease domain of the DNA Polymerase. It was said that the activity of the endonuclease alone improves the error rate of dsDNA synthesis. I wondered if a biochemical model can demonstrate that or even quantify the effect of the endonuclease. So my question is thinking in terms of a pathway makes sense. I think of implementing a model in MATLAB to see if just by changing the exonuclease's affinity for the mismatches improves the fidelity of the synthesis. I appreciate any comment.

well I tried to implement this pathway in MATLAB and it seems to me that it makes some sense. Here are two versions of the reaction progress simulation, one with low and the other with high affinity of the 3' to 5' exonuclease domain for the mismatches. The violet curve of the simulation corresponds the amount of synthesized dsDNA and the green curve corresponds to the error-free amount of that dsDNA.
The next figure shows that with low affinity of the exonuclease for the mismatches, the error rate is high (12%).

The figure below shows that the dsDNA synthesis error rate decreased with the increase of the affinity of the exonuclease for the mismatches.

The MATLAB code of this simulation is provided
https://matlab.mathworks.com/users/mwa0000016879211/Published/x551/x551.html
Your comments and suggestions are most appreciated.
Thanks,


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nontechnical understanding of a mammalian expression system
I just started working as an intern in the pharmaceutical industry. My background is in economics and I have pretty much zero knowledge of biology/chemistry. I am trying to build a basic understanding of some of the products I work with to better understand their place in the market. One (the most important) such product is a mammalian protein expression system. My questions are the following:
As I understand it the "output" of such a system is a protein, the "input" is DNA and the system itself is a cell, is this correct?
In the context of producing pharmaceuticals, would this system be used primarily for R&D, manufacturing or both?
I have read that an expression system consists of host cell lines, vectors, media and know-how. Would it be possible to explain in layman's terms what each of these elements is, and how they fit together?
Thanks

If you are talking about a commercial product, it would help if you could give us the name on the label, and a link to it. If it is a the name of a system assembled in some laboratory, could you give us details. I ask this because, not being familiar with a commercial product of that name, all it indicates to me generically is a system where protein is the output and mammalian describes either the origin of the machinery that makes the protein or the protein itself.

The general principle of the expression system is simple: it is a biological machine that uses cell media as its input (i.e. a broth of simple nutrients, including the protein building blocks) to generate its output, a specific protein of interest, according to its "settings", if you will, which is the DNA plasmid that describe which protein will be made. The cogs of the machine are carefully engineered mammalian cells that both create protein from nutrient, and multiply themselves to increase production capacity.
In a perfect expression system, there would be no need to know the underlying biology of the system: just provide the specified broth with a correctly formatted DNA plasmid, let it simmer for a specified duration at a given temperature, and voila!
The value proposition of a commercial system for its users is being as close as possible to this perfect system, i.e. not having to "roll your own" from first principle (after all, the general processes underlying protein expression are covered in an undergrad biology education) which would entail a great deal of effort and expenses. In some way, this is similar to the business model of cloud providers like AWS: abstract the low-level sysadmin-type stuff to provide a reliable platform for applications.
This is useful in both an R&D context (you can iterate on the protein and specific process steps for your product, not on the expression system) and a production context (you have a reliable expression system, that conform to regulatory requirements, with vendor technical support).
However, even the vendors have not entirely abstracted the biology of protein expression, and the specific working of the system is part of the differentiating features of a specific commercial product versus other products in the same line, and competing solutions from other vendors. You have asked clarification on a few technical terms:

