text:
Is it possible to have cancer and normal blood count at the same time?
Does cancer always cause abnormal full blood count? I've read on the internet that some people who had advanced cancer, also had normal blood count. I can't find anything on the internet about this topic.

Cancer doesn't have to have a profound effect on the blood. Remember that a cancer generally starts off as an abnormal tissue growth or a neoplasm. As the tumor progresses into a malignancy, it has the potential to gain or lose functions, develop new cell types that shouldn't be present in a given organ, invade other tissues, etc. Because of this, in some cases of cancer patients may be subject to paraneoplastic syndrome, or cross-reactivity between something the cancer is doing and the normal tissues.
In the above-linked source, some hematologic paraneoplastic syndromes include (1) eosinophilia, commonly associated with a number of cancers, (2) granulocytosis, often associated w/ lung cancer, (3) Pure Red Cell Aplasia, commonly associated w/ thymomas. The list goes on, but in some cases blood testing is capable of assisting in diagnosis, especially in cases where cancer of the blood is the culprit (very obviously). To also be kept in mind, they note paraneoplastic syndrome only affects around 8% of all cancer patients.
In other cases, you'll be monitoring treatment. As we know, chemotherapy is destructive, and can cause a depletion of platelets or neutrophils, damage organs, etc. Complete blood count (CBC) testing will help oncologists monitor treatments in cancer patients.
Being said: Because individuals with a tumor/cancer may fall within normal ranges in a CBC test, and because these tests must be analyzed scrupulously due to several factors that influence them such as diet, multiple tests are often needed to arrive at a meaningful conclusion. On the basis of cancer itself, however, if it's a solid mass lodged in the liver for example, it's completely possible that blood counts are normal. What you may find, however, are biomarkers in the blood that are saying "hey, the liver is being damaged or dying" such as the enzyme aspartate transaminase. If the tumors are currently small, you may not find anything meaningful in blood tests, or that the blood is "normal." (the possibilities aren't exhaustive)
As a matter of real data I was able to find, Spell et al. was at least able to find some efficacy in CBC testing for colon cancer, to 84% sensitivity and 88% specificity, but you should suspect that individuals may still be asymptomatic under such tests regardless.


text:
Indian tropical fruit trees and fruit bearing

Most Indian tropical fruit trees produce fruits in April-May. The best possible explanation for this is

optimum water availability for fruit production.
the heat allows quicker ripening of fruit.
animals have no other source of food in summer.
the impending monsoon provides optimum conditions for propagation

This was asked in a competitive examination, and being a mathematician with interest in plants, this caught my attention. Please note that this was asked in aptitude section, and I feel it more aptly belongs this SE, correct me if I am wrong.
My thoughts:

April-May is summer in (tropical) India (where I live, Kerala) hence optimum water availability looks out of option.
Considering fruit production being a part of process of propagation, though this is a favourable factor, I doubt if it is a determining factor
Animals help disperse the fruits, and less availability of food may be a favouring factor attracting animals to fruits, it is not a determining factor.
which for me looks like the factor influencing increased fruit production more than the other two.

Sorry for the layman language, I would be grateful if someone can correct me if my reasoning is wrong and explain it more precisely (preferably in layman language, though I can understand some botanical terms)

Trees fruit before the monsoon season to maximize seed germination and seedling recruitment. previous studies have shown that in many species, fruiting occurs just before the wet season such that seeds germinate and establish during the wet season when conditions are most favourable.
Smythe N. 1970 Relationships between fruiting seasons and seed dispersal methods in a Neotropical forest. Am. Nat. 104, 25–35. (doi:10.1086/282638)
So the answer is 4.

So you say faster ripening influences the tree to produce more trees in summer?

Adding: Something to be noted here is that question is about "increased fruit production" and not (just) "ripening"!

Evolutionarily, these tropical fruit trees would want to maximize the amount of offspring that are produced and that survive to reproduce. This would increase their fitness and ensure that their genes are passed on to the next generation.

Tropical fruit trees would "want" (they're not actively strategizing) to produce their fruit at a time when other sources of food for animals are limited as this would increase the likelihood of most of their fruit being eaten and these seeds being dispersed (through the feces of animals) to many different areas to grow and reproduce themselves. This ensures the continuation of these species of trees.

So you say (3) is the best possible reason for increased production of fruits in April-May? I doubt!

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text:
Is hypoxia/anoxia the ultimate cause of death?
I know there are different causes of death for humans like heart disease, cancer, stroke, injury and so on, but i was thinking if in every case in the last instance death is due to hypoxia/anoxia.
Am i missing other mechanisms ?
What i'm searching are the last mechanism that cause the organism to collapse and die.
E.g. (non detailed just an example)
In the case of heart disease, a plaque could lead to the block of a myocardial artery followed by local hypoxia/anoxya that kills the heart tissue followed by cardiac arrest and death by general anoxia.

Copy of this http://biology.stackexchange.com/questions/41207/why-do-you-die-if-you-cannot-breathe ?

There is no one ultimate cause of death. For instance, there are neurotoxins which kill brain cells while oxygen remains plentiful, and there is complete disruption of the brain, as with a suicide-bomber.

You will first need to define death, Mauro. Good luck. You might say, when the organism stops moving for good, but I have shot deer that keep moving well after I shot them. Like 15mins after. You could say when the heart stops, but I know people whos hearts have stopped at one point and they are still alive today. So our first task would be to define death, so that you may later classify an organism as dead or not dead. Let us know what you come up with.

@Nathan Thanks for pointing that out, i would check it later to deepen my knowledge about hypoxia... there are indeed common parts in the two question, but the one that you linked is focused only on hypoxia while my question is more broad in the sense that i'm searching for other mechanism different from hypoxia that cause the death of a person.

@mgkrebbs Thanks for the comment, could you gently suggest me some reading about one of these neurotoxyns ? But if a neurotoxin badly damage the brain is there a chance this in the end lead to the failure of lung function (by poisoning of the respiration centre) and consequently general hypoxia ?

@DonJulian When i thought about this question i remember an MD (i was young and not really into science so i'm sorry to bring this without reference) that said something like: In the end we all die of heart failure. I think he was referring to the fact that independently from the primary cause of damage (a trauma, a pathology, a poison etc) in the last instance the collapse of the organism was caused by failure of heart function and blod flow to the entire body.

Having the head removed by an axe or sword is fairly ultimate...

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text:
Is there any evidence of animals wanting to die?
Is there any evidence of animals wanting to die? Specifically, animal communication which says "come and eat me".

Why do you call animals wanting to do 'cannibalistic' and not e.g. 'suicidal'? In any case, this seems to be more biology than philosophy.

@CamilStaps these sorts of things come up... obviously closes are very subjective

@CamilStaps btw in answer to your question i just find the idea of an animal telling another it's going to kill itself, more fantastic than "please kil me"

I don't understand what you mean by your last sentence I like the idea that internal reflection needs to be able to express the absence of an object, if it is to have object-hood but I am assuming those are concepts of philosophy that are irrelevant for the question. If it is the case, you probably want to delete that sentence.

If you are thinking in terms of mammals, then the behavior is probably more along the lines of where the individual organism that may be sick, injured and likely dying will isolate itself from its group. And if leaving the security of its group makes it vulnerable to predation, then maybe you could interpret that as a form of communication,

In biological terms, it would be more useful to frame this in terms of behaviour and not the vague "wanting to die" (which is subjective and/or meaningless for non-human animals).

Is it possible that an individual would benefit form being eaten?
In theory it is possible that such behaviour would evolve. An individual may improve the probability of its genes to be passed on by letting a related individual (which carries similar gene variants) to feed on it. When counting the fitness of an individual as being the sum of the fitness of all related individuals weighted by their coefficient of relatedness as inclusive fitness. We refer to the selection pressure that is due to a differential in inclusive fitness as kin selection. The field that study the evolution of altruistic behaviours is called social evolution and is an active field of research.
Example
For example, a male could much enhance the probability of survival of its offspring by being eaten by the mother. The type of cannibalism where one mate eat the other is called sexual cannibalism. A famous example of sexual cannibalism is the mantis prey. Note that it has been suggested that in natural conditions sexual cannibalism could be rarer than expected previously thought. Note also that the question of whether the male benefits from being eaten by the female in prey mantis is still controversial and could result from a sexual conflict.

In fact there are many cases of animals expressing a behaviour which benefit their predators, although it is controversial whether they "want" it. I mean arthropods and mammals infected with "mind-controlling" parasites. For example, an ant could become host of the liver fluke Dicrocoelium dendriticum. Then every night it would wait patiently on the top of a grass leaf to be eaten by a grazing animal, in whose liver the fluke could reproduce. When the temperature rises during the day, if still alive, the ant would return to its normal behaviour. Here you can find other examples.


text:
How does the brain train its neural network?
One question that came up learning how artificial neural networks are working was how the brain can train its neural network?
When we say we have an artificial neural network, the problem behind it is a typical, but uncommon minimizing problem. The math behind it is logical and pretty easy. But it's math, so an computer can calculate it by doing millions of iterations. But the brain can't do that (I would be surprised)
So, how does the brain solve this task. Trial & Error, we don't know or is there an even more complex system behind it?
Thanks in advance.
GA

I'm voting to close this question as off-topic because it belongs on Cognitive Sciences S.E.

@AMR - not more on topic there than here. Wouldn't migrate. Wouldn't close here either.

@Christiaan This really isn't asking about a purely biological process. Sure you could talk about reinforcing neuronal connections through repeated usage and the underlying chemistry, but that doesn't get at the learning aspect, and I think that the mechanisms of learning are Cog Sci more than straight biology.

