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Why do people eat meat?
My main question is why do people eat meat?
Can we not survive without meat?
I recently became a vegetarian and I have not yet felt any impact on my health. Can any one explain this phenomenon from the perspective of nutrition?

You might note that the health problems caused by dietary deficiencies may take months, years, or even decades to show obvious symptoms.

The spiritual benefit of not eating meat outweighs the potential nutritional deficits. But there really is nothing special in meat that the body cannot make itself or obtain from non-animal sources. ["As to food, his breakfast was chiefly of honey..." --Porphyry (about Pythagoras)]

What do you mean by "spiritual benefits"?

There are many reasons for why people eat meat. Some of them are to be discussed here and some of them have nothing to do with biology.
Reasons that have nothing to do with biology
There are many reasons that are not to be discussed on Biology.SE. These include cultural reasons, the reasons related to taste and appreciation, farming and availability, price and economy and of course for reason related to political ecology (incl. water and energy consumption of meat production).
Reasons that has to do with biology / medicine
We can talk about nutritional value though. According to a number of websites (sorry nothing peer reviewed; monitor.co.uk; rd.com; sparkpeople.com), people not eating meat may suffer from lack of

protein
iron
zinc
calcium
vitamin D
vitamin B12
omega–3 fatty acids

It is not impossible to get all of these nutrients without meats. However, when becoming vegetarian, some people need to be careful and rethink their diet to ensure not to suffer from the lack of these nutrients.

Where do these six come from? Can you support this with a source?

I don't think calcium and vitamin D deficiency are common in vegetarians.

@Remi b - can you highlight the vegan product to get vitamin B12

@Lasantha You can just google it. Amandmilk, coconutmilk and soymilk contain a lot of vitamin B12.

Tribal peoples throughout the world have revered meat since the times of cave paintings, over 30,000 years ago and the oldest stone arrowheads are 66,000 years old.
Chimpanzees also eat meat. They can hunt like wolves and devour small prey. (see videos)
Meat is a highly useful or essential nutrient source to those who cannot source enough local protein for the level of activity.
The importance of meat depends on geographical factors. Eskimos live in snow and eat more than 90% meat. There are no plants there. Equatorial people like Indians have plentiful plant growth and can live fine as vegetarians on replenishing foods like lentils and greens.
Northern people have less choice of vegetables and fruits, whereas tropical fruits like melons grow year round, and northern plants grow slowly, whereas northern grazers can grow fast.
Energy budget in the north is limited by the sun, which is deficient to grow grains and oils. Fat is the highest energy source, and it is very easily sourced from livestock.

Just a minor quibble - India is tropical.

@Roni Saiba: Depends on what part of India you're looking at.  It's a big place, with lots of climate variation, especially when you take elevation into account  :-)

People eat meat for the same reasons they eat non-meat food. Taste, nutrition, availability etc. Nutrition comparison is a medical question.

Disclaimer: I am not an anthropologist, this attempt at an answer is only my crude 2 cents, I haven't looked for references to support this supposition.
Nowadays we can survive without meat, but this has not always been so. We know that early human groups were hunter-gatherers. Hunting is obviously much more difficult than gathering: it takes more energy because you have to run, it is more dangerous because you can be hurt in the process. Therefore, the primary reason why early humans hunted and ate meat must be because they had no choice; likely because they could not gather fruits and plants in enough amounts or variety to support a healthy diet. Later on, when they transitioned to agriculture they also naturally transitioned to raising domesticated animals for meat production because that's what their diet was already like.

WRT hunter-gatherers, I don't think it is really because they can't gather enough plant foods, it's that meat offers more food for less effort.  You don't have to run to hunt (unless you want to): you lie in ambush, set snares or pit traps, drive the mammoths over a cliff, &c.  Likewise with subsistence farming: once domesticated, animals like cows, pigs, chickens and such can turn things that really aren't edible by humans (like grass, acorns, small bugs...) into tasty food, with much less effort than is required by plowing, planting, & harvesting crops.


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Is it possible to make anaerobic media too reducing?
I've been struggling to grow an anaerobe (P. gingivalis), I take every precaution to keep the culture conditions free of oxygen, I was wondering if the conditions can be so reducing that they inhibit microbial growth of an obligate anaerobe.
To make the liquid media I do the following:

TSB supplemented with yeast extract
plus 0.5g/L L-cysteine HCl as a reducing agent
plus resazurin as a redox indicator
heat-sparge with nitrogen until the resazurin goes completely colourless
add hemin (5 mg/L) and vitamin K1 (1 mg/L) from stock solutions (1mL/L hemin in water, 200uL/L vit K1 in ethanol)
filter-inject this media into glass tubes which have had the gas in them removed (this takes place in an anaerobic hood)
all materials (syringes, needles, filters, tubes) had been left in the anaerobic hood before use so that no residual oxygen is left in/on them
swap the headspace for a gas mix of 80:10:10 N2:CO2:H2

I don't get any growth after over 72 hours @ 37oC.
Other protocols I have found are much more vague/lax about removing the oxygen, many just say that the cysteine should be added, and the media should be incubated in an anaerobic hood for 24 hours with the lid loose before being used. This got me thinking that maybe I'm removing too much of the oxygen.
What do you think?

For the record I got the culture growing today, I checked the pH after sparging and noticed it was a bit low (6.6, it should really be 7.4) so I pH balanced it to around 8.0 before sparging and the pH ended up around 7.0. I think I could do better and have media with a final pH of 7.4, but hey, it works!

I notice that you don't specify pH, which might be important.
I don't know if you can put in too much reducing agent (I suspect not), but a large excess is often required as the equilibrium constants for disulfide exchange reactions are typically close to unity (see Cleland, 1963).
I also don't know if any of following has any relevant to your problem (again, I suspect not), but I want to briefly comment on two aspects of using thiols to as reducing agents in general.
Firstly, the oxidized (disulfide) form of thiols may react with a protein sulfhydryl. Using β-mercaptoethanol as an example (Scopes, 1993, p 320), something like the following may occur, where the reducing agent becomes (reversibly) bound to protein. If the reactive sulfhydryl is at an enzyme active site, this may lead to inactivation.
$$\ce{2 HSCH2-CH2OH  +  O2 -> HOCH2CH2-S-S-CH2CH2OH + H2O2\tag{1}}$$
$$\ce{HOCH2CH2-S-S-CH2CH2OH + HS-{Protein} <=>HSCH2-CH2OH + HOCH2CH2-S-S-{Protein}  \tag{2}}$$
As stated, equilibrium constants for thiol exchange reactions are often close to unity (Cleland, 1963).,
 $$\ce{R1-S-S-R2 + R3-SH <=> R1-S-S-R3 + R2-SH \tag{3}}$$
  For this reason, many protein chemists prefer to use dithiol analogs of threitol (dithiothreitol, DTT, or Cleland's reagent) or erythritol as reducing agent, as the oxidized form of these compounds are cyclic disulfides, where the equilibrium constant is displaced to the right  (see Cleland, 1963).
There is also the question of stability.
The half-life of thiols in solution are markedly pH and temperature dependent, as the  table below shows. The half-life of β-mercaptoethanol at pH 6.5 and 20℃ is greater than 100 hours, but at pH 8.5  and 20℃ it is only 4 hours.

The above table was taken from  Stevens, R, Stevens, L & Price, N.C (1983) The stabilities of various thiol compounds used in protein purifications, published in (the now-defunct) Biochemical Education. The full article is freely available as a pdf from the Wiley website

Thanks that's really interesting, I'll look into using DTT as a default reducing agent. I think in the end the problem was pH, I would adjust it to 7.4 before sorting but this would drop to around 6.6 after sparging. I'm not sure why this would be, could be evaporation, or some CO2 might be dissolving. Anyway it seems that Porphyromonas gingivalis prefers a pH more around 7.5

I think I agree with you: that you probably can't have anaerobic media that is to reducing for an obligate anaerobe. So I consider this question answered.

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Is there a point in our life when ALL the atoms from our childhood's body get replaced?
The evolutionary biologist and Oxford professor Richard Dawkins makes on his TED talk the rather interesting suggestion that we human beings, are in nature more similar to a wave than an object. In the sense that we are a persistent structure travelling trough a constant flow of atoms that only transiently form part of our body.
Citing Steve Grand and his book Creation: Life and How to Make It, he argues that the body of a grown up man doesn't preserve any of the atoms that formed his body by the time of his earliest childhood's memories.
Is that fact widely accepted by the scientific community?
I know that this question is a duplicate of Are all body atoms really recycled several times during a life? (or this one), however I want to put the emphasis on the atom constituents of cells, as the accepted answer there doesn't fully answer that question.
Following those answers and the references within, a consensus seems to exist that most of the body is in constant renovation, with the exception of the cells in the cerebral cortex and the inner lens of the eye, whose cells persist trough life. But to what extent cellular metabolism replaces individual constituent molecules and atoms throughout those cell's life? Is that true also for DNA? What about mitochondrial DNA?
Are the processes that repair DNA damage operating only in damaged areas? Or do they constantly "repair" also healthy areas leading to the constant replacement of the atoms that constitute the DNA?
Others argue that tooth enamel does not regenerate or get replaced, been that what allows carbon dating to be accurate to the year of birth plus or minus a few months. However, as my question begins with a philosophical issue, I'm mostly interested in the atom constituents of the cerebral cortex. I am in particular aiming to figure out if we are more precisely described as a brain travelling through time or just a wave in a sea of atoms.

What defines childhood? Anytime before puberty?

@Sudachi Considering the context of the example I've pointed, it would be any age you can preserve memories of in adulthood. So I would guess from 3-4 years of age onward.

Is there a point in our life when ALL the atoms from our childhood's body gets replaced?

