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Is anaerobic activity during ketosis possible?
When a person's glucose and glycogen stores are depleted, which can occur due to fasting or due to a diet consisting largely of fat (like eskimo diets), the body produces its energy by breaking down triglycerides into fatty acids.  Fatty acids can be then converted to Acetyl-CoA, which can consequently enter the citric acid cycle, generating ATP.*
Now normally when a cell does not receive sufficient oxygen to undergo its natural processes, it usually breaks down glucose anaerobically to generate ATP and lactic acid.  However, in the case where the body is running off fatty acids (e.g. fast, or fat/protein only diet), how does the body respond to such anaerobic situations?
*(Note:  In this situation many fatty acids are first taken up into the liver and converted to ketone bodies, which are subsequently converted to Acetyl-CoA after being taken up in the required tissues, hence causing "ketosis" as in the title)

You are correct in thinking that fatty acids cannot be metabolised anaerobically. However, in the type of metabolic state that you are describing, blood glucose will be maintained by the liver to support tissues or cells which are more or less dependent upon anaerobic metabolism. The classic example of such a cell type is the red blood cell which as no mitochondria and so cannot use the TCA cycle. The brain is also heavily dependent upon glucose.
The liver exports glucose that it has produced via gluconeogenesis from amino acid skeletons, as well as from glycerol produced as a result of fat metabolism.

In reality, a cell will die almost immediately in such anaerobic conditions.  The question itself can be taken another way.  That is, how does the body fuel anaerobic metabolism in the relative absence of glucose.  It is important to understand that stored ATP and CP (creatine phosphate) provide energy anaerobically, but can be refueled by beta oxidation of fatty acids that occurs between bouts where energy needs exceed oxygen supply.  So someone on a high fat diet with virtually zero carbs is going to perform their anaerobic work mostly from ATP-CP without having to turn to gluconeogenesis.  Glucose obligate tissues, primarily the brain, nerves, liver and pancreas will require glucose (or ketones) in the absence of endogenous glucose, and so they will need to receive these via gluconeogenesis of canabalized tissues or consummed protein, however the brain does not last for more than about 30 seconds on fast glycolysis anyway so to say that the body makes glucose from protein to allow anaerobic metabolism to go on is not accurate.  The body turns to gluconeogenesis primarily to provide substrates for glucose dependent tissues to use in oxidative phosphoylation, not in anaerobic pathways.
At any rate, the ANSWER to the question as posed "Is anaerobic activity during ketosis possible," YES because you have stores of CP and ATP that don't require oxygen to access, but gluconeogenesis during ketosis is not activated by a need for anaerobic energy sources (fast glycolysis) but by glucose dependent tissues need for glucose for oxidative phosphorylation.

Two points to you as a new contributor. 1. It's best to provide sources in support of assertions, e.g. "the brain does not last for more than about 30 seconds on fast glycolysis" (what do you mean by fast glycolysis, anyway?). 2. Wbat do you mean by "the oxidative phosphorylation needs of the brain"? Oxidative phosphorylation is a means to an end (production of ATP), not a need in itself.

It may take a few posts on this S.E. to get a feel fort what is considered to be a baseline level of knowledge in biochem.

Will work on an edit. "Oxidative Phosphorylation needs" should be "aerobic energy needs" "Fast Glycolysis" is glycolysis that results immediately in lactate/pyruvate rather than "slow glycolysis" which is going to send substrates directly into the TCA cycle.

http://www.biomechanix.net/a-quick-breakdown-of-fast-and-slow-glycolysis/

Something wrong with your link. It points to a page that gives me a "401 Forbidden".

The link gives me the article with no problem

Just rechecked on my iPhone (previously was from my Mac desktop or laptop) and still get the 401. Not sure why this would be. Seldom get 401s.

Actually it's giving me a 403 (forbidden) on my office Mac using Safari, Chrome or Firefox, and on a Windows machine I had never previously used with IE. Looking up Biomechanix on the web gives me commercial sites in US and Oz concerned  with physical therapy and "professional trainers" (the latter giving me a 403). Having read the Google extract "CSCS professional trainers are the absolute highest level of trainer you can work with and we take pride in the fact that BioMechanix Strength and Conditioning", I wouldn't think anything they say about glycolysis would be of interest here.

It is a textbook cited article on a commercial sports performance website.  To summarize, fast glycolysis is a term that refers to glycolysis that proceeds to lactic acid because the cell has insufficient oxidative capacity to process all of the glucose through the Krebs cycle.  In humans is is primarily present in high work output type IIb msucle cells which are low in mitochondrial density.  It fuels short bursts of work output that exceed the cells ability to produce energy through oxidative glycolysis, or when oxygen can not be brought to the cell fast enough.

Fast glycolysis then is the exercise physiology term used for anaerobic glycolysis, but it generally refers to the pre-Krebs cycle portion of glycolysis even if it ends in Acetyl-CoA entering the mitochondria.  I suppose that in exercise physiology it has garnered the name "fast" glycolysis because it is mostly important in providing short term energy for energy needs that outpace oxidative glycolysis.


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How does HCl not burn our stomach?
How does the digestive acid (HCl) not burn the surrounding membrane of our stomach? It digests the majority of raw food we eat but how does it stay safely in our stomach?
Also, how does the stomach maintain the ability for a human body to retain HCl for all lifetime?

What do you mean by "how does the stomach retain the safety procedures for a human body to retain it for all lifetime"?

Just as a note, ulcers occur when stomach acid does break through the mucus layer.

Mucous-producing cells at the neck of the gastric pits create a layer of protective mucous covering the stomach lining. This mucous layer includes bicarbonate ions which act as a chemical barrier against the protons in gastric juice.  See here for some evidence.
The stomach lining stays protected because the mucous layer is continuously replenished.

This is why stomach acid will burn and break your stomach after you die - the mucous layer is no longer replenished then. Since it isn't any enzyme but acid that is breaking down the organs, I don't think this can be called autolysis though.

Cause of this secret are tight junctions and mucous.
As Wikipedia explains:

Tight junctions, or zonula occludens, are the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates. The corresponding junctions that occur in invertebrates are septate junctions.

They perform vital functions:They hold cells together.Barrier function, which can be further subdivided into protective barriers and functional barriers serving purposes such as material transport and maintenance of osmotic balance:They help to maintain the polarity of cells by preventing the lateral diffusion of integral membrane proteins between the apical and lateral/basal surfaces, allowing the specialized functions of each surface (for example receptor-mediated endocytosis at the apical surface and exocytosis at the basolateral surface) to be preserved. This aims to preserve the transcellular transport.They prevent the passage of molecules and ions through the space between cells. So materials must actually enter the cells (by diffusion or active transport) in order to pass through the tissue. This pathway provides control over what substances are allowed through. (Tight junctions play this role in maintaining the blood–brain barrier.) At the present time, it is still unclear whether the control is active or passive and how these pathways are formed. In one study for paracellular transport across the tight junction in kidney proximal tubule, a dual pathway model is proposed: large slit breaks formed by infrequent discontinuities in the TJ complex and numerous small circular pores.1In human physiology there are two main types of epithelia using distinct types of barrier mechanism. Dermal structures such as skin form a barrier from many layers of keratinised squamous cells. Internal epithelia on the other hand more often rely on tight cells junctions for their barrier function. This kind of barriers is mostly formed by only one or two layers of cells. Until recently it was not clear whether tight cell junctions also play any role in the barrier function of the skin and similar external epithelia, recent research suggests that this is indeed the case.

In the next step mucous protect epithelial cells from released HCl.
Here  you will find more things.

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Why have humans evolved conciousness?
Why did humans/animals evolve to become self-aware of their own thoughts.  That is, why don't humans act and compute like a machine, or walking zombie.  In my mind, such creatures would still be as smart and equally capable of surviving, the only difference being they don't experience the phenomenon of self-awareness. (To understand my question think: unconsciously sleep walking)

What kind of answer are you looking for? If the answer "It is evolutionary advantageous" or "You might not be able to have one without the other" will not work for you, can you give an idea of what you expect?

"such creatures would still be as smart" - if you aren't conscious can you be aware of others' motivations in the same way? Isn't the ability to develop a theory of mind a big part of "being smart"?

How can you demonstrate that humans are self-aware? How can you demonstrate that computers or worms are not? These are hard philosophical questions not really suited for this site.

@MCM, The answer I personally think is that evolution cannot explain why we have awareness.  I posted the question in-case people who know more about evolution could give an explanation.

@terdon, I can feel my own self-awareness, and I just make the assumption that other humans are self-aware because we look the same, grow up together etc.  But I know I'm self aware, so why I did I evolve to have this self-awareness, which provides me no benefit.

@AlanBoyd, a computer can play chess equally well as a human, and the computer isn't conscious.  I'm sure an unconcious "walking, computing zombie" could navigate his way though motivations of others and appear to be identical to us in everyway.  The only difference is that there would be noone who experiences his subjective point of view.

@Chris - I'm not asking what your opinion is, I'm asking what's an acceptable answer for you. "Why are humans self-aware?" and expecting something other than a variation on "Because it's extremely beneficial evolutionarily speaking" is asking a lot. If you think Natural Selection isn't a satisfactory explanation, you need to explain why.