@AMR - good point. But CogSci often deals with it from a holistic perspective, while this question tends to aim at the network level. As such, given the low-level nature, it's ontopic on both ends from my pov

@Christiaan well, if you think there is an answer, then you are the expert. It just seems that also trying to make this relevant to the neural biochemistry of learning as well, may make the answer a tad long....

@AMR a close vote based on too broad would be perfectly acceptable to me for sure. I just wouldn't like to see this migrated.

this is one of the biggest open questions of the AGI field, a solution apparently nearly leads to AGI. there is some research trying to link gradient descent to brain neurology. also jeff hawkins postulates cortical columns are representing ML algorithms. Deepmind has some research relating to the hippocampus. may try to cook up some survey at some pt, but its an extremely challenging area to cite/ summarize current knowledge. the dopamine system has a lot to do with human rewards & presumably plays a large role. etc

The answer to this question is probably Hebbian Learning.
Hebbian learning can be nicely summarised with "Cells that fire together, wire together". So basically the synapses of neurons are strengthened if they fire in sync, and weakened otherwise.
One can easily see that a) this kind of local learning mechanism makes a lot more sense for the brain then some global method like gradient descent and b) this mechanism leads to stable representations of patterns.
In artificial neural networks this kind of learning is modelled in Hopfield networks and Restricted Boltzmann Machines.
Of course this simple rule barely scratches at the surface of what goes on in the human brain, when we are learning something. A complete picture would probably involve complex feedback mechanisms of inhibitory and excitatory connections between neurons, functional modules of neurons, and different parts of the brain.
But I fear these details are not yet well understood …

Oh. MY. GOD. I didn't through anybody would ever answer on this question anymore. :D Thx.


text:
Blood sampling at home
I want to collect small blood samples at regular intervals (e.g. every 8 hours or more often) over a longer period (weeks to months). To avoid having to go to a lab or doctor to have this done, I want to do it at home. I will need to extract mRNA from PBMC from the samples.
Assume a test tube in which you have a piece of filtration paper. You prick your finger and let a couple of drops of blood soak into the filtration paper, and then seal the sample in the tube, and immediately place it in your regular freezer.
How long will the mRNA survive under these conditions?
Will it be better just to let the sample dry out inside the tube (e.g. using a desscant), or store it at room temperature?
Will it be possible to store it for e.g. a week before sending the batch in for analysis?


text:
Why does my grass luminesce when I step on it?
I live in Austin Texas. My grass is in pretty bad shape but I have noticed small luminous spots on some areas after I step on them.
I'm guessing this will be seasonal so, for the record, this is during November and December that I've noticed it.  It's been quite wet and about 40F to 60F at night. I've seen it a dozen times over the last several weeks. I've attempted to collect samples and when I bring it inside to study it, there is nothing there but grass and maybe some young root systems.  I've googled and haven't seen anything like this discussed.  Does anybody have an explanation?
I can see about 5 spots after trampling a few square feet of my grass.  Using a DSLR and a time exposure, this is the best photo I've been able to get of one:

On one attempt, I pinched the glowy part, held it in my hand, confirmed it was glowing, brought it inside, and this is what I had:

Can anyone explain this?  Is this significant?  Or perhaps the right question is where should I go for a question like this?

Neat! How long does the glowing last? And can you not see the luminescence when under artificial lighting?

I'd guess that you have some kind of glow worms/fire flies - when you walk across the grass you are disturbing them causing light to be emitted. It's going to need a much better photograph to capture the luminescence event (I appreciate that is very difficult!) to be answerable.

It lasts for about 30 to 90 seconds.  It's conceivable that I'm squishing something, like glow worms. Are glow worms tiny like a quarter of an inch?  And would this be the right season, weather, and location for there to be several of them per square foot? And would their ..uhm.. juices glow when they get squished?  Oh, and this is so faint that anything more than moonlight and you wouldn't see it.

I know this is a late reply, but I observed the same phenomenon this morning. I live on 12 acres with horses. It is my ritual to jog with my horse in the morning early before I get started with my day. It was before sunrise and very dark (the moon wasn't out). I had a red-filter flash light so I could see what I was doing, but once I started my jog I turned it off. I saw a speck on the ground that I thought at first had to be the neighbor's security light shining through some trees. After I looked closer I was certain it was it's own light source, so maybe a firefly then? A firefly usually has

first of all, this is not an answer to the question. This is also not a question on its own.Usually, I vote to remove these kind of answers but in your case, I will make an exception since its a well written anecdote and others get to know that this is not an uncommon occurrence.

If it were fireflies or glow-worms, you would have seen them pretty quickly with your searching and collection of grass. I would guess that this is some kind of bioluminescence caused by bacteria or Dinoflagellate.  I have seen this effect when walking on wet sand at the ocean. It is quite fascinating and fun to watch. According to wikipedia, bioluminescent bacteria and Dinoflagellate can exist in fresh water. The moisture in your yard might be enough to support their growth.
https://en.wikipedia.org/wiki/Bioluminescent_bacteria
https://en.wikipedia.org/wiki/Dinoflagellate :

The luminescence occurs as a brief (0.1 sec) blue flash (max 476 nm) when stimulated, usually by mechanical disturbance. Therefore, when mechanically stimulated—by boat, swimming, or waves, for example—a blue sparkling light can be seen emanating from the sea surface.[66]


text:
Can Allergy and Auto-immune diseases be the signs of hyper-vigilant immune system?
Allergy sufferers are much less likely to get some types of cancers. Theories regarding  allergy - cancer link are mixed.
Many say it is due to hyper-sensitive immune response.  But the correlation between allergy and lowered glioma risk is also difficult to explain, due to blood -brain barrier.
However there was one interesting theory, saying that, allergy is an evolutionary anti-cancer protection. Allergy sufferers simply do not let some of the carcinogens to come into their body.
I am computer engineer. When we setup a protection at a system (antispam, antivirus, firewall) there is  sensitivity level that we have to select.  Higher sensitivity offers better protection but also results in more false positives.  However not all false positives are due to higher sensitivity. Some can simply be due to faulty protection system.
So my question is,  can  allergy or auto-immune diseases be sign of high-sensitive immune system which will have advantages and  disadvantages  or just a sign of simply faulty immune system which will have only disadvantages?

Could you add some citations of where you came across these theories?

@MattDMo  http://jnci.oxfordjournals.org/content/early/2012/02/20/jnci.djs153.full


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In the video, "Inner Life of a Cell", what's the empty space between the molecules?
In the video, "Inner Life of a Cell" there's a lot of empty space between the proteins. Is it just a simplification (i.e. they omit smaller molecules)? If so, what are the smaller molecules supposed to be? Or is it just a vacuum small enough to be ignored?
I've done some reading up on it, and found that it's called cytosol which is a complicated mixture of random proteins and molecules.

It is a vast oversimplification. At a minimum the space between proteins will be mostly water. There will be plenty of small molecules, ions, and dissolved gases as well. Also, the cytosol is a pretty crowded place.. Also, it might be helpful if you linked to the video so we can see what you're talking about more easily.

@Loogai you answer the question in your question: "I've done some reading up on it, and found that it's called cytosol which is a complicated mixture of random proteins and molecules." - therefore, it's unclear to me why you've posted this as a question, and unclear what question remains.

I was seeking clarification for the cytosol answer and if the proteins in the video comprise the cytosol, if so the space between them is vacuum. I thought I implied it but I wasn't clear enough. Sorry. Also: "what are the smaller molecules supposed to be?"

If the video were realistic and showed all the molecules in the cell, you couldn't see anything because water would always get in the way.

It could be plasma containing water.

This is a common simplification of videos and textbook illustrations. In reality a cell is much more crowded and there is hardly any space between proteins. You can find a more realistic drawing here (I linked the pictures, because I am not sure about the license).
Regarding the cytosol:
Quoting wikipedia:

The cytosol or cytoplasmic matrix is the liquid found inside cells.
  [...]
  Most of the cytosol is water, which makes up about 70% of the total volume of a typical cell
  [...]
  The amount of protein in cells is extremely high, and approaches 200 mg/ml, occupying about 20-30% of the volume of the cytosol


text:
Does physical exercise of a specific part affect muscles in the other parts of the body?
There is a theory among bodybuilders, that is, if you train big muscle groups (e.g. legs, chest), it will increase the overall growth of muscles all over the body; the trained muscle will release signals (what are they?) into the blood stream and in turn, triggers the release of muscle growth/repair hormones (insulin-like growth factor?) which have effects on any (skeleton) muscle cells.

Is this story true?
Will the muscle growth/repair hormones also enhance the smooth muscle or cardiac muscle?

Definitely a question that should be asked on bodybuilding.SE.

@Remi.b, the OP is interested in knowing if the popular notion amongst bodybuilders has some authentic biological basis.

Maybe I am wrong but I would assume that on bodybuilding.SE they care about verifying their claims.

@Remi.b thank you for the link. But I just want to find out whether these popular claims are supported by rigorous study. I looked at some references cited by bodybuilding experts, they are pretty crappy.

http://jap.physiology.org/content/65/6/2406 here is a paper on training and increase in testosterone.

@ChenChao what were the references by the bodybuilding experts?


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How to predict cancer-related proteins in Protein-Protein Interaction networks
Protein-Protein Interaction networks are known. It's an undirected graph. Each row of the networks is like this (Protein 2 - Protein 6), and It represents the interaction between Protein 2 and Protein 6.
networks:
Protein 2 - Protein 6
Protein 4 - Protein 5
Protein 6 - Protein 5
Protein 5 - Protein 7
...

