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Questions about the evolution theory
I'm not sure whether I can ask those questions about evolution in one post or should separate them into multiple posts, but I am just curious about the evolutiontheory. (I am new here)
Sorry for my english and my many questions :)
My questions:

They say humans and monkeys have a mutual ancestor. Was it literally one ancestor? Because if so, then it would need a partner to regenerate children right?
Even if they would have children, then these children would be brothers and sisters right, which means they cannot have sex to regenerate their children?
They say that humans and monkeys have a mutual ancestor, does that mean that a certain brother's family became monkeys and the other brother's family became human?

https://en.wikipedia.org/wiki/Chimpanzee%E2%80%93human_last_common_ancestor

If humans and monkeys have a mutual ancestor, then how come humans and monkeys are so different in terms of intelligence, hygiene, clothing?
They say humans lost our fur because we don't need it anymore, but how come we still need cloths to wear to protect us from cold?
Why do humans have to brush our teeth, cut our nails, use toilets and work for our food and drinks, while any other animals don't?
Why do men and women have those specific features that make a man a man and a woman and woman? Why do women have to give birth and not men? Why do men have more facial hair growth and are built stronger than woman (while male and female chimpansees (our closest ancestors) both grow facial hair Why do men grow facial hair?)? Some people say men have more facial hair growth and are built stronger because they used to hunt (why did men hunt and not women?), but some say men hunt because they have more facial hair and are built stronger. Wouldn't it be a circle reasoning?

https://www.reddit.com/r/explainlikeimfive/comments/31zou1/eli5_what_evolutionary_advantage_does_having_long/ (facial hair because hunt)
http://www.answers.com/Q/Why_did_men_hunt_and_women_gather_in_prehistoric_times (hunt because built strong)

Why do human male and female look different compared to other animals? Why do human individuals look different from each other, but all other animals look like each other (geometrically)?

Could it be possible that we relate humans to animals, because we associate animal behavior with human behavior due to our human reasoning (which we can't help of course)? But human and animal behavior that look similar, does not mean that they have the same meaning right?
Does 'survival of the fittest' mean the following?: Humans have finger nails and a protruding nose, because animals that didn't have nails or protruding noses are extinct?
Why do humans have a chin, curly hair, eyebrows, lips and facial hair above the lips while monkeys don't?
Why do humans have this specific hairline (separation line between hair and skin)

https://www.reddit.com/r/askscience/comments/v3w3b/why_do_humans_have_such_distinct_hairlines_as/

Why can human hair and finger nails grow forever, but monkey's hair and nails don't grow that long?

https://www.quora.com/Why-dont-the-other-primates-have-long-hair

Some human emotions such as guilt and fear sometimes result in not doing anything at all, but isn't that evolutionary a disadvantage?
Humans have so little fur compared to monkeys. Which means that at some point, starting from the ancestor, the next generation lost more and more fur. At some moment there was so little fur left that generation felt cold and wore some clothing? But what about their naked parents who have about the same amount of fur?
Why are there humans and monkeys, but not intermediate forms that slowly changed from the ancestor to human or ancestor to monkey? Because they would have human characteristics but also monkey characteristic which are still there nowadays?
Could it be possible that new species are not arisen, but just discovered?
Could it be possible that all the species do not arise in series (after each other), but parallel (at the same time). Because if it would be the former, then the food chain would be incomplete?
Why do we have puberty, and why don't boys already have facial hair when they are kids (for warmth)?
They say humans find a lover because, evolutionary speaking, they want to produce children. But how come some couples choose not to have children?
Why do humans talk and write (have a language), while monkeys don't?
They say the big bang was the cause of everything, but how can material appear from nothing? (Which basically means 0=1) Even if organic molecules came from an-organic molecules, they it would still not mean that the organic molecules were living? (example: a wooden door is organic, but does not live)
They say evolution is driven by mutations. Are protruding noses and nails the consequence of mutations? But most mutations are of disadvantages (example: diseases)

First: This is ways too broad. Please limit a question to one (or maybe two closely related questions) but not 23. Here at biology.se we require people to do at least some own research to solve the question. What have you found out?

I'm voting to close because this is TOO broad - please ask your questions individually and not all lumped into one question that is unanswerable.

Do you mean I should separate it into 23 posts?

@FacebFaceb Theoretically yes, but a lot of your separate questions would still be closed because we require you to do some previous research of your own and state how it did not answer your question. (Like Chris already said.) For example your last question can easily be answered by reading the wikipedia article about mutations. https://en.wikipedia.org/wiki/Mutation

Yes, separate into 23 post if you want good answers for each question. And answering convention here mandates citation and such... so researching the answer of all 23 questions will be too much for most people.

Most definitely absolutely way too broad! Also some of these questions have nothing to do with biology (e.g. there is one question about the big bang). I am voting to close.

You might want to follow a very quick intro course to evolutionary biology such as Understanding Evolution by UC Berkeley for example. It will already allow you to answer to several of your own questions.

Also, a lot of your questions are patently ridiculous.  As for instance #2.  It's perfectly possible for brothers and sisters to have sex, and produce offspring.  In fact, it's a fairly common practice (known as line breeding) in animal breeding.  Or #8: animals, when you get to know them, are quite as distinct as individuals as humans, maybe more so.  Think for instance of the many colors & patterns that horses have.  Far more distinctive than e.g. interchangeable blonde Hollywood actresses :-)

a lot of the questions about hairlessness are pretty repetitive. I don't think you have 23 questions

Please break these up and and post specific questions, some of these are quite reasonable questions for a layman, but many have nothing to do with each other.

The post is way too broad. Many questions are unclear and many questions lack research from your part. But I still wanted to give you some info that may help you. Answers will be short but it would take a whole book to fully answer all questions.
You are often using "They" to refer to some undefined group of people and give a random straw man. Please always backup your claims with a reference. As a consequence most of your questions are opinion-based (which make them off-topic).
Intro course to evolutionary biology
First and before everything else, you should have a look at a short intro course to evolutionary biology such as Understanding Evolution by UC Berkeley for example.
Please do follow some intro course before reading the following. You will get much more from the below answers this way.
Your questions
You should read about coalescent theory.

They say humans and monkeys have a mutual ancestor. Was it literally one ancestor? Because if so, then it would need a partner to regenerate children right?

Yes, any two organisms on earth literally have a common ancestor which is a single individual. However, when thinking about closely related species as humans and chimps, the dating of the most recent common ancestor might rather correspond to a population than a single individual. It would be a single individual if there were only asexual reproduction with no genetic recombination.

Even if they would have children, then these children would be brothers and sisters right, which means they cannot have sex to regenerate their children?

See above.

They say that humans and monkeys have a mutual ancestor, does that mean that a certain brother's family became monkeys and the other brother's family became human?

If reproduction was asexual and if there were no recombination (which at this scale is not too an awful model depending on what predictions you are trying to achieve), yes one individual is ancestor of the human lineage while the other sibling is ancestor of the chimp lineage.

If humans and monkeys have a mutual ancestor, then how come humans and monkeys are so different in terms of intelligence, hygiene, clothing?

They say humans lost our fur because we don't need it anymore, but how come we still need cloths to wear to protect us from cold?

Why do humans have to brush our teeth, cut our nails, use toilets and work for our food and drinks, while any other animals don't?

I will just make one short comment for all 3 questions.
If an oak tree and a pigeon have a common ancestor, then how come they are so different? You could ask the same question with any pair of species. the appreciation of the differences is completely arbitrary.
The terms you use are all very related (all related to intelligence) and fast to acquire. You typically talk about hygiene. Showering / bathing is a very recent human activity. Just a few centuries ago, no one was ever showering (not even the kings) and people were throwing their dejections in the street in cities.

Why do men and women have those specific features that make a man a man and a woman and woman? Why do women have to give birth and not men?

For these questions, you will need to learn what a sex is, learn about sexual selection and eventually about Bateman's principle. You will note that these questions are not specific to humans.

Why do men have more facial hair growth and are built stronger than woman (while male and female chimpansees (our closest ancestors) both grow facial hair Why do men grow facial hair?)? Some people say men have more facial hair growth and are built stronger because they used to hunt (why did men hunt and not women?), but some say men hunt because they have more facial hair and are built stronger. Wouldn't it be a circle reasoning?

You are imagining a cause-consequence considering only extremes of the two variables. The reality is much more of a smooth process where gender roles happened slowly. Also, there are many factors that affect gender-specific general body size. In most species, females are bigger as females produce bigger gametes and, for the case of mammals typically, carry the baby. Gender roles such as defense, hunting and many other things explain such dimorphism. You will note that there is also similar dimorphism in chimps.

Why do human male and female look different compared to other animals? Why do human individuals look different from each other, but all other animals look like each other (geometrically)?

The first question could be asked for any species again. For the second question, please have a look at the post Why do different humans look different?.

Could it be possible that we relate humans to animals, because we associate animal behavior with human behavior due to our human reasoning (which we can't help of course)? But human and animal behavior that look similar, does not mean that they have the same meaning right?

I don't understand the question and it sounds very much a matter of opinion rather than a matter of evidences.

Does 'survival of the fittest' mean the following?: Humans have finger nails and a protruding nose, because animals that didn't have nails or protruding noses are extinct?

"survival of the fittest" is a typical expression that refers to the process of natural selection. Natural selection is a process that causes a change in allele frequency over time caused by a fitness differential associated with genetic variance. If this decision does not make sense to you, make sure to have a look at an intro course to evolutionary biology.

Why do humans have a chin, curly hair, eyebrows, lips and facial hair above the lips while monkeys don't?

Why do humans have this specific hairline (separation line between hair and skin)

Just one comment for the above two questions.
These questions only are already too broad. You will need to focus on a single trait. You will also need to get some intro knowledge to evolutionary biology as it feels like you would make the mistake of being too adaptionist and misconsidering spandrels.