No. There is no point where ALL atoms have been replaced.
This has been shown by tracing distinct carbon isotopes in DNA [which reflect upon atmospheric 14C at the year of their generation (which reflect the extent of human atom bomb testing)]; Bergmann et al. 2009, Science: Evidence for Cardiomyocyte Renewal in Humans.

for your other questions:

Is that fact widely accepted by the scientific community?

The phrasing of Richard Dawkins, which you also list, uses "more similar" (rather than the absolute ALL). These words provide quite an accurate approximation to express that  most building blocks of cells undergo a constant renewal. The choice of words of Grand seems a bit unlucky, if read out of context.

Are the processes that repair DNA damage operating only in damaged areas?

As a first approximation: yes. For instance the image below shows the localized detection of H2A.X histones upon damage at the DNA (red: H2A.X staining -> much stronger in treated cells which have high level of damage; blue: DNA staining)

Or do they constantly "repair" also healthy areas leading to the constant replacement of the atoms

As one approximation this would be true, e.g.: proteostasis  (a process whose failure contributes to aging).

that constitute the DNA?

Note that DNA molecules are vastly outnumbered by other molecules in a cell.
DNA is quite static (see above publication), although individual parts could possibly be repaired (see above image on H2A.X);
Also there might be a selective retainment of more "healthy" DNA strands with less mutations (the immortal strand hypothesis).

Just adding my two cents about this particular point:

Others argue that tooth enamel does not regenerate or get replaced. If that is true what makes carbon dating to the year of birth +/- months possible?

Because the principle of carbon dating is not counting atoms being replaced, but measuring the same atom decaying into a different isotope of its element, which is physically totally different. Wikipedia has more info about radioactive decay.

That's not what I said. The meaning of that sentence was changed by who edited it. Look at the original text on the edition history. I've corrected it. But thanks anyway for the clarification.

Note that in the study cited in my above answer, carbon dating primarily does not measure decay of radioactivity, but inclusion of a (radioactive) isotope that happed do be created by unusual conditions (such as atom bomb tests), and its "decay / inclusion" in DNA molecules which are known to replicate in a semi-conservative way (that essentially depends upon biology and differs from pure physics / chemistry).

@CamiloRada sorry about that, I indeed did not read the original question before it was edited. I will remember to do that from now on (I started using SE only recently).

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Which nervous system is the Sensory system a sub-unit of?
I'm wondering about this because on one hand, the actual sensory information from something such as sight or sound transmits to the brain, which is part of the central nervous system.
On the other hand, the actual muscles that control eye movement but have absolutely nothing to do with processing incoming information are part of the somatic nervous system, meanwhile the actual motion of tissues within sensory organs can also be involuntary.


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How a particular composition of molecules result into life in form of cell?
I had read biology in childhood only, but as far as I can remember every living thing/being is made up of cells in the lowest level. Cells again are made up of some particular composition of molecules. But my question is how a particular composition of molecules become alive? Or What's that which turn compositions of molecules sentient?  I'm trying to understand when or how insentient compositions of molecules become sentient.

Welcome to Biology.SE. I don't think one can answer this question differently than giving an entire intro course to molecular biology. I am voting to close as too broad.

For ressources, have a look at Books for beginners

Okay @Remi.b Can you answer that in 1 or more comments? I don't want thorough answer or suggest me the proper SE where I can ask this question.

Taking a biological course is highly impractical just to know the answer. :)

I suspect you might expect a magical simple answer but there is no such thing to this question. There is no essence of life or any specific process that transform non-living matter into living matter. There is just matter interacting in a complex manner that end up making some entities that we like to call life.

Science does not have an answer to how the first reproducing cell came about.  The actual event has left no traces except life as we see it today. There are theories about parts of how it might have happened, but evidence about it essentially doesn't exist.  If you want to get a flavor of recent ideas of scientists in this area, here is a video of a lecture on "The Origin of Cellular Life on Earth".


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qPCR (weird ntc curve, amplifies before templates and reaches plateau quickly)
I'm new to qPCR, and I’ve been testing the AR expression on canine tissues. I’m currently using a pair of primers that have been tested in other article for canines.The issue I’m having is  that I have very early amplification of ntc AR (before the amplification of cDNA templates) but also this amplification curve looks weird since it reaches quickly the plateau phase (flattened). This problem persisted even after changing to a much more specific cycling. If anyone has any tips, or ideas on how I may be able to explain this, I’ll be very gratefull.

The cause of the signal in the no template control will be contamination. It could be that the reason for the different plateau positions is the presence of reaction inhibitors, depletion of reagents, or possibly different binding efficiencies between template (and contaminating DNA) and the primers. I'm not sure about that last one but it kinda makes sense in my head: any contaminating DNA that binds to the primers probably won't bind as efficiently as the template that the primers have been designed for so the reaction is inhibited by accumulation of dsDNA faster.
Either way the cause is going to be excessive contamination. Try using more template in your samples (increasing you signal to "noise" ratio), or be more careful when preparing your samples.
There are extraordinary measures that can be taken to remove contaminating DNA (e.g. treating the water with DNase and then deactivating it) but these often aren't necessary and the added steps can actually increase contamination, it's usually best to keep it simple.


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Can my dog really understand me?
Are dogs capable to understands human language ( for example after order sit it sit because he know that word) Or can sence our order by body language and intonation if so why this type of communication developed only at dogs?

What do you mean by recognize human language? Do you mean "able to tell which language is being spoken" or do you mean "understand words in a specific language?"

I mean if he is actually capable to recognize my orders only in my mother language or he is used to my intonation and the sight for the specific order.  I thought the understanding of single word is came in hand with this question.

Your dog understand you facial and body expression and gestures along the tune of your voice and the actual word being said. If you change the word and keep the rest, your dog might still understand the rest. In fact, many dogs tend to have an easier time to learn gesture than vocal commands. My dog will sit, lie down, give the paw, go to his bed and twirle much more easily if I make the gesture than if I say the command.

I think tyou are right. But i remember experiment, where researcher tried to learn dog by giving him a reward. He lerned him to bring specific item by his order (i saw it in documentary but dont know name). Fact what i tried to explain that he said bring for example doll and the dog bring it to him (but with hard drill).

@Remi.b: WRT tone and body language, how does this really differ from humans?

It does not. Both humans and dogs use somewhat similar cues to interpret someone else attempt to communicate. Why?

@Remi.b: Because your comment seems to be saying that dogs respond much more to tone & body language than to actual words.

(https://www.petmd.com/dog/behavior/dog-brain-facts-understanding-canine-cognition) according to this remi.b you should be right, but i am not stil sitysfied with the communication part. Its kind of strenge things about that the dog evolve the abillity to communicate with us because we gave them food, and our love. But if dometication can do this with dog, why not with others ??

Some researchers say that dogs have the intelligence of a two-year old.
Many dogs can understand more than 150 words and intentionally deceive other dogs and people to get treats, according to psychologist and leading canine researcher Stanley Coren, PhD, of the University of British Columbia.
He is a reasonable and serious scientist who is biased towards overstating dog intelligence. he sais:
The average dog can learn 165 words, including signals, and the “super dogs” (those in the top 20 percent of dog intelligence) can learn 250 words, Coren says. “The upper limit of dogs’ ability to learn language is partly based on a study of a border collie named Rico who showed knowledge of 200 spoken words and demonstrated ’fast-track learning,’ which scientists believed to be found only in humans and language learning apes,”
Dogs can also count up to four or five,
http://www.apa.org/news/press/releases/2009/08/dogs-think.aspx


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What factors affect the number of individuals in an animal group?
Social animals can live in groups whose numbers vary greatly according to species (for instance wolves vs deer herds vs buffalo stampedes vs lemmings).
Is this number regulated only by environmental factors (resource abundance, position in the food web etc) or is there a genetic upper bound to this number which prevents overcrowding? Put in other words, would a species with endless food resources (but finite space) grow endlessly?
If the genetic regulation is common, then why humans don't seem to be subject to it?

What is the relationship between your title and the content of your post? Can you please try to make this clear?

Also, generally speaking, avoid saying "I heard" or "I've read" but always try to cite a source for your claims ("according to www.canislupus.com/groupSize, ...")

I am terrible sorry i am still know on this site and my english is not good as it was. But this idea come to my mind in a late night. I have just want to know if a specific number of members in groupe was evolved. I am not quite sure that wolf ancestor hunt always in 6 ( that was number from my memory, i didnt know that i have to always source for my opinion, the number is not important to me). But the question should be is the number of members important to species fylogenesis?

Don't worry, you don't have to be sorry for your english or for not asking perfect questions. It takes time to learn a language and to learn the details of the working of the SE websites.

"We are only species on this planet which have tendency to increase our population". Wrong. Every species tends to do so. Thats pretty much what reproduction is for.

Again i hit a language barier. The last comment was quite insolting. I am just want to know if some kind of animals which commit group suicide od their population Is overgrove!! I am not from preschoole. If you dont want to help me. Vote And dont let comment like this!!

@Remi.b since I think I understood what the OP wanted to ask, I decided to give it a shot and I've rewritten completely the question. L.Dodo, feel free to roll back the edit if this is not your intended question.

@LinuxBlanket Wow, there is quite a stretch between the original question and your rephrasing. Apparently the OP is happy with your rephrasing so good job!

You know the main idea was actually this, but not much people understands me even in my language. I just tried to say example, but obviously it was not the right way.  But this is exactly how my question would sound in my mother language. Anyway guys i am glad u gave me this lesson and hope i ll get answer.