In this networks, It is known that some of proteins are cancer-related proteins, some are nonCancer-related proteins,
The known proteins:
Protein 4,Cancer
Protein 6,nonCancer
Protein 7,nonCancer
Protein 10,Cancer
...

But the vast majority of proteins is unknown whether is cancer-related protein or noncancer-related protein. How to use these known cancer-related proteins and nonCancer-related proteins to predict the protein whether is or not a cancer-related protein.
I do not know how to solve this problem. I need your help. Thank you very much.


text:
Are there testosterone receptors in female mammary tissue?
Does female mammary tissue have receptors for testosterone hormones?
Do male hormones influence female mammary glands, as female hormones influenced the male mammary tissue, such as in gynecomastia?

The female mammary gland tissue contains androgen receptors (testosterone is an androgen). So this tissue is sensitive to androgens, and they inhibit the estrogen-induced proliferation. The inactivation of the androgen receptor on the other hand leads to an accelerated growth of the pubertal mammary gland and to the upregulation of estrogen receptor α expression in female mice. See references 1-3.
And the androgen receptor also seem very important in the formation of the nipples, as testosterone here directs apoptosis in the forming breast tissue. Mice without a functioning androgen receptor were born without nipples. See reference 4 and 5 for details.
To answer your question shortly: Yes, androgen hormones (among them testosterone) have a profound influence on the female mammary gland.
References:

Testosterone inhibits estrogen-induced mammary epithelial
proliferation and suppresses estrogen receptor expression.
Minireview: The Androgen Receptor in Breast Tissues: Growth
Inhibitor, Tumor Suppressor, Oncogene
Androgen receptor inactivation resulted in acceleration in pubertal
mammary gland growth, upregulation of ERα expression, and
Wnt/β-catenin signaling in female mice.
Hormone Action in the Mammary Gland
Specificity of tissue interaction and origin of mesenchymal cells in
the androgen response of the embryonic mammary gland.

@esi72
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What is the term for "technical extinction" of yet alive animals?
What is the term for an event in which a species is still alive, but has no chance of future reproduction and the species will be considered extinct once the current generation dies out?
For example a species of a tiger that has the last 5 surviving members left and which are all related and all male. Hence, even though they are still alive, there is no chance that the species will be able continue their bloodline and hence are already "technically" extinct.

This is technically called Functional extinction. With no viable reproducing population the species will almost certainly become extinct. Note that humans could potentially mess with this through the use of reproductive technologies.

Are humans functionally extinct?  It is all but certain the species will become extinct.  Probably long before the sun dies.  But even if the humans figure out how to migrate to another solar system, that is just putting off the inevitable.

@emory All species were created at some point in time, and all become extinct eventually, whether that be hundreds, millions, billions of years into the future. Humans are not functionally extinct, at least not by any useful definition of the term.

Functional extinction is a bit more broadly defined. I don't know if it accurately describes the last living individuals of a species past the tipping point, but it's still a good answer (upvoted).

For this matter, I'll call it Ecological Extinction. That means you still have an extant population, but the individuals in which you are focusing on do not interact any longer with their surroundings and environment as they should. For ex., they're no longer preying or being predators, they no longer reproduce because effective population (Ne) isn't enough.
There's an example in which you can make some research on, and it's about the Ecological Extinction of Nomascus leucogenys (white cheeked gibbon) in Yunnan Province, China.
There are some papers about it, which you'll easily find if you go to Google Scholar.
Hope I helped.

David, fantastic example. Do yo have anymore of these?


text:
Are there animals / mammals which only have one eye?
Do all animals (of a certain size and not thinking about worms) have the possibility to perceive depth?
Do all mammals have at least two eyes? Are there mammals with more than two eyes?

Not all two-eyed mammals have depth perception. Many herbivores have eyes on the opposite sides of their head to increase their range of vision for predators, and are so widely separated that they barely overlap at the front, if at all.

Also, please clarify "all animals (of a certain size and not thinking about worms)".

@MattDMo Thank you for your first comment; I didn't think of that. For the second: I am aware of the fact that some worms (all?) don't have eyes. Also, I'm not interested of animals which consist of a very small number of cells (by a quick search I found Myxozoa as an example). So for the sake of clarity, lets say the animal has to have at least 5cm of height when standing on the ground.


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Can you grow more Biomass in a brickhouse only powered by solar cells than in a greenhouse? Will we ever be able to?
So I asked following question some physicists but they couldn't really help me though:

Right now I read that 1m² of solar cells generates roughly 100Watts of
  energy. There are really efficient Grow LEDs that use only two spikes
  in the lightspectrum to make plants
  grow.
I have seen some graphs like the Quantum Efficiency of Sola
  Cells
  that suggest that solar cells can absorb energy in the range of 400nm
  up to 1200nm (in varying degrees of efficiency).
By my logic (given a high enough overall efficiency of the solar
  cell), a solar cell can make light that is most of the time reflected
  by plants in the range of e.g. 500nm-600nm / or 800nm+, into
  electrical energy, and that electrical energy can be used, in turn, to
  produce light in the range of 400nm and 700nm that the plants can use
  again for photosynthesis.
Additionally, i could imagine that the sun sometimes hits the range of
  diminishing returns in terms of brightness (lux, lumen?) when it's
  really really bright and hot and shining directly on the plants.
  Instead it would maybe be more efficient to capture that energy
  (photon) and convert them only to the wavelength needed in enough
  brightness that plants can grow (again, given a high enough solar cell
  efficiency, right now it's 20%, i heard 40% is a theoretical limit?)
You could phrase the question a little bit different: I have 1m² of
  land and two possibilities:

build a greenhouse and plant 1m² of crops
build a brickhouse as high as I want with as many layers of 1m² levels. But they are only allowed to be lighted with LEDs and no
  direct sunlight. And the LEDs are only allowed to be powered by 1m² of
  solar cell on the roof.

What is the needed solar cell efficiency (generated watts/m²) for the
  solar cell to reach the break even point of total biomass production /
  timeunit between case 1. and 2.
If there are other environmental conditions that would benefit only
  one of these cases, assume in favor of case 2 and mention the
  variable.
I was in a heated discussion about this yesterday and I would love for
  someone who knows more then me to help me wrap my head around this.

So, to give some extra Information for you guys or to rephrase it again to increase the chance to get an answer: current solar cells operate anywhere from 100W-200W/m² with an upper limit somewhere around 400W to 450W for the way we do it right now. (100W is 10% efficiency, 20% are high quality PVCells right now)
Thanks a lot!


text:
Where can I find a file listing the genetic differences in humans?
I don't know much about genetics. For an arts project I'm looking for a human genome.
I read that:

Only about 0.1% of the genome is different among individuals, which equates to about 3 million variants (aka mutations) in the average human genome. This means we can make a “diff file” of just the places where any given individual differs from the normal “reference” genome. In practice, this is usually done in a .VCF file format, which in its simplest format looks something like so:
chr20 14370 rs6054257 G A 29 PASS 0|0
Where each line uses ~45 bytes, and you times this by the ~3 million variants in a given genome, and you get a .VCF file size of about 135,000,000 bytes or ~125 megabytes.

Is that correct?
Do you know a database to download a VCF file or something similar? It would be amazing if you could provide a link to the file mentioned above!

You may need to rethink your number, that 0.1% number might be a little low... If you are interested in the genetics, you may be interested in this answer, http://biology.stackexchange.com/a/41975/16651. Also, NCBI's databases are open to the public and you should be able to download whatever you want from them.

Technically speaking (and in SI and IEC terms) 135,000,000 is 135 Megabytes (MB) or approximately 129 Mebibytes (MiB).

Have you tried poking around the 1000 genomes project?
Try this link
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/snps/


text:
Why only human have noticeable difference in face?
Our facial appearance is pretty much different from each other unless we are talking about twin. Credit goes to crossing over of chromosome. But why can't we distinguish between other animals of same species? Yes there are some very little differences but not that much clear and obvious difference like we have. Why is that?

So it's because we are human. Therefore  we can distinguish between two human easily?


text:
How are individual neuron firing rates characterized?
I'm reading this paper that the Human Brain Project published in Cell and I'm confused how they recorded the firing rates shown in the firing below:

In the publication, they mention that they use the Petilla convention. However, upon reviewing that publication, I was unable to determine the procedure of characterising neuronal firing rates. How are they able to isolate a neuron's firing behaviour away from the network it is usually contained in? Where do they measure the outputted firing rate?
I am aware that usually to characterize a neuron in a network, Spike Sorting or single-neuron recording can be used, however this doesn't seem like a valid way to characterize the physiological properties of an individual neuron.
If you consult the experimental procedures section of the paper, you can find that they used methods previously established in three papers. However, upon reviewing these papers, it appears that the neurons were stimulated while still inside the tissue, but after the tissue had been sliced. However, this seems so absurd that I must be misreading it.
How were the electrophysiological properties of these neurons characterised?

However, upon reviewing these papers, it appears that the neurons were
  stimulated while still inside the tissue, but after the tissue had
  been sliced. However, this seems so absurd that I must be misreading
  it.