host cell lines: The carefully engineered mammalian cells, which have been tuned to product protein in great quantity, while maintaining quality (e.g. avoiding aggregates) and, typically, specific requirement on post-translational modifications necessary for the application the protein was designed for. It must be easily to culture in large batch. There cells are a blank slate in which the DNA plasmid will be inserted to start useful production. A vendor's expression system will feature a cell line that tries to fulfil these something conflicting requirements.
vectors: How to format the DNA plasmid (= protein recipe) and get it into the host cell line. For mamalian system this will typically be viruses that can infect the host cell line to deliver the plasmid. The reliability and ease of use of the vector system, as well as compliance with regulatory standards in a pharmaceutical environment is also a differencing feature of an expression system.
cell culture media: Specific cell line will have different "nutritional requirement", as such vendors will have specific "recipes" for the nutrient broth in which to grow the cells of the system. This is more or less directly dependant on cell line, so less of a differentiating factor per se.
know-how: Biological processes tend to be messy, so some troubleshooting is expected even in commercial systems. Documentation as well as expert technical support can be an important selling point.

Ultimately you will need to understand to some degree the biology underlying the particular
expression system to be able to compare it horizontally to competing solutions from other vendors,
and vertically to other methods of producing proteins (e.g. prokaryotic expression system, cell-free systems), and, if you are in a customer-facing position, to be able to answer some domain-specific question on the spot. Here is an overview, here is another from a different vendor. I would suggest asking more specific question after perusing these.

Vector is based on a plasmid which is covalently closed circular DNA that can naturally exist in the host cell.
The plasmid has its origin of replication and a promoter, both of which are recognized by the host cell.
In order to express your mammalian gene in the host cell (e.g. in E.Coli bacteria), you must insert the gene of the interest downstream of the bacterial promoter of your plasmid. The bacteria will express the gene, without caring that the expressed protein has nothing to do with its own functions.
You also must insert into your plasmid another selectable marker, which is also a gene that will allow the cell to survive in the selectable media (chosen by you). For example, you can have a penicillin resistance gene.
Now when your vector is ready, you can add them to your cell culture. The bacteria will engulf these vectors (almost most naturally) and will start expressing the genes present in the vector.
But you are not sure yet which bacteria engulfed your vectors and which not.
In order to select only the cells that succeeded in engulfing your vectors, you must plate your cells on a selectable media. In our example a media containing penicillin. The cells that did not succeed in engulfing the vectors will die. You will have only the cells containing the vectors, and therefore the cells expressing your mammalian protein.
Grow the cells. When the cells divide, the vectors (little plasmids), will divide with them. So you can establish a production. Lyse your cells after creating a large enough population and purify your mammalian protein through the biochemical purification steps.
Hope it helps.


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Can you eat more calories than the body can store?
I believe I have read that if the body takes in too many certain nutrients/vitamins, the body simply excretes them.
How does this behave with calories? If I have a daily consumption of exactly 2,000 calories, would the body gain more weight if I took 6,000 calories in one day or if I took 2,500 calories over 8 days?
I know that excess calories can be stored by the body, but is there a point where the body can't keep up and excrete the rest?

you will run into the issue of eating more than the body can digest first.

Even if you only eat chocolate or something similar? For example, I have a bar of chocolate here that has ~550 calories per 100 grams. There would be 4,000 extra calories 'only' 700 grams of chocolate. But I think that there are also things that have much more than that.

After googling I found out that Macadamia Nuts has 718 calories per 100 grams. Thats even more.

As @John already pointed out, efficiency of digestion can be assumed to decrease in case of extreme uptake of excessive calories. (diarrhea)
In terms of the excretory system: Proteins are generally strongly retained by the kidneys, while glucose famously could leave the body through urine (diabetes) but should be taken up by your cells under normal circumstances. Fats, as carried by transporter proteins, should not be excreeted either. So I don't think you would excrete many calories.
Also I remember some papers stating, that short-term excessive caloric uptake is correlated with down-regulation of glucose transporters to your brain, while prolonged uptake of excessive calories (more than around 3-7 days) leads to changes in the brain-barriers permeability properties. It was observed that this change in permeability has long-term fatalistic effects: It will cause hippocampal damage and in turn further cause high caloric intake as a behavioral change due to reduced internal cues that depend on the hippocampus.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381074/


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Has anyone yet figured out how sensory signals for eyes and ears are encoded by our organ into electrical signals?
The most obvious way to give sight to blind and hearing to deaf is to give them a replacement organ for these. In order to do that we would need to understand how our eyes and ears encode sensory information into electrical signals which then go into the brain. My question is, how close are to understand this mechanism at this time?