Thanks @Remi.b! I think that it is actually a very good question and I'm eager to see what the others have to say about it (I remember reading something about this topic some time ago). Now I hope that the downvoted can be reversed to get some attention!

this depends on what you mean by group.
If you mean population then it is mostly environmental factors, although part of the environment can be other member of your species, some groups have a minimum functional size, such as passenger pigeons and breeding in groups behavior, or have density controls(if you are too spread out you might never run into another member of your species to breed with) , these internal factors are fairly rare however compared to basic resources availability, things like food, water, territory, shelter, nutrients, ect.
If you mean size of individual packs, herds, ect, then it is a mix of both, behavior which is almost always genetic is the main cause. However this behavior can be alter or triggered by environmental factors and its ultimate evolution is strongly affected by those factors as well. for instance large herd behavior will never evolve if the environment cannot support it, and if the environment changes the behavior may stop being beneficial.


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If motor neurons are part of the CNS, what is the PNS made of?
It is my understanding that motor neurons transmit messages to the myocytes of skeletal muscles all over the body. This should make them part of the peripheral nervous system that transmits both the voluntary and involuntary movement of muscles. Now, I came across this site that says motor neurons are part of the Central Nervous system. https://qbi.uq.edu.au/brain/brain-anatomy/types-neurons. Which is right? My book specifying the peripheral information, or the website?

Comments are not for extended discussion; this conversation has been moved to chat.

The peripheral nervous system refers to parts of the nervous system outside the brain and spinal cord. It includes the cranial nerves, spinal nerves and their roots and branches, peripheral nerves, and neuromuscular junctions. The anterior horn cells, although technically part of the central nervous system (CNS), are sometimes discussed with the peripheral nervous system because they are part of the motor unit.

It appears that even though the motor neurone body lies inside the CNS, the spinal nerves are by definition part of the PNS.  Clearly some authors don't follow the convention hence the conflicting views.
https://emedicine.medscape.com/article/1948687-overview

I've sent feedback to the University of Queensland to inform them!

Eww a commercial source.

As far as I know universities are run as commercial entities as well.


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What are the optimal conditions for storing frozen glycerol stocks of bacteria?
The common method of storing bacteria long-term is to collect saturated liquid culture, such as LB, and mix it with sterile glycerol so as to obtain 10-30% final glycerol concentration. The resulting mixture is then frozen, usually at -80 or -20C. Bacteria stored in this way are said to be viable for years. I am curious as to what affects the success of such a storage strategy?

Obviously the temperature should be below freezing, but how exactly is viability affected? Is colder always better (assuming the tube can withstand it)? Is there rapidly diminishing returns after -80C? Is there an optimal temperature? I'm expecting something like a plot of viability after 1 year of storage vs. temperature, ideally with multiple species.
What is the optimal glycerol concentration?
How much does viability drop per freeze-thaw cycle?
Does it matter how quickly you freeze after adding glycerol?
While letting a frozen sample thawed is considered unadvisable, after it does thaw, does it matter how long? Does every second count, or is there little difference so long as it's not several multiples of the lag phase duration?

However, I found it very difficult to locate specific information about the optimal conditions for such storage. For instance, Addgene claims that optimal glycerol concentration is unknown. Moreover, a lot of the older papers on this topic are paywalled (even from my institution). But the experiment to determine it would be so trivial that I can't believe nobody has done it. I am interested primarily in data from actual experiments, and I am interested in glycerol alone as a cryopreservant.

Here’s something.


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Where can I find a compendium of microorganisms?
I recently bought a microscope hoping to learn more about algae and bacteria and stuff. I've collected a few samples of pond water and found tons of algae and stuff, but I have no idea what to call the things I have found. I am wondering if there is a list of every known algae with a picture and some characteristics that would help me identify what I am looking at. I've looked around on the internet and haven't found much. Thanks

So you're looking for maybe a book or list with some common microorganisms that you would find in water so that you know what it is?

that is exactly what i'm looking for

It sounds like what you need is an identification key. The most common form of a biological identification key is a dichotomous key. In such a key the sequence and structure of identification steps is fixed by the author. At each point in the decision process, multiple alternatives are offered, each leading to a result or a further choice.
Key can be very region-specific so I suggest to search for a key that focusses on the group of animals you wish to identify and the region/country you live in.

Where are you from? I've got a good suggestion, but apparently it has not been translated in English...

This website will probably provide you with more information than you need at this stage of your investigations but is it one of the most complete and free resources for microbes of various kinds. http://microbe-canvas.com/

I do not know how complex of a key you want, but this one is a good identification guide for beginners. It contains a lot of common freshwater pond algae, what they look like, and some basic characteristics. From here, you can identify your specimen and then be able to look them up further. Hope this helps!


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Does cow urine have medicinal properties?
It is a common belief in India that cow urine has medicinal properties.
It is said to be anti-biotic.
It cures diabetes, cancer and many other diseases if not all.
Because this is biology I would like to focus on the anti-biotic property and set aside other claims cos they many be related to medicine and not biology.
Is it anti-biotic?
Does urine not cause infections?
Especially since it is applied the belly of new born babies by orthodox Hinuds.

it's a question for skeptics.se

there's a bunch of questions on skeptics on this topic already, for example this one : https://skeptics.stackexchange.com/questions/36282/is-there-a-hindu-cult-in-india-that-drink-cow-urine-to-cure-diseases

@gilleain Note that only asks is such a practice exists not the medical validity of it.

Don't use these medicines please. It only goes into the vicious cycle of spreading more fraud.

Interesting question anomdsgf. There are substances present in Bos taurus urine that promote antimicrobial activity. Studies like this and this have shown how the urine can inhibit the growth of certain bacterial strains.
However, with all that said, Bos taurus urine could still contain other harmful bacteria that are not inhibited simply because it was excreted out of a cows urethra and could cause infections. Read more on possible harmful effects here.


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Passing virus/diseases immunity to newborn
From my understanding, our white blood cells 'learn' to fight off viruses and other pathogens that make us sick (or that they encounter because of vaccination) so that the subsequent encounters with same strain will not make us as sick; our immune system is able to fend off much better.
Newborns are protected with mother's antibodies via placenta and breast milk. My question is, can immunity be passed from mother to child via hereditary mechanisms, or does the child have a completely fresh set of 'default' defenses? Is that the reason why we get sick so easily when young?

So what happens to bottle fed infants?

^ that's something to ponder too

well, you have your answer.

(@GrahamChiu that's a comment - if you want to post it as an answer go ahead, but I suspect it might need more work...)

Welcome to Biology.SE! It sounds like you've tried doing some research already and know something about adaptive immunity and maternal antibody transfer - can you include the sources you found so we can work out how much you already understand? (Showing how much research you've already done usually helps get positive responses, too.)

And innate immunity, as well as possibly microchimeric cells

@arboviral I dont have much sources, it's just a question that is stuck in my mind without any answers.

@GrahamChiu what happens to bottle fed infants? Humans get passive immunity across the placenta, so human bottle-fed newborns are OK. Many other species do require colostrum for passive protection; if they're bottle-fed and never receive first milk, then they're more susceptible to infection until their own immune system is fully mature.

@iayork that wasn't my point which was to say that adaptive immunity exists

@GrahamChiu yeah your detailed question certainly made that clear and justifies your condescending smugness.

@iayork I guess you've never heard of Socrates then.

Newborn mammals get something called "passive immunity", in which the mother's antibodies are passed across to the fetus or newborn. Depending on the species, this can happen by the antibodies crossing the placenta, or more commonly by being transferred in the first milk the mother forms, "colostrum", which is very rich in antibodies. (At the same time, the newborn has special adaptations to absorb antibodies from the colostrum into its body; this only works for a short period after birth.)

Passive immunity
IgG Placental Transfer in Healthy and Pathological Pregnancies
Colostrum

This allows the newborn to have a temporary resistance to whatever pathogens happen to be common in its immediate environment (because presumably the mother would have been exposed to them). It's very much temporary, lasting typically a few weeks or so before the transferred antibodies half-life away. During this time, the newborn has a chance to start developing its own active immunity, which is dynamic and lasts much longer.
Edit to add:
Are there other modes of heritable immunity? Sort of but probably not what you're thinking of. Innate immune responses are often triggered through recognition of molecular patterns that are common to many different pathogens ("Pathogen-associated molecular patterns" or PAMPS). The receptors that recognize these patterns are inherited, and they are essential for starting innate immune responses which are in turn very important for starting acquired immune responses. So yes, every newborn mammal, and reptile, fish, sea urchin, arthropod, nematode, etc. inherits mechanisms for recognizing pathogens.
However, it's important to understand that these don't change during the mother's lifetime. This system doesn't provide any inheritance of recognition of pathogens that are locally important, or that the mother has met during her lifetime. This is the basic toolkit that every individual of the species (often, that every individual in the genus, or kingdom) has, that's needed to answer the general question "Is this a dangerous situation? Should I activate the immune response?"
In other words, as far as the innate system is concerned, "the child has a completely fresh set of 'default' defenses"; the only non-default information that's passed from mother to newborn is via the passive immunity described above.

I'm not sure this answers the question - it sounds like OP already knows something about maternal antibodies (("Newborns are protected with mother's antibodies via placenta and breast milk") but is asking whether other mechanisms for passing on immunity also exist.

http://europepmc.org/articles/PMC3959733

maybe this would be another question itself. U state that the receptors that recognize these patterns are inherited. but why would a mum that is vaccinated against a certain virus, would not pass that knowledge to the child? Since vaccination works by teaching the immune system to recognise the viral signature. Or this inherited immunity is for other kind of illnesses?

why would a mum that is vaccinated against a certain virus, would not pass that knowledge to the child -- She does, via the passive immunity I mentioned at the start. Why not pass down dynamic immunity? Probably because it's better to develop your own immunity to the pathogens you actually see yourself, rather than the ones your mother saw in 1962, or your great-great-grandfather saw in 1880. Passive immunity gives a brief coverage of possibly-relevant agents until you develop your own to the guaranteed-relevant ones.