If I knew of the acceptable answer, I wouldn't be asking the question.  An acceptable answer is one that explains why consciousness helps an organism, or explains why consciousness is essential for intelligence.  Basically an acceptable answer is one that answers the question.

Why do I think natural selection can't explain it?  Because I thought that intelligence doesn't necessarily require self-awareness, and therefore while I see how natural selection would push creatures in the direction of high intelligence, I can't see the survival benefit of being aware of one's thoughts.  Many say that we only become aware of our thoughts after our brain has come up with the thought, so why is such an awareness even necessary, if the subconcious is happy thinking on its own.

The thing is that "feeling" something does not demonstrate it as true. Also, it is virtually impossible to demonstrate that animals are or are not self aware.

Its my self awareness that allows me to be aware of my feelings.  If I had no self-awareness, there would be no "I" who is the subjective observer of my body.  But I am "I", the subjective observer of my body.  The fact I feel the emotions attributed to a specific body, my one, illustrates to me my own consciousness, so my feelings do prove that I am self aware, but to myself only.  I know I am self-aware, but I don't know if you are, or anyone else, and I can't prove that I am to anyone, as noone else can experience my experiences.

-1. Your question and comments are philosophical, not biological, and therefore not appropriate for this site. You seem to believe that evolution can't possibly explain it, and therefore there is really no science to be discussed. Read up on the philosopher David Chalmers, who agrees with you. Then read up on his main rival, Daniel Dennett. Note that when you get into these sorts of questions, your intuition about whether you "know" that you are "self-aware" and how to "prove" it are destined to fail.

np.  I see you are a neuroscientist.  Could you please have a look at this question?  http://biology.stackexchange.com/questions/6794/do-adjacent-axons-in-a-nerve-influence-each-other

Imagine a sleep walker trying to deal with a leopard or learn a new skill and you see the problem right away. A complex brain makes a model of the universe (the world around it) and tries to predict what is going to happen when it does different things, It allows learning by something other than trial and error. As soon as a creature starts including its own possible reactions in its model, it is self aware.

@John I guess then I'm not convinced that self awareness is the same as consciousness.

@Kenshin define conscious and self-aware then, becasue you used both interchangeably in the OP.

@John suppose a robot knows how to catch a ball.  It clearly must be aware of it's own position and the ball's position so it is self aware, but I don't think the robot is conscious, do you?

have you seen the attempts to build a robot that can catch a ball? and no you don't need to model yourself to catch a ball reflexes will do it, but the downside of reflexes is they are not flexible. You should really read up on ethology and animal behavior before you try human behavior, much like learning how a lawn mower engine works before you try and understand a nuclear turbine.

catching a ball does not require consciousness but it is an incredibly complex behavior one that requires some of the most advanced AI we have ever built. http://www.livescience.com/45528-robot-arm-catches-flying-objects.html. By model itself I do not me model your body I mean model your open brain, your own thought process. An example of an advantage is being able to lie and catch lies effectively both require a detailed model of  a brain someone else's or your own through process.

There have been many proposals over the years as to why human consciousness has emerged and how, or even what it is.
Most of us will not be surprised to know that there is no consensus about an answer here.  Its hard to draw a trend from a single example.
Here is a little survey of the one's I've heard.

We are intelligent because we have opposable thumbs and can use tools, which evolved our brains.  This is an old one - maybe as old as Darwin's time.  I think its mostly ignored now because so many animals - including pandas and other non primates have opposable thumbs or use tools or both.  (monkeys and chimps use tools, and recently crows have also been observed to use tools.)
brain size.  We do have a large brain to body size ratio.  There are other animals with similar ratios and they don't have internets.
We are 'self-aware'.  That is to say we recognize ourselves as an individual.  It was proven that other primates can recognize themselves in mirrors (putting a red dot on their forehead. when they see their reflection, they touch their own forehead).  So that's not exclusive either.  its not a bad idea, but so far it doesn't seem to make the
'We ate something' I once read a discussion of how humans might have ingested psychotropic plants or fungi.  As you can see, this was 2010.  Its not the worst idea, but its hard to prove.  Lots of experiments on cats since the '60s have not produced cat's who care to tell us if they are intelligent.  Maybe they are just too smart in the first place.

These theories, from when I was a student are so discounted now, you can't find too much record of anymore since they were pre-internet and also they seem so unlikely now.
More modern theories have locked onto social configurations of human societies which drive intelligent adaptations.  This is stemming from observations that human evolution (the rate at which genetic variants are retained in the gene pool) are accelerating since humans have become social.
These new theories while standing on some amazing evidence are still feeling around in the dark - stuff about how social interactions have created a preference for intelligence-like traits. There is probably something to that - once intelligence gets a toehold it is a clear advantage.  But how did it show up only once and why us? I think that's the hard part that science has, for the moment, given a rest.

Given how we clearly would have no hardship eradicating everything else on earth (though funnily moral objections against doing so), it could be that intelligence/conscience/... is an "absolute advantage" trait similar to, for example, using enzymes rather than ribozymes or DNA in conjunction with RNA - except that we're not yet at the stage where all alternatives are eradicated.

heh - we're so superior we might end up doing the job on ourselves too!  I agree though - nothing seems to be able to stop or trump intelligence...

@Armatus - Are you sure we could easily eradicate everything else (well, all other life) on earth? Viruses might be a tough game, especially those that live in humans. And extremely small things that replicate often and mutate successfully relatively often may adapt pretty quickly to our efforts to eradicate them (not that it would be easy in the first place).

If only the Obama administration had really listened to the Death Star Petition we'd have a running start at it.  Seriously there is an idea that bacteria might have come to earth by hitching a ride on a martian meteorite, so some clearly believe its possible microorgs can survive planetary devastation. (search term: "Panspermia")

A Death Star might be the way to go if we wanted to include ourselves in the noble quest of extermination, but imagine the horror if some tough bacterium would get a foothold on the death star itself! : )
(As for all alternatives that don't include us humans -- it will be tough to get all the bacteria in intestines, mouth, stomach etc out of there)

-1. The substantive part of this answer assumes the common misconception that only humans are intelligent and conscious, and that we somehow know this for a fact.

Why did humans/animals evolve to become self-aware of their own
  thoughts.

Answer is pretty simple. Most mammals are self aware... it is just a matter of degree. It is a lot more advance in humans, but it is there in animals. like pride of Lioness hunting... setting up an ambush together... which means a lion can predict what zebra will do in a situation. And what other lioness will do.
And why have it? The answer is simple... being aware of you own thought, is basically being able to prediction the thoughts of others. And this is pretty useful.
We have the example of lioness pride ambush hunting. It requires a degree of self awareness in order to communicate and in heat of the chase predict what the other members of your pride will do and what will the prey animal will do.
Being alpha (wolf, lion, chimp, elephant, hyena, meerkats) is great. There are many biological benefit (first to eat, drink and have babies). However for a there to be an alpha, there must first be a  group to be alpha over. And when there is a group, there is a beta, and while beta might not be able to beat you individually, beta might team up with delta..to remove you.
So  as you can see, living in groups quickly leads to complications. And if you can understand others, you can use others to benefit yourself. Much selection pressure there for to evolve consciousness.

"being aware of you own thought, is basically being able to prediction the thoughts of others" I don't think these two things are necessarily related. As an extreme counterexample: Many algorithms can predict behaviour (e.g. youtube and amazon suggest videos/items you might be interested in). That doesn't mean they are self-aware. I know I reasoned in the opposite direction as you did (you: self-awareness causes prediction; me: prediction can exist without self-awareness), but I still think yours was not a valid logical conclusion. Or at the very least not an obvious one.

It seems to me like the answer that addresses the core of the question: 1) we need to define what is self-awareness and 2) how humans are different in this respect from other animals.

I don't think you can ever ask or answer for that matter WHY questions in biology. The only answer there is: because it works. Asking why questions implies that there was a reason, and reason cannot exist alone by itself. Reason is held by someone or something. And reason is something that doesn't exist, it is something we created and use for our own purposes and we cannot attribute it to anything else having one. Now, if you asked "how?", that's an answer biology was created for.
There could have been many outcomes to everything in biology but this is the one that appeared and works. This doesn't mean that it is some sort of theoretical or practically optimum, but the law of this universe is survive long enough to improve if needed.
I know that this is an opinion, but it's as close to the answer that you can get. If someone gives an answer to the WHY question, you could never prove it, or you could find evidence for all the possible reasons. And we can't also tap into the reasons of the universe because our intellect and modes of expression are way lower than the universe has.

Asking why doesn't have to imply reason, it can imply a cause.

yes, "why" is different from "what for"

Probably density of cortical columns. I tested this on a mouse recently, it was aware I was trying to help it and actually walked calmly into the jar.
Released it but did wonder if it will make an appearance again one day.
Perhaps in this case, neural nets are not complicated enough unless the connectivity threshold is in a critical range. This is apparently why we are one of only three intelligent species on this planet, sharing this with dolphins and African Grey parrots.
Four if you count octopi.
I speculated a while back based on my knowledge that connectivity modulators like psilocin, xenon and other compounds could be used to trace the actual neural connections responsible. This has been linked to Orch-OR and other QC like phenomena, also allowing for strong AI to be developed by synchronizing classical processors with a quantum link using entangled photons.

Welcome to Bio. Thank you for your contribution. However, we appreciate well-sourced answers and by the looks of it they are more a collection of thoughts and opinions, rather than plausible answers. Perhaps even more importantly, you are targeting a how question and the OP is asking why.