You're not misreading it. I can't access the paper you refer to, but this is a standard way to measure the electrophysiological properties of individual neurons, and has been for more than 25 years. (I'm really curious what you find "so absurd" about this).
I'll take an educated guess (since I can't read the methods online) that these recordings are from rats (or possibly mice), using whole cell patch clamp technique in thin slices of the young rat neocortex. Briefly put: the animal is sacrificed, the brain is removed, it is sliced into about 400 micron thin slices using a vibrating razor blade, and the slices are kept in a artificial cerebrospinal solution that allows the neurons to remain functional for a day's worth of experiments. Then individual neurons are imaged under a microscope and "patched onto" with a glass micropipette that contains a silver wire. Electrical events in the neuron can thereby be recorded into one's computer and plotted as shown in the figure you provided.
In this case, what's shown are what are known as current clamp recordings, in which current is injected into a neuron and the resulting voltage changes are recorded. Here, they are injecting a depolarizing current to make the neurons spike (have action potentials) and seeing that the neurons they sampled vary in their spiking properties. Some are fast spiking, some are slower spiking, some have different spike waveforms or patterns of spiking.

"absurd" was a bit of a strong word. I really just meant to say that if the measurements are taken while the neuron is still connected to other neurons, how do they know the spiking pattern is due to the neurophysiological properties of the neuron and not because of the neuron's placement in the network?

Also, why are you unable to read the methods online? I think all the papers are free.

@Seanny123 1st question: they could do these recordings in a pharmacological blockade of excitatory synaptic transmission to eliminate any spontaneous excitatory drive from the network (Did they?). 2nd question: No, it's behind a paywall for me ("To view the full text, please login as a subscribed user or purchase a subscription."). Maybe you're accessing it from on a campus that has a subscription to Science Direct, or something like that?

Could you email me or tweet me so I can send you the papers?


text:
Is an egg classified based on the species inside it, or by the species that laid it?
Basically what I'm asking is if an animal of species x were to lay an egg, and the animal inside that egg happened to be the first member of a genetically new species y, would the egg be considered an x egg or y egg?

Parent species is certainly what they'll call it, unless there was some reason to check the genetics.

What you are proposing does not happen in higher Eukaryotic organisms. See UC Berkley site on Speciation for more detail.

Asap Science answer to this question

Species are generally defined in terms of populations (see e.g. the wikipedia page), and it is therefore relatively meaningless to talk about individuals as species. That species is defined in terms of populations is true for many species concepts, e.g. as groups that can produce fertile offspring (biological species concept) or as a evolutionary distinct lineage (phylogenetic species concept). The question is therefore somewhat ill-posed, since it is only framed in terms of individual parents and offspring.
A possible exception could be speciation in apomictic species or speciation events following a change in ploidy level, but this is mostly relevant for certain types of asexual species and probably not what you are after since you are talking about egg-laying animals.

Linguistic
An Ostrich egg. A chicken egg. A quail egg...whether you call an egg based on who laid it or who is inside of it is not a question of science but a question of linguistic.
Non-fertilized chicken eggs do not contain any chicken. We still call these eggs chicken eggs. Following the same logic, I would call an egg based on who laid it. But really this has nothing to do with science.
But, the first question one should ask is whether the scenario you are describing makes any sense. Is it possible for an offspring to be of a different species than its parent?
Can the offspring belong to a different species than the parent?
The concept of species is very poorly defined. The reason is not that we fail to agree on a definition but that the categorization of living things into discrete categories often does not make sense.
Let's think of an individual of species A. Imagine we were to look back at the ancestry of this individual for a relatively high number of generations. You chose one specific ancestor in the lineage and realize that this ancestor looks very different. Maybe we have already named the species that this individual belongs to. Let's say the ancestor belongs to species B. So, at some point there was necessarily an individual from species B who had an offspring who belonged to species A, right? ...not really. The reason is that the concept of species makes little sense. There is no such thing as absolutely clearly defined groups of individuals that you can gather into one single species.
You should read this post on the concept of species and then read this post on species ring and come back here once you finished reading....
We often think of the concept of ring species when thinking about population separated spatially. But the same concept hold true for population separated temporally. If we come back to the two individuals belonging to species A and species B. These two individuals probably cannot reproduce together and are very different. It seems legitimate to classify them in different species. However, all individuals along the way were probably able to reproduce with their own parent and offspring.

This is really convoluted. The simple answer is that unless giving birth to a hybrid, a species will only produce offspring of that species.

Hidden behind your simple answer is hidden the conceptual issue of the species. Saying it is impossible to give birth to an individual belonging to a new species (except hybridization) seems to contradict the existence of speciation events.

What are you talking about?

Well... that is a broad question that you are asking @AMR! Saying a species will only produce offspring of that species is contradictory to a species can evolve to become another one and the reason is that the term species is poorly defined.

In a single generation an organism of a defined species will not give birth to another species, unless the mating is between two individuals of such compatibility as they can produce a hybrid, and more often than not, in those situations the hybrids are sterile. Any single generation will not be that different from the prior one or the next one. It is over time and gene pool separation that different species can be distinguished when making a comparison. So it is not contradictory.

If you move from area A to area B you need to pass by the border at some point. If you evolve from species A to species B you need to make an offspring who is not of the same species. I wanted to make sure the OP understood why this analogy is misleading and the reason is that the concept of species is bad. We are not talking about speciation here, we're only talking about a single lineage that changes through time sufficiently so that we would tend to call the lineage differently at two time step (regardless of whether the lineage actually split in two or more).

This question is interesting. First of all, I recommend you to look a little bit about the most popular definitions of species and, more importantly, how speciation can occur.
I can picture a problem of hybridization when I think of your question. Since speciation takes many (plentiful) generations to happen, and as I can remember, can involve sympatric speciaton and/or extinction of the parent's species since the new one won't be enormously different in matters of food request, habitat and other physiological needs (generally) and so there will be a conquest/fight for resources (you can look out for more details in Charles Darwin's On the Origin of Species). All this to say you won't have a newton coming out of a frog's egg. :)
But hybridization can lead to speciation, and you can have a hybrid coming out of an egg of a well descripted species. This happens with more frequency in fishes, insects and amphibians. For example, you can study individuals that are phenotipically different from their parents, with other types of adaptation (sometimes better) to the environment, and that emerge from different (and phylogenetically proximate) diploid sexually reproducing species... and the resulting individuals can have, of course, di/tri/tetraploid genomes... So, morphological and genetically different from their parents!!
And when referring to these situations, scientists generally call them genus name of the species involved + complex. For ex, the Pelophylax complex, involving 3 types of frogs.
If you really have an urge to search about this, try to go to this paper.
Hope I helped.
PS: You can also research about the Squalius alburnoides complex, which is about a group fishes extant in the Iberian Peninsula, with an amazing (and complex) process of speciation where you have a well characterized hybrid coming out of eggs layed by hybrids or parent species.


text:
Bootstrapping (symmetry breaking) in evolution
Many fascinating phenomena in nature show different behaviours on the micro and the macro level. Here I am especially referring to phenomena that are symmetric on the micro and asymmetric on the macro level. Let me give an examples from physics:

Arrow of time: Physical processes at the micro level are
  completely time-symmetric, if you reversed time, all laws would remain
  the same. Yet on a macro level they are not time-symmetric, we have an
  obvious direction (flow) of time.

It seems to me that we have a similar situation with evolution:
On the micro level it is really only about adaption (and not about improvement): You put some beings into an environment and they adapt, you change this environment and they adapt. No improvement, just blind "back and forth".
Yet looking at the whole tree of life on the macro level we have a different picture, we see all kinds of emergent phenomena:

explosion in diversity
emergence of complex interconnected ecosystems with completely new dynamics of their own
true innovations in functionality (sensors, actuators, information processing etc.)
and finally of course higher order functions like abstract intelligence (and  even qualia)

To make the difference more concrete I will give a gedankenexperiment of two planet simulators. In both cases you accelerate time so that one hour translates into one billion years. Both simulators function differently in a subtle way but you don't know how. You throw some simple sims onto both planets and let the evolution simulation run. You don't switch your computer off and go to bed, the next morning you decelerate time and take a look:

Planet 1: The simple sims quickly adapted to the environment as expected (but they stayed simple because evolution is not about improvement but about adaption).
Planet 2: Some strange looking sims wish you a good morning and want to discuss the technicalities of the Riemann hypothesis with you.

My question
What are the minimal conditions that have to be met to get this kind of bootstrapping (symmetry breaking from micro to macro level) started. And what is going on at the core of this transition from micro to macro.
Edit
My specific point is about the symmetry breaking process in the sense of system dynamics. To give an example of a possible answer it could be something like Parrondo's paradox, a fascinating phenomenon from game theory where you combine two symmetric (losing) processes to get a (winning) asymmetric process. More can be found here: Parrondo's paradox.

This would require an entire book. There are several books on biochemical as well as mathematical explanation to how diversification could have happened. Most of our understanding is also incomplete. You have to ask a precise question or it is highly likely that this question would be closed for being too broad. Also, it is really essential for you to know some basic concepts of molecular biology, biochemistry and evolution.

I wish to reiterate that we are not being hostile towards you. Any good answer on this topic would require a good knowledge of biology. The issue with general evolution questions is that anyone who has read a popscience book comes up with a handwaving answer. So, please focus on a specific point instead of asking how and why the world is as it is.

@vonjd just because you produced an answer doesn't mean that the question itself isn't too broad, and I'm not even sure that it answers the question in a self-contained manner. You also need to stop ascribing motivations to people that may not have them, as many of your previous comments have done. This just makes other users less and less likely to answer your questions. No one on this site has a vendetta against you, but we all care about the quality and focus of this site, and so vote accordingly.