Why can human hair and finger nails grow forever, but monkey's hair and nails don't grow that long?

Is this true? You will need a reference for that. I doubt chimps hair really stop growing. They probably just fall as they get long enough. I don't know much about that but I would definitely need some references to really understand in what terms are human hairs different from chimp hairs.

Some human emotions such as guilt and fear sometimes result in not doing anything at all, but isn't that evolutionary a disadvantage?

Yes, very likely. The field that studies such thing is called evolutionary psychology.

Humans have so little fur compared to monkeys. Which means that at some point, starting from the ancestor, the next generation lost more and more fur. At some moment there was so little fur left that generation felt cold and wore some clothing? But what about their naked parents who have about the same amount of fur?

I am not sure I understand the question. It feels like you are seeking for a sudden change where everybody suddenly went from being naked to wearing uniforms with bow ties.

Why are there humans and monkeys, but not intermediate forms that slowly changed from the ancestor to human or ancestor to monkey? Because they would have human characteristics but also monkey characteristic which are still there nowadays?

You should have a look at Where are the evolutionary “inbetweeners”? and Why aren't there any transitional animals today?.

Could it be possible that new species are not arisen, but just discovered?

Most species that are discovered have not arised any time recently indeed.

Could it be possible that all the species do not arise in series (after each other), but parallel (at the same time). Because if it would be the former, then the food chain would be incomplete?

I don't understand your relationship with the food chain but yes speciation events occurs in any lineages, not totally independent of each other but in a way that "feels" like something we would call a parallel process and not a serial process.

Why do we have puberty, and why don't boys already have facial hair when they are kids (for warmth)?

Have a look at an intro course to developmental biology.

They say humans find a lover because, evolutionary speaking, they want to produce children. But how come some couples choose not to have children?

While evolutionary processes can eventually select for not reproducing (see kin selection), the likely main reason for why many coupled don't want kids have to do with our culture and not with the evolutionary forces.

Why do humans talk and write (have a language), while monkeys don't?

Because we're intelligent. Many monkeys have some form of primitive communication though with a few words and a few signs.

They say the big bang was the cause of everything, but how can material appear from nothing?

This is completely unrelated to biology.

(Which basically means 0=1) Even if organic molecules came from an-organic molecules, they it would still not mean that the organic molecules were living? (example: a wooden door is organic, but does not live)

I don't understand your question. But you should have a look at an introduction to abiogenesis

They say evolution is driven by mutations. Are protruding noses and nails the consequence of mutations? But most mutations are of disadvantages (example: diseases)

The statement "evolution is driven by mutations" is very misleading if not simply wrong. Just have a look at an intro course to evolutionary biology!
In short, evolution is a change of allele frequency over time. There are various processes that can cause such changes. One of which is natural selection (NS). NS is caused by a fitness differential associated with different genotypes. It causes genotypes associated with higher fitness to raise in frequency, therefore removing genotype associated with lower fitnesses from the population.
NS therefore results in a decrease of the within population genetic variance. Mutations brings up new genetic variance in the population. It is true that most mutations are neutral or deleterious and are therefore (by definition of what deleterious mean) counter selected and will eventually disappear from the population. The few beneficial mutations that occurs may eventually increase in frequency through NS and eventually reach fixation (that is a frequency of 1) in the population.

Re "Why do men have more facial hair growth...", one might ask why male deer have antlers and females don't,  or why male lions have manes, peacocks have gaudy tails... Which gets you into the whole subject of evolution by sexual selection.

This is impressive. Well done.

1    They say humans and monkeys have a mutual ancestor. Was it
  literally one ancestor? Because if so, then it would need a partner to
  regenerate children right?

First off.. human and monkeys do not a mutual ancestors. Ape and monkeys have a mutual ancestor. Humans are a type of ape. Gorilla's are a type of ape.
It was an ancestral population. If we had a time machine, what we would see an ancestral population, then at some point in time the population got divided. The populations continue to have babies and accumulate mutations. Until so many genetic difference were accumulated the the two populations could no longer produce fertile offspring. That tipping point occurred 25-30 million years ago in Africa.
http://www.livescience.com/32029-oldest-monkey-fossil-found.html

2    Even if they would have children, then these children would be
  brothers and sisters right, which means they cannot have sex to
  regenerate their children?

No reason why not? Evolution does not care about dead babies or morality. Only humans do.

3    They say that humans and monkeys have a mutual ancestor, does
  that mean that a certain brother's family became monkeys and the other
  brother's family became human?

Not exactly. Ape and monkeys have a mutual ancestor. Let say 31 millions ago, there might have been a family of pre ape-monkey. Said family might have had two brothers. Then 1 million years later, the descendants of one brother might have been come apes while the other become monkeys.

If humans and monkeys have a mutual ancestor, then how come humans and monkeys are so different in terms of intelligence, hygiene, clothing?

Well the last common ancestor was 30,000,000 years ago. 30 million years is a long time. The average life span in the us is about 75 years. The human species is only 200,000 years old. Domestication of dog only 25,000 years.

They say humans lost our fur because we don't need it anymore, but how come we still need cloths to wear to protect us from cold?

Well humans evolved from homonids who evolved on the Savannah of Africa. Nice and warm. 5 million years of evolution to survive in a place where the danger of death by heat stroke was real. Humans only left africa about 60,000 years ago. Only left the tropics and ventured into higher latitudes of asia and europe 20,000 years ago.  https://genographic.nationalgeographic.com/human-journey/
Just not enough time to evolve fur coats.

Why do humans have to brush our teeth, cut our nails, use toilets and work for our food and drinks, while any other animals don't?

Civilization. And the fact that you don't want to stave to death once you lose your adult teeth. And animals do clean and groom themselves. Cats, ape, monkeys, birds and dogs.
Why do men and women have those specific features that make a man a man and a woman and woman? Why do women have to give birth and not men? Why do men have more facial hair growth and are built stronger than woman (while male and female chimpansees (our closest ancestors) both grow facial hair Why do men grow facial hair?)? Some people say men have more facial hair growth and are built stronger because they used to hunt (why did men hunt and not women?), but some say men hunt because they have more facial hair and are built stronger. Wouldn't it be a circle reasoning?

Sexual dimorphism. Most animals have it. In fact the sexual dimorphism in human is rather small only about 10-15%. Sexual dimorphism in gorilla for example is nearly 260% where males gorilla range between 350 pounds (160 kg.) and reach 400 pounds (181 kg.), while females only about 155 pounds (70 kg.) and much less muscular. http://anthro.palomar.edu/primate/prim_7.htm
The question you should ask is not why men are stronger than women. Most male apes are bigger and stronger than female apes, most extremely so. The question you should ask is why women are nearly as strong as men. Why is sexual dimorphism in humans astonishingly small. The gibbon is one other ape that has such small dimorphism. The interesting thing between human and gibbons, both species are mostly monogamous. ie on average one male does not physically dominate all other males and mate with all the females in the tribe.

Why do human male and female look different compared to other animals? Why do human individuals look different from each other, but

all other animals look like each other (geometrically)?
  Because you are human. I am sure to other animals all humans look alike. In birds the difference between gender is very obvious. Males have one plumage, different colours and feathers. While females have another. In lions and dear and asian elephants, walrus, elephant seals and narwhals, the difference between males and females are also very obvious.

Look at dogs, cats. The variation in dogs far exceeds that in humans.

Could it be possible that we relate humans to animals, because we associate animal behavior with human behavior due to our human

reasoning (which we can't help of course)? But human and animal
  behavior that look similar, does not mean that they have the same
  meaning right?
  The difference between animals and humans are a matter of degree.
Does 'survival of the fittest' mean the following?: Humans have finger nails and a protruding nose, because animals that didn't have

nails or protruding noses are extinct?

No. Survival of the fittest also have the aspect of context. A fish is vastly more fit in the sea compared to a human. A bear is vastly more fit than a weaponless human on a river side.

Why do humans have a chin, curly hair, eyebrows, lips and facial hair above the lips while monkeys don't?

They do. they also have fur.
Why do humans have this specific hairline (separation line between hair and skin)

No idea what you are asking.
Some human emotions such as guilt and fear sometimes result in not
  doing anything at all, but isn't that evolutionary a disadvantage?
  Humans lived in tribe. In fact we evolve from an animal that lived in tribes. A lone homonid on the open savannah was easy food for a lot of animals. I have a strong suspicions that there was immense selection pressure for individuals who stayed with the tribe, and had behaviors that maintained the tribe.
Humans have so little fur compared to monkeys. Which means that at
  some point, starting from the ancestor, the next generation lost more
  and more fur. At some moment there was so little fur left that
  generation felt cold and wore some clothing? But what about their
  naked parents who have about the same amount of fur?

Cause the naked parent lived in the tropic of Africa. While the clothed offspring lived 40,000 years later in the higher latitudes of Asia and Europe, after 1000s of years of slowly moving northwards.

Why are there humans and monkeys, but not intermediate forms that
  slowly changed from the ancestor to human or ancestor to monkey?
  Because they would have human characteristics but also monkey
  characteristic which are still there nowadays?

Because nobody can sit still. Evolution continues to happen. Even the intermediate forms will continue to change. Why do you think apes are?

Why do we have puberty, and why don't boys already have facial hair
  when they are kids (for warmth)?

Because all mammals have puberty. It takes resources to grow up, become an adult and have your own babies. Childhood is the time to accumulate puppy fat and learn skill (even lions and wolves need to learn how to hunt). The question that should ask is why human childhood is so long.

They say humans find a lover because, evolutionary speaking, they want
  to produce children. But how come some couples choose not to have
  children?

Some couples are infertile. Development might not have gone right, so one member or both are either completely infertile or both have reduced fertility. Also sometimes it is better/more successful to help a sibling raise their children and have your own. Many reasons.