Natural selection doesn't select for the type of consciousness. It selects for brains that work for its purposes. The brain I think is like a Conway's game of life. It theoretically can pull off all kinds of tasks, and that can be explained just by the laws of physics acting on the brain.
The question of how the brain creates consciousness is an entirely different question maybe a philosophical one. I have aspergers. I sometimes do some abstract thinking. I sometimes sort of feeling like I'm conceiving of an object with properties that most intuitive theories prove cannot exist. They would say it's just my brain inventing the sentence "This object has those properties" and they're probably right. However, I sometimes actually have a small bit of feel for thinking in one and would feel like I'm conceiving of a real object which is distinct from its formalization which people would see if they looked at an image of my brain. I think we then decide to define consciousness according to the way the brain is in that kind of way.

Animals are not self aware, sentience is the quality of placing yourself in time and space, and the capability of introspection. We humans know we exist, we know we live in a universe, we ponder what's the meaning of life, where we came from and how we came to exist, where we go after we die, animals don't, they act by instinct and have different levels of intelligence, their behavior is written in their DNA code, but they aren't self-aware, this is the basic trait that separates us from animals.
Concerning how we became self-aware, that will depend on your beliefs (another trait of our advanced intelligence), but those who believe in evolution pretty much agree that we developed sentience because our brains developed much further than that of any other species, our advanced cortex and cognitive system gave us this ability. Different religions also have different accounts to our origin and history, in the proto-Indo-European cosmology for example, we are descendant of aliens, called pleiadians or nordic aliens, they came to earth through a portal in the sun, and brought their seed to our planet and gave origin to us, all our knowledge and manifestation of our humanity, like science, art... come from them.

Animals can be self-aware. There's quite a list of animals that have passed the mirror test.

I down voted this answer because it doesn't answer the question.

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Why do we feel tired if we sleep excessively?
When we eat, finally we feel full. I know which mechanism causes the sensation of being full. But when we sleep excessively we often still want more sleep. Why does this happen? Is there a mechanism underlying this?

Is this a universal phenomenon?

What you think dear Kevin? you didn't experienced?

i doubt there is a good answer to this one.  I recently read an interview with the retiring head of the UCSF sleep center and he said 'to the best of our knowledge, the reason we need to sleep is because we get sleepy.'  Not sure if there is a strong answer to a question like this ;)

No answers, but some speculations: Perhaps "excessive sleep" simply usually happens when people are excessively tired? Or perhaps people who once in a while sleep excessively do it to "make up for lost sleep", but that it is not really possible to make up for lost sleep, and lost sleep in general might lead to lower quality of sleep. Low quality of sleep may make you want to sleep more. In normal cases where you get up early there is perhaps some sense of acuteness or danger that makes you relatively alert (at a cost, perhaps).

People sleep in ~90minute long sleep cycles. Technically, if you decide to "sleep in" by 30-50 minutes, you may start the next sleep cycle and feel worse awakening from that. The logic behind this is that you wake up from deeper sleep. I don't know if there is hard science to back this up though

Studies have proven somewhat the opposite of what you're asking

For example a study from 2004 - "The impact of extended sleep on daytime alertness, vigilance, and mood" found that,

Average daily POMS vigor and fatigue scores also improved during the sleep extension period

And thus concluded

Extended sleep leads to substantial improvements in daytime alertness, reaction time, and mood.

Whilst an older study from '73 -"Performance and Mood Following Variations in the Length and Timing of Sleep" found that,

Neither sleep duration, nor any other sleep parameter consistently correlated with the performance or mood measures.

The study does go on to state however,

Therefore, it seems reasonable to assume that the detrimental effects of acute changes in the length and/or timing of sleep were not directly related to any specific changes in the length or electrophysiological patterns of sleep, but to as yet unknown physiological changes resulting from the disruption of an established circadian rhythm of the sleep and wakefulness.

This perhaps suggests that the question which should be asked should not be why does oversleeping makes us feel tired, but why does the disruption of normal sleeping patterns make us feel tired?


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Papers linking telomeres and aging
I'm currently writing a piece of work about telomeres and aging, and wondered if you could share some good papers you've either read or know of.

This question is not really a good fit for the Q&A format, the topic is rather broad, there is a nearly endless list of possible responses with no real criteria on what is a better answer. If you have any specific questions you encounter in your research you are certainly welcome to ask them.

the editors are kind of a pain here.  a good example would be why do we believe that telomeres are related to ageing? or What is the evidence that telomeres are related to aging.

http://biology.stackexchange.com/questions/186/is-telomere-length-a-reliable-measure-of-health-lifespan?rq=1  did you look at this one?

also take a look at this link: http://learn.genetics.utah.edu/content/begin/traits/telomeres/


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Are humans still competing in the same way now that the first life forms did?
I'm not sure if this is actually a philosophical question, but I was reading a timeline of life on earth and I came to this:

4500-3500 Ma The earliest life appears, possibly at Alkaline vents
  with the creation of the Last Universal Common Ancestor, possibly
  derived from self-reproducing RNA molecules.[6][7] The replication of
  these organisms requires resources like energy, space, and smaller
  building blocks, which soon become limited, resulting in competition,
  with natural selection favouring those molecules which are more
  efficient at replication. DNA molecules then take over as the main
  replicators and these archaic genomes soon develop inside enclosing
  membranes which provide a stable physical and chemical environment
  conducive to their replication: proto-cells.

..and I thought to myself, are we still essentially doing that as we live our lives?  I think I'm trying to connect the idea of a human "being competitive" with "evolution".. is there any truth to that?

It's important to realise that evolutionatry competition and the common usage of the word competition do not mean quite the same thing. For example, you could talk about Usain Bolt competing in the 100m but this is only evolutionary competition with the other athletes in they are in competition in terms of evolutionary fitness. Evolutionary fitness encompasses ideas of survival, reproduction and the nurturing of offspring. The only thing that matters, from an evolutionary point of view, is how many successful offspring are produced1. Where human competition does not relate to this, it is not related to competition in the evolutionary sense.
People certainly do still compete in the evolutionary sense for mates, resources, etc. but in the West, in particular, much of human competition has become a very long way removed from anything that relates to evolutionary competition except in the most tangential of ways.
1 - my favoured definition for fitness is number of grandchildren.

If you have kids and set a horrible example they might be afraid of screwing their own offspring up and decide not to propagate.

Your question is a little vague, but if I understand it correctly yes.
The crux of evolution is that in essence the resources we need to survive and reproduce are in lower supply than necessary for all to survive- therefore there is competition for such resources.
Those who are more genetically adept to gain those resources are more likely to pass on their genetic material to the next generation.
If you're speaking specifically about Humans there is of course still competition between individuals for resources (money being a primary one now). Competition is just an entirely different game now. Beyond that level of answer it's a philosophical can of worms I don't feel equipped to properly answer, and arguably it doesn't belong here but over in the philosophy stackoverflow.
Hope this helps a bit...


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Where does all the food go?
Food goes in, excrement come out. This seems obvious.
But it seems like the mass of the excrement is less than the one of the food.
Most people I asked answered: "There's a difference because it's transformed into energy, like heat...". I think that's bull-excrement.
There's still the law of conservation of mass: our body does no nuclear reactions, or does it?
Example:
Someone's on a "high protein / low carb" diet, he may ingest like 1kg of food, he isn't really productive on the toilet (it's difficult to find any fibers in those diets), he loses 500g in a day... My question is: where does the 1.5kg of matter go?

Whatever the diet, the food intake contains macronutrients: carbohydrate, fat and protein. When they are metabolised all of these molecules will end up, for the most part, as carbon dioxide, water, and ammonia, unless they are incorporated into components of the body.
These waste products are, of course, lost via breathing, and via the urine. That's where the "missing mass" goes.
A related question is here.

Thank you, the fact that we aren't carrying around a nuclear reactor is reassuring for me.

Yup, faeces is only the matter that wasn't taken up by the digestive system - plus some stuff excreted via bile by the liver.

If the total mass of everything released (as carbon dioxide, urine, faeces, etc.) was equal to the mass of the intake then animals wouldn't function. Your friend is wrong, Roman, in that the conversion of mass to energy does not account for the energy difference but it does occur albeit it at very low levels. It is this conversion of mass to energy that provides the energy needed for the body to function with the energy eventually being lost as heat.

Metabolic heat comes ultimately from thermodynamically favorable chemical reactions---breaking chemical bonds whose energy of formation is high, creating chemical bonds whose energy of formation is lower. Technically, yes, the mass of one glucose molecule is ever so slightly more than the mass of six carbon dioxide molecules and six water molecules, the difference corresponding exactly to the energy released when the glucose is catabolized, but we usually don't think of this as mass-energy conversion; we think of it as releasing energy stored in chemical bonds.

(ugh, months later I notice that I should have said "the mass of one glucose molecule and six oxygen molecules...")


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Do neurons secrete multiple neurotransmitters, or just one type?
I know that neurons communicate between each other by filling the junction between dendrites with neurotransmitters.
What interests me is if a single neuron only works with one type of neurotransmitter(ex: serotonin), or if it can secrete/receive all of them (serotonin, dopamine, etc).
If a neuron can secrete all, then can all dendrites secrete and respond to all neurotransmitters, or is it one per dendrite (one branch only works with dopamine, another one with serotonin, etc)?