@WYSIWYG It is why SE has a voting system to promote good answers. Closing down questions for fear that they may attract bad answers seems to put the cart before the horse. I don't understand this kind of censorship. I won't even try to use the argument that anyone who doesn't like broad questions has no obligation to read this one.

Good well written questions would attract clear good quality answers - yours don't, they're consistently attracting junk. Anyone can turn up and vote on SE - they might know nothing about evolution, or (like me) might be an active researcher in the evolutionary biology community with a phd and masters degree in the subject... you should be more selective about whose voices you listen to if you want to learn.

@AleksandrDubinsky We are not censoring anything. I am just asking the OP to be precise. Broad questions are off-topic in any SE. Btw, I personally just pointed out to the OP that they should refine the question. I didn't close the question as you can see. Please go through the help center to know wat "broad questions" are.

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

@WYSIWYG: Yes, you asked me to be precise and I therefore edited my question accordingly and asked for your feedback. I got no feedback but this comment was deleted. Then the question was over-hastily closed (not by you). That this question is not too broad can be seen by the fact that I gave a short and precise answer. Additionally people are giving precise answers in the comments. Now those answers have been moved to chat. I think there is something fundamentally going wrong in this community. I am active in many different SE communities and I have never encountered something like this :-(

@vonjd 1. Comments are not used for answering 2. Your question is broad even after the edit and if you think your own answer was what you were expecting then I don't think that is clear from the question. Please see MattDMo's comment. There is nothing wrong with this community; many people here also participate in other SEs. Vague and broad questions are not accepted in any SE. Perhaps you are better aware of other subjects so you don't end up asking vague questions in other SEs. None of your "supporters" are active here and probably even bio graduates. Your question is broad. Period.

Comments are moved to chat on other SEs all the time. They are also deleted as soon as they are not useful anymore all the time.

@vonjd THIS IS YELLING. This is strong emphasis. This is emphasis. WYSIWYG (who happens to be a site moderator, if you hadn't noticed the ♦ next to his username), was merely emphasizing SE rules, which are common across all sites, and which you appear to be selectively ignoring. That is all.

I found a paper which gives four conditions that have to be met:

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

Source: Soros, Stanley (2014): Identifying Necessary Conditions for Open-Ended Evolution through the Artificial Life World of Chromaria
Chromaria is "an experimental platform that allows the exploration of evolutionary theories in an intuitive and visually engaging way" from EPLEX, the Evolutionary Complexity Research Group at the University of Central Florida (UCF)

Condition 2 does not have to be the case. Prokaryotes, single celled Eukaryotes, and some organism with fertile hermaphrodites more often than not create exact clones of themselves. Condition 3 does not happen in life. Even bacteria communicate chemically at a minimum creating quorum sensing behavior within the colony. Condition 4 doesn't hold for life as most organisms will operate at some optimal level. They will lose traits that are not used, especially those that are not required for survival.

@vonjd "Later I found that it is still a huge research topic to find out what we are missing (keyword: "open-ended evolution")" You are still misstating this - it's not that we are missing big chunks of information about how evolution works, algorithms simulating evolution are missing a lot. That's what people have been trying to tell you.

@YviDe: I get that but how can you be so sure without even be willing to think about it? It is as though you thought you knew everything about aerodynamics and when you build a plane it instantly stalls in the air and crashes. You did everything according to the theory of aerodynamics. Then you ask the aerodynamics experts and they tell you: "No, no, we know everything. We don't know why your plane crashed but our theory is complete. It must be your fault and we don't want to think nor talk about it - case closed." Would you accept that? I don't - and I don't think it is good science either.

@vonjd you seem to be completely comfortable just taking the other view, though, that Biologists must be missing something that's "breaking symmetry". As for why I am comfortable saying that the fault is in the models and not in our understanding - because I actually used to study Evolutionary Bioinformatics (MSc) and we acknowledged that we lacked computer power to model everything when doing simulations.

@YviDe: NB: I am talking about the first plane ever built. If you built a plane today and it crashes it is of course an engineering problem not a problem with the theory. But in evolution despite decades of research we are still far from producing anything that faintly resembles real evolution. So, yes, you could be right but the case is far from closed. The evidence that evolution happened on this planet is overwhelming but the argument that we understand the whole process sufficiently well is far from conclusive.

It's called Occam's razor. We know our simulations are lacking, so if they don't produce the desired result we need to first look at our models and computations to find the fault, and only if we can exclude that (which we can't) should we look at the theory behind the simulations.

@YviDe: "we lacked computer power to model everything when doing simulations" - this could be true too. But it can also be the case that we miss something fundamentally different. That we do the abstractions at the wrong places. I mean we are able to simulate the creation of galaxies in the early universe because we know how to simplify the model enough to get to the bottom of things. If you wanted to simulate that with every single atom involved you would also lack the computing power. We have not yet understood what a good simplification/abstraction of evolution could look like.

@YviDe: and e.g. one of my master students is working on a multi-agent simulation of the stock market at the moment. This model is able to reproduce many important stylized facts of markets. And, believe me, markets are also very, very complicated beasts. People could tell you that you had to simulate millions of brains that are involved in the process - but that of course misses the point. All models are wrong, some are useful: We have not yet found the right abstract model (from an algorithmics point of view) of real evolution that does just the simplifications at the right places.

@vonjd If you want to ask about a right model to simulate the evolutionary process then your question should have these: 1. Kind of outcomes do you expect (i.e what exactly you are looking for) 2. The scale of the model 3. Assumptions you can allow 4. Kind of model (deterministic or stochastic) 5. Computational resource available (optional).
You should explain what you have thought of and then ask. You should also go through the existing algorithms. If you are unaware of those then your question should be a reference request asking for papers on evolutionary simulations.

@vonjd "This model is able to reproduce many important stylized facts of markets." And if it didn't, would your first question be "what are we missing about the workings of the stock market" or would it be "let me look at that model and see how good your model is"?

As it was, your first question was "What are we missing about the real workings of the evolutionary process?" which is still about what we are missing about the actual process, not the simulations - turns out, even from your own research into the topic, that that question was based on wrong assumptions. See the paper you referenced in that other question and how they talk about porevious work done on the subject. "If we cannot simulate a process we have not understood it properly" is wrong - we might actually be simulating what we know badly.

@vonjd As for why you got such a strong response, I am guessing it's because our inability to simulate evolution well has led to it being used as an argument against evolution again and again. See, for example http://biology.stackexchange.com/questions/40845/do-the-claims-in-this-paper-have-any-degree-of-validity

I've removed the comments that focused on persons, and not on the post and the content. Criticism is welcome, but please keep it constructive.


text:
Determining the Accuracy of DNA Testing
The DNA Testing firm in the below article claims that its tests were "99.99 per cent" accurate.
http://www.telegraph.co.uk/news/uknews/1322077/False-DNA-test-led-father-to-reject-daughter.html
Googling "dna test accuracy" has led to numerous websites many of which claim an accuracy of their DNA testing to be 99.9%, with some even 100%!
How does a firm calculate this percentage accuracy? It seems to me that experimental data would not be useful in determining this percentage accuracy as there is no way to really confirm the fact that Bob is the son of John and vice versa as that is what we're trying to find out. Do they do so by factoring in slight inaccuracies in the laboratory procedure?
Acquiring experimental data would not be useful as I described above for paternity testing, a useful application of DNA testing, but could, to my knowledge, be used to determine the percentage accuracy of DNA testing in the recognition sense. By DNA testing various cells of the same person, and then seeing how many of them result to be from the same individual according to the DNA test (understanding that scientifically every cell should have the same DNA but then experimentally acquiring results that show that 999 in every 1000 cells show to link back to the same person) seems to be a working method...Is this how it works? Is this the notion conveyed with the idea of the percentage accuracy of DNA testing?

Essentially, yes. These tests are usually based on enzymes that replicate DNA, and they have a certain (small) probability of getting a base wrong now and then. You can estimate the error frequency by doing many repetitions of sequencing of the same DNA sample and counting the number of discrepancies. Of course, this assumes that there are no systematic errors, only random variation, which may not be entirely true.
The Sanger sequencing technique is estimated to have error rates on the order of 0.001% (or, is 99.999% correct). I don't know exactly how these firms calculate their numbers, but I would guess it is similar.


text:
Why are nucleic acids negatively charged at physiological pH?
Why do nucleic acids and mononucleotides have a negative charge physiological ph?

Are you asking about nucleic acids or nucleotides?

This sounds like a homework question. Have you tried looking at the structure of a nucleotide?

http://www.tud.ttu.ee/im/Tonu.Reintamm/shabarova/4.1.html

The phosphate group/s present in the mononucleotide or nucleic acid result in the structure having an overall slightly negative charge.
Positively charged proteins that are also present in the cell such as histones help to keep the negatively charged nucleic acid stable 'in vivo'.


text:
What are the identifying characteristics of a Jellyfish?
I was walking down the beach today (Wollongong Australia, near Sydney) and saw this Jellyfish washed up on the beach.

Then I saw another.

I wanted to work out what type it was but didn't know where to start.  I'm looking for a process to determine the category of Jellyfish this is.
I've had a look at this chart:

which tells me it is probably a Catastylus Mosaicus (Blubber fish).
I've also looked at this chart:

which tells me it is probably a Rhizostoma Octopus - Barrel or Root Mouth JellyFish (name only - still a jellyfish).
The biggest identifying characteristic seems to be the eight legs. (Clearly a jelly fish - but still a very confusing trait).
My question is: What are the identifying characteristics of a Jellyfish?

Did you do any research at all about jellyfish? What did you find? What was confusing?