Re "... between human and gibbons, both species are mostly monogamous."  Huh?  Don't know much about gibbons, but most humans sure aren't, unless forced to be by legal or religious pressure.

Even in cultures that  today still legally allow polygamy... most people are monogamous. Most guys are not  wealthy enough to maintain more than one woman and her children. And most man are not such a great catch that the woman is willing to be a sister wife and share his fortune. Only the wealthy and powerful ever practice polygamy in human cultures.

Well, you pretty well prove my point when you say the wealthy and powerful practice polygamy when they can, which makes it a matter of resources/opportunity rather than an inherent monogamous nature :-)  But I am not talking about maintaining women & children (which is economics), but about sex.  For instance, studies showing that various percentages of children weren't actually sired by the legal parent, or the common practice (in the West) of serial polygamy through divorce and remarriage.

And can you name a human culture where 95% of the men fail to have children. And most women are in married and have children only with the remaining 5% of men. That is what a polygamous species is like. Most males fail to breed. Most offspring are fathered by a very few males. I don't understand your point. There still places in the world where polygamy is legal both in the court and religion. And even then most people are monogamous in those cultures.

We are obviously using different definitons of the word 'monogamous'.  I prefer the dictionary definition of  "having only one mate".  You seem to be defining polygamous as a very extreme case, while in fact very few species are truely monogamous.  The reality seems to be that where they have a reasonably free choice, humans make a pretense of social & serial monogamy, while a significant number have sex outside that relationship.  Also realize that among humans, reproduction is only a secondary factor in sex.

I guess I am seeing the word from a biological perspective. Human are by and large a mostly monogamous species. Most of the males do get to father children. Monopoly of female fertility by high status males is not as absolute as say elephant seals.


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Are epicanthic folds a dominant trait?
My state (Tripura) originally had a mostly mongoloid-feature-possessing population (ethnic group: Tripuri). Recently a large number of non-mongoloid people (ethnic group: Bengali) have migrated to Tripura.
Assuming that reproductive barriers are not present between these two subpopulations in future, are epicanthic folds likely to be a prominent feature of the new hybridized population?
I've found some non-scientific discussions here and here.
In this newspaper article, an anthropologist is cited as saying the following:

Poirier attributes the fold to pleiotropic genes--single genes that control more than one characteristic or function--but he has no explanation for its origin

This is an interesting question. What did you find when you googled this question? Please show us your research results. Thanks!

@anongoodnurse, There were several sites where I found answers which are not backed by research  and no genetic rationale but by everyday observation.So I didn't put them in question.

@ItachíUchiha You can link those sites anyway stating that you don't know whether the sources can be trusted. These sources may always help one to answer.

I did some preliminary searches but could find nothing about the genetics of epicanthal folds in normal people. The only references I could find were about epicanthal folds in a variety of genetic disorders. Sorry. :(

@anongoodnurse,please don't be sorry.Thanks a lot for your efforts. ^_^

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What kind of (cinnamon?) tree is this?
This tree was found in the rainforest on subtropical Japanese islands. At first I thought that it was a camphor tree, which are indeed common in Japan. However, the leaves are slightly different and elongated, and the fruit  has a sharp tip and is much larger than that of camphor trees. The bark is very aromatic and smells like good cinnamon, perhaps a bit peppery. Any ideas?

It has 250 species!

This is the Japanese cinnamon, Cinnamomum tenuifolium, or "Yabu Nikkei" in Japanese. It smells like cinnamon and is found from the middle of Honshu (Fukushima prefecture and southward) throughout Shikoku, Kyushu, Okinawa, and into China. It is the native and more commonly found cinnamon species in Japan that grows wild in forests. The other species is Cinnamomum sieboldi, which was introduced to Japan in the early 18th century from its native Indochina via China. C. tenuifolium is distinguishable from C. sieboldi by its much more symmetrical arrangement of leaves, as depicted in your photograph.
This page also details the differences and similarities to other related species in Japan, however it is only in Japanese:
Camphor/Cinnamon species in Japan.

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Book recommendation to know and understand the brain and the phenomena and processes related to it
I need a book recommendation or, more properly, any source recommendation to know and understand more about the phenomena related to the brain, as far as we know how the brain works. I'm interested in the very structure the brain has and how it leads to what we experience. Due to the way biological processes happen, how the things we define for ourselves are related to each other. It would be cool if it adds more to the biophysics of those processes and the possible picture of their evolution, as well as the physical characteristics of those biological structures.

I have been away from stackexchange for long if the question is not according to the site's guidelines please edit it or if you can make the question better please do it (I know I wasn't that good at it). I didn't find any other question or answer helping so I asked it, if there's any question or answer already that can help please add it into comments.

Your question would be a better fit on CognitiveSciences.SE. In fact your question is possibly a duplicate of this post.

I'd agree with @Remi.b to check CogSci - the recommendations in the linked question will probably get most of what you want, but your question touches on a lot of areas that probably won't all be found in detail in the same book; you will probably find more on biophysics in a more basic neuroscience textbook like this question; I'd expect more coverage of evolution of behavior in an Animal Behavior textbook.

My other advice is that I'd recommend staying away from "evolutionary psychology" because that field is tainted with a lot of pseudoscience and disguised speculation, and it will be difficult to evaluate the claims critically without a lot of background knowledge.

@Remi.b the books suggested into the answers to that question possibly aren't answering the questions i do have, neither there's much of discussion about the books in the answer. I checked on CogSci.SE few simillar questions were there but the recommended books weren't really getting around what i want as I have mentioned in the question, and few were bit perspective based.

@BryanKrause Yeah what I want I might not get in the single book , It's not necessary for it to be a single book but the ones which are really good getting around the questions. Ok I will remember your advice. And the question you mentioned helped. I found recommendation of those same books before coming to SE,they seem to be bit expensive purchase but yeah they seem going with the subject. It will be helpful if somebody can recommend some similar books not that long and expensive but as cool as them. If you think I will get better answers to the question on CogSci can my question be migrated?

Probably the best options for general knowledge are going to be textbooks, which unfortunately are going to be expensive. However, there are also lots of used textbooks, so you might be able to find a used, older edition of the books that people recommend that is much more affordable. There are some more affordable books in the pop-science category, but those can be problematic; Steven Pinker for example is an entertaining writer, but his books are meant to be persuasive: he won't give you an unbiased perspective of the literature (and one of the reasons I warned about evolutionary psychology)


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Is there a term for a procedure in which the chromatography column is washed with 20% alcohol
From a method description in a Russian document:

After the chromatographic analysis is complete, the column is flushed with at least 2-3 volumes of water at a rate of 0.4 ml/min. The column is then mothballed (?) by washing it with at least 10-15 volumes of 20% alcohol at a rate slowly declining from 0.4 ml/min to 0 ml/min.

The word I translated as "mothballed" is konservirovat (консервировать колонку) in Russian. It has the general meaning of "preparing something for storage" (for instance, "preparing vegetables for storage by pickling").
In an effort to determine the correct terminology, I would like to know the reason why a chromatography column would be washed with 20% ethanol. Any recommendation on the standard biochemical terminology for this procedure, if it exists, would also be welcome.

You have accepted an answer (which alternative?) that allows you to do what I consider the wrong thing. The right thing would be not to try to translate but to explain what it is the 20% alcohol does. What does it do? Remove uneluted protein, prevent bacterial growth, or what? If you know, say, followed by "before storage".

@David thank you for the good advice, but I don't always have time to investigate the issue that deep when translating a large text. I write questions to the authors, but that takes some time too.

@tomd Perhaps you can add this as an answer.

Prepared or conditioned for storage would probably be perfectly acceptable.
If you're looking for a single-word equivalent, in this case, I would translate as stabilized. From dictionary.com:

stabilize
[stey-buh-lahyz]
verb (used with object), stabilized, stabilizing.

to make or hold stable, firm, or steadfast.

This seems appropriate, since one wants to ensure maintenance of the proper condition of the column for later usage, when taken out of storage.

I don't like "stabilize" because it implies that the column is unstable otherwise, which it isn't.

@David , I'm not familiar with the technique in detail, so I'm poorly equipped to evaluate it from that perspective. Is it stable in storage without the ethanol washout procedure?

I suspect it will either get clogged up or bacteria may grow on it, but I'm not sure. I don't think the beads will disintegrate though.

The ethanol is indeed to prevent microbial growth.

@canadianer Hmm, so preserve might be better than stabilize?

Possibly. I don't think information about how the columns are stored is really very necessary when describing methods.

This is a routine procedure in FPLC to prepare columns for storage. 20% ethanol is used to prevent microbial growth. See this technical note:

All SEC columns are delivered in 20% ethanol to prevent microbial growth.

I have always found it strange that we only use 20% ethanol, why not add 0.05% sodium azide for further protection as some microorganism will grow in 20% ethanol alone.

@JeppeNielsen It's an interesting point which I don't have an answer to. I store gravity flow columns in sodium azide.


text:
Relationship between food decay and electric current
I am planning to do a little experiment on investigating the relationship between food (organic) decay and the electric current.
I am going to place the food (ex.banana) on top of an aluminum foil, then hook the foil to a battery.

However, this doesn't seem convincing that it's going to work.
Is there any better way to experiment this?

I'm not sure if this falls under "biology" category
Also, it doesn't have to be banana, it could be avocado, lettuce, apple etc.
Thank you

What do you expect will happen?

I expect that food decay will slow down since the current might zap the bacterias @bpedit

Nice drawing of the experiment. However, I do not expect you will find anything. As a reference: electroporation is an extremely common method used in laboratories, many bacterial cells survive, and a pulse of ~12500 V/cm is used. Please don't try this at home, because I expect already a fraction of this pulse will lead to exploding bananas.