My knowledge isn't detailed enough for this specifically but as far as I know: each postsynaptic membrane has receptors to one specific neurotransmitter and each terminal only secretes one specific transmitter - which doesn't exclude that other terminals of the same neuron might secrete different transmitters. Once the postsynaptic receptor generates a membrane change from the interaction, it's all just potentials, so a neuron is not limited in number to how many different transmitters it can receive.

I've googled this for a biology class I taught, and the quick answer is that both possibilities happen in different instances.  Some specialized neurons secrete more than one type, even though the ruling concept used to be one neurotransmitter for one neuron.

If you could reference the works in which you read this, it would make for a better answer.

Check this link out, It's a little simplistic but hopefully, will give the info you want so you can search elsewhere.


text:
What's the simplest set-up to demonstrate soiless plant growth to middle school students?
I'm looking for a simple, inexpensive way to demonstrate that soil is not needed for plant growth to middle school students.  I plan to germinate bean seeds in cotton, but where do I take it from there?

You can take a glass mason jar, a bean seed, and a moist paper towel. Place the seed between the paper towel and the glass. If you press the paper towel so that it lines the inside of the glass jar, the seed with grow and the students can see this process through the glass.


text:
Are there any mammals in which polyspermy produces viable zygotes?
Are there any mammals in which polyspermy produces viable zygotes? In the wikipedia page it is mentioned that there is a delicate equilibrium between female defenses against many sperms, which ocassionally results in low fertility rates (which in not all cases might be an evolutionary disadvantage, but i disgress)
My question is if there are cases where a ovum can be fertilized by several sperms, and the zygote somehow manages to select fairly between a subset of all chromosomes, avoiding polyploidy and producing a viable embryo.

The short answer appears to be "no".
The longer answer seems to be dependent on what you mean by "viable". Triploid humans do exist that apparently arise from dispermy, but most such fetuses die shortly after birth. Those that do not die soon after birth have a variety of health issues such as intellectual disability; "The few [triploid] infants that do survive to term have multiple severe birth defects." They're almost certainly sterile, though that source doesn't say anything about it.
The existence of elaborate physiological mechanisms for blocking polyspermy in sexual organisms generally, and further mechanical means for limiting sperm number in mammals, argue that polyspermy is something that we spend a lot of effort because it's bad. Here is a recent review of polyspermy in mammals; it has a lot more information about both mechanisms and statistics on the outcomes of dispermy.


text:
Connect the inner and outer space of cell with a wire, will there be electricity?
There is a potential difference, but ions can not go through wires, right? Though there is a electric field, but there is no electron source, I am thinking the answer is no, or will there be some chemical reaction?

Let's start with the basics.  The inside of the cell contains predominantly positive potassium ions, and negative phosphate ions, and other negative ions (e.g. from amino acids).  The outside of the cell contains predominantly positive sodium ions, and negative chloride ions.
The cell however sets up a resting membrane potential, due to the cell's semi-permeable membrane, allowing predominantly only potassium to pass through the membrane.  This causes potassium to flow along its concentration gradient towards the outside of the cell, until it is balanced by the electric potential that is consequently set up.
So we now have POSITIVE potassium ions on the outside of the cell and NEGATIVE phosphate ions (or other negative ions) on the inside of the cell, which aren't balanced.  Now as the wire is placed between the inside and the outside of the cell, electrons from the negative phosphate ions will travel through the wire, towards the positive potassium ions on the outside of the cell.
Once this occurs, the potassium from the cell's interior can now continue to flow against its concentration gradient, because the previous potassium ions in the exterior no longer contribute to an opposing electric potential.
Additional note:  As the K+ ion in the extra-cellular fluid gains electrons from the wire to form K, it will react almost immediately with water to form KOH and H2 (hydrogen gas).  The K and OH will be soluble in the extra-cellular fluid, forming K+ and OH- ions.  Over time the K+ ions will be "pumped" back into the cell's cytoplasm.  (The left over OH- ions will temporarily increase the flow of K+ down its concentration gradient, etc.)

Mmmm... I like a good, thorough answer.

I am very skeptical of this answer. Electrons do not simply flow away from phosphate ions because they are negative, nor do they attach to K ions freely (I don't think potassium and phosphate ions react in solution). Patch clamp systems actually do conduct current between the inter and exterior of neurons, but they generally achieve this by exchanging Cl- ions with an AgCl wire, not by exchanging electrons with K/PO4.

Just to clarify your ion/electron question - a neutral atom or molecule becomes ionized when it either loses one or more electrons, becoming positively charged, or gains electron(s), becoming negatively charged. Since the negatively charged phosphate (PO42-) ions have a surplus of electrons, they (the electrons) are free to flow "up" the wire and to the outside of the cell.

For electrons to flow trough the wire you'll need that the wire can have a redox reaction with the required solution, a simple voltage difference is not enough. Given that you may use a silver chloride wire or a platinum wire which can have these kind of reactions with the ions inside of the cell. If there`s no redox reaction, you can still see a transient capacitive current going trough the wire.


text:
What Effect Does the Endocannabinoid System have on Monoaminergic Neurotransmission?
I know that Δ9-tetrahydrocannabinol and other cannabinoids increase dopaminergic neurotransmission in the nucleus accumbens and that this is what results in the euphoria experienced by cannabis users. Other than this I do not know what effect cannabinoids have on monoaminergic neurotransmission. I would assume that it increases monoaminergic neurotransmission seeing how rimonabant $-$ a selective CB1 inverse agonist $-$ leads to depression and anxiety which according to the monoamine hypothesis can likely be linked to changes in the activity of monoaminergic pathways in the brain.


text:
How might one determine if bacteria are nitrogen fixing or not?
If you had an isolate bacteria sample how would you determine if they were nitrogen fixing?

Would stable isotope probing be useful?

@zenbomb more of a comment than an answer :)

Never mind found the answer myself you can use the acetylene reduction assay.

as a quick screen, often nitrogen fixing bacteria die or stop fixing nitrogen when exposed to oxygen.

This is true, nitrogenase has a very low half life in the presence of oxygen- around 30 seconds. Never thought of that could be useful for further lab testing... Thanks.

I'd suggest doing a bioinformatic search of the bacterial genomes first before doing the experiments. You should be able to find homologues of the "nif" (nitrogen fixation) genes there.

Not ideal if you have no idea what the colony is at all though.


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What are the physiological effects of wine?
I have read that alcohol in general and wine in particular can have advantageous as well as detrimental effects on human health. Is this true? What are the physiological effects of consuming wine in moderate quantities?

Are you asking for physiological benefits of alcohol? If so, then it's probably worth editing your question to reflect that. I doubt biology has anything to say about gambling or sin.

Hello Kevin, I am Asking benefits and Disadvantages of Wine (Not only its alcohol, maybe it have some thing else, I dont Know)

I think you should limit your question to the wine aspect. There are certainly answers for that part of the question.

So please edit it. maybe you do better

In it's current shape I'm downvoting this due to lack of research effort and the inclusion of a, to be honest, entirely irrelevant religious verse detracting from your question.

@MySky It's your question, not mine.

I think maybe you can edit it better. I am not native

Dear Rory, I am abiologist and also a beliver. I like Know more in both directions. it is not a relegious question, it is really a biological concern for me.

I have completely rewritten the question to focus on the biological aspects alone. @MySky, I hope you don't take offense but as written your question would soon have been closed.

It is maybe better

There are two components to wine: 1) alcohol, 2) the remains of grape. And regarding these two, there exist pretty definite answers: 1) alcohol brings destruction to body system on multiple levels 2) the residue that's left from the source grape (particularly, its seeds) is what grants wine its useful properties. The same and even more useful effect can be acheived by simply eating raw grape with seeds, crunching them, without any alcohol.

It is undisputed that heavy alcohol consumption (of any variety) leads to many deleterious effects on health.
It has also been claimed, however, that low to moderate alcohol intake can in fact be protective against some medical conditions (in particular, cardiovascular and cerebrovascular events). That is, there is often said to be a 'j-shaped' curve relating alcohol consumption to mortality and morbidity: low to moderate intake actually slightly reduces risk of adverse events relative to people who abstain completely from alcohol, but the risk increases markedly as consumption becomes heavy. See Plunk et al (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872245/
Sometimes the protective association is attributed to the alcohol content itself (i.e. the ethanol), and sometimes to non-alcohol compounds (often specifically those found in red wine). The existence of such a possible protective effect at moderate doses is not a controversial position but it is also not settled science as yet. You should make up your own mind by reading reviews and ideally meta-analyses in the area. As a starting point, this 2013 review by Chiva-Blanch et al. in the journal Alcohol & Alcoholism has been well-cited by other researchers and is available to read in full here: https://academic.oup.com/alcalc/article/48/3/270/244770


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Why does having cold hands hurt?
(1). Why does having cold hands create a painful sensation?
Is it a physical effect, maybe a protection mechanism from evolution?
(2). Why, if one's hands are cold, does it feel as if they are more susceptible to pain?
Note: I have (2) as a separate question because the painful sensation in (1) refers to that from the coldness, whereas in (2), I mean that certain 'ordinary tasks' would feel painful, for example, holding a shopping bag.