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Can I use commercial DNA loading dye for my RNA samples without degrading them?
I was wondering if I have to use special RNA loading dye or can I run RNA samples with regular loading dye that is used for DNA?

What are you running?

I did electrophoresis of my RNA probes for in situ hybridization several times, and every time they were degraded. I am trying to figure out what was wrong, so I realized I used DNA loading dye every time. I just wanted to check if that could be the problem.

Handling of RNA requires extra care, especially using RNase-free pipette tips, tubes and reagents, to prevent RNase contamination. Common labware and reagents usually indicate whether they are RNase-free certified. If there is no such mention written on the box or label, then you should assume it is not RNase-free and you should not use it to handle your RNA.
Check whether your loading dye is certified RNase-free (this should be written on the tube, or easy to find out on the manufacturer's website using the product reference number). If it is, and you exclusively used RNase-free certified tools and reagents all the way, then maybe the loading dye tube or something else got contaminated by one of your co-workers.


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can you create an offspring from ancient human's DNA?
If a DNA from an ancient human, for example the cheddar man, is still intact, can you make an offspring today using that intact DNA?
https://www.theguardian.com/science/2018/feb/07/first-modern-britons-dark-black-skin-cheddar-man-dna-analysis-reveals

You could, however the DNA is not that intact, there is a steady rate of loss of the genes...
mtDNA is degraded to an average length of 1 base pair after 6,830,000 years at −5 °C (see wiki: ancient dna). that's a speed of 1 base pair every 412 years. The cheddar caves are not frozen, I'd guess that the DNA lost one base pair every 10 or 20 years, so it has lost at least 400 or 800 base pairs. at 5 degrees, it may have lost 2 percent of it's informations, except that they sequenced it many times and reconstructed the original version.
The technology does exist to design synthetic chromosomes. https://www.nature.com/news/synthetic-yeast-chromosomes-help-probe-mysteries-of-evolution-1.21615
https://www.scientificamerican.com/article/scientists-downsize-bold-plan-to-make-human-genome-from-scratch/
I figure that once science has a sure footing on genetic taboos, the do's and dont's, a company will one day try to give birth to neanderthals the cheddar specimen. There is too much scientific value for it to never be realized.

A species is generally defined as a group of organisms that can breed and produce fertile offspring. So, if you are extracting DNA from the an ancient human that is indeed the same species as us (homo sapiens), then by definition, you will be able to combine it with modern human DNA and generate offspring.
This is just stating the theory, the actual biology behind extracting that DNA and using it to fertilize offspring will be... messy.

You don't need to combine with another human, just clone https://www.usatoday.com/story/tech/science/2018/01/24/cloned-monkeys-scientists-china-first/1062649001/

scientifically yes, legally probably not as it would fall under human cloning/experimentation laws in most countries.
Artificial insemination with sperm with inserted genomes or artificial sperm already exists in mammals. Reconstructing genomes is possible and that together is all you really need.

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Snail species identification from the United Kingdom
Can anybody identify the species of this snail?
From this website, it looks like a Common Snail.
Could it be the dextral type of Cornu aspersum?
These snails have been found in a garden, have survived a month on lettuce in a home environment, retreat in their shell sometimes. Their shell measures about 2 cm diameter.

To me it look like that your guess is correct, but I'm not an expert.

This snail is Cornu aspersum its common name is garden snail, it belongs to Helicidae family click here for more information

Given that the OP thought this was the correct species but was unsure, good answers to this question should explicitly describe the characteristics or evidence that support that this is in fact the correct ID. Please [edit] your post to provide explicitly-stated evidence for why your ID is correct. Thank you.


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What species is most prolific?
What species represents the largest biomass on earth, ie, how much does the entire population weigh? Also, what species has the most members?

have you googled?

This article covers your desires. Briefly, the single species that weights the most is the cow (520 million tonnes in 2011, now probably way more). About the most members, it looks like that the prize could go to the Antarctic krill (7.8 x 10^14 according to Wikipedia. [
This BBC article, instead, argues that collembola might be the most numerous group on Earth, being present in the number of 10000 per square meter (I leave the calculation to the reader). Collembola, however, are made up of ~6000 species. The same goes for ants and termites.
Regarding bacteria, the same article mentions
cyanobacteria, and more interestingly Wolbachia, an intracytoplasmic parasite that can bend the sex of the progeny of its host to spread more effectively.

The discovery of this giant Armillaria ostoyae in 1998 heralded a new record holder for the title of the world's largest known organism, believed by most to be the 110-foot- (33.5-meter-) long, 200-ton blue whale. Based on its current growth rate, the fungus is estimated to be 2,400 years old but could be as ancient as 8,650 years, which would earn it a place among the oldest living organisms as well.
And in 2003 Catherine Parks of the USFS in Oregon and her colleagues published their discovery of the current behemoth 2,384-acre Armillaria ostoyae

No weight is given.
https://www.scientificamerican.com/article/strange-but-true-largest-organism-is-fungus/

But this is about the size of an individual, not of the entire species.

Humans are the obvious and boring answer. 7.5 billion at 50 kg each is a lot of species, and getting heavier all the time from fast foods

...But humans is not the answer. We could be the second heaviest species, but the first is the cow, as I mention in my answer.

I don't see how your comment addresses mine.


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Why is full cell/high antigen dose pertussis vaccine dangerous for adults?
I do remember that I have read (or heard) somewhere that as a human is older, the whole cell vaccine (and high antigen dose one) has more and more adverse effects.
As it is consistent with the target age group mentioned in the leaflets attached to the vaccines:

whole-cell DTP vaccine (Instytut Biotechnologii Surowic i Szczepionek BIOMED S.A.) is suitable "for children not older then 3 years",
high antigen doseInfanrix-DTPa (GlaxoSmithKline Biologicals S.A.) "shall not be used for children older than 7 years",
low antigen dose Boostrix (GlaxoSmithKline Biologicals S.A.) is "suitable for a person older than 4 years",

I suspect it is true. Unfortunately I lack a reliable source to both confirm that and read more about the effects. Can anyone provide a reference.
As there is a strain of pertussis "resistant" to acellular vaccine, IMHO it would make much more sense to use whole-cell vaccine for adults too.

It seems it is not about pertussis.
I have found information in the Infanrix-DTPa characteristic that it is not recommended for adults due to high dose of diphteria toxoid.
Both Infanrix-DTPa and whole-cell DTP vaccines contain over 30 international units (whatever it is) of diphteria toxoid while Boostrix contains "not less than 2 i.u.".

Yes, it is true that the whole cell vaccine can have more adverse side effects on older patients (and much younger patients also). This is because their immune systems can be weaker and they are more susceptible to side effects. Some of the vaccine adjuvants (preservatives) can also be dangerous for at-risk patients, and can have more serious long-term effects. According to the CDC, the ingredients include:
Each 0.5-mL dose of Daptacel® (Sanofi Pasteur) contains 15 Lf diphtheria toxoid, 5 Lf tetanus toxoid, and acellular pertussis antigens [10 µg detoxified pertussis toxin (PT), 5 µg filamentous hemagglutinin (FHA), 3 µg pertactin, and 5 µg fimbriae types 2 and 3 (FIM)]. Other ingredients per 0.5-mL dose include 1.5 mg aluminum phosphate (0.33 mg of aluminum) as the adjuvant, ≤5 µg residual formaldehyde, <50 nanogram (ng) residual glutaraldehyde and 3.3 mg [0.6% volume per volume (v/v)] 2-phenoxyethanol (not as a preservative).
With any vaccine, one must weigh out whether it would be riskier to get the actual disease or the side effects of the vaccine.
For further reading:

about the whole cell pertussis vaccine
another informative article
more about the ingredients

The problem is that whole-cell DTP vaccine is suitable "for children not older then 3 years" (Instytut Biotechnologii Surowic i Szczepionek BIOMED S.A.). Also Infanrix-DTPa (GlaxoSmithKline Biologicals S.A.) "shall not be used for children older than 7 years" while Boostrix (GlaxoSmithKline Biologicals S.A.) is "suitable for a person older than 4 years".
Thus it looks like the problem is with a mature immunesystem. I would bet it may be overreacting or so.

This is because their immune systems can be weaker What does this refer to?

I think we can safely say that the average person reading this response can just assume it is always safer to vaccinate.  In the unfortunate age where Jenny McCarthy's mommy instinct is given equal weight to actual experts, we should avoid ambiguity and plainly identify failure to vaccinate for what it is: irresponsible bordering on negligent / child abuse. Vaccines save lives. Diseases take them. It's almost like living with the benefits of vaccines has afforded people the luxury of forgetting why we need them.

@JustinMasters Any kind of propaganda (even one supporting vaccination) is a misconduct that should be avoided. It may easily backfire. It is fact that vaccination may have adverse side effects. In some cases (eg. TB in Canada) it is safer to not vaccinate. It is also probably the case with vaccines containing high doses of diphteria toxoid in adults. Failure to acknowledge it leads to be accused as a member of vaccine genocide lobby and no longer trusted as reliable source by people interested in facts.

When did we start talking about TB vaccines?  I can't remember ever having a doctor recommend that I be vaccinated against TB, but I can assure you that if I ever had to go anywhere where I had a high probability of being exposed to TB, I would take the vaccine prior to going. It's the only responsible thing to do.