Bananas, unless you like mush, become inedible long before any bacterial decay. The brown spots and softening that occur are due to ripening  processes in the banana. Some of the amino acids in the banana are metabolized to produce ethylene. As with other fruits, ethylene acts as a hormone to accelerate the conversion of starches to sugars. The banana gets sweeter while at the same time getting musher. http://www.livestrong.com/article/466183-is-eating-a-banana-with-brown-spots-bad-for-you/
As far as your experimental design, you would need to stick electrodes into the banana to attempt to run a current through it. But I doubt this will work because, to conduct the current inside the banana, there needs to be a certain amount of water, free ions and the structure to allow the ions to move. In my opinion, bananas have too little moisture content for this to occur.
Aiming to affect bacteria on the surface of the banana might be a doable experiment. But the methods that come to my mind involve immersing the banana in an electrolytic solution possibly leading to un-yumminess and not at all guaranteed to work.


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Is vermiform appendix no more a vestigial organ?
The appendix has a role in the immune response.
So is it therefore recently removed from the list of vestigial organs?

Short Answer: No, the appendix is still considered a vestigial organ.
Long Answer: The idea that that vermiform appendix is vestigial originated when Kumar et al (1989) removed it from the body, but failed to find any side-effects. From then on, it got widely established that vermiform appendix is a vestigial organ and has lost all its functions during the course of evolution. The reason behind appendix becoming vestigial was given by Darwin himself in The Descent of Man, and Selection in Relation to Sex where he stated that appendix was used by early primates to digest leaves, and slowly became vestigial as ancient humans shifted towards foods like cereals and meat. This theory was also supported by presence of very long cecum in herbivores like koala and horse.
The only problem with this idea was that the role of appendix in only digestion was being considered. As appendix was connected to large intestine, so early scientists (kinda) presumed that it should be related to only digestion.
This theory got its first challenge when Parker et al (2007) suggested the appendix to be a safe-house of healthy bacteria when illness (such as diarrhea) flushes them out of the GI tract. It was based on the understanding, which came in 2000s by Sonnenburg et al (2004) and Everett et al (2004), about how the immune system supports the growth of beneficial intestinal bacteria. This was experimentally established when Dunn et al found that individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile colitis.
After this, more functions of appendix were discovered, especially those related to immune system. It is because of the efforts of Zahid et al (2004) (the one you cite) and Rankin et al (2016) that appendix is now identified to be more related to immune system than digestive system in humans.
Also, research by Laurin et al (2011) and Smith et al (2013) concluded that during the evolutionary course, appendix has evolved about 38 times and lost as many as 6 times, suggesting that the cecal appendix has a selective advantage in many situations and argues strongly against its vestigial nature.
Conclusion:

Vermiform appendix is identified as Gut Associated Lymphoid Tissue (GALT) and important component in mammalian mucosal immune function, B-cell mediated immune response and extrathymically derived T-cells.
This structure helps in the proper movement and removal of waste matter in the digestive system, contains lymphatic vessels that regulate pathogens, and lastly, might even produce early defences that prevent deadly diseases.
It is thought that appendix may provide more immune defences from invading pathogens and getting the lymphatic system's B and T cells to fight the viruses and bacteria that infect that portion of the bowel and training them, so that immune responses are targeted and more able to reliably and less dangerously fight off pathogens.

Discussion: The problem is in the definition itself of vestigial organs. The point is that being vestigial is not equal to being useless. See this definition by Wikipedia (emphasis mine):

In the context of human evolution, human vestigiality involves those traits (such as organs or behaviors) occurring in humans that have lost all or most of their original function through evolution. Although structures called vestigial often appear functionless, a vestigial structure may retain lesser functions or develop minor new ones. In some cases, structures once identified as vestigial simply had an unrecognized function.

Now, since vermiform appendix does not perform its (suggested) original function of digesting cellulose and other indigestible materials, and performs much less of its (possible) function in immune system, it is still officially considered as vestigial organ.
References:
• Vermiform Appendix - Wikipedia
• Human Vestigiality - Wikipedia
• Kumar, Vinay; Robbins, Stanley L.; Cotran, Ramzi S. (1989). Robbins' pathologic basis of disease (4th ed.)
• Darwin, Charles (1871) "Jim's Jesus". The Descent of Man, and Selection in Relation to Sex
• Bollinger, R.R.; Barbas, A.S.; Bush, E.L.; Lin, S.S.; Parker, W. (21 December 2007). "Biofilms in the large bowel suggest an apparent function of the human vermiform appendix"
• Sonnenburg J.L.; Angenent L.T.; Gordon J.I. (June 2004). "Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?"
• Everett M.L.; Palestrant D.; Miller S.E.; Bollinger R.R.; Parker W. (2004). "Immune exclusion and immune inclusion: a new model of host-bacterial interactions in the gut"
• Dunn, Rob. "Your Appendix Could Save Your Life"
• Zahid, Aliya (2004-04-01). "The vermiform appendix: not a useless organ"
• Rankin, Lucille C.; Girard-Madoux, Mathilde J. H.; Seillet, Cyril; Mielke, Lisa A.; Kerdiles, Yann; Fenis, Aurore; Wieduwild, Elisabeth; Putoczki, Tracy; Mondot, Stanislas (2016-02-01). "Complementarity and redundancy of IL-22-producing innate lymphoid cells"
• Laurin M.; Everett, M.L.; Parker W. (2011). "The cecal appendix: one more immune component with a function disturbed by post-industrial culture"
• Smith H. F.; Parker W.; Kotzé, S. H.; Laurin, M. (2013). "Multiple independent appearances of the cecal appendix in mammalian evolution and an investigation of related ecological and anatomical factors"

How is it concluded that vermiform appendix had original function of digestion?

@jm97 I ain't sure about this...I suppose Darwin's theory?

@JM97 many herbivores have a large appendix that functions as a sort of protected space for their gut bacteria, so a single bad food or illness cannot deplete their gut bacteria.

Short answer
The appendix is a vestigial organ.
Background
According to the Oxford Dictionaries vestigial means:

Degenerate, rudimentary, or atrophied, having become function-less in the course of evolution.

This doesn't mean that a vestigial organ necessarily has to have no function at all, as in the case of the vestigial wings in mutant fruit flies for example that serve no purpose whatsoever.
The appendix has lost all of its original food digestive functions, and therefore it is,  per definition,  a vestigial  organ.  However,  it still has a role in immune responses.

It turns out that the vermiform appendix is NOT a vestigial organ based on Darwin's definition.
Without rehashing what the appendix actually does, I'll quickly address the faulty arguments that it is a vestige.
Point 1: Darwin called the appendix a vestige because it was a remnant of a larger cecum used for digestion:
RESPONSE to Point 1: In most cases of evolution of the appendix (as we assessed with our collaborators in France and Arizona), the appendix is actually getting larger (or appearing) as the cecum gets larger. The appearance of the appendix in the anthropoid apes is an exception. So the appendix, in general, cannot be characterized as the remains of a cecum in the ancestral state.
We covered this in a paper published about 5 years back: World J Gastroenterol
2013; 19(34): 5607-5614.
Point 2: Related to point 1, the idea is that the appendix still has some function, but has lost it's digestive function.
RESPONSE to Point 2: Based on what we know about its function, the vermiform appendix has ENHANCED functions in terms of maintaining beneficial bacteria compared to a cecum without an appendix. In other words, in some regards, it has more function, not less function, than the ancestral state. (Thus explaining the tendency of it to occur repeatedly in evolution more than it is lost.)
Discussion: The human arm is probably akin to our appendix in many ways. We would never think of our arms as a vestige even though we do not use our arms for locomotion as did our ancestors. But we still use them, in some ways probably more than our ancestors, and we still need them.
The definition of a vestige in biology does cause confusion. In my lab, we prefer to think of a vestige as a structure that is best understood based on a function that has been lost rather than on a current function. Darwin meant it to be descriptive, not to cause confusion. In English (non-biology), a vestige means simply a remainder of something that is gone or disappearing. (e.g., the vestiges of colonial rule) It is best to think of the odd wiring of facial nerves, the wings of flightless birds, or the hip bones in certain legless animals as vestiges. These are much more clear-cut cases, where the current structure is best understood when one understands both the structure and the function in the ancestral state.  This does not apply to the human arm or to the vermiform appendix, of course.


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Are antibodies and hepatitis viruses of similar adaptability?
Antibodies and Hepatitis viruses both have hypervariable regions.
Is one more adaptable than the other?
Precisely how adaptable are they?
I have read that antibodies can be trained to bind to almost any antigen, is the same true for Hepatitis?
Long-Term Evolution of the Hypervariable Region of Hepatitis C Virus in a Common-Source-Infected Cohort
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC110045/
I guess the first step to answering this is to find/conduct a study in which the Hepatitus virus is mutated and selected for a particular antigen. I am not sure if this has been done, but it definately has been done for antibodies.

Can you please add some references for the variable region of the hepatitis virus?

My initial thought is that this question is either too opinion-based or too broad, the comparison between members of different categories, and the measure of "how adaptable" is non-specific and environment-dependent.

@BryanKrause Can It be trained to attach to a particular antigen? how adaptable means how many antigens can it be trained to identify.

First off, you probably mean antibody-producing cells; a given antibody can't be trained or adapted, it's just a protein, and it will bind whatever fits in its antigen-binding region. I don't think it's really reasonable to count the number of antigens, because there doesn't necessarily have to be a one-to-one ratio: a given structure can potentially bind many different antigens, as long as there exists an appropriate motif that "fits."


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Cocoon like bug on exterior walls south florida

Can anyone tell me what this is? One side of my house has 30 to 40 of them. when I try to pick them off they leave either brown spots or fibers from the cocoon. Is there anyway to deter them?

Could you provide approximate size/dimensions. Also, given that you have so many, could you post a picture of what's inside?

Are they all "plastered" to the the side of the house as this one appears to be, or are they dangling down, too?