You may want to have a look at: http://biology.stackexchange.com/questions/371/how-is-temperature-sensed/

For question 1 it's just a biochemical response from thermoreceptor nerves in the skin, temperatures that are likely to cause lasting damage from prolonged exposure cause a neurological response - in this case it's pain.
In address to question 2 it is most likely down to the physiological response of vasoconstriction.
When the body is cold the body undergoes constriction of the blood vessels in the extremities to preserve core temperature where it is more essential for the proper functioning of vital organs. By constricting blood flow to the extremities (in this case the hands) there is less volume of blood present, because of this nerves present in the hand are closer to the surface and thus more sensitive to pain.

It doesn't matter if its hand or any other human body organ, cold would hurt, the reason being that we humans being warm blooded animal require an optimal temperature-pressure balance to be maintained for our nervous system to work in its natural order.
So when we have, in your case, cold hands its like a thermal shock to our hand as the above mentioned functional optimality is hampered, and just similar to a hot ceramic cracking due to cold water poured on it, our hand(would not crack, however might in extreme cases) reacts to  this with the sensation termed as Pain.
This is a common answer to your questions, cold is directly proportional to pain being felt during our daily engagements(like holding a bag).
Pressure plays a vital role in this too as when your hand is cold the pressure exerted to the epidermis is at a reduced rate, which is another reason for the same.
Hence commonly my conclusion would be the Temperature-Pressure Factor.

It has to do with the way that body parts are more rigid when it is cold. This makes them less flexible and more prone to superficial injury....even without frost nip setting in. In the event that actual frost nip set in, this would be even more sensitive, as you have tiny crystals beginning to form in your cells, like little shards of glass......and, smacking them, rubbing them, or scraping them would be like SMACKING, RUBBING, or SCRAPING your neutral temperature hand against shards of glass.
When it is cold, your nerves are very sensitive to the temperature, as it isn’t numb yet, and still....blood flow is slowed down tremendously. In fact, your body has begun "vaso-constricting" all blood flow away from your extremities, resulting in nerves being pressed upon by the less supple skin and vascular tissues.


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What is the surface area of the human heart?
I heard that the human heart had a surface area of 1000 square feet, and I thought that that cannot be true. So what is the surface area of the human heart and what are the different ways it can be measured?

The number you are looking for might be quite large depending on the level of detail you demand for the measurement.  There is no single number for the area of most objects in fact.
The importance of fractals is much related to the question of what is the perimeter or surface area of something.  The classic example is trying to determine the length of Britain's coastline.  If you took a surveyors sight and set a point every 500 ft you would get a certain number, if you paced it out in strides you would end up taking more curves and turns and you would get a longer number.  If you took out a ruler and measured down to the inch you would get a still larger number.  In these two wikipedia pictures you would get a perimeter of 2400 km and 3400 km for points set every 200 and 50 km respectively:

As you can see that makes a big difference.  So in the same thought organs also need to be measured using fractal sorts of measurements- depending on the level of detail desired. For a heart, if you were to cover the organ with a tight stretch of Saran wrap, you'd have maybe 1-2 square feet, but if you estimate the surface area for not only the inner chambers, but the blood vessels and capillaries, it would be much larger.  The latter is probably relevant if you are a physiologist and want to know how much oxygen the heart is taking in as it beats.
I can't find a reference for a human heart, but fractal calculations for the human lungs tell me that 1000 sq ft seems reasonable.  If you take the oxygen accessible area of lungs, including every bronchial passage and aveoli, the answer is 50-100 m^2. This is about 538- 1,076 sq feet.
The heart does not need to have as much surface area as the lung, but the capillaries and arteries that feed the heart need to be spaced a few millimeters apart to keep the tissue oxygen saturated.  1000 sq feet seems a possible range for the heart compared to the lung's surface area, maybe on the high end...

pardon changing the area numbers for lung- just caught my error of 100x.  I think the conclusion still holds water though.


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Has any large-scale origin-of-life simulation/experiment been done?
I have been thinking a little about the origins of life, and was further inspired by this question: How did the first self replicating organism come into existence?
I can accept that we don't quite know exactly how, but has any large-scale/long-term simulation been carried out?
There have been experiments but they seem to have been on a small scale. As an example, according to the Abiogenesis page on Wikipedia, some experiment which spontaneously formed peptide structures was carried out by Sidney Fox during the 50s and 60s.
What would be really interesting is if there had been some experiments or simulations carried out during a very long time, plausibly allowing for extremely low-probability structures to form. I doesn't matter whether this simulation/experiment has been carried out in a lab or as a computer simulation. There is of course the interesting but old "Conway's Game of Life" simulation, but according to my search efforts nobody has really tested it on a very large scale and in 3D.
Again, I'm looking for something extensive, like a decades-long single lab experiment or a simulation that has been run for years.

much more recent experiments have been done with astounding success. https://www.nature.com/news/2009/090513/full/news.2009.471.html

What you are possibly thinking of is large versions of the Miller Urey Experiment where a mixture of reducing gasses carbon dioxide, ammonia, nitrogen and the like are subjected to electrical arcs in a closed flask reaction, resulting in some biological molecules being produced.
Opinions have changed - Miller Urey did get the atmosphere wrong and so their finding of amino acids is not as strong as supposed.  Variations of this experiment continue to be done, with different conditions in the reaction vessel which reflect typical or even unusual conditions.  I've found some nice collections and reviews. There continues to be an enthusiastic effort even today.
Looking over several of these overviews, it's clear that many different conditions are being tried - reactions on mineral surfaces, examining chemicals on meteorites, near volcanic vents, different kinds of radiation.  What I don't see is anyone going to a huge tank.
I think that this might not have been tried (perhaps someone else will find a counter example), but if it were not me, I would probably not try longer experiments either.
There's some good reasons for this, if true.
Firstly all the published descendants of the Miller experiment have produced biologically relevant compounds after a few days.  Extending the experiment a few orders of magnitude may not prove anything new.
Secondly, the longer a reaction is run the more likely the sealed containers and heaters and other apparatus has to fail, causing you to restart or include contaminants that would ruin it.
Thirdly, one is not going to run an experiment that will ever come close to reproducing the time spans or volumes over which life emerged on earth - that was perhaps a few hundred million years over the area of the planet.
That's not to say you won't find out something new - an extra week could produce a new set of compounds or even a replicating system - we don't know if we haven't done it, but the nature of science is that you have a little time and money for a project like this and you would like to prove feasibility  - 'it could have happened this way'.  By selecting the conditions and doing a series of modest experiments which allows some to fail so that you can find something new.
I would say the observation of other planets and analysis of meteorites are getting closer to your idea - they are huge systems and been going for billions of years.  Titan is especially promising.  They just aren't the same conditions as Earth.
In brief, nothing is both affordable and perfect in proto-biotic research.


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Which blood vessel carries the most impure blood?
There is a question in my Biology textbook:

"Which blood vessel in the human body carries most impure blood after
  few hours of meal."

The answer is given as Renal artery.
But I think the answer should be Hepatic Vein, because the liver produces urea and other waste materials and then it pours it all in the right ventricle of the heart for oxygenation. And then the heart distributes the blood to various parts of the body. So the impure blood brought by the Hepatic Vein and other blood vessels gets distributed through the aorta. This will automatically imply that the Renal Artery will contain lesser impure blood than the Hepatic Vein.
Impure blood is the blood with urea, uric acid and other components of urine.
It would be good if you give your opinion and also a reason for it.

The problem with this question is that "impure" is too non-specific a term. What blood components are impurities?

@AlanBoyd Impurities include urea uric acid and other components which are there in urine.

yup toxins from the liver breaking down and concentrating impurities from the blood.  in physiology its not as vague as it sounds...

It's the renal artery because it will contain everything from the liver as you describe plus all waste accumulated on the way from the liver to the kidney. Here it gets filtered, so there cannot be a place after the kidney that is less "pure".

please read the question again and make necessary changes in the answer. I have revised the question in order to include more details.

+1 - "...plus all the waste accumulated on the way from the liver to the kidney." And there's the rub.

@PranitBauva the changes don't really affect the answer as written

But the urea containing blood liver distributed through the body from the heart , as some of the blood goes to the kidney so renal might not contain that much of urea right? As OP has mentioned


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Is this an Emperor Penguin or a King Penguin?
I have a book from Dorling Kindersley called Animal Encyclopedia (the German version that I have is called Das große Tierlexikon) with images from animals.
One is titled Emperor Penguin (Kaiserpinguin) which is in my opinion clearly recognizable as a King Penguin (Königspinguin).
This is the image:

I wrote to Dorling Kindersley and they told my that their investigation revealed that it really is an Emperor Penguin.
I am not a biologist nor a penguin expert, but from all the descriptions and images I could find (even in the same book on other pages!) I think the publishing company is wrong and just too lazy or arrogant to admit this error and too miserly to release a revised version of the book.
Who is wrong? Me or Dorling Kindersley? Emperor or King?
Update 2020
They seem to inherently admit it themselves, that the book was wrong (and that they lied to me), as they used the same picture on one of their websites and with king penguin in the caption of the picture:

I know this is verrrryyy old. But yes it's a king. You can tell from the long straight beak. Emperors have a shorter curved beak

@erik Haha love the update. Much appreciated after 7 years of personal torment I'm sure! :p.  Seriously, though, thanks for updating!

Might I also suggest just accepting Alan's answer here or adding one of your own.