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What is the primary energy source for sprouting plants?
To what extent are young plants powered by the potential energy stored in the seeds and when does solar energy take over? Are there other energy sources involved?
I was observing sprouts in a germinator [is this a word?], pushing up the lid after being left alone over three-four days. As this is a considerable amount of work (for such young plants) I wondered how long the plant can access the original energy stored in the bean/seed and how it compares to the amount of energy it can get. As you can see in the picture, the sprouts have only access to water and some sunlight.
I suspect the potential energy it draws somehow decreases monotonically (perhaps linearly, quadratically, exponentially?) over time, while the solar energy pics up.
Is this mental model correct?
I'd appreciate an answer that a non-expert can understand.

I think these were radish sprouts, but my question is more general.

This depends largely on the plant, some seed stores can last a very long time, but a few general trends can be discussed.
sprouting plants run off stored carbohydrates in the seed, they are using respiration, photosynthesis begins as soon as they are able and they will switch over to it as quickly as possible it is however gradual as the plant never stops using respiration it just starts using photosynthetically produced sugars instead of stored ones. The stored energy will run out so the faster a plant can stop relying on it the better, so even a small production is helpful, you yest it is a gradual process, even if it is a fast gradual process ins some plants.

Your first question has an easy answer.
Q: "when does solar energy take over?"
A: as soon as a green part of the plant receives sunlight. Chlorophyll is the main light-harvesting pigment, and responsible for the green color of the plant.

Clearly. But is it the primary power source for the early development? The surface area of the plant is comparably small and it's just beginning to develop leaves.


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found this flying ant like insect in pune, help me identify it?

Is it species of wasp or ant or fly? I found it in Pune/India. I need its common name at least.
Here is another photo I managed to take...Found at same place as previous one.

It looks like a a species of a genus Baccha (which are hoverflies). Maybe Baccha elongata.

Can you please add more information. What approximate size is it? Where did you see it (country, region, type of ecosystem)? What did you see of its behaviour? Typically, is it able to hover?

@Remi.b Comparing the eyes of Baccha elongata from the wikipedia link to the picture given, the species in question does not look like a hoover fly.

I do believe this to be a fly, but it is probably not a hoverfly (Syrphidae); the antennae appear to have more than three segments.  If you see it again (or already have other photos from different angles), adding them would be a help.

It was found in Pune, India. It was not able to hover, but it was moving swiftly. I think it is a fly but could not find any matching known species from my region. It was about 1.5cm long, found it in garden. I have only one picture of it, i'll see if i can find it again.

This is not a syrphid. It is a fly in the family Megamerinidae, genus Texara. Very little is known about their biology, and they are rather uncommon.

You might very well be right. Could you add a source or a picture for verification?

This isn't a Megamerinid fly; the same objection I made to "hoverfly" (see my note of February 25th) apply here, and would apply to any Dipteran family belonging to the infraorder Muscomorpha.

Sorry I didn't add a verification - I only just noticed the request for that. In any case, yes, it is definitely Texara (a megamerinid fly) - see this https://lkcnhm.nus.edu.sg/app/uploads/2017/04/sbr2016-148.pdf, as well as google searching. I've collected a fair number of specimens of this group of flies in Asia, and even photographed it myself. [Edit: regarding the antenna - the elongated part is the arista, not the full antenna]


text:
Do PC-12 cells have to be stored in nitrogen?
My lab has been storing their PC 12 cells in the -80 freezer... upon arriving here and investigating a new project I see that it specifically stated to be stored in nitrogen vapor? Is this the absolute case or is -80 for short term storage okay as well?

The temperature at which nitrogen evaporates is about −195°C. Given the considerable difference in temperature between the current freezer and nitrogen vapor, I'm inclined to say probably not.
I suspect that it may be dependent on what exactly you are using the PC 12 cells for. Without knowing more detail about the situation, I would do my best to get ahold of some liquid nitrogen for your samples as soon as possible. When in doubt, it is always best to follow procedure.
Until you can acquire nitrogen, -80 is still far better than room temperature. Be sure to take note of the discrepancy in your notes and hope for the best.

From talk among the powers that be in my old lab, many of the common cell lines have become divergent anyway. I think HeLa cells were notorious for behaving differently in different hands due to different storage conditions and culture mediums.
PC12 cells were believed to be similar, so I think that whether or not it's OK will depend on what you want to do with them. If you want to set up simple assays for comparing the effects of small molecules, then you'll probably be fine (obviously note down the storage conditions when starting your cultures up again).
However, if you want to replicate a differentiation procedure from another lab exactly, then you should be replicating their conditions as exactly as possible. Therefore your -80 stored cells might not be OK for that.
So as Astrolamb said, have a go, see how they behave, but maybe be prepared to beg someone to give you some more if the -80 ones don't do what you want them to.


text:
Is there human Anatomy software that provides great detail?
Is there Anatomy software that is exact representation of human body, like let's say virtual reality tour inside human body from head to foot, detailing all organs even small, covering all systems, nervous, blood vessels, muscular, skeleton systems, could be zoomed even to deepest skin layers, neurons,  that can be applied unapplied like layers in Photoshop?
If this does not exist, then which is the most advanced human Anatomy software?

try this page https://www.google.fr/search?q=very+detailed+human+Anatomy+software%3F&oq=very+detailed+human+Anatomy+software%3F&aqs=chrome..69i57j69i60&sourceid=chrome&ie=UTF-8

In English the indefinite article "a" is never used with the word "software". (The definite article can be used in appropriate circumstances.) I have corrected your question accordingly.

Isn't the question off topic?

My favorite is this one and it is quite detailed and interactive. It does not use virtual reality technology, but it is a good resource for anatomy students. Then there is this one, but it is more virtually animated and less real. Hope this helps!


text:
Renal threshold for glucose
Wikipedia in its article on 'Glycosuria' says that the renal threshold for glucose (RTG) reabsorption in the kidney is around 160-180 mg/dL. Beyond which the glucose starts to excrete in the urine. But in diabetic people blood glucose exceeds in range of 300-400 mg/dL is prevalent. How this is possible? What prevents the the excretion of excess glucose into urine?
Does it mean more glucose is reabsorbed in the nephrons above its threshold limit? Also, as the glucose is co-transported with sodium, does it mean that glucose reabsorption is tightly coupled with sodium reabsorption? Does sodium play any role in crossing the glucose threshold limit?
Or is it possible that the excess glucose (beyond RTG) is actually excreted out of blood in the kidney but the hyperglycemia is caused by the fresh gluconeogenesis of the body?
Or is it possible that both these mechanisms (RTG is exceeded as well as fresh gluconeogenesis) cause in furthering the hyperglycemia?
Is it possible to measure this state?
Thanks in advance.

Classic symptoms of untreated diabetes include excessive thirst and urination, and glycosuria. Think about the solute gradient. At some arbitrary number the level of glucose becomes saturated. The kidneys are forced to get rid of the extra glucose in urine. This increases the concentration of solutes in the urine, so where does the water go? Right? So that high blood glucose concentration translates into frequent trips to the bathroom, and frequent need to consume fluids. This can also lead to a fluid/electrolyte imbalance, which is potentially dangerous.
There's actually a limit to what can be reabsorbed, denoted the transport maximum,
but, you can only eliminate so much solute over time, so here's a figure from a Pearson physiology chapter:

Source
You've got your renal threshold around that 180 mg/dL but look at that excretion kinetic. It's known that the excretion rate increases linearly with the filtration rate above the renal threshold (ref). So say i'm an average male with 400 mg/dL plasma glucose and 50 dL of blood or 20 g of net plasma glucose. All other things held equal, it looks like it could take around 2 hours to clear that glucose on excretion alone, which doesn't typically happen. Clearance is also outlined in that Pearson chapter, and you can measure that by knowing the excretion rate, and the concentration of glucose in the urine and in the plasma.
Data shows, however, that the filtration/reabsorbtion process is maladapted in a diabetes model, and increased plasma glucose levels are maintained by an up-regulation in glucose transporters (thus an increase in the transport maximum), and an increase in the renal threshold (and thus the kidneys only begin to excrete glucose at a significantly higher level) (ref).


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Can the human body utilize electricity?
In any way could the body store electricity supplied externally?

Electron is a measure of charge, not a charge carrier, in the same way yard is a measure of distance, not a thing with the length of one yard.

@MartinKlvana The electron is a subatomic particle, symbol e− or β−, whose electric charge is negative one elementary charge.

electron transfer in mtDNA and nerves (although in nerves, the moving charges are ions, not electrons).

I don't understand your second sentence. It contains no verb. What exactly are you trying to ask here. I don't understand either the purpose or meaning of the picture. Can you clarify this?

@Remi.b I hope that is better.

You seem to be interested in a medical application. Is your question "Can our body sense an electrical current?", "Can our body produce an electrical current?", "Can we cure breast cancer with an electrical current?", "Do different organelles communciate through an electrical current?"etc...

@Remi.b more like if our body has a external consistent charge will our body adapt or has the ability to make use of it

@Remi.b: What is "negative" and what is "elementary" and what is "particle"? And what do you call that which has a charge different from "negative one elementary charge"? How can elementary charge become delocalized? And so on and so on. "Electron does not exist." --Kenneth Lee Wheeler (citing Nikola Tesla, among others) https://www.youtube.com/channel/UCVcxJ9k14bi__-uA1cGkEcA

@Remi.b very nice.

I would like this to be migrated to health SE. please

@MartinKlvana Well you might want to discuss this on physics.SE or philosophy.SE but all commonly accepted source of information on the subject suggest that an electron is a particle which carry a charge (which has arbitrarily decided to be negative). An obscure youtube channel with 4 videos, none of them where seen more than 8k won't be a good argument. But let's not further this discussion here, it is not the place.

@Remi.b: "electron" is an example of "reification of attributes" fallacy. What is "commonly accepted" is usually wrong. (4 videos? More like 400.)