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Which organelle is the easiest to see in a cell?
I was asked a question in class: "Which organelles are easiest to see in any cells while using a microscope?"
This seems a little bit like a trick question, and since I'm not an expert in cellular biology, I'm not sure which organelle to go for. A cursory google search only lays out what organelles exist, and isn't clear on practical lab details.

Can you be more clear about why you are interested in this question? I would say the nucleus is the most obvious feature of most cell types unless stained for something particular, but good luck finding one in a red blood cell... Words like "any" and "all" are always going to be dangerous in biology.

I need this answered for hw in general what would be the eaiest organelle to see on a microscope.

You said you looked everywhere online, did you try searching for something like "easiest organelle to see"?

Could you elaborate your problem a little more?

This reads like a homework question without much in the way of attempts-to-solve — I'm thinking maybe it should be closed?

@AsherF. I agree this question should be closed. A google search for exactly the title gives the same answer (nucleus) in basically every one of the top results besides this one, and this is really just an introductory cell biology, hey let's start thinking about what the components of a cell are question rather than a serious biological question.

Request to reopen. Though it looks like homework question; it is rather different type. It might help the learners to get practical experience on the cell, and to apply the common sense. The general answer is nucleus, due to a larger size; in plant cells the vacuoles could be even much more larger; and chloroplasts; though not as large as nucleus; or sometimes close in size; but larger than most other organelles, are clearly distinguishable due to their colour.

A quick google revealed this slideshow that says the nucleus is the easiest organelle to see. Generally, this is what is taught in schools worldwide. Note that mature red blood cells don't have a nucleus, so this isn't a universal rule. The visibility of the nucleus also changes throughout the cell cycle.
In case they are trying to trip you up, double check what the definition of an organelle is. The easiest cellular structure to see is the cytoskeleton by proxy of the cytoplasm. The cytoplasm forms the largest portion of the cell, it can be easily identified as the space between all the other organelles, and it is universally present in all cells. Indeed, many definitions of an organelle allow cytoplasm and all should allow the cytoskeleton.

any of a number of organized or specialized structures within a living cell. -Google

or

a structural and functional unit, such as a mitochondrion, in a cell or unicellular organism - Dictionary

However this is the kind of answer akin to "skin is the largest organ in the human body", and isn't what your homework is guiding you towards.

I don't think the cytoplasm is typically considered an organelle; I would suggest editing that out of your post unless you can find a reliable source that shows that some sources do indeed classify "cytoplasm" as an organelle. I'd like to avoid confusion.

@BryanKrause It's certainly a cellular structure rather than a classic organelle. The part that is more traditionally considered an organelle is the cytoskeleton. I'm not really too fussed about semantics, and it's clear in the answer that the cytoplasm isn't really a good answer. That being said, definitions themselves don't seem to rule out the cytoplasm. I'm curious; did you have a specific definition of an organelle that rules the cytoplasm out?

While there are a lot of definitions of organelle, particularly between eukaryotes and prokaryotes, my main objection about the cytoplasm is that it isn't really...anything. It's sort of defined only by what it isn't: it isn't the nucleus. Everything else is cytoplasm. So while the cytoplasm definitely contains organelles it doesn't seem like it is an organelle itself; you couldn't define a function of the cytoplasm, sort of like you wouldn't call the "abdomen" an organ. I would agree with you that the cytoskeleton is an organelle.

@BryanKrause I've made a quick edit, but I think in all likeliness this question will be closed (I would initiate the vote if I hadn't already answered). Currently, it's a fruitless semantic argument - the cytoplasm is membrane bound and does carry out specialised functions within the cell. We would need to really tighten definitions up. Clearly, it's important in a research topic to understand what something does, not what it counts classically as. For us to answer in this case if cytoplasm should be counted among the ER etc, we need more clarification from OP (which I doubt will happen).

Yes I agree with respect to the ultimate fate of this post. I guess to me the difference is that you could, at least theoretically, "remove" the ER from a cell and then say "What was the result?" Same thing with a ribosome, etc. You can't really do that with cytoplasm; if you did you would just have a nucleus. Anyways we apparently already have a question on this - both bpedit and Joce do better in their answers at explaining their positions than I am here.

@BryanKrause It's a fun question! I tutted when I read whereas cytoplasm is just a fluid in which the other cells are surrounded (ie, passive). Just a passive fluid, is it? It's the bedrock of all life as we know it! "Passive" indeed... I honestly think that there are a few broken words in biology. "Organelle" is one, "subspecies" is another. They were invented in simpler times and the respective fields have moved on so far in understanding the complexity of the true situation. Yet we are relentlessly trying to force things into these out-of-date boxes... I'll kick off the close vote.

Let us continue this discussion in chat.


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Which organisms require the least fluctuation in ambient temperature?
Note that I am NOT asking "which organism can survive the most extreme temperatures." Many extremophiles like the tardigrade can survives extreme heat, but also extreme cold. Many heat adapted animals like the camel can also tolerate fairly cold conditions. I want to know what species that are adapted to hot climes are hot climate obligates (or the corollary for cold climate obligates) and which extreme temps-obligates have the narrowest tolerance.

the icefish must have a pretty narrow band of temp tolerance since they have no hemaglobin and the really cold antarctic water is loaded with O2

I don't have a precise answer for this, but if you want to do some more research on your own to try to find answers, I have two guesses for directions to take: 1) Parasites of warm-blooded hosts. I would expect these to have some mechanism for survival between hosts, like a spore or egg phase, but they would do all their growth, reproduction, etc, inside a nice, comfy host and they would have enzymes adapted for the host condition. 2) Extremophiles, like you mention, that are so adapted for strange conditions such as ocean vents that they cannot survive outside these areas.

(also, if you are wondering about animals you really need to specify animals; otherwise, unless you are talking about sizes of individuals or something like that, "what is the most" or "what is the least" questions have a high probability of leading to bacteria/archaea, or if you need a eukaryote then protists)

@BryanKrause obligate-symbionts is a really good thought since their host takes care of providing a homeostatic environment. Thanks for that thought!
I thought about ocean vents, but in reality, those environments fluctuates quite a bit since the temp varies wildly at the boundary layer between deep-ocean cold water and magma-hot water.
Also, just to note, I'm not specifically asking about animals, but I suspect sedentary organisms probably adapt for greater fluxes since they cannot cope with temp changes through vagility.


text:
Can Oxaloacetate cross the outer mitochondrial membrane?
I am aware of the Malate–Aspartate Shuttle, but something is not clear to me and different sources seem to contradict each other. Some show oxaloacetate (OAA) being reduced to malate in the mitochondrial inter-membrane space (IMS), whereas others show the reduction happening in the cytosol.
Where does the OAA → malate reduction happen? i.e., can OAA cross the outer mitochondrial membrane (from the cytosol into the IMS) so that it can be reduced in the IMS, or must it be reduced in the cytosol before crossing either of the two mitochondrial membranes?

I've edited your question a little. I defined the abbreviations you used. This makes the question clearer and I mention it in the hope that it will help you in formulating future questions. (It is not necessary to abbreviate malate to mal to save three characters, so I spelled this out in full.)

In general the outer mitochondrial membrane is thought to be basically permeable (through porins) to small molecules such as OAA. As is typical in biology, the situation may actually be more complex -- see for example this paper. But I think the default assumption is that metabolites freely cross the mitochondrial outer membrane.
You might also ask whether either the mitochondrial MDH or the cytoplasmic MDH enzyme is likely to be found or be active inside the intermembrane space.

Good point about considering which enzyme is active. Thank you for the concise answer.

Oxaloacetate (OAA) cannot cross the inner mitochondrial membrane.
The process of oxidative phosphorylation and the electron transport system (ETS) occur in the mitochondrion, whereas $\ce{NADH}$ generated by the reduction of $\ce{NAD+}$ in glycolysis is in the cytoplasm. The problem is that the inner mitochondrial membrane is not permeable to $\ce{NADH}$ , so a shuttle system is required for the transport of the reducing equivalents through the mitochondrial membrane. There are two of these, one of which is the ‘Malate–Aspertate’ shuttle.

In the process (see above) oxaloacetate (OAA) takes up the reducing equivalents from $\ce{NADH}$ to form malate in a reaction catalysed by malate dehydrogenase. The inner mitochondrial membrane is permeable to malate, which passes through carrier proteins (Malate-$\alpha$-ketogluterate transporter) into the mitochondrial matrix where it is converted back to OAA. As this happens the concentration of OAA decreases in the inter-membrane space, and as OAA cannot pass directly through the inner mitochondrial membrane it is converted into aspartate in the mitochondrial matrix by reacting with glutamate to produce $\alpha$-ketoglutarate and aspartate. The aspartate then travels  to the inter-membrane space through specific carriers(Glutamate-aspartate Transporter). In the inter membrane space the aspartate combines with $\alpha$-ketoglutarate to form glutamate and OAA (the reverse of  what happened in the mitochondrial matrix). Thus the concentration of OAA is maintained in the inter-membrane space, and the reaction continues.
Conclusion
OAA is converted into malate in the inter-membrane space. In the mitochondrial matrix malate is converted back to OAA, as illustrated in the illustration below.

Image source : Malate–Aspartate Shuttle, Wikipedia

I have edited your answer extensively. Although what you wrote about OAA and malate seems reasonable, your remarks about reduction were incorrect (reduction is the addition of an electron, not an electron and a proton) and there is no such molecule as NADH+. Further an illustration in Wikipedia cannot prove a 'fact'. A fact is a fact, and is established by experiment.

Thank You for the edit. But I have one question, addition of an electron is definitely reduction, but can't I say the addition of an hydrogen as addition of an electron and proton, in that case it is also reduction. I am not arguing ( and definitely it was my fault) but it can be said like that. And about the 'fact' - some people prefer such sources , they think that an answer is incomplete without a citation from a notable site or book and they don't even judge whether the answer is reasonable or not.