Found this image here. I've also seen references to the "closed orange ear patch" of the King Penguin, which fits with the image. So my vote is for the DK image being a King Penguin.

Are you an expert at this? Ornithologist or something? That would be of more value for me. I have the same opinion as you have because of the closed orange ear patch. But maybe there are other indicators which are not that obvious for us amateurs.

No I'm not an expert, just an amateur like you.

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


text:
Refutation of Darwin's Random Evolution Theory
I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?

Refutation of the Theory of Random Evolution
As for the theory of evolution, which says that living things evolved progressively from
  mud - first organism - bacteria - fish - animals - humans through tiny
  random mutations which were advantageous and naturally selected;
  there's a lot to say on this. All currently living life forms appears
  to be highly related, sharing the same DNA system and cell structure.
  This would suggest a common first ancestor as the theory suggests (or
  better yet - one Designer), however, the most obvious flaw with the
  theory is that the first organism must have had highly sophisticated
  intelligent design. There is a minimum requirement for even the most
  primitive possible life form, without which it could not possibly
  survive.
Minimum Requirements for First Organism

The first organism must have a system of producing and/or sourcing energy along with subsystems of distribution and management
  of that energy which interact and work together, otherwise it cannot
  power critical tasks such as reproduction.
It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information
  copying, and information reading/processing which interact with each
  other and work together. This reproductive system is dependent on a
  power source, so it must be coordinated with the power system. The
  reproductive system must also copy/rebuild all critical infrastructure
  such as the power system and the reproduction system along with the
  "circuitry" and feedback mechanisms between them, otherwise the child
  organism will be dead..
It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations.
  This growth system necessitates subsystems of ingestion of materials
  from the outside world, processing of those materials, distribution,
  and absorption of those materials to the proper place, building the
  right thing at the right place and in the right amount. It must also
  have an expulsion system for waste materials.
The growth system must also be coordinated with the reproduction system. Otherwise, if the reproduction trigger happens faster than the
  growth, it will reduce size faster than it grows in size and vanish
  after a few generations. The growth system also requires connection to
  the power infrastructure to perform its tasks.
All the "circuitry", signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate
  together and work together must be in place before the organism can
  "come alive". The reproduction system won't work without coordination
  with the growth and power systems. Likewise, the power system by
  itself is useless without the growth and reproduction systems and
  cannot survive. Only when all the "circuitry", etc. is in place and
  the power is turned on is there hope for the hundreds of
  interdependent tasks to start working together. Otherwise, it is like
  turning on a computer which has no interconnections between the power
  supply, CPU, memory, hard drive, video, operating system, etc -
  nothing to write home about.
We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some
  kind of membrane otherwise its precious contents will drift away in
  the water due to natural diffusion or drifting of water due to
  temperature variations in the water from sunlight, etc. or from heat
  generated through its own power, or wind, moon, etc. If so, this makes
  the assembly of such an organism more problematic, since it would need
  to be closed shut before it can build itself in a stable way. Yet, to
  build itself it would need to be open for a long time until all
  systems are built and interconnected.

From the above minimum requirements it is clear that the simplest
  possible surviving organism is by no means simple. You would need
  thousands of different proteins/lipids etc., in the right proportions,
  all intricately folded and actively interacting with each other and
  with sophisticated organelles. Contemplate this and you will see the
  necessary complexity of this primitive organism is far more
  sophisticated than anything modern technology has ever produced. Even
  the most sophisticated Intel CPU is mere child's play compared with
  the design of such an organism.

See this question

As explained by @5th below, this is really about the origin of self-replicating systems. See here for an outline discussion of this difficult problem. (added later - I have just seen your other question, so now realise that you know all of this anyway!)

thank you to all who answered/commented. I see its not so simple as I thought. still seems to me a far jump to go from things like self replicating RNA to fulll fledged single cell organisms. intuitively, i just dont see how it can evolve one tiny step at a time due too many interdependent things. will need to think it over

@user1909257 I think your stumbling block is that you don’t account for the vast time span involved. I’s very hard to grasp how much time evolution had. We can estimate the rate of evolution from experiments and observation, and let me tell you, even though evolution is happening really slowly, there was plenty of time since the beginning of the world. It’s simply unimaginable how old Earth is. The book Climbing Mount Improbable illustrates how tiny changes can accumulate over time.

Theory of evolution has not to be called theory of random evolution! Mutation is a random process (more or less) while natural selection is not random but is a deterministic consequence of the effect of alleles on their own replication abilities. Then, origin of life is not part of the theory of evolution. Theory of evolution has a domain of definition (just like any theory). It explains how living things evolve and it does not say anything about the big bang or the origin of life. But still, talking about the origin of life is worth and for this point your question is interesting.

Apparently it's still active. I think it should have been closed initially but better late than never.

I like @5th 's answer but I thought it might be worthwhile to clarify on some points and pull the logic out a bit more.
First there is some contesting the overall logic that it assumes all these qualities of life are showing up at once.  If they had to, it probably is true that life could not evolve, but the general assumption is that there is a path to do so.  Let me try to be convincing of this.
Dawkin's theory of the replicator is axiomatic and not entirely helpful at this point, but it does have a lot to say.  Once you have self replicating systems, the rest of biology and evolution and selection does seem reasonable, even with the emergence of complicated structures like the eye, the flageller motor and other seemingly unplausibly multi component systems seem to magically come together and do something new in the course of evolution.  Dawkins wrote a book on this topic "Climbing Mount Improbable" on this topic which tries to answer this question for several cases.
To outline why biological systems can and do seem to leap to new abilities, organs and unprecedented assemblies. In fact the do not, but there are so many possible trials (quintillions? ) over the trillions of years, that eventually some adaptive path to these features, which has usually been found when we go looking for it.  As such there is no clear reason why new cases of this argument need to carry extra weight.   The argument of statistically improbable combinations has been tried and remains unconvincing with respect to evolution several times.
After this, I think it would be fair to say that the origins of life, although coming clear still has many details to be resolved, but progress is being made. Precambrian evidence of primitive life was very different as seen in fossil records.  We can see that at one time there were only bacteria and single celled organisms.  There is evidence that at one time there appears to be only simple very large single celled organisms that lay in shallow water and soaked up the sunlight, growing and growing.
We can see that going back about 1.2-2 billion years, life shows a pretty clear progression where selection and adaptation creates complexity in living things and transitions life from exclusively chemotrophs (metabolizing Sulfur from geological processes) to anoxic (no oxygen environment) photosynthesis, and then oxygen breathing organisms.
In the precellular world, the RNA World hypothesis describes how all that life needed was one sort of molecule - RNA.  That is chemically a very simple replicator.  Evidence is pretty strong that RNA world was possible.  Many chemists are interested in proving that RNA can be created more or less spontaneously from early earth chemical environments and recent experiments show that spontaneous soups containing RNA are a reasonable picture of earth at one point.
All this being said its probably true that exactly what happened and how it happened will never be 100% known and the argument can be made that something unnatural happened at some point. But I hope you can also see that while the argument may still hold some water, the need for any magical interventions in the action of life is retreating to a point of origin - the beginning of time.  Scientific inquiry is very much focused on filling the picture of the origins of life on earth though and given the success of finding probable paths through to the origins of life, the odds actually are in favor for making a statement of the physical mechanisms of life's origins.
Just a couple of side notes.. (1) biologists are not stuck on everything being random.  There is lots of work on mechanisms evolved to adapt in non-random ways.
(2) Darwin is not a sacred cow - just about any working biologist would love to show Darwin was wrong even in a little way.  The same is true for Einstein, Newton and the rest.  After a few years of trying though what one usually finds that its kinda difficult.  Its not a matter of who makes the argument or what it means, but it has to be convincing and that turns out to be difficult.

i agree that the answer is not so clear cut, and ultimately may remain a mystery

science is more guessing than proof in many cases, theories are built on lots of different evidence that somehow turns into a story.

(A few words about your source: it's little use to come a serious site about science and quote sources whose objective is to prove the existence of god. If you want to learn more about the beauty of life and the theory of evolution, I suggest you read the book "The Blind Watchmaker" by Richard Dawkins, it's an excellent introduction to the topic.)
There is no such thing as "Darwin's Random Evolution Theory". Further, Darwin put forward a theory of the origin of species (which is the opposite of random!), not of the origin of life (I do believe he did not write anything at all about how life develops from "mud".)
Thus, there is nothing to "crack" in that "logic", because the question is not valid in the first place.
Disregarding that the question is not valid in the first place, I think you're trying to refute the idea that self-replicating life-like things could emerge spontaneously. I'm not sure there is anything particularly random about how the world behaves, it's rather a label for what human imagination and ingenuity cannot predict. However, in the sense of random you are using, self-replicating patterns (I won't be the one to determine whether it passes as life) have been shown to be possible in a much simpler world than ours: Conway's Game of Life. A pattern that uses a kind of instruction tape, replicates and destroys its parent (repeating this every 34 million generations) was found in 2010 by Andrew J. Wade.
http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life#Self-replication
If this can occur, although to a large part it was probably designed in this case, you cannot say it is impossible in a world on a much larger scale and over eons of time (these kinds of time periods cannot easily be imagined - a good reason why we tend to believe it is very unlikely that something very improbable will happen during the period).

what is the difference between origin of species and origin of life?