Not to be a smartass, but do you not consider the mitochondrial electron transport chain to already sort of do that? When we consider that actual movement of electrons to be a step in the conversion of chemical potential in fatty acids and carbohydrates to phosphorylating ADP for later mechanical energy. Just a thought.
Although I'm assuming you mean somehow utilizing a current flow through the body from an outside source.

No, the human body cannot utilize externally applied electricity.  Applying electricity to the body will either have no effect, if the amount is small, or will disrupt normal functions of the body or cause injury if the amount is larger.
An overview of the effects of electricity (for doctors) can be found in "Conduction of Electrical Current to and Through the Human Body: A Review".

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text:
Veritasium video about mosquitoes
In the recent veritasium video about mosquitoes , the host says that the researchers used identical female twins and fraternal female twins to understand the effect of genes on attractiveness to mosquitoes.
Is there a scientific reason to use only female test subjects for the experiment?
The video:
https://youtu.be/38gVZgE39K8

My guess is that there is no reason for choosing female per se. Rather, I'm guessing that they simply wanted to avoid complications regarding sex differences, so they simply created the experiment with participants being of the same sex. So I suspect the experiment could just as well have been created with only males.

Female and male mosquitoes are quite different, studying both would be like studying different species in many ways and females are the ones that bite, so likely that is why.


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Using evolutionary algorithms in molecular biology?
I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also interested in machine learning, mostly in evolutionary algorithms (evolutionary strategy alg.s, genetic alg.s) and Bayesian optimization, from both of which I have written multiple, working programs in C# at home. Due to the massive need for people trained in informatics I'd like to convince my supervisor to include this topic into my future research, especially as I have already acquired some basic skills in these areas. However I have only seen research examples that are purely computational and these didn't include any laboratory work. Can you provide me some insight into the use of these techniques in molecular biology and ways of connecting these with laboratory work?

Why are you coding in C-sharp? This is a language almost never used in bioinformatics or molecular biology, not least because it is specific for Microsoft Windows, a platform that is generally avoided in this area. Sounds rather as if you are putting the cart before the horse. If your supervisor can't suggest a wet project that requires computational analysis, this list isn't going to. Perhaps you need to find a new supervisor.

@David I don't restrict the language options only to C#. I can also program in Python at some level, but I am willing to learn new languages. The main reason I'm asking this is that my supervisor hasn't got much experience with machine learning but he is at home on for example MD simulations, model fitting, etc., and machine learning can come in handy in these areas. I know how to write GAs, I know how to do research in the lab, I know that these two can be somehow used together, but I cannot give concrete examples. It's just I have acquired this skill that I dont want to completely neglect.

OK, but in my experience people tend to do "all informatics" PhDs, or do a PhD where they generate the sort of data (e.g. RNAseq) where it helps if you can use Unix and write the odd glue script, but for the most part you are using powerful programs written by professional computing scientists. I'm not sure it's as easy as some of your respondants make out.

@David What languages are mostly used for this sort of stuff?

@Zebrafish — These days everbody in bioinformatics (except oldies like me) seems to use Python wherever they can. The heavy-weight stuff is often written in C++ (e.g. parts of Trinity). Java is still used (because it is taught by CS Departments), but less than a few years ago. Web stuff tends to use MySQL or other relational databases and various JavaScript and other frameworks. PHP is less popular than in other areas. But that's just my impression — others may have a different view.

There are countless really worthwhile ways to use evolutionary computation (EC) in molecular biology.  The chief advantage of EC is that it can find solutions to problems that are too complicated, too nonlinear, etc., to solve by more direct methods.  I've used genetic algorithms to evolve models, to find patterns in data, to design optical systems, you name it; and almost always a GA finds solutions I'd never find on my own.  Sometimes it's a challenge to find a representation for the solution space that fits the problem well, or to find recombination/mutation operators that work well, but that's where human insight is important. Bottom line: if you can list some problems that fascinate you (or better, fascinate both you and your supervisor), I'd be happy to give you some concrete suggestions.

Our groups research focuses mainly on the structural investigation of miniproteins (such as the Trp-cage motif) through NMR, XRD and CD studies, but we are pretty diverse when it comes to research; my current thesis-work is about bacterial expression optimization in a biorector, we also synthesize small peptides, sugar-derivatives (through classical organic chemical synthesis), do MD calculations and all of these topics are coordinated by my supervisor (so we could say that all of these fascinate him). As for me, I am willing to do almost any research in these areas.

I've opened a chat room, "EC in Molecular Biology", which should be a better place to carry on the conversation.  Optimizing bacterial expression in a bioreactor is probably a great place to start looking for an application for evolutionary computation.

The first thing that springs to mind is modeling and simulating the evolution and specificity determinants in protein - protein binding. You can easily include an experimental  part and make it as big as you like (the bigger, the better). For a useful set of physiologically important protein - protein interactions and background info on the specificity and affinity determinants in those systems, see Ivanov et al., 2017 and Ivanov et al., 2016, and the references therein.


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Would current-day human-initiated panspermia be effective?
With current technology, we are able to easily send a probe to the Alpha Centauri star system at a speed of about 20 km/s (velocity of voyager probe), which means it would take about 65000 years to get there.

In light of this, suppose we sent a probe capable of delivering 100g of biological material to an Earth-like planet in α-Centauri.

Are there organisms that:
1) Could survive the journey, perhaps frozen or in a dormant state;
2) Would have a fair probability of surviving in the barren oceans (or land if preferred);
3) Eventually have a change of evolving to more complex lifeforms?

If possible, give a rough estimate of how likely you think that would be -- would we need to send 10 probes for a good chance, or billions of probes?
The lifeless environment seems to necessitate either photosynthesis or chemosynthesis to survive. But what about the necessary food (organic matter)? Would any of those restriction make it virtually impossible to achieve long term life with current goals?

Do you have a source for the "easily send a probe to AC" statement?

I would note there is a person at nasa with the job of exactly preventing seeding life on other celestial objects.

@arboviral By easy I meant feasible for a large space agency. According to NASA the voyager program cost around $865m USD ( from May 1972 through the Neptune encounter), which I assume includes cost of all systems, personnel and communications. Each probe had about 815 kg launch mass.

The technical problems with delivery to a specific planet seems outside the scope of a biology specific site - launching something that will pass within watery planet's distance of a star, eventually, may be "easy" but delivery to the planet's surface will be lots harder.

How this might affect any existing life - including a life detection/abort mechanism is a space tech question but whether to include it would be an ethical question.

@KenFabian Agreed but actually I've posted a question on this to Space.SE; it's linked in my answer. If I get anything pertinent in the answers I'll add it.

Rather than relying on shipping (few) organisms, one may prefer to ship chemicals and a ribonucleotide synthesizer that could be programmatically instructed (as commented in a recent book by Craig Venter)

Okay, there are technically four questions here, but I'm willing to have a stab anyway.

[Are there organisms that c]ould survive [65,000 years], perhaps
  frozen or in a dormant state;

Probably/possibly (prossibly?). There are claims of the recovery of viable bacteria from samples that have been frozen for millions of years, and viable green algae have been growth from permafrost samples at least 5,000-7,000 years old. Dormant bacteria have also been  reportedly recovered from 25-40 million year-old amber and salt crystals formed 250 million years ago. Several of these results are controversial, since in some cases the organisms's genomes are suspiciously modern, and it's not clear whether they could represent sample contamination, but confidence in several of the ones in the range of 10-100,000 years seems to be fairly high (for example, this Carnobacterium recovered from 32,000-year-old permafrost . Using freezing methods optimised for viability, it should be possible to achieve better viability levels than occur naturally (but you'd have to test your samples after 65,000 years to make sure!).
It's also (with a fairly high degree of confidence) probably possible to create micro-environments containing viable bacterial communities that can survive for thousands of years without light or nutrients, but this looks like it would require liquid water, and the maximum lifespan of most radioisotope thermal generators (RTGs), which would be the lowest-maintenance form of heat generation, is only a few thousand years (I am not a physicist though - you might want to post this on Space.SE).

[are there organisms that w]ould have a fair probability of surviving
  in the barren oceans (or land if preferred)

Yes, if you have liquid water and CO2. If you don't, you might need to engineer something. There are various currently-available technologies for inferring the atmosphere of exoplanets.
I'd recommend sending as many species as possible to encourage the formation of a complex ecosystem (and increasing the chance that one of them survives!). The gypsum-crystal samples mentioned above contained around 40 strains of bacteria plus several viruses, so that's a start. Maybe try freeze-thawing that first. Happily (pretty much by definition) any crystals proven to contain bacteria are water-soluble, so if the planet has an ocean of water then they'll eventually dissolve, releasing their (hopefully) highly invasive payload.

[Are there organisms that would e]ventually have a change of evolving
  to more complex lifeforms?

This is the easiest one to answer: an unqualified yes. Any organism relying on error-prone information storage (so DNA, RNA, or pretty much anything else) is capable of evolution.

If possible, give a rough estimate of how likely you think that would
  be -- would we need to send 10 probes for a good chance, or billions
  of probes?

This is the problem. The reasons go rather beyond this SE (again, maybe try Space.SE) but literally any machine you can conceive based on anything more complex than chemistry or melting points is going to fail after 65,000 years in space. Forget computers, moving parts, rockets, etc. So how do you do it? You really want something that starts to melt as it approaches the other star and releases tens of thousands of packets, each containing copies of everything you're trying to seed the planet with and capable of surviving re-entry (for this, you should post another question on Space.SE - those guys are going to love you). Even so, I don't have the figures for this (again, Space.SE) but I have a very, very strong suspicion that since you're basically throwing darts at a pinhead millions of miles away you'd need to build a moon-based factory or something and fire synthetic comets/meteors containing your payload every few minutes for thousands of years. But since that's trivial compared to the travel time, and that in turn is miniscule compared to the time it'd take for the arrivals to evolve into anything worth visiting, I imagine that's fine. Launch early, launch often.
(I have posted a related question on Space.SE)

Regarding actually getting the payload to the new planet, orbital mechanics is relatively easy; doing the math to get the payload to Alpha Centauri is fairly simple. The bigger issues are:

Fuel required to push the payload to the velocities required and
Fine-tuning the approach once in the AC solar system to target the preferred planet
#2 is the real kicker because, as @arboviral and I have mentioned, spacecraft don't do that well in a vacuum, and most propulsion systems (and guidance systems, for that matter) would almost certainly fail by the time the craft reached AC.