This is the textbook answer, but there are also studies suggesting that oxaloacetate can cross the inner mitochondrial membrane, see for example http://www.sciencedirect.com/science/article/pii/0003986177900200
It might be that this is cell type and/or condition dependent. Or perhaps the transport rate for oxaloacetate is too slow.

In reply to your response to my comment. 1. On the reduction reaction. First, it is not necessary to discuss it in answering this question, which doesn't even mention it. It is, of course, relevant to explain that the problem is the transfer of NADH into the mitochondrion and NAD+ out. But, as I wrote, there is no such molecule as NADH+, so this mistake detracted from the virtues of the answer. Indeed the figures you reproduce show NADH. As for your question, there is no addition of a proton, but of two hydrogen atoms, and the balanced equation is: NAD+ + 2H ⇋  NADH + H+.

In reply to the second point in your comment. Of course, it is expected that you quote sources in support of your answer, and Wikipedia is useful because it is free to access. In fact your figure wasn't support for your argument, but an aid to the reader in understanding it. The fact that someone had gone to a some trouble drawing it lends authority to your point of view, but many of us are rather suspicious of Wikipedia entries (any one can edit them) and so are unhappy about statements that they support facts. (I realize that it is also a question of facility in English and experience.)

jyoti: Thank you for your detailed explanation. However, it does not directly answer my question and I tried to show I was already assuming this information by staying "I am aware of the Malate-Aspartate Shuttle". My interest in whether OAA can cross the /outer/ mitochondrial membrane. You seem to have deliberately avoided addressing this, mentioning how NADH must be imported then suddenly you speak about OAA already being in the IMS (without mentioning how it got there).

(continued) I find it interesting that you picked two illustrations that both show OAA in the IMS, when most of the other diagrams I saw through Google do not depict the IMS at all and rather show the OAA reduction occuring in the cytosol. Either way, I think we may be beyond textbook illustrations as they may not have been created with the subtleties of this issue in mind. Namely, how does OAA cross the outer mitochondrial membrane (if it does at all)? Is the outer membrane somehow more "leaky" than the inner? Could this be related to the endosymbiont origin of the mitochondrion?

There are porin channels in the outer membrane which make it more permeable than the inner one


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What type of insect is this? Is it ant or something else?
I was sitting under morning sunshine when I saw this:

At first, I thought that it is a common Indian black ant. But it was moving much faster. Also, it seemed to have 2 (or probably more) eyes (sorry, couldn't take images as 'twas too fast). The most surprising part was when it leapt over the chair WITH A WEB! (just like a spider). Also, its mandibles(?) are much bigger than an ant's. Is it some kind of hybrid of ant and spider. I recently read that in some caves new varieties of spiders, which look like beetles (or maybe opposite) have been discovered. Is this related to them?
Details: I found it in Northern Plains, India. Its length is almost 1 cm (maybe bigger) and breadth is about 0.5 cm (actually slightly smaller than that).

This one is an ant,Common Indian black ant.Ant being an insect has 3 pairs of legs but this one his has 2 pairs,must have got it's body cut. The small projections at front are the antennae.

@another'Homosapien' I see you found the other half :p. Cool find.

Such a queer species. I thought it was an ant. But it is actually a spider.
These spiders belong to Salticidae family,commonly called ant-mimicking spiders / jumping spiders.

They are  Batesian mimics of ants, such as Sphecotypus in the Clubionidae.

They do not feed on their model organisms and keep them at an acceptable distance.
This one is from Myrmarachne sp. There are more than 20 species found in India.

Source:

Wikipedia
Myrmarachne

@another'Homosapien' If you are not an expert on the group, or can find extremely conclusive evidence that points to one specific species, you shouldn't push to add a specific species name. Species information on the internet is scattered at best, and you cannot expect to be able to identify every single species based on google searches and a couple of websites. There is no problem of leaving it at the family name or Genus sp., if that is what is relatively certain.


text:
what chromatin factors are the most potent supressors of meiotic crossover?
I think linker histone H1 is probably involved, but the literature is scant.  What else prevents crossovers from becoming hyper-frequent during meiosis?


text:
What is the step by step procedure that leads the T cell to release chemokines?
When T cell receptors bind to the receptor of an antigen presenting cell, is this what leads to the release of chemokines? I know that T cell release of chemokines leads to the migration of other T cells to the area of infection. What is the step by step procedure that leads to this release of chemokines from a T cell?


text:
where i can download reference MSU7 rice genome?
I am working with RNA Seq data analysis. I have to download MSU7 rice genome. somehow i downloaded from
"http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/ "
. But i am not able to find Annotation (.gtf) file and reference genome (.fa) file . so how can i find and how can i download..help me

You can find this on the phytozome website. You will have to make a free JGI account to access it


text:
what is the meaning of the genotype values in each snp
I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are
C,T.
My question is what is the meaning of 0,1,2 genotypes under each snp id (rs#) , and how it is related to the snp ?

I won't post this as an answer, as I really can't find any comprehensive source. Basically you are looking at SNPs from a diploid individual. Therefore it can either be homozygous for an allele or heterozygous. Heterozygous SNPs are encoded by 1. For homozygous ones it is usually 0 if the individual is heterozygous for the major allele (in the population or the one found in the reference in pairwise comparison) and 2 if it is heterozygous for the minor allele. Although this might in fact be different in different formats. 0 and 2 are always homozygous and 1 heterozygous, though.

Note that there is now a beta bioinformatics stackexchange site where this question might receive answers: https://bioinformatics.stackexchange.com/


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Why spermatogenesis is an independent process while formation of ovum is dependent on fertilization by sperm?
At the time of ovulation,secondary oocyte is arrested at Metaphase II and goes into the fallopian tube.If fertilization occurs, sperm binds with secondary oocyte and releases Anaphase promoting factor which leads to completion of meiosis II,ovum is formed and it subsequently gets converted into zygote.
My question is that why formation of ovum is dependent on fertilization by sperm and why formation of sperms is independent process? Has it some benefits for nature?

This can only be answered logically. Imagine bellow paragraph.
If secondary oocyte does not require fertilization for completing 2nd meiotic division then it will become an ootid (female gamete). Once formed lots of hormonal changes occur in female example individual's diet increase, mammary glands differentiate and all necessary changes for pregnancy which will be unnecessary at end of every month.
I hope u understood and comment if u want to ask about above imaginary paragraph.

Downvoters do not necessarily need to explain, in part because those explanations often result in rude comments like the one you just posted. Don't do that. You've posted a bunch of answers recently that are below the standards of the site and that's likely why you are getting downvoters. Please improve your answers as suggested by the post notices if you want your answers to be received positively.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Hedgehog AP Bio question
Could someone please explain this AP Biology question? I know the answer is C but I do not understand why. Doesn't Smo prevent gene transcription? If you "block its activity" then wouldn't it cause gene transcription, whereas the goal of treating cancer is to prevent transcription? Please help!

Reread the line: "When Hedgehog is absent, Ptc inhibits another protein known as Smo"; Hedgehog is present in the cancer cells, so what you want to do is to mimic Hedgehog's absence. The question is hard because there is a lot of inhibitory and disinhibitory activity in this pathway, so that's what you have to do, try to follow all those +s and -s; it might be helpful to draw the whole thing out as a block diagram, and to take that approach with similar questions in the future.

Thank you! This was actually helpful, I think the information was worded a little weirdly - "When Hedgehog is absent, Ptc inhibits another protein known as Smo, which, in turn, blocks the activation of a group of proteins..." I think I was thrown off by the end of this sentence, because the way the sentence is constructed makes it seem like when Smo is inhibited it blocks the activation of a group of proteins, when it was actually the opposite idea!

I'm just going to outline the alternatives, I'll leave validating why choice C to you.
Choice A. If the new molecule acts in the same fashion as Hh, the results will be identical. If the new molecule bound to Pct but did not effect a response, that might work.
Choice D. Addition of Ci into the nucleus initiates transcription which seems to be the issue here.
Choice B. Best wrong answer! Can you inject enough stem cells to make a difference? Will the cells have some adverse effect? More importantly, the binding of messengers to receptors is a reversible process. The Hh will be able to detach from Ptc on the stem cells and eventually interact with Ptc on the native cells.
So, what effect will Hh have if the Smo in unable to respond?

Thank you! This was great! Especially your justification for B and explanation that binding to receptors is a reversible process. Now I why that choice was incorrect! :)


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How to dialyze large amounts of precipitated enzyme solution (ammonium sulfate)?
I am no biochemist, but I want to purify some liters of solution through dialysis. What I know are those dialysis tubes in glas vessels on stir plates for labs. But how is this done in industry for bigger quantities in an affordable way?
Background: The solution contains a precipitated enzyme (183 kDa) with ammonium sulfate (132 Da). I want to take away the ammonium sulfate to get back the active state of the enzyme.

Ammonium Sulfate (AS) precipitation is used to concentrate protein. After AS precipitation, you would centrifuge the sample to pellet the protein and then resuspend it in a small volume of water or buffer. You can then dialyze this small volume.
There are other methods of concentrating large volumes of protein, including chromatography and ultrafiltration.


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What is the purpose of two cell divisions in meiosis?
At the moment, my thoughts are that the two cell divisions are necessary for recombination to occur, although I am not sure. I cannot really see why technically, the chromosome from each parent cannot just recombine with the other chromsome when each is a single DNA strand and not in the form of two sister chromatids joined at the centromere. Something tells me that there are several reasons why there are two cell divisions. Perhaps the S phase of interphase triiggers some further stages of cell division such as cytokinesis, and the splitting of the cell will not occur unless some DNA replication has taken place? However in meiosis 2 there is no further DNA replication, so this can't quite be right...