The first talks on how and why life changes over time. The second talks about how to make life. It is the difference between how prosperous nations are run and how to win a nation its independence.

I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?

Certainly. First and foremost: The refutation is not simple. It is a complex argument that draws consistently on baseless assumptions and relies on the lack of education of the reader to get its point across. I do not mean that the reader is dumb, merely that the author's target audience is probably ill-informed about the details of Biology, Chemistry, Physics, and similar fields. The author relies on being long and convoluted, appealing to faulty logic, and a whole slew of fallacies that might be missed if the reader hadn't already encountered them in the context of Evolution.

As for the theory of evolution, which says that living things evolved progressively from mud...

Well, as 5th has already said, this is a bad start. The Theory of Evolution (via Natural Selection if we want to get the full name out there) says nothing about the beginnings of life. That would be Abiogenesis.
The Theory of Evolution merely dictates that subsequent generations adapt to their environment, and that those who have adapted best will pass their inheritable traits to the next generation.

1. The first organism must have a system of producing and/or sourcing
  energy along with subsystems of distribution and management of that
  energy which interact and work together, otherwise it cannot power
  critical tasks such as reproduction.

This isn't a difficult task. Currently the most abundant source of energy on the planet is the Sun. It has been shining for billions of years before the Earth was formed, and will be shining for billions of years after you've read this paragraph.
If we exclude sunlight for the LCA (Last Common Ancestor) of all life, then we're mostly talking about geothermal energy or chemical reactions. Ultimately, though, extant organisms store energy in chemical bonds. The primary "Energy Carrier" of the cell is ATP - Adenosine Tri-Phosphate, and it's the third of the three Phosphates that is often "harvested" for its energy - leaving ADP as a product of metabolic reactions.
That a system of sourcing and managing energy distributions could arise from even simple situations is not so far fetched. Consider the Earth's atmosphere and weather patterns; initially they appear extremely complex and result in myriads of environments that even modern science cannot accurately predict more than a few days ahead.
However, the entire system is driven by the interaction of the planet's geography, the gases composing the atmosphere, and the Sun as it heats the system. Regulation is taken care of by Physics - hot air rises, cold air sinks, geographical location determines exposure to the energy source, etc.
Power is not an issue. Basic regulation is not an issue. Once the basics are down, more complex forms can Evolve.

2. It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information copying, and information reading/processing which interact with each other and work together. This reproductive system is dependent on a power source, so it must be coordinated with the power system. The reproductive system must also copy/rebuild all critical infrastructure such as the power system and the reproduction system along with the "circuitry" and feedback mechanisms between them, otherwise the child organism will be dead..

If you're willing to accept that chemical reactions between amino acids and similar molecules can occur on primitive Earth, then the jump to this question isn't that hard.
First, you should know that DNA almost certainly wasn't the initial genetic storage form. A commonly accepted and incredibly intriguing theory is the RNA World Hypothesis. RNA can also store genetic information - albeit at a less accurate rate for a shorter amount of time. More importantly, RNA has also been observed folding into itself to create proteins and catalysts. It's sort of a jack-of-all-trades, and since it's basic constituents have been discovered amongst the vacuum of spaces, all the pieces were here on Earth 4 B.Y.A. to make some of the first steps towards organic life. All that had to happen is that the right molecules had to come together, then physics takes over and you have some astonishing reactions. Given the right conditions and a few hundred million years, who's to say it isn't possible?

3. It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations. This growth system necessitates subsystems of ingestion of materials from the outside world, processing of those materials, distribution, and absorption of those materials to the proper place, building the right thing at the right place and in the right amount. It must also have an expulsion system for waste materials.

Let me introduce you to the Micelle: A naturally occurring structure that looks an awful lot like today's cell membranes. It doesn't require exotic materials, it doesn't require fancy catalysts; it requires amphipathic molecules and that's about it.
While complex organisms do require subsystems and various ways to ingest food to harness nutrition, for the most basic forms of life "Digestion" is little more than taking in outside material into the cell and then putting what's left back outside.
To that end, Micelles merge on their own when distance allows. The mechanism is powered by the entropy of the water molecules surrounding the micelle's structure and doesn't require any sort of metabolism or organic control to occur. In addition, hydrophobic molecules can slip through unhindered fairly easily (depending on size), and many of amino acids used to make proteins and micronutrients our current bodies require are hydrophobic.
So it's entirely possible to have a basic membrane that can "eat" other things without being strictly alive. Everything after that is just added complexity that was retained due to improved functionality. It's important to remind yourself that we're talking of a span of hundreds of millions of years. Almost nothing currently living on the planet has gone more than a few hundred thousand or few million years without drastically changing how it looks. A hundred million years ago humans were little more than rats or furry lizards. Imagine what could happen with 5x that span!

4. All the "circuitry", signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate together and work together must be in place before the organism can "come alive"...

This very, very much depends on your definition of alive - which is still difficult to define for Biologists to this day.
Are viruses alive? They certainly do not retain any reproductive ability of their own and must hijack the operations of a living cell to create the next generation - but they still have inheritable genetic material, they still create structures and adapt to their environment, and still - in an odd way - consume resources to reproduce.
What's the difference between the spread of iron oxide (rust) -- which, you could argue, requires an interaction of existing elements to perpetuate and has built-in feedback (it is inhibited when there is a lack of a substance - a completely viable and well-known trope of feedback mechanisms) -- and the spread of a fungus, which you could describe just as simply?
Defining "Life" by what exists today is a mistake often made by those who dispute the Theory of Evolution. Only the most basic assumptions and connections can be made between life as-it-exists and life-as-it-started. The planet is different, the air is different, the Moon is significantly further away, and countless other things have occurred.
That said, we have definitely observed complex interactions of molecules and systems in situ within conditions similar to those of early Earth. One of the most famous is the Miller-Urey experiment. If you're asking why they didn't succeed in creating life, remember that it took about 500 million years for the LCA to spring into existence... And the LCA is not necessarily the first form of life, just the one that gave rise to all current forms. Miller and Urey experimented for two weeks, not 500 million years, but still made significant discoveries in that short a time-span.

5. We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some kind of membrane otherwise its precious contents will drift away in the water due to natural diffusion or drifting of water due to temperature variations in the water from sunlight, etc. or from heat generated through its own power, or wind, moon, etc.

We have already discussed the Micelle above.

This refutation contains a fundamental error.
The first living organism need not be anything complex, it just has to bea molecule that creates copies of itself which inherit its characteristics.
From there its population grows exponentially and evolution starts.
Therefore there is no need for any of those items he is listing as requirements for the first life.

your system works for simple molecules. but to go from there to interdependent intelligent design is a long way. consider upgrading your software through random mutations of the hard drive. it's just impossible for anything to improve unless its coordinated with other changes in an intelligent way

for example, you cannot improve the code for windows xp by randomly changing one line of code. the reason being that this change would affect other lines of code and you'd need to modify those in a coordinated way. make sense?

I am pointing out that this so-called refutation is flawed as it assumes that first life must be someting complex. As for the continued evolution of life you can start a different thread.

simple molecules is not first life.

No but molecules that create copies of themselves which inherit their characteristics are. And that is all that is necessary for first life.

thanks but dont you think, you need some kind of "intelligent design" at some point. meaning, something which is highly interdependent and sophisticated. don't see how that could work thru random mutations. you'd need some kind of coordinated design.

At some point is a different matter. The question is about the origin of life. If you want to have a discussion about the process after life has originated then that should be in a different thread.

Continuing to say "you need some kind of intelligence" doesn't mean you have demonstrated it to be so.  Yes, it's a long stretch from self-replicating chemicals in a micell to full-blown organisms with brains capable of intelligence, but you also have a VAST amount of time, and a VAST amount of attempts with which to make incremental changes.

@user1909257.. yes you can... make a random change in XP code. Do so for 1000 copies. Send it to users. The copies that work, have their code copied 1000 times more with additional random changes. The copies of XP that do not work are thrown away. Do this every day for least 10 million of years.we actually have self evolving code... that have done things like build a TV antenna, fly a fighter plane, and even play chess. What you are missing is selection after that random mutation. Only the best live and breed, everyone else dies.


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Why does yawning impair hearing?
When I yawn I can't hear anything happening around me. I also feel some kind of muscles inside my head contract and hear a faint hum, but it is not loud enough to explain not hearing other sounds. I can force those muscles to contract even without yawning and it produces the same effect of humming and no other sound, so I suppose they cause this effect, but how?
What really happens? What muscles do I feel?

There may be some clues here. it sounds as if you may have some voluntary control over the opening of your Eustachian tubes as described in the article.

It is related to Eustachian tube. It links the back of throat and the middle ear and allows air pressure to equalize in the middle ear. When you yawn air pressure goes up in this and it bends the ear drum and causes impair hearing (notice, just impair and not stop).
Yawning also helps to open Eustachian tube.

This answer contradicts itself. You are correct in saying that yawning opens the Eustachian tube, and it does this precisely to keep the pressures equalised - so why would yawning 'bend' the ear drum when the tube is open? (This is the same effect that you experience in an aeroplane during landing - anything that you can do to open the tube, including yawning, will restore impaired hearing caused by pressure changes.

Function of Eustachian tube is equalization of pressure. But yawning create pressure in Eustachian tube and cause bend.