@anongoodnurse I am wondering if they are using "category" in the colloquial sense and what they really mean is that they are interested in finding out how you can look at a jellyfish and visually identify its species.

@AMR - I think you're right, but it's kind of broad. Intro to jelly fish is better approached on one's own, and this site can help with the difficulties. Just my opinion.

Thanks that's helpful. I've added some comments on my own personal investigation.

Blubber fish is far more likely. https://en.wikipedia.org/wiki/Rhizostoma_pulmo and http://oceanaddicts.ie/blog/rhizostoma-octopus-barrel-jellyfish

Thanks @AMR - can you expand that into an answer?

On that @AMR - the linked article implies it is not common in the Pacific ocean (although my feeling is the article is incorrect) could you comment on that?

All I was showing you was that the Barrell or Root Mouth doesn't appear to be endemic to your area, so it is more likely your first choice, the Catastylus Mosaicus (Blubber fish).


text:
Why are human titin and mice titin considered the same protein?
I have a book that says:

In humans titin is a chain of 34,350 amino acids, but in mice it is even longer with 35,213 amino acids.

If two polypeptides had different amino acid sequence lengths, how can they be considered the same protein? Or is it because they share in common one or more amino acid sequences - which, if a polypeptide contains, biologists consider it a particular type of protein - that they are both considered the same protein?

Plenty of proteins have different isoforms that are produced from the same gene (for example by alternative splicing). They can be different in size and function and we'll still call them by the same name.

If they perform the exact same function, they can be considered the same functionally.
Hemoglobin in most humans is the same, down to the amino acid sequence; the hemoglobin in sickle cell anemia, Hemoglobin C, Hemoglobin SC, thalassemia, and others are all different by at least one amino acid, yet they are all hemoglobins, and all do the same job: they carry and release oxygen. Insulin in humans and pigs are not identical (human insulin differs from porcine insulin by a single amino acid - Thr instead of Ala - at the C-terminal residue of the B-chain - but they are both insulin, have an identical function in each animal.
Clearly two proteins of different lengths are not identical. (Did the book claim that they were identical? If it did, it was an error.) If they perform the exact function, they can both be called by the same name and be considered functionally the same protein.

Human and mouse titin are orthologs, and can be confirmed through an NCBI query for TTN.
Orthologous proteins are not the same, per se. They retain the same function, and basically result from speciation: the common ancestral gene got divided between two species. However, the sequence may potentially differ because obviously the species have diverged.
Homology between the two can be confirmed computationally, through phylogenetic and alignment analyses, but I believe the naming convention Titin for both mouse and Human stems largely from the function of the protein in either organism.
Naming convention and explanations of homology are nicely outlined in this Bio.SE post.


text:
Why only mitochondria and plastids?
Why are there only two unique semi-independent organelles? Why are there no others, symbiogenesis seems like it should be a relatively common thing. So do most organelles just lose all their DNA? Or is it something that occurs fairly rarely?

There are. But they are not that universal. See kappa-particle in Paramecium and Wolbachia in insects. Also, there are different origins of plastids (compare red algae and green algae). Some organisms like Rhopallodia gibba even have plastids of multiple origin.

So do most organelles just lose all their DNA? Or is it something that
  occurs fairly rarely?

The organelles of endosymbiotic origin lose their genes gradually. The extent and rate of loss is correlated with the number of organelle the cell harbours. The limited transfer window hypothesis speculates a probable mechanism.


text:
Why sympathetic and parasympathetic nerves originate in different parts of CNS?
Curious if there is a reason for having:

parasympathetic nerves originating from brain stem and pelvic part of spinal cord
sympathetic nerves originating from thoracic and lumbar parts

It looks well-organized, so maybe there is a good reason for that.


text:
Do "scars" in humans replace all the skin layers or only some layers?
When someone has a cut or surgical incision that results in a "scar", is the scar tissue replacing all 3 layers of the skin (epidermis, dermis, hypodermis)? Or only the first one or two of them?

Do you want to know why scars don't go away? If not please do tell me what you want to know. I'm a bit lost here

Scarring can be internal also so it would depend how deep the cut was and how successfully it healed along with many other variables.

@Tusky it is clear what the OP is asking. Problem is there's to many critical variables to consider to be able to provide a straight answer. The OP didn't mention anything about why scars don't go away.

Exactly my point. We need more detail

This depends on how deep was the initial wound, and how that wound healed. There are mainly two ways a wound could heal, either by primary intention (like in surgically closed wounds), or by secondary intention (like in wound left to scar up with the edges not closed properly).
In very well closed wounds that involves all layers of skin, such as primary intention healing following plastic surgery on previously healthy skin, the skin would regenerate all the layers after a long process that could last for 2 years or longer and involves constant life long remodelling of the remaining scar.
In wounds healed by secondary intention, such as following a third degree burn without treatment with skin grafts, there is extensive scaring (mainly consistent of collagen which could be thought of as a filler and adhesive that allows the epithelial skin layer only to grow over it, without renewing the deeper layers). In such cases the scar is large, adherent to underlying tissue, and has only a thin overlying layer of epithelial skin cells. This scar might also be insensate (numb) as a result of superficial nerve injury due to the initial wound.
Most scars are somewhere on the spectrum between the two extremes mentioned above. A badly sutured surgical wound, or a surgical wound that gets infected later, might still heal by secondary intention causing extensive scaring that doesn't replace all the skin layers. A good plastic surgeon might later remove that scar and allow the wound to heal by primary intension to improve the outcome.
If you would like to expand on how wounds heal, here are a couple of links to start you off:
http://teachmesurgery.com/skills/wounds/wound-healing/
https://emedicine.medscape.com/article/1298129-overview

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


text:
Could a trans-female person ever become pregnant?
I was told that a transgender person, which I will define as anyone assigned male or female at birth that identifies opposite to that assignment, could never become pregnant conceptually, due to the lack of hormonal pathways present in cis-male / trans-female person.
Are there modern medical methods that would allow for someone born male and is now trans-female to ever become pregnant or is it the case that medical science is not, nor ever will be capable of allowing for this?
Edit: I would say this is a different question than the suggested duplicate because someone who has AIS or CAIS would have a different anatomy than men assigned at birth, although not by much.

One thing I would point out in your question is that a female identifying as trans-male who has not undergone hormone replacement or reassignment can become pregnant, assuming there are no medical conditions that would prevent a pregnancy. It is only after they are trans-male that they would be incapable of becoming pregnant, unless of course their internal sexual organs were preserved. I think the bigger issue would be that as the person does not identify as female, they would probably not desire to become pregnant, either before or after reassignment.

Possible duplicate of Can androgen-insensitive genetic-males get pregnant?

@Christiaan The question here is phrased differently. It asks whether or not current medical technology could allow a trans-female to ever become pregnant. With Uterus transplantation, carefully controlled hormone therapies, in vitro fertilization, and cesarean delivery, the answer could be yes rather soon, though there may be some ethical hurdles to overcome.

Medical science has reached the point where it is able to consider performing uterine transplants in genetically female (cis-female) patients born without a uterus.
In the MedlinePlus report, First Uterus Transplant Planned in U.S. doctors at The Cleveland Clinic have plans to perform the first uterus transplant in the US sometime in 2016.
The article does however go on to state that the women will need to have been born with ovaries. The same matching process of blood and tissue typing that goes along with any organ transplant would still be in effect for this surgery.
It is also unlikely that the procedure would be open to women that lost their uterus due to cancer, as the recipients would be required to be on immunosuppression medication, and the risk of cancer recurrence would be too great.
As for your question about transplantation into Male-to-Female transgender patients, it is unlikely, at least with present technology that the person would be able to receive the transplant. There is a complex cascade of hormone signaling required for implantation of the embryo.
There could also be implications as to the formation of the placenta and how the person's body react to that. We have many examples of surrogacy, so we know that a woman can carry the embryo formed from the egg of another woman, but how the transgender person's somatic cells would react, given that they all have y-chromosomes is unknown.
According to a Yahoo! news article that interviewed Dr. Karine Chung, director of the fertility preservation program at the University of Southern California’s Keck School of Medicine and Dr. Christine McGinn, a New Hope, Pa., plastic surgeon who performs transgender surgeries on men and women, they foresee possibilities that this could happen in the future, however they do not cite any research that has been performed to date.
One of the issues would be the differing pelvic vasculature that a cis-male has to a cis-female, and what would need to be done to provide an adequate blood supply to sustain not only the uterus but the growing fetus as well.

...biological women have a leg up on biological males when it comes to accepting and nurturing a transplanted uterus. Women already have: vasculature needed to feed the uterus with blood, pelvic ligaments designed to support a uterus, a vagina and cervix, and natural hormones that prepare the uterus for implantation and support the pregnancy.
Men have none of those support systems — naturally — but none are impossible to create. “Male and female anatomy is not that different,” says Chung. “Probably at some point, somebody will figure out how to make that work.” (2)

The article does go on to point out that

Hormone therapy can shut off testosterone and introduce progesterone and estrogen needed to prepare the uterus for pregnancy.

Even though males do not have uterine veins and arteries needed to nurture the womb, it’s possible to attach a branch of a large vessel, like the internal iliac, to the uterus. “It’s doable, it just hasn’t been done,” Chung says.

Although it’s preferable for a vagina to support the uterus, it’s possible to attach a transplanted uterus to other ligaments in the pelvis.

So if I understand correctly we can not emulate the hormonal signals at all or well enough to allow for the formation of a placenta in a possible successfully transplanted uterus in a Male to Female transgender person? Is research being done in this regard or no?