For developing a 2N cell, we need a N cell from each parent. In any division(meiosos or meitosis), chromosomes are doubled at first. In firs meiosis a 2N cell in divided into two N cells and as you know these N chromosomes are doubled( 2N chromatids). In second meiosis a N cell is divided into two N cells but this time chromosomes are not doubled(in fact N chromatid cells)
1.Firs division in meiosis is needed because we need N cells to combine, if they are 2N the result of recombination is a 4N cell.
2.Maybe your question is: why a 2N cell is not directly divided into two N cells without doubling? the reason is same in mitosis and meiosos, it is because of a stage of division as you know it is called anaphase in which a kind of protein, connects centromer to centriol, this stage is needed because we need one chromatid of each chromosome in each cells so if this part is not done there is no guarantee to have all N chromosomes in both cells and in fact a kind of distribution is made.
( I hope that I could understand you, well.)


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What is allele-specific binding?
So far all I have found is this:
https://www.biostars.org/p/132527/
My guess is that some alleles, for whatever reason, bind to things like transcription factors 'moreso' (for want of better word - affinity maybe) than others. Or maybe some alleles are more likely to get methylated, for example.
I feel my understanding is very much bare bones. Is anyone able to go through it a  little more comprehensively? Thanks


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Save endangered parasitic species?
It seems to be an important issue the parasitic control and even some pursue the eradication of some species. Most of the researchers in parasitology are focused on the host damage and population regulation. How do we perceive and value the function of parasites? Is it really needed a change in paradigms and views of dependent species? How important is to conserve them?

are there any parasites that are endangered of extinction? Even smallpox is extinct only in the wild.

This is an interesting subject but it sounds like you're focusing on the ethical aspects, which are probably too opinion-based to be a good fit for this site. Can you clarify what you're looking for a bit more?

Although we think of parasites as harmful and tend not to consider them for conservation, they do peform valuable functions including population regulation and the development of immune systems. More philosophically, under the 'intrinsic value' argument sometimes used for conservation, every species should be considered to have an intrinsic right to existence, regardless of its ecosystem function, harmful effects on other species or appeal to humans.
Conveniently, this article has just been published on this very subject. :)


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Sex linked genes?
I am learning about genetics and sex-linked traits. All of the X-linked traits we have considered (eye colour in Drosophila, Duchene Muscular Dystrophy to name a couple)follow the rule that, a female will only express the phenotype if she has both of the alleles and a male will necessarily express the phenotype if his X chromosome contains the allele.
However this got me thinking, is there a gene that requires two copies to be expressed (and not just due to dominance considerations)? I.e., are there any x-linked genes which, even if the male has this gene, it will not be expressed as there is one copy of it only (despite the fact that this gene is on a non-homologous region of the X chromosome and therefore there is no second allele to this gene present in the male). In that case only the females could express this trait if they are homozygous for the allele, and men would never exhibit the trait.

then why is the other x chromosome gets inactivated?...

@JM97 I'm afraid I didn't understand your question :/

What @JM97 appears to be saying is that in females there is a process called X-chromosome inactivation which shuts down one of the chromosomes to prevent females having a double dose of a particular gene product. This would invalidate your premise that genes that require a double-dose of expression (as it were) could be only expressed in females.

It is not easy for an individual to figure out if it is haploid or diploid at a given sequence. To my knowledge, this is feasible only by searching for specific case of heterozygosity.
The most famous case is mating types in yeasts. In yeasts, haploid cells have mating types. Individuals are either "a" or "$\alpha$". Individuals can only fuse with individuals of a different mating type. As a result all diploid cells contain both the "a" allele on one chromosome and the "$\alpha$" allele on the other chromosome. The "a" sequence codes for proteins that can bind only the proteins coded by the "$\alpha$" sequence. If "a-$\alpha$" dimers are formed, then the cell "knows" it is diploid. Read more about it on wikipedia > mating of yeast.
Following this, a cell could figure out what sexual chromosome it has by searching for heterozygosity. This is typically NOT how gender determination works in mammals. I can't think of a specific example where this would be a thing but I would surprise if it is not.


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Why haven't environmentally-reactive bodies developed as an evolutionary advantage?
Regardless of region, earth's tilt results in yearly seasonal changes, which organisms deal with through processes like migration/hibernation. Both seem like attempts to avoid the extreme fluctuations... so why haven't certain organisms developed environmentally-reactive bodies, changing with the seasons throughout the year (based on measures like temperature- I.E., additional fur growth during the winter), and why hasn't this continued as an evolutionary advantage to allow organisms to thrive in longer
environmental ranges (like staying in place instead of migrating) or even go a step beyond and take advantage of the qualities specific to each season?

What on Earth makes you think they haven't?  Certainly my dogs & horses grow much thicker coats during the winter, and shed them during the spring.  I believe that's true of many wild animals - e.g. fur trappers think winter pelts are better quality.  Also a number of Arctic animals change color, becoming white during the winter.

@jamesqf it's also true of humans. For example, small capillaries are rerouted away from the skin after spending time in cold weather and back towards it if spending time in the heat.

@jamesqf great information. Can you think of any reasons migration has been favored over more extreme body-variations regarding these seasonal changes? Is there an advantage to moving as opposed to staying put? Most animals are constantly on the move regardless and I assume that's an advantage in survival.

@Taytee: I think (I'm certainly no expert) that it'd mostly be a matter of food supply.  If you're a large grazing animal, in winter your food is dead grass under the snow, so it's economically beneficial to migrate.  (Also migration can be between elevations in mountain ranges.)  Likewise if you're a seed/fruit eating bird, or a nectar-sipping hummingbird. It's easier to go where there's food, than to try to survive a foodless winter.  Same reason bears &c hibernate.

@jamesqf totally makes sense! Animals likely migrated historically due to reasons along those lines, and since those specific species migrated and ended up in an acceptable environment again, it was never beneficial to develop a focus of seasonally-reactive biology. Interesting to note as well that it may be an early sign of animals engaging in a behavioral pattern to solve a problem instead of leaving it up to natural selection.

Hibernation itself is also a pretty good example of an environmentally-reactive physiology. It's not just behavior (sleeping longer), but a huge amount of metabolic and other changes (recycling urine in bears!).  https://en.wikipedia.org/wiki/Hibernation Without that set of body changes, the behavior would be harmful.

What you call environmentally-reactive is called phenotypic plasticity.

You could improve this question if you could give some evidence to support your assumption that this hasn't been favored over things like migration. I am pretty sure that's very simply wrong. I don't have numbers handy, but I would guess most species that live for a year or more have developed precisely the sort of thing you describe. Migration isn't as common as all that (I am ignoring hibernation since it is a perfect example of "environmentally-reactive bodies", pretty much the definition, actually).

This question shouldn't be closed. It has been answered in the comments.

As Jamesqf pointed out, food supply was likely a big contributor. As a general expansion onto that, I believe a sufficiently reasonable answer could be that animals likely found solutions (I.e. migration and hibernation) to deal could with seasonal factors out of their control (like lack of resources) before natural selection leading to more defined adaption could/would've taken place. Their behavior dealt with the problem- which leads to another interesting idea that it could have been an early sign of organisms using their intelligence to survive and change the course of natural selection.


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Where do mushrooms get their energy from?
I'm wondering where field mushrooms get their energy from.
I've heard that they can easily grow on soil in a dark room. So, it seems to me that there wouldn't be any photosynthesizing plants from which they could get energy. Also, as far as I know, they don't have seeds from which they could directly get energy initially.
So, I have two questions:

Where do mushrooms get their initial energy from? (The spores, if that is the right term)
Where do they get their energy from in later stages? (If there is a difference at all)

Plant-physiology is an incorrect tag because fungi aren't plants.

The difference between plants is also related to your question because plants get their energy directly from light and fungi from organic material.

Mushrooms are the fruiting bodies of fungi. Fungi get their energy by decomposing dead or decaying organic material, such as fallen leaves or dung.
Some background: spores of fungi germinate forming mycelia consisting of threadlike hyphae. When the hyphae of different fungi meet, they may have sex and form mushrooms. The mushrooms produce the spores. See https://en.wikipedia.org/wiki/Fungus.
So, each of these stages get their energy ultimately from decomposition, although the mushrooms get their energy from the mycelium. Spores rely on their internal energy storage to germinate and start decomposing. Even though spores are tiny, the have energy stored, like all cells do.

Why don't you add a link for further reading?

The Wikipedia pages on this are OK, but not really an authoritative source.

@Daan in that case, maybe alternative sources?

Add them still. Thez are accepted as sources for general topics and really helpful for further reading, especially for laymen.

Research mushroom " metabolism/enzymes/catabolism/respiration/glycolysis" to read nice texts of concise info for that topic.
Mushrooms use enzymes to break down cellulose and substrates into smaller substances and eventually they use CO2 for respiration, glycolysis, and ATP production.
https://books.google.fr/books?id=xmB_DYPp9LIC&pg=PA49&lpg=PA49&dq=mushroom+metabolism&source=bl&ots=mEkG_WGfaY&sig=9XAXzpPgSMHkRg_8kPjE1LIYatQ&hl=en&sa=X&ved=2ahUKEwjfwJvjmLLdAhXjx4UKHUiiA_UQ6AEwA3oECAkQAQ#v=onepage&q=mushroom%20metabolism&f=false
Cellulose is not that different from sugar and mushrooms get sugar from it using cellulase and lignase enzymes, although some mushrooms dont have cellulase. https://www.google.fr/url?sa=t&source=web&rct=j&url=https://www.researchgate.net/post/What_are_the_nutrients_required_for_the_growth_of_mushrooms_like_oyster_and_shiitake/amp&ved=2ahUKEwj4pLC3m7LdAhWRyIUKHf27DD0QFjACegQICBAB&usg=AOvVaw2b-TTVDZHQBcS8l-TMYmz0&ampcf=1
Its the digestion process is probably a complex physical absorption by the hyphae, so research hyphae structrures, they must be cool.
https://www.ck12.org/biology/fungi-nutrition/lesson/How-Fungi-Eat-BIO/


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In reconstructions, how are various shapes of facial features determined from skull only?
I have seen reconstructions (with skin, eyes, muscles etc) of some first humans based on skulls and skeletons. But how can the shape of nose (protruding part), shape of eyelids, shape of eyebrow, hairline be determined base on the skull only?
Examples of these reconstructions:

Disclaimer: I am an evolutionary geneticist. I know nothing about anatomy and forensic methods....
You should just have a look at wikipedia > forensic facial recognition. There are a number of different facial reconstruction methods, one of which is the so-called Manchester method (see a review of the Machester method in Wilkinson 2010).
In any method of facial reconstruction, there is some part of artistic representation to fill the gap of what we fail to infer from the tissues available. It is typically not so uncommon esp. for recent(-ish) fossils to have remains of soft tissues as well. In absence of such soft tissue, the morphology of the mouth and ears are typically left to artistic interpretation.