Yawning increases pressure in eustachian tube because it takes place during inspiratory phase of respiration, so pushes Ear drum on the outer side

Welcome to Biology SE! I think this is a great answer, but could you elaborate a bit more? For example, why would a (more or less) static pressure difference affect frequency analysis in the kilo-Hertz domain? Also, a reference would be nice, or a picture, a website...

Plus, it may not add anything to the existing answers in its current form. Please elaborate.


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Why do humans alone have the capability to have religious/spiritual experiences?
What is it in our brain that makes having such experiences possible? I assume other species don't have these. Sure there are instances in the natural world where you can see individuals of the species gather around the dead one. Sometime even the alpha male in the group allows the kin/relatives of the dead individual to approach it (for whatever reason).
The kind of thing I don't see in the wild-life kingdom is an individual becoming "enlightened" or the likes.
Sure our cerebrum is highly developed and all. But "what" is it in our brain that makes it capable for humans to have such experiences?
I've read articles saying we have identified such regions in the brain. Just want to know what these structures are. Did such research establish that such structures also exist in other species too?

This recent paper looks like a good starting point.

But I'm not sure what an enlightened gorilla (for example) would look like.

I never realized that religious/spiritual experiences already existed and were certainly proven in a scientifical framework?!

what if the world is much more magic and full of spirits for animals than for men? For example, deer and horses see monsters everywhere. Animals have the capacity to fear imaginary beings that peer from unknown hiding places. It is said that human religion derives from the animal instinct that there is some very big powerful animal that could be watching you, tracking your every move. That instinct in humans if intellectualized into the surveillance of god, and his power over your life. The human rational cognition of the afterlife perhaps has similar animal cognitive roots

Its not clear that this is true.
Working with animals has been a little disconcerting over the past 50-60 years.  In the distant past, I think most evolutionary anthropologists and their like bought into the idea that humans were completely uniquely intelligent and spiritual.  But the more we try to define human sensibilities apart from other animals, the more we find its difficult to see animals as being completely incapable of human feelings and even thoughts.
I refer you to this question which describes the shift in intelligence theories over the years: Why have humans evolved conciousness?
The above reference is just to say that every definition of intelligence that is fairly broad has been overturned by animals (thumbs, socialization, tool use, self awareness, communication and language).
If you want to say 'I know we're special, but I just can't say how' you are in lots of good company... it's become pretty hard to lay down a definition that includes all human beings and excludes animals.
Lately it seems as if the definition of spiritual experience is similarly hard to define. What is your definition?  The capacity to receive and reciprocate affection or love is almost never brought up - that seems to be half of the internet.  Yet, that's a common component to many ideas of spirituality.   It was found a while ago that primates have some form of self-awareness to identify themselves as distinct from other individuals.  True this was only demonstrating that they know themselves in a mirror, but other experiments show it probably is deeper than just that.
I think the most confounding evidence is the work with animals who have been trained from infanthood to communicate to humans through sign language or symbols.  The most astounding example I know if is Koko the gorilla. She had the vocabulary of a 5 year old and the capacity to joke around, reason, and adopted pets as children including a cat called All Ball.  When All Ball who was killed by a car she mourned and remembered her adopted cat for years.  This page outlines all that, though there is a book that describes Koko's life.

The human staff sought to discover what Koko thought about death.  So they asked, “Where do gorillas go when they die?”  Koko answered, “Comfortable / hole / goodbye.”
  They asked, “When do gorillas die?”  Koko answered, “Trouble / old.”
  They asked, “How do gorillas feel when they die:  happy, sad, afraid?”  Koko answered, “Sleep.”

So this has been taken as evidence that gorillas have a concept of their own mortality or possibly even life after death.
So what is left?  Not clear to me.  Any thoughts?
Some regions of the brain and control of electrical activity in the brain have been associated with spiritual experiences or acts like prayer and meditation.  The temporal lobe is exciting because magnetic stimulation of that region can create the sensation that there is a presence in the room with you. there appear to be many regions which are active in different instances though, which is something you might expect.
There is no evidence yet that animals do not experience similar effects in their brains, though primates have very much the same structures as we do.   Its too bad Koko has died - she might have told us.


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Why can silicone reduce keloid?
I heard people use silicone sheet for reducing raised scars (i.e., keloids). I was wondering what is the rational behind it, and whether it actually works.

Keloid scars are formed when the scar tissue extends beyond the margin of the original wound and is the most extreme type of scarring. When this scar type occurs, a small wound such as an insect bite or piercing can result in the formation of a much larger elevated area of tissue which even after surgical revision can reform. Keloid scars are not to be confused with hypertrophic scars which are raised and often discolored, but do not extend beyond the boundary of the initial wound. This article discusses in great detail all the biological properties and mechanisms of scar formation and how silicone enhances the recovery.
Role of silicone in scar reduction
The epidermis may take around 2 weeks to sufficiently regenerate after a full-thickness wound has occurred due to it penetrating through the epidermis and into the dermis layers. During this time, intervention with scar development will have little to no effect as high collagen levels are required at this early wound healing stage.12
After this period, the new immature stratum corneum allows abnormally high levels of transepidermal water loss. This dehydration of the stratum corneum signals the keratinoctyes to produce cytokines, which signals to fibroblasts to synthesize and release collagen.
The newly formed collagen rushes to the scar site and is the cause of many undesirable physical and aesthetic properties associated with scarring. The application of SGS replicates the stratum corneum's occlusion properties, normalizing hydration of the scar site to that of healthy skin, perhaps inhibiting the instruction sent to the fibroblasts to produce excess collagen cells.

I cannot say the mechanism, but I can confirm it works, and can say that is generally accepted as working, not as some weird dubious treatment. I had surgery to install a rod in my leg after a broken bone. On the advice of my physical therapist, I purchased "Scar Away" brand silicone oil with roller applicator. Placing a thin layer and massaging with the applicator twice a day for four weeks turned my giant cheloids into small sections of skin which were distinguishable only by their smoothness and lack of hair, not color. He said he used to work for some basketball team and it was common practice to be used in professional basketball.

Thanks! What products did you use and/or recommend?

According to several papers (Sawada and Sone, 1992; Wong et al., 1996), increased hydration appears to be the main mechanism by which silicone oil acts on raised scars. Combined with an occlusive dressing, this preparation would increase hydration of the scar site. Sawada and Sone (1992) compared silicone oil treatment to vaseline treatment and found significantly improved healing with silicone oil, concluding that it was the hydrating action of silicone oil that led to improvement.
Sawada Y, Sone K. 1992. Hydration and occlusion treatment for hypertrophic scars and keloids. Br J Plast Surg 45(8):599-603.
Wong TW, Chiu HC, Chang CH, Lin LJ, Liu CC, Chen JS. 1996. Silicone cream occlusive dressing--a novel noninvasive regimen in the treatment of keloid.. Dermatology 192(4):329-33.

Thanks! By hydration, you mean keep the raised scars wet?

That's the idea.


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How does toluene inhalation damage the brain?
We just had a discussion about toluene abuse. It is known, that people inhaling toluene for a long time have significant brain damage, including  decreased intelligence.
I found that toluene is a lipid solvent, and that it can damage the myelin. However, myelin is only present in the white matter, but intelligence is related to the grey matter which does not contain myelin.
Is there any indirect damage, or did we miss some important point in this case? Second, how does toluene get to the brain? Is it able to infiltrate from the nose through the mucous membrane, or is it carried in the blood? I am just curious.

Unfortunately, saying that white matter doesn't relate to intelligence is like saying that the only factor in how long it will take to drive from New York to California is the condition of your car.

After crossing the blood-brain barrier, toluene, along with other volatile anesthetic agents, had been previously thought to inhibit neuronal transmission by causing a change in membrane or membrane protein conformation. Recent research has shown that interactions with several key brain neurotransmitters, mainly γ-aminobutyric acidA (GABA), to a lessor degree glycine, and possibly dopamine, are responsible for the clinical effects seen. Postmortem studies along with magnetic resonance imaging (MRI) findings have shown diffuse white matter demyelination and gliosis (solvent vapor/toluene leukoencephalopathy), which is postulated to be the end product by which chronic toxicity occurs, although the exact mechanism by which this occurs remains unclear

(McKeown at al. Toluene Toxicity).


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Effect of Ethanol on Brain Volume Measurements
I want to compare the brain sizes of two populations of fish. However, all the samples I have were fixed in 95% ethanol. As far as I know, 4% formalin is the normal fixative for soft tissues. Can I conduct my study, or do I need to obtain samples in formalin? I've scoured the literature, and I can't find any useful recommendations.

Are all the samples fixed in ethanol? Or some in ethanol and some in formalin?

I just spoke with my histological colleague about your question. He said that you should be fine for gross examination but not for microscopy. Why? He says, "When working with specimens, the higher resolution microscopy you try to achieve, the more 'potent' the fixative needs to be. A preservative will preserve what tissues are there. However, fixatives (like paraformaldehyde or glutaraldehyde) bind proteins together and, thus, are used to try to 'fix' a tissue posthumous in the manner that it was structured in life. For gross examination, a preserved specimen (without prior fixation) can act as a decent voucher for macroscopic evaluation of its internal organs; however, it will not suffice for any type of detailed histology at the light microscopy or electron microscopy level."
So, the short answer is that it depends on the type of work you need to accomplish.