I am not familiar with what is being done beyond the information contained in the article, and one or two others I have read with basically the same information. I would have to assume that to clear their Medical Ethics committee and gain approval for the procedure, the doctor's would have needed to limit the study to only women born without uteri. I do not know if they would have even gone so far as to consider the possibility of performing this procedure in the transexual population. As for what is being done elsewhere, this is the first I have heard of the procedure, so I cannot say.

The point of the ovaries is likely two-fold. First is likely hormonal, and the second is likely practical. If the woman has no ovaries, then she would not be able to give birth to a child that was genetically her's, so I would think that ethicists would weigh the risks versus the benefits as far too great to allow the procedure to proceed for the purpose of giving the person the ability to have the experience of being pregnant.

@RoSiv This article from Yahoo! news interviews doctors that feel that it may be possible within the next five to ten years, but here, they are guessing. https://www.yahoo.com/health/surgery-could-give-men-wombs-1302360099545142.html


text:
About acetyl-coA in the Krebs Cycle of respiration
In respiration, Krebs cycle starts with acetyl coenzyme A which is made from pyruvate.
However, it is said that the cycle keeps repeat it self with oxaloacetate turning back to citrate and cycle starts again, so why is acetyl coenzyme A constantly supplied to the cycle?
According to that logic, shouldn't there be no need for acetyl-coA after the first round?

Pyruvate transfers an acetyl group to coenzyme A.
The acetyl group from acetyl co-A is the molecule that provides the 2 carbon atoms that get added to oxaloacetate to form citrate, and as you said, citrate starts the cycle over again.
Without coenzyme A, pyruvate cannot transfer the acetyl group to oxaloacetate to form citrate so without coenzyme A/acetyl co-A, the process would stop.
This is a slightly busy version of the diagram, but it does let you see how molecules in the cycle are formed and where carrier molecules interact with the molecules in the cycle.

- By Narayanese, WikiUserPedia, YassineMrabet, TotoBaggins [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons


text:
probe amplification in MLPA
I'm reading an article about MLPA (Multiplex ligation-dependent probe amplification) and I got stuck on this sentence:

The advantage of splitting the probe into two parts is that only the ligated oligonucleotides, but not the unbound probe oligonucleotides, are amplified.

The principle I don't understand is why won't the unligated oligonucleotides be amplified? As is my current understanding of the PCR, the primers should normally anneal and produce fragments which would end at the end of an oligonucleotide (at the "ligation site" - so they would be shorter, but they should be there), am I wrong?

Please [edit] your question and add a citation to the paper you are reading so we may see the sentence in context.

It's the wikipedia article which is linked to MLPA word.

I work for MRC-Holland, the developer of MLPA, and what Kacper explains is indeed the case. Any RPO (right probe oligo) that is not ligated is also amplified in the MLPA reaction, as the reverse primer can bind to the primer binding site of the RPO. HOWEVER, since this unligated RPO oligo LACKS the binding site for the (fluoresently labelled) forward primer, the amplification ends here. LIGATED probes, in contrast, contain the binding site for BOTH primers, and hence are amplified exponentially. Furthermore, the fluorescent label is only incorporated in the amplicons that results from ligated probes.

I suppose unligated oligonucleotide would also be "amplified" but on much lesser scale(?only one part of probe?). For instance after 6th run of PCR you would get 2^6=64 amplicons of ligated probe but only 6 for one unligated part(?second starter is designed to anneal to second part of antisense oligonucletide of probe?). After 30 runs there is massive diference that allow you to only detect properly ligated probe. I'm not sure if I'm right but this is how I understood it.
Peace:)

Why is the down-vote please? I find this pretty reasonable. À propos, thanks for the answer.


text:
What are the minimum conditions required for "open-ended evolution"?
According to a paper about artificial life systems, the following four conditions have to be fulfilled for "open-ended evolution":

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

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

Could you clarify point 2 for me please, individuals don't evolve. Do you mean that mutations/immigrants is allowed to affect variation in fitness?

Also on point 1, in principle open ended evolution can occur without a minimal criterion. If all individuals within a population contributed the same number of offspring to the next generation then there would be no minimal criterion (no variance in reproductive output through i.e. no drit or selection) but evolution could still occur by mutation.

@rg255: I don't want to unnecessarily inflate this post but you can find a clarification in the linked paper on page 3 where condition 2 is explained in a short paragraph on the left hand side. The example given therein is about giraffes.

@rg255: I would ask you to give your answer below and not in the comments - Thank you.

Even reading that paper I can't figure out what they mean with condition 3. Do they mean the individual is completely free to interact with all of its environment?

@Downvoter: Please explain the downvote as is good practice. How can I improve the question?

@vonjd Please read Why is voting important?, especially the last paragraph. Additionally, mouse over the vote buttons on both questions and answers and read the tooltips that pop up. Voters are under absolutely no obligation whatsoever to explain their votes if they don't want to, instead relying on the tooltips to do the explaining for them. They may also comment and/or edit with improvements, if such a thing is possible and they have the volition. Demanding explanations for every downvote is not a generally-accepted practice.

In principle open-ended evolution can occur with condition one violated. Because evolution is simply a change from one generation to the next (see answers here, here, and here), the is no requisite for a "non-trivial minimal criterion". Such a minimal criterion (e.g. survival to sexual maturuity) would imply that evolution is occurring by drift or selection, because being non-trivial implies that some members of the evolving population will fail to reproduce. However, evolution also occurs by mutation (and migration).
For example, we can have a population at generation $1$, and each individual within that population produces one offspring, present in the next generation. This means no variation in reproduction exists. If generation $2$, the offspring of generation $1$, carry new mutations then the characteristics of generation $1$ and $2$ can differ, and the descendant generation has evolved from the ancestral state. This can be seen in mutation accumulation lines as an example:

"In a typical mutation accumulation experiment a single inbred and
  highly homozygous line is replicated.  Each of the replicated lines is
  maintained at a very small population size (usually brother sister
  mating, or in plants, selfing).  These lines are maintained for many
  generations.  During that time mutations accumulate, and the lines
  generally decline in fitness, and the variance among lines increases." - UVM Blog

So the answer to your question, these conditions are not necessarily met in nature. However, that doesn't mean evolution can't be open ended - the conditions outlined in the paper are flawed when trying to compare to nature. Evolution can occur when the "minimal criterion" is trivial (when all individuals are capable of meeting the criteria). The existence of a non-trivial MC only implies drift (e.g. some don't reach survival to sexual maturity by bad luck) or selection (e.g. some don't reach sexual maturity because they carry a genetic disease which kills them first). A trivial MC says that there is no drift or selection, but says nothing of mutation. I have since spoken with one of the authors who describes a non-trivial MC as the same thing:

"Regarding nontriviality, it should at least be possible that some
  individuals do not meet the MC"

Note: I have only focussed on condition 1, because this condition is not necessarily met in nature, thus your question is answered (are all conditions satisfied in nature)

I am now in touch with the authors of the paper. A big problem seems to be that there are different definitions and approaches in the biology and the Alife community. So I guess from a biological point of view (so to speak) your answer makes absolute sense and therefore I undownvoted it and upvoted/accepted it. The authors gave me another paper which might also be interesting for you to understand their point of view a little better: http://eplex.cs.ucf.edu/papers/lehman_alife14.pdf

@vonjd I also reached out to the authors for clarification of their non-trivial MC - see edits

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


text:
how to calculate dilution factor and CFU
I'm very confused
I did a bacterial experiment where i added 5 grams to 70ml of distilled water that contains 10g of fresh meat. I left it in a sampler container over 24 hours then i cultured bacteria from the broth using an incubating loop onto nutrient agar. I left them to culture then observed 29 colonies of bacteria.
I observed 1 bacterial colony under a light microscope and counted 19 bacterias.
How do i calculate the dilution factor and CFU?
i need to calculate how many bacterias were on the agar plate?
please help!

Do you know what CFU stands for?

What are your workings out so far? Did you record what magnification you viewed the colonies under? ( Eg. 200x ). Did you use a hemocytometer?   If you did, Google hemocytometer and lots of info will come up about finding the number of CFU including the formula/s required.


text:
Which steps occur in each phase of Meiosis and Mitosis
MITOSIS

In mitosis am I correct in saying that the spindles attach to the centromeres at the end of prophase/prometaphase? (I read this in an answer to another question)

MEIOSIS

Does the nuclear envelope disintegrate during prophase (as occurs in mitosis), or during metaphase? (this is what it says on my textbook)
When do the spindles attach to the chromosomes during the first phase? (during prophase I, or anaphase I? On my textbook it says anaphase I)
And when do they attach to the sister chromatids in phase II? (on my textbook it says metaphase II).

Why would you doubt the answers you are reading in your textbook? It should be accurate, at least for a phenomena as well characterized as Mitosis and Meiosis.

Please limit yourself to one question per post.

Is there some reason that you doubt the textbook?

@rg255 I doubt the textbook because other reliable sources were giving contradicting information, and my teacher even mentioned that in some parts it was not specific/accurate enough.

Then you should give the sources for the both sides of the contradictory information

Mitosis:
1. Yes, the spindle fibers attach to centromeres at the prometaphase
http://www.biology.arizona.edu/cell_bio/tutorials/cell_cycle/cells3.html
Meiosis:
1. The nuclear membrane breaks down in Metaphase 1 and reforms during Telophase. It breaks down again in Prophase 2, reforming after that in Telophase 2 in the daughter cells.