Nice answer, thanks. Concerning the estimate of likelihood, I'd actually prefer you simply assumed the payloads could be delivered to the surface intact -- because we're indeed on a biology SE and because this allows isolating different fields, such that you can assemble a systemic estimate a-posteriori (i.e. combining engineering and biology knowledge).

There are many organisms capable of surviving in extreme environments. While 65,000 years is a long time for any organism, it is possible for some, or even all, of a 100g sample to survive long enough to reach it's destination, especially if the spacecraft were capable of keeping the sample's temperature high enough above absolute zero. I would argue that the extreme cold of space, especially interstellar space, is the most difficult obstacle to overcome in a situation such as this.
TL;DR If it can survive the journey to another planet, it almost certainly can survive on the planet. Let's assume that our organisms could survive the journey. So now let's consider the planet our little friends will be trying to colonize. Water is absolutely necessary for earth-based life to survive. You are going under the assumption that the planet is Earth-like, so we will assume that there is water. We can also safely assume that the elements required for Earth-based life is available, since these elements have been found on planets in our own solar system, and based on how planets are formed, there is no reason to think differently for another earth-like planet. The organisms' most difficult challenge may be releasing those chemicals from their original state (state at time of arrival) into a usable state. The other major issue that comes to mind is if only one species is sent and there is one major obstacle that that species isn't equipped to deal with, and they die off. There is no good way to predict all of the possibilities in this case, the best bet is to send several species and hope they get along and work well enough together to thrive. I'd say photosynthesis-utilizing organisms would have a better chance of surviving, given that the planet is Earth-like and therefore in the Goldilocks zone. Most planets have atmosphere's (even Pluto has one!), and many of them have carbon dioxide in their atmospheres. Bacteria are very adaptable and some of them are extremely resilient, and given the above assumptions, I see no reason why they couldn't survive.
Given how long it took for multicellular organisms to evolve on Earth, it'd probably take at least as long elsewhere. That being said, life is an amazing thing, and finds ways to do lots of things, so my personal opinion is that if 1 and 2 were successful, 3 is a certainty given enough time.

As for the number of probes we would need to send for this to have a statistically good chance of succeeding, I don't have any hard numbers for you, but I suspect even just one probe has a fairly good chance of working (ignoring possible issues with the spacecraft itself, spacecraft don't exactly have a great track record for longevity), and I think two probes would be sufficient.

Please note that I make several assumptions in my analysis which may or may not be accurate. Additionally, my conclusion that two probes would be sufficient is entirely my opinion, and may  be drastically insufficient in reality.


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Where is cleavage site located?
I feel a bit confused about cleaving!
Is cleavage site always located on the substrate or on the enzyme?

Hi. Your question seems incomplete. Please provide some context to your question. Also I really think this question can be googled and found easily their. Thanks.

The cleavage site is always located on the substrate. It is specific sequence of bases (if we speak about DNA or RNA) or amino acids (proteins) that is recognized by the particular enzyme and cut.

Yes, and the site on the enzyme's side is called the "active site" or "catalytic site".


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Are there organisms sensing conformations, which we humans can't sense directly?
Are there organisms which can sense the conformations, which we humans can't sense directly, i.e. without using any equipment?
If there are organisms which can sense conformations ("the shape or structure of something"; objects; example: elementary particles, atoms or anything) of sizes which we human's can't sense directly, can we know on what they are sensing, to compare on what is being known theoretically or by indirect means via equipment, for knowing them more precisely than before?
Sensing (in this context) = Knowing on how objects are at lower scale; knowing there shape, smell (!), taste, touch, sound, etc.
What is to be sensed? = It may be the properties of the conformations at lower scale, which may not be sensed directly by humans.
Organism (from wiki) = an organism (from Greek: οργανισμός, organismos) is any individual entity that exhibits the properties of life. It is a synonym for "life form".
NOTE: I had before asked on the organisms sensing conformations which humans may not have, even by using equipment. As the utility which is needed, is to know the elementary particles precisely, I have changed the question to know on organisms sensing the conformations which we humans can't sense directly, to compare with what is known from theory or equipment, and to know accurate details. And if I would have had limited the question to what organisms can sense which humans can't even by equipment, it seems to have become completely narrowed one, as humans, as said by others in the comments and answer, can sense most of smallest by equipment.

I am not a biology student, if there are sources which would allow me knowing on this, and if mentioned, it might help me.

Are you claiming that some species can sense individual protons and neutrons? I really don't understand your question. What can who sense? Are you claiming some species can sense something or are you asking if they could sense (hypothetically), then how would they do so?

Thank you for the comment. I am asking your last question if they could sense (hypothetically), then how would they do so?, and how to know on what they are sensing? This might give experiences for knowing on what QM,or any other elementary physics is trying to know.

I'm voting to close this question as off-topic because you question is based on a hypothetical situation that does not exist (and that is unclear btw) and it is therefore impossible to offer an answer that is empoirically inspired. You could give a try on worldbuilding.SE but you'll have to be way more accurate about the thing they can sense. You'll also have to be more accurate about the means of sensing. Humans can sense a whole lot of things with our complex tools (electronic microscope, LHC and others).

Sorry, I might have been not clear. I don't know on whether such organisms sensing lower scale conformations exist or not, and that is what I am asking in the main question; as said in my question, if they exist, only if they exist, how to know on what they are sensing? I might have misunderstood or not understood on the complete meaning of hypothesis, before mentioning it in the above comment. And organisms need not sense the extreme smallest elementary particles, I mentioned them as example, you can consider any small scale (atoms, compounds, etc) which humans can't sense....

So, your question is "Is there an organism that can sense 'such thing'?" and the you may ask as a follow-up how it is doing it. Make sure to be very clear by what you mean by sensing and what is the thing being sensed. Does the single proton sensing of humans count? Does electronic microscopy count? How small must the thing be that you want to sense?

Thank you for the comment. I have edited the question. I meant to say any conformation, which human's can't sense, even by using any of the equipment.

@Remi.b: I have changed the question.

Animals can sense magnetic fields

technically speaking, Large hadron Collider allowed humans to sense quite a bit of information about particles. Also, we can sense pretty well how electrons and photons behave, using other tools. We even can sense how they behave in absence of particles (it's called theoretical physics).
Closer to your point, however, it is verified that human eye (and brain) can detect single photons. There are probably similar studies about smells, maybe even electrons or electric currents.
My main point is that you need to specify exactly what you are asking. Right now it is unclear.

Sorry, if the question is not clear. I have edited the question now. If it is still not clear, can you please say on where I need to clarify?


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What animal makes these spherical sand clusters?
I encountered these structures on a beach in Hong Kong (the Ham Tin Wan beach in Sai Kung country park). There were many of these structures and I have photographed two of them in detail and attached a larger image which shows the extent to which these were spread on the beach.
It seems these were made by an animal of some sort. All these sand deposits were organised around a single hole in the ground which presumably is the animal's home or hide out. And all such structures had a clear "walking" path which was almost a straight line. These paths had no sand deposits in them.
Am I right in assuming that these structures were made by an animal? If so, then which animal makes them? And what is the purpose of the round(ish) deposits of sand around the main hole? Are they an obstacle for predators?

Image 1: A structure in detail

Image 2: Another structure in detail

Image 3: Overview of structures

Sand bubbler crabs make those sand pellets. The formations are called sand ball flowers or sand ball galaxies. The purpose is that they scrape the surface of the sand to filter and consume microanimals; then form a little sand pellet and kick it off.

Sand bubbler crabs (or sand-bubblers) are crabs of the genera Scopimera and Dotilla in the family Dotillidae. They are small crabs that live on sandy beaches in the tropical Indo-Pacific. During the low tide, they form inflated sand pellets that are disintegrated by the incoming high tide. - Wikipedia

You can watch the video below that shows how they make it:
https://www.youtube.com/watch?v=6XJtq2d_lFs

Not sure what exact species it is, but those definitely look like crab holes. They create the holes in the sand to get away from the heat and predators. They clean their homes by depositing unwanted ~sand around their door (the hole).
So yes, you're totally right in assuming those were made by an animal.

These holes were a few centimeters in diameter. Could that be a really small crab then?

Yes, those are crab holes.


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Are microwaves harmful to us?
They closed my question on the Physics Stack Exchange because it wasn't a purely physics question, so I'm trying here.
Recently I've come across the topic of scrapping microwaves, and the various warnings about the potential dangers. I've found out that generally speaking higher frequency radiation is more harmful, also that frequency itself is not the sole factor of harmfulness; as one question on the Physics site remarks the fact that microwaves and Wi-Fi use the same 2.4 GHz range, yet Wi-Fi doesn't cook. Anyway, I saw on a website:

Don’t take apart the magnetron or play with it for several good
  reasons! First, there is the obvious danger of 2.45 GHz microwave
  radiation.

There are two problems I see with this warning. First of all isn't 2.45 GHz well into the radio wave category? And also radiation of 2.45 GHz wouldn't be harmful in and of itself, right?
Also a comment from the Physics site:

wifi would be dangerous because of the microwaves, but it is limited
  to very low powers

This seems to imply that microwaves in and of themselves are harmful.