I don't understand your question -- My confusion is reflected in the responses to your post; Bryan Krause's quite excellent comment below delves into implant world, while some answers allude to normal physiology. I think this is because the post's body and title don't match -- they reflect the ambiguity in the question. In other words, like Bryan suggests -- current prosthetics don't treat hearing loss or blindness by reproducing normal physiological processes.

See what I want to know is, do we understand exactly how the vision is converted into electrical signals and how to interpret those signals? I am an electronic engineer myself and have studied a few communication protocols. My question arose during my contemplation of how we encode information in electronic systems.

Well, do we know it 'exactly'... no. But we do know a lot. But the visual system is large and complex. From physical stimulus to 'interpretation', as you say you wish to learn, is a lot to ask for. It spans the full range from sensation to perception to association - impossible to capture in a single answer. Dependent on your background knowledge, it may take a full uni course to even just understand the very basics I reckon.

I am only curious to know to what extent we can create an artificial eye that behaves like the real one at the present time

That answer to that Q is very simple - we can't :) Bryan has abstracted that below. I've worked with folks with retinal implants - while promising, it's not even close to normal vision.

I think the encoding is quite well understood, and in fact there are artifical cochleas available for deaf people: https://en.wikipedia.org/wiki/Cochlear_implant
For retina replacements, I think the hurdle is establishing the connections from any device to the nerve.  There are roughly 120 million rods and 6 million cones in the human eye. (Per Wikipedia: https://en.wikipedia.org/wiki/Photoreceptor_cell )  These connect to about 1.2 million optic nerves, so making the proper connections would seem to be a non-trivial matter.

Cochlear implants work by stimulating the nerves that normally innervate the hair cells. They give very low resolution - only about 20 total sites over the entire frequency spectrum. It would be just as much a hurdle to connect to the 30,000 auditory nerve fibers. However, there is enough redundancy in speech that the 30,000 -> 20 mapping is enough to resolve some speech from one talker (some other cues for direction and resolving multiple talkers are much more difficult). You can do the same thing in the retina, the problem is that you don't get much useful vision out of that low resolution.

See also: https://en.wikipedia.org/wiki/Visual_prosthesis

@Bryan Krause: I'd disagree that it's just as much of a hurdle. 20 into 30,000 nerves is rather easier than 20 into a million.  The problem is that hearing is linear, while sight is two dimensional, so for equivalent resolution you need to square the number of sensors/connections.

Even 20x20 pixels isn't much. It's less about 2D and more about temporal vs spatial resolution; it's a lot easier to put temporal information into one channel than it is for spatial. Paul Bach-y-Rita did make a tongue stimulation device for vision ( https://en.wikipedia.org/wiki/Brainport ) that gives about that 20x20 resolution. It's enough to help not bump into stuff but you aren't going to read. The rest of the information is conveyed with pre-processing rather than trying to render an actual image.

In general I would say a lot is known:
Seeing starts with the photo-receptors. See "signal transduction" section of the Wiki:
Signal transduction works though rhodopsin and subsequent closing and opening of ion channels.
Then the signal is transferred from the optic nerve to the brain.
Hearing works though hair cells and mechanotransduction.


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Auto-immune problems if immature B-cells released if bone marrow bone is fractured?
A fracture of a bone containing bone marrow with B-cells not yet taught to not recognize self-antigen, if the bone is fractured, can those cells get released and cause problems?

Most likely not, because immature cells require other signals from the marrow to survive, so "spilled" cells likely wouldn't last long.

Thanks good answer, sounds evolutionarilly probable.