The spindles attach to the centromere is Metaphase 1
Yes the spindles attach to the sister chromatids in Metaphase 2

Check out this animation, it might be pretty useful


text:
Short videos on evolutionary biology
What I am looking for
I'm considering to eventually start my teaching sessions with short emotional, awe-inspiring or exciting videos that are somehow related to evolutionary biology incl. diversity of life, history of evolution on earth, specific evolutionary processes (sexual conflict, evolution of ageing, evolution of mutation rate, speciation rate, ...), diversity in mating systems, major transitions, etc...
3-minute long movies would be perfect. 15 minutes would be too long. The videos should be easily accessible for Bachelor students having little background in evolutionary biology.
Examples
Asap Science video about the evolutionary history of life would be a good fit.
The beginning of We are all related by vsauce would be a good fit.
This video from SciShow is typically too long
This video on the evolution of human face would do but I am not quite sure how exact it is and it feels a little weird that the end product is a white male!
It'd be great if not all suggestions were about recent human history or about dinosaurs :)
Do you have any suggestions?

This question might very well be off-topic here. Let me know and I'll delete it. Advice on where to ask such questions would be very welcome.

The question is fine and will likely produce a good resource for the community.

Upvoted! Normally those kinds of questions get asked when an SE communitiy starts out so I would say it is high time :-)

@Remi.b I'm curious, is there anything wrong with your first example that you say is a good fit?

@Insane. No, it is a good fit but I am hoping to have several such good fits.

I think you should show your students a video by a creationist on why evolution is not true. That would certainly inspire them to appreciate the logic of evolution ;)

I lead a workshop on protein packing that opened with this video of the inner workings of the cell by Biovisions at Harvard. I narrated what is happening whilst the video was playing (I sometimes found it awkward when lecturers and teachers just watched the video too!). It's off topic at first glance, but It could set the tone for the complexity of life at a molecular level, and how evolution acts at a molecular level.

@biogirl Don't be so sure that intelligent design videos can't be compelling and inspiring. This clip is one of the prettiest and most informative ATP synthase videos available and it argues for intelligent design.

@James Oh you are right. But I think you can use that video in a productive way. Show it to "inspire" students and then prick the balloon by carefully explaining why the argument is not acceptable to biologists even if it is so seductive.

I suggest the Stated Clearly channel, but the videos are longer than 3 minutes

I find it discouraging that nobody else realizes that the subjectivity of this question (what you consider exciting is not necessary what I consider exciting) renders it off topic. Furthermore I think it is bad to try to appeal to the emotions rather than the intellect. That is the approach of the irrationalists. Evolution is yesterday's scientific news. Ignore the flat earthers and move on.

I saw this HHMI video today. It is called The Animated Life of A.R. Wallace, and it discusses the contributions that Alfred R. Wallace made to evolutionary theory. It is a little long for your stated time of 3-minutes. but it talks about how in fits of malaria he came up with his ideas on evolution.
HHMI also has a whole series of videos and modules on Evolution, though Wallace's came to mind as it showed his ambition and desire to solve the problem, even though he had not received formal training in the sciences.

Nice video. It is nice also to bring some fame to Wallace and not only to Darwin. I'm looking at the other videos on the website. +1

It is not really a video but it is a real life simulation in the browser about vehicles that evolve to master a race track. I project it onto the screen while I introduce genetic algorithms in my data science classes. I then ask people to identify key features of the evolutionary process and we talk about it while the "cars" are still evolving:
http://boxcar2d.com/
People told me that this is really motivating. After that we start programming our first genetic algorithm.
This is a video that I sometimes show additionally (5 min. about robots in an artificial world learning to walk):
https://www.youtube.com/watch?v=pgaEE27nsQw

Not quite what I expected but it is nice. I particularly appreciate the evolving car simulator. What population size, type of terrain and mutation rate do you recommend to maximize the speed of improvement? Can you maybe say a word about how you coded the information about the car and how to interpret a mutation? Would be great to have a snapshot of the parent population on the side to understand that we have a population and not just a series of random individuals. +1

@Remi.b: Thank you, I appreciate your feedback. I have to run now but I will answer your questions later!

https://youtu.be/hOfRN0KihOU Sorry, this video is not short, but perfect. From Kurzgesagt chanel youtube

Thanks a lot for the suggestion. I agree Kurzgesagt (a.k.a. In a nutshell) is a great channel. The video is a bit long though (as you said). It is also a little too introductory and too general and not very "emotional, awe-inspiring or exciting".

Here are a bunch of fun videos about evolution! They might not be very educative at first sight but they might still bring more than just a laugh to students.
MinuteEarth videos
The youtube channel MinuteEarth has plenty of evolution related videos of about 2-6 minutes each. Look for example at

Males vs. Females: Sexual Conflict
Why Do Animals Eat Their Babies?
Do We Have to Get Old and Die?
Are We Really 99% Chimp?
Why are Males often More Physically Aggressive?
Epigenetics: Why Inheritance Is Weirder Than We Thought

PBS Eons
PBS Eons have a lot of cool videos on the history of life on earth. Videos might be a bit long for your needs though, around 5-10 minutes long on average.
MaxBird feat Jamie

Les dinosaures ont disparu ? in 7'51'' (in french)

How is evolution often misrepresented

South Park - Mr. Garrison's Evolution Theory in 51''

and of course

Simpsons - Homer's evolution in 1'29''

One can also just type Evolution on google Image to get only this misleading and anthropocentric view of representation of evolution

Why Pokemon evolution is not like evolution in nature

Dirty Biology - Darwin chez les Pokemon (in french)

Song

Evo-Devo A capella on Despacito by acapellascience.

Creationist argument (although this is not really the way the OP wants to go to)

Simpsons - Missing link (start at 1'14'' to 2'10)

In the category 'Response to creationist argument' it is easy to find funny videos just by showing burlesque creationist argument such as

Ray Comfort - banana proves God (from 1'12'' to 2'20 although the whole video is pretty funny). The video mixes up questions of believing in God and of evolution which I don't mean to do myself and could (rightly) be taken as offensive by students so be careful.

BBC and other CG animation programs about Ediacaran life, trilobites, other old life forms, are very engaging to see. There are a lot of CG progams bringing to life ediacaran seas.
https://www.youtube.com/watch?v=znO8q5Ht17g
David Attenboroughs CG animation of the chinese microraptor, where it steps out of it's fossil and flies around the room.
microraptor chasing other flying reptile:
https://www.youtube.com/watch?v=-fyxUxGdrns
https://www.youtube.com/watch?v=SmcqnAWKLJQ

I like the David Attenboroughs link! Thanks +1. Note that the last link on 'Microraptor' is in french. Don't remove it but you should probably highlight it in your answer and explain what it is.

sry didn't have time to find the original english version.. https://www.youtube.com/watch?v=-fyxUxGdrns here it is, first result for "microraptor chase"... it's narrated by john hurt, the recently defunct actor of midnight expess and the storyteller series.

This Evo-Devo music video from A Capella Science is very good: https://www.youtube.com/watch?v=ydqReeTV_vk&feature=youtu.be

Thank you! The link is already present in my answer though.


text:
How do small birds survive the winter?
I live in a region with cold winters (ca. -40 C) and many quite small birds (sparrows, crows, ducks) stay for the winter.
How can the birds survive this?
As I understand it, smaller bodies will be less able to produce and retain heat. Despite this, birds seem to cope much better than humans, sitting in the cold all winter and even swimming in cold water. In comparison, humans lose mobility in their muscles when cold, and can suffer severe frostbite causing them to lose fingers, toes, or limbs from relatively short exposure to the same conditions.
What specific adaptations allow birds to cope so well in these conditions?

Are you actually seeing these species where you live during winter? Birds tend to be migratory. Feathers and fats tend to make fairly good insulators though. They would need a food source and some form of shelter. But I would assume if you do not see them in the winter, then they have migrated towards the equator.

Also, if it is actually water, then it is greater than 0°C, so the water may actually be warmer than the air temp. And like I said above, fat and feathers make for good insulation.

@AMR: yes, I actually see them. Maybe there are less birds than in summer, but there definitely are many. I know they should migrate, but for some reason they don't really always do that.. idk, the migration thing seems broken, I see really many birds in winter in the city. Yeah, they can find heat sources in the city, but still they spend quite much time just wandering around in the cold. Good point about the water temperature.. Idk how, but sometimes, when it's -20C, some parts of the city channels are not iced, probably someting warms the water..

@AMR: also - what about their legs? They are in no way protected... still their muscules and joints do not suffer, they can just as easy grip to their sitting place, like a branch or a wire..

The coldest water is around 0 Celsius. Beyond that it's ice.

@ott-- yes, right. I guess I wanted to say that as water is more dense than air, it's thermal conductivity is also higher, and it would draw heat more eagerly than air. Same as a metal usually feels colder although it's of the same temperature as everything else around.

Which birds,  many birds have very different responses and adaptations to winter.

Not even close to a full answer, so I'll only post a comment. Here you can read about a cold adaptation of the circulatory system in bird legs that allows a heron to keep standing in icy cold water and be fine.

During cold weather, birds will go into torpor where they will reduce their metabolic rate to conserve energy over the night. This burns fewer calories and maintains fat reserves that help insulate them from cold temperatures. Behaviorally, many bird species will roost communally to share heat among each other.

Welcome to BiologySE! Thanks for your efforts - you may want to review the help page on how to write a good answer. You could improve your answer significantly and earn more reputation points for it! Check it out... http://biology.stackexchange.com/help/how-to-answer