Higher frequency radiations are more likely to cause chemical damage (like to your DNA) because individual photons have higher energy. Lower frequency radiations are easily absorbed as heat but don't cause chemical damage. They are not dangerous at low power, but the high power can obviously burn.

$2.45~\rm GHz$ is well into the microwave region, which is usually defined as radio waves with a frequency of greater than $1~\rm GHz$.
Microwaves can be harmful. If you stood in front of a $1~\rm MW$ microwave dish, you would be cooked basically instantly. But that doesn't mean they are harmful in small doses: if you stand in front of a $1~\rm MW$ visible light source, you would also be cooked. You can hold your hands in front of a fire, but sticking your hands in would be bad. Like heat and visible light, microwaves aren't intrinsically harmful in moderation, but they can be deadly if you have enough of them.

Thank you, this seems to answer my question. The microwave when powered does indeed operate at a high power, but the sentence the: "obvious danger of 2.45 GHz microwave radiation" doesn't make sense if  the microwave isn't powered.  Also the sentence: "wifi would be dangerous because of the microwaves, but it is limited to very low powers", seems to imply that microwaves themselves are harmful, when in actual fact they should be less harmful than for example visible light at the same intensity... I believe.


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Why add hydrogens in molecular dynamics simulations?
In my molecular dynamics lecture, our prof said, that we always have to add hydrogen atoms to titratable groups, before we start the force field simulations, and that it is especially important for Histidine.
But why is that? Why do we always have to add the hydrogen atoms? And do we only have to do that for titratable groups, or for all?

I refer to this presentation: https://www.mpibpc.mpg.de/15151147/Lecture3_JH_20151117.pdf (On the second slide on the bottom)

Ok, and why do we only have to do that for the titratable groups?

The RCSB Protein Data Bank (PDB) presently has 137,917 structures deposited in it, of which less than 10% have been solved by nuclear magnetic resonance (NMR). Most techniques in structural biology simply cannot resolve the positions of hydrogens in macromolecular structures; only NMR and neutron diffraction provide the positions of hydrogens "by default." Therefore, all-atom molecular dynamics force fields, the most notable of which are the OPLS, CHARMM, and AMBER series, require that the positions of hydrogens be deduced from the starting macromolecular structures and geometric criteria and patterns, that hydrogen bonds are known to generally follow, if the starting structure doesn't have hydrogens. "Generally" is an important word to point out here, as there often is no unique, unambiguous way to place the hydrogens in a structure. This is especially true of histidine, where the local environment of residues and/or cofactors may perturb its pKa in often unexpected ways. Simulating histidine in the wrong protonation state, when that histidine is an active site and crucial to the mechanism and process under study, may lead to spurious, misleading, and/or potentially nonsensical results. Hydrogens are required for a faithful, (relatively) realistic description of macromolecular structure, simply because they are always present in macromolecules and are crucial for macromolecular structure and functioning - recall that hydrogen bonds stabilize the secondary structure of proteins, the DNA double helix, etc., moreover, they often mediate intermacromolecular recognition and function. Thus, an explicit representation of hydrogens is required. The so-called coarse grained force fields, the most popular of which I believe are the various versions of MARTINI, group hydrogens along with heavier atoms to achieve an increase in the simulation time step and to reduce the number of particles in the system, but these force fields are a very poor choice when modeling specific recognition and interactions.
The ambiguities of protonation are not a matter of opinion, I'm afraid. One can go through all the structures in the PDB, only to find that the majority of  them have no hydrogens at all. One can explore the link to the PDB I've provided; one will find that out of the 131,917 structures in the PDB, 123,461 have been resolved by X-ray crystallography, of which only 10,749 have a resolution below 1.5 Å. To resolve hydrogens, a resolution below 1 Å is required. Indeed, high resolution crystal structures, NMR structures, and neutron diffraction structures (only 60 in the entire PDB!) are less than 20% of the entire structural archive. Techniques like electron microscopy have resolutions between 4 and 10 Å; in such cases, people are unsure about the positions of the heavy atoms; they don't even dare think about the hydrogens. So, it's not just the titratable groups that are problematic, in most structures one can't see ANY hydrogens. Of course, for backbones and alanine side chains, one probably has a pretty good guess where the hydrogens are, given the positions of the heavy atoms. But to answer the question - in MD, most often one needs to add hydrogens everywhere, not just in the titratable groups, because the starting PDB structure doesn't have any hydrogens. In fact, often times structures from the PDB have missing heavy backbone or side chain atoms, because those couldn't be resolved; sometimes termini are missing, sometimes large stretches of protein; these often need to be modeled-in.

@xusr, please see the edit to my answer, it was too long to post as a comment.

Your statement that "only NMR provides the positions of hydrogens by default" is not true. Neutron diffraction also indicates positions of hydrogen atoms (precisely enough to be able to assign orientations of organized water molecules!).

Thank you for your comment @Guillaume, I will edit my answer accordingly.


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Why do tears fall from our eyes when we ride a bike too fast?
When we ride a bike too fast why do tears fall from our eyes. What is going on biologically and what may the evolutionary story be behind this?
This quora Q&A gives a few ideas, none of which satisfy my question fully.

This is similar to a response to smoke.

But this is clean air? Why doesn't this happen all the time?

Our eyes always need to be lubricated.

But why the need for excess tears?

Our eyes need to be covered with a thin film of liquid all the time. When riding fast, the wind flow pushes the liquid away from your cornea. Your eye compensates for that by producing more tear.


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Family eye genetics
Both my parents have brown eyes.  My older and younger siblings have brown eyes.  I have green eyes.  Is this genetically possible?  Back in 1962, this was questionable and led to family problems, which have long since been resolved.

Of course it is possible. Your parents obviously have two different allels for the eye color (heterozygous), one recessive for green/blue eyes and one dominant, for brown eyes, which is expressed in this case beacuse dominant allel determines eye color if present.  You and your siblings have inherited one allel from each parent. Your siblings have inherited at least one dominant (brown) allel from one of the parents, so they have brown eyes as well. You have inherited recessive allels for green eyes from both of them (homozygous). The chance to inherit two recessive allels in this case were 25%. I hope this helped you a bit :)

@TamaraSpipka do you have any reason to think that eye colour genetics is that simple? In fact it does not seem to be that easy Zhu et al. (2012)

There are at least three major effect QTL according to Mengel-From et al. 2009

I agree with you that it is not that simple, especially because there are more complex eye colors besides clear brown, green or blue. But the color example in the question and the question itself were very simple: 'Is it possible?' and it was quite explicable in the simple way. Don't you agree with this?

I would tend to agree it is possible (although I'd love to have a reference for it) but I disagree with the explanation provided.


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what is the difference between osciloscope and electrocardiograph?
I am completely confused about these two devices! as far as I know, oscilloscope and electrocardiograph, both, show the heat waves(P, QRS, T) so what is the difference between their job?

I would say that electrocardiograph is a specific case of oscilloscope. The main difference, perhaps is that "oscilloscope" is a device for visualization on a display ("scope" from greek "look out"), whereas "electrocardiograph" is primarily used to record ("-graph" from greek "to write").
Oscilloscope is design to visualize an electrical signal, that changes in time (generally speaking). Nature of that signal is not important, it can be radio signal, electrical signal from some device (Arduino), or sensor (thermometer). You can detect earthquakes if you have particular sensor for vibration.
It is just that these devices should output signals of particular frequency, usually general laboratory oscilloscopes are designed to work with signals up to few MHz. If you attach sensor that "feels" muscle contraction, you will have a tool for electromyography.
Electrocardiograph, by definition, is a device that visualizes electrical signals acquired via electrocardiography. It is just that usually when people and doctors perform electrocardiography, they use specialized devices, not general-purpose oscilloscope. For example, cardiac signals are usually well below 0.5-1KHz, you can save a lot of money and complexity by not having to worry about higher frequencies in your device.


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Are all hybrids infertile?
I'm familiar with the concept of hybrid infertility, but my question is: Are ALL hybrids infertile, or is it just so extremely unlikely that the chances are basically nil that they can actually produce a viable sperm/egg?
Thanks.

From today's news, an article about hybridizing between elephants and mastodons: https://gizmodo.com/ancient-elephants-and-mastodons-were-totally-down-with-1823328857#15196834320111&%7B%22sender%22:%22offer-0-WKRZx%22,%22displayMode%22:%22modal%22,%22recipient%22:%22opener%22,%22event%22:%22loaded%22,%22params%22:%7B%22width%22:735,%22height%22:854,%22iframeId%22:%22offer-0-WKRZx%22%7D%7D

Species definition
The whole problem is based upon your definition of hybrid and therefore your definition of species. If a hybrid is the offspring of two individuals belonging to different species and if we define species based on reproductive isolation, then a hybrid can, by definition, not be fertile.
However, we often call two lineages as being two different species even if they can reproduce. To get into more difficulties we could differentiate between pre-zygotic and post-zygotic reproductive isolation assisted reproduction.
You should definitely have a look at the post How could humans have interbred with Neanderthals if we're a different species? for a discussion on the concept of species.
In practice
In practice we often call two lineages as different species even though they are not reproductively isolated. In such cases, yes hybrids are fertile. In fact, hybrid can even have a very high fitness, a phenomenon called heterosis (aka. hybrid vigour). A historically important example is one described by Darwin in The Variation of Animals and Plants under Domestication; the hybrids between the common pheasant and domestic fowl are larger nd more resistant than both parents.
Note also, Haldane's rule that states if in a species hybrid only one sex is inviable or sterile, that sex is more likely to be the heterogametic sex. This is for example the case of the Yakalo (hybrid of yak and bison).
There are also cases where the hybrids are reproductively isolated from both parent species and end up creating a third species. This is called hybrid speciation.