'artistic interpretation' sounds rather subjective and so says Wikipedia. But that means that the reconstruction does not necessarily represent the original

Yes, that's what it means. It means that there are things we don't know and we just go with our feeling.


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Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?
I have a data set of de novo assembled RNA-seq datasets across different sample types.
When BLASTing, many of the matches of the individual transcripts match to the same gene on the reference genome. However, each individual transcript has its own unique FPKM value.
I'm confused, firstly, as to how you can have multiple sequences from the same gene with different FPKM values — and of course, I'm also wondering what would be a suitable approach for the subsequent analysis. Should I just add the FPKM values together for the sequences with the same matches?

If the quantification is done at the transcript level, each identified transcript of a given gene will have a different number of reads attributed to it, hence a different RPKM value.
For the subsequent analysis, you can continue at the transcript level.
I think you cannot sum the FPKM values directly, because they are inversely proportional to the transcript lengths ("K" stands for "by kilobase"). If you want to do the subsequent analysis at the gene level and use FPKM values, you would have to multiply the FPKM values of the transcripts by the corresponding transcript lengths before summing. Then you will have to divide this sum by the gene length, or something like that.

Indeed you can't sum FPKMs, and nowadays you should probably try to void using them in the first place (they have some bias, but are still widely used). But even if you get the raw counts per transcript, you should not directly sum them to get counts per genes.
If you got your counts using Kallisto or Salmon, the easiest way is to either use sleuth to work directly on transcripts, or tximport to sum counts and input them into DESeq, edgeR or another program.


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How is epinephrine and norepinephrine different?
Is there any difference between epinephrine and norepinephrine?
https://www.quora.com/What-is-the-difference-between-epinephrine-and-norepinephrine
This site says that norepinephrine is also a neurotransmitter.
Is there any major difference between them?

Epinephrine: https://en.wikipedia.org/wiki/Epinephrine
Norepinephrine: https://en.wikipedia.org/wiki/Norepinephrine

Please can you list the major differences.

But little amount of epinephrine also serve as a neurotransmitter.
Iam mentioning here some of the differences I found out myself when I had the same question.
If you need further reading you can visit the site  as mentioned by @Spartacus9
https://en.wikipedia.org/wiki/Epinephrine
https://en.wikipedia.org/wiki/Norepinephrine
1)Norepinephrine is mostly made inside nerve axons and released when an action potential travels down the nerve.
Epinephrine is made from norepinephrine inside the adrenal medulla.
2)Norepinephrine acts mostly on alpha receptors.
Epinephrine is relatively non specific,stimulating both alpha,beta1,beta2,beta3 receptors more or less equally.
3)In medicine, norepinephrine is used to increase and maintain blood pressure related to cardiac arrest,spinal anaesthesia,septicaemia,etc.
Epinephrine is used in medicine to treat low blood pressure associated with septic shock and also for the emergency treatment of allergic reactions.


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Why does pink colour reduce aggressiveness?
According to this Wikipedia page, a shade of pink colour known as "Baker-Miller_Pink" has been known to reduce aggressive behaviour.
Is there any biochemical reaction responsible for this?
Specifically, are any hormones responsible for this?
If yes, then which ones?

Where did you find this claim? A source would be good...

You can just see in the wikipedia

Please put your sources in here, your question might otherwise be close as "primarily opinion based" or unclear.

The page on Wikipedia says - research has shown conflicting results....,  also see this ( http://www.orthomolecular.org/library/jom/1988/pdf/1988-v03n04-p202.pdf )

Thanks I read about that.But my question is different.

Some research have been done recently by a set of scientists different from what JM97 mentioned and their results too contradicted what was believed to be the effect of this shade of pink from the earlier experiments performed in 1970-1980. The paper.

I'm voting to close this question as the quoted hypothesis is not valid according to recent published papers.

I think this question should remain open - a good answer should probably contain proposed hypotheses for the effect and any data towards a mechanism and/or a refutation of the existence of the phenomenon. I don't think a question should be closed based only on a faulty premise.


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Influence of carbon dioxide concentration on the rate of photosynthesis
The experiment to prove that carbon dioxide concentration influences the rate of photosynthesis:
Click here to see the image
The experiment is repeated after adding some sodium hydrogencarbonate (which dissolves in water to produce carbon dioxide) to the water. It is observed that more oxygen bubbles are produced, and thus this shows the increased photosynthesis rate.
My question: The equation for the dissolution of sodium hydrogencarbonate is NaHCO₃ (s) ⟶ NaOH (aq) + CO₂ (aq). But won't the sodium hydroxide turn the solution basic and also influence the rate of photosynthesis?
Thanks in advance,
Ramana

@ bpedit. One of my friends (who is a biologist) said that when hydrogencarbonate dissolves, it forms carbonic acid which turns the solution acidic. But how? He says that the hydrogencarbonate combines with the hydrogen ions in solution to form carbonic acid......

Unimaginable that this question passes unanswered for over three years. It is very important to understand the advantages of increased carbon dioxide levels.


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What is the brain's preferred energy source? Glucose or ketones?
As with all cells in our body, I know that the brain can get fed from both glucose and ketones, so my question is, given both of them, which one would the brain prefer to utilize first?

Can you explain what you mean by "preferred"? The brain mostly metabolizes glucose only.

By preferred, I mean, given the choice for either, which one would it use first  @BryanKrause

"The brain gets a portion of its fuel requirements from ketone bodies when glucose is less available than normal (e.g., during fasting, strenuous exercise, low carbohydrate, ketogenic diet and in neonates)" from https://en.wikipedia.org/wiki/Ketone_bodies @BryanKrause

Exactly - it is only during those special cases that ketones are even available for metabolism, and the reason ketones are made available is a drop in blood glucose below sufficient levels.

My question comes from learning about https://en.wikipedia.org/wiki/Caprylic_acid which apparently increases ketone bodies in your body even if you aren't in one of those states @BryanKrause

First of all, for those readers with less knowledge of the general principles of biology, I want to state an important, even if obvious, point: The brain doesn't
"prefer" anything. Despite being the smartest organ in the body, it is subjected (like any other biological system) to changes in the concentrations of the substances in question, that is, glucose and ketone bodies.
According to a study in rats from 2010, it seems that ketone bodies suppress glucose metabolism in order to conserve glucose when its concentration is too low for the body to be used regularly. Therefore, the ketone bodies are regarded as neuroprotective, since their metabolism prevents the brain cells from starving.
Another study in rats from 2013 emphasizes this point further. Please note the following excerpt from the discussion section:
The brain's ability to switch from glucose oxidation towards ketone bodies requires a type of ‘cerebral metabolic adaptation'. This process is not well understood but is thought to be highly associated with the duration and level of ketosis. Ketones are considered to supply up to 70% of the total energy demands once maximal metabolic adaptation occurs. Blood ketones become elevated during prolonged fasting or with a ketogenic diet reaching a state [of] ketosis and glucose sparing. During this process, monoca[r]boxylic transporters upregulate at the blood–brain barrier with increasing demand for ketone utilization by brain. Recently, investigators have recognized additional therapeutic properties of ketosis, such as neuroprotection after stroke or injury. What remains unclear is whether the neuroprotective or therapeutic properties of ketosis is as a result of changes in the regulation of metabolic signaling pathways...
This means that when the balance of concentrations shifts toward the ketone bodies, they will have precedence over glucose in order to conserve the latter. The mechanism is probably upregulation of ketone bodies receptors and transporters that increase its transport into the brain, as stated above.
Therefore, when the brain is given both ketone bodies and glucose (which actually happens in the fasted state - ketone bodies transport and metabolism in the brain begins when blood glucose is low, not zero), there will be "preference" for the ketone bodies, but this depends on the glucose concentration. If it shifts back, above a certain glucose concentration glucose metabolism is supposed to be renewed.

Thanks for your answer, I guess this partly answers my question. What's left to know is how much of a difference in concentration does it need to be in order for the brain to use ketones, like someone doing low-carb and consuming Caprylic-Acid, how low carb does that person need to go to get the brain consuming ketone bodies.

Long story short. Burning glucose it’s the easiest, most « efficient » and laziest way your body supply energy to your brain. Fat on the other hand is harder to break for the body. But, the ketones produced during the combustion of the fat cells have unsuspected properties making them of a much greater benefit to the brain health, with benefits that includes: better decision making, acute intuition and sereinity.
I hope this helps.
YO
P.s; Fat is the preferred source of energy but the body will use glucose first (Fast for 3 days, enter ketosis, maintains carb intake under 50g and enjoy feeding u brain ketones for as long as you can). Plus, while writing I remembered that the brain is made out of fat to start with. What is more natural, intuitive and logic than feeding the brain with what look alike?!

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