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Questions about the Evolution Theory
I'm trying to understand more about evolution theory.
(I am coming from a mathematical background)
What i understand till now is that the "improvement" of the dna is a purely random development and the Selection criteria if the improvement was not negative is by surviving.
The better the improvment was the higher the likelyhood of surviving is.
What i don't understand is that the likelyhood that something useful comes from random changes in the dna is very low?
This reminds me of the http://en.wikipedia.org/wiki/Infinite_monkey_theorem it has surely a finite likelyhood but considering the complexity i still doesn't understand how for example wings of birds evolve.
Consider a pre-bird without wings, to get wings it has to have interstage with some useless pre-wings and then it has to learn how to flight.
Maybe someone can help me solve these mysteries :)
The other thing i am wondering is the smallest living element is the cell.
How did the first cell evolve?
Thank you very much

This question has a large answer but in short, mutations occur at a certain rate, which can depend on the environment and how exposed organism is to mutagenic factors but there are intrinsic mechanisms for creation of variation such as SNPs and chromosomal crossover. Many mutations don't have any negative impact on survival (more importantly passing your genes). The ones that do will get selected against but the ones that increase chances of survival will remain and tend to become prevalent amongst the species over time. Cell is the smallest living unit in an organism. Look at the RNA world.

Your two questions (1. How can useful features initially evolve, 2. How did life start) are two of the largest debates in biology, with endless arguments going back and forth throughout academia and laydiscussion. It's not currently possible to definitively answer either of them, and people have written entire books trying to summarise the state of the debate at that time. Google these to your heart's content - some keywords of potential interest include "origin of life", "intelligent design" and "RNA world" - but unfortunately Bio.SE is not a suitable platform for discussing this.

Welcome to BiologyBeta.SE!
On stackExchange sites, an OP should always limit his/her post to one question and should make his/her question is not too broad. But before you split up your question I invite you to have a look to some other post that will give you some answers. For this reason your question will very likely get closed as too broad. But I am giving some indices below. Also your post is a bit poorly written. This also lead people to close posts. Please come back with better posts, show some efforts in seeking for some information and it will be my pleasure to help you!

Origin of life

There are already a bunch of posts on the origin of life for example. Note that the origin of life is not a field that is part of evolutionary biology as evolutionary biology only explain the evolution of life and not its origin. As a mathematician you may prefer saying something like the domain of definition of evolutionary biology does not include the origin of life just like the shannon's theory of information says nothing about the euclidian geometry.

What i understand till now is that the "improvement" of the dna is a purely random development and the Selection criteria if the improvement was not negative is by surviving

Hum… that's sounds very weird. If I didn't know I would hardly recognize that you talk about evolution. You should have a look to some introduction to the field. Also, you should not confound the concepts of evolution, natural selection and mutations that I guess you confuse. A good, extremely simplistic view of evolution is that mutations occurs and create variance in the population. This traits are heritable. The variants that replicate the best increase in frequency in the population while the other variants will decrease in frequency up to the point to disappear. This is called natural selection.

Consider a pre-bird without wings, to get wings it has to have interstage with some useless pre-wings and then it has to learn how to flight

You also seem to ask a question about how some traits may come to exist while what seem to be necessary intermediate would not be beneficial. This question has been answered probably a thousands of time as it is a common creationist argument.

Because your questions really sounds like creationist arguments I am a bit afraid that you are not trying to understand evolution but you wondering whether evolution does occur or not.
Note also that evolutionary biology is a very big field. You cannot expect to have a more or less good understanding of the whole science of evolutionary biology in less than a year. But if you are trying to just understand the very basic, sufficiently to persuade you that evolution does occur, then few weeks will probably be enough if you show some effort
Please don't forget the questions you may have. Seek by yourself for more knowledge and if you can't find something, then you're really welcome to come back to this site with an accurate question.
EDIT
Have a look to the definition of scientific theory. Also, please read @Chris comment below.
You misunderstand the meaning of "direct observation" that canadianer used. Observations we do in evolutionary biology are just as valid as those that has been made to confirm the theory of gravity. The only point concerns the easiness of understand these observations for non-literate in the field.
Yes, you are totally right. Just like the theory of gravity, the theory of evolution does not explain everything. It only applies to a subset of the phenomenons existing on earth. The theory of evolution is true, we know for a fact that evolution occurs but our theory is not global enough to explain things like the big bang or the surface tension and will never do so. The theory of evolution will never prove or disprove the existence of God as well (supposing you're concerned about that) because again it is not within its scope and will never be. However, the sociological impact of this theory tells much about the human behavior and our difficulties to accept something we know to be true if it contradicts some pre-establish believes even when these pre-established believes are not based on any logical developments.
Your question has been closed because it is too broad. The issue also is that your questions concern much more than evolutionary biology and biology. It also concerns the very nature of science and this is a common reason why creationist missundestand evolution. They don't (only) missunderstand evolution but they missunderstand what science is.

thank you very much. That intermediate changes might have some other function is something i did not thought about, but it sounds reasonably. I want to understand Evolution-theory more because i have the feeling i have no idea about it. In mathematics i learned that asking the critical question leads to far better improvement than looking at the obvious examples and that is often the point where some of the "theories" fail. And in my personal opinion as long as something is not proven (might be never the case) you should always look at the critical points without the bias evo is true/false

Direct observations of populations changing were and are made and then the theory of evolution was created to describe the process. There is no debate about evolution being true or false. What you're saying sounds the same as watching an apple falling from a tree, creating a theory of gravity to describe it and then having a debate about whether apples falling from trees is true or false.

why is it then called theory?

to make your comparison more correct i'd would say it's more about if the theory of gravity is right/wrong. While Newton's Law is true it is only partial true as an approximation for a more general law. (and Newton's Law was discovered through Direct observations) So maybe even while Evolution seems to be true it might not explain the picture fully.

@jonsonBen See my updated answer. Hope that helps!

@jonsonBen Just because it is called theory, it doesen't mean it is theoretical and can not be proven. The opposite is true. A theory describes the theoretical foundation of a special part of science. As does Newton with its theory of Gravitation or Einstein does with its Theory of Relativity. What you are looking it is the term "hypothesis". This can be proven wrong or right. If the first is true, scientists set up a new hypothesis to work with. Standard procedure, no drama included.

What i don't understand is that the likelyhood that something useful
  comes from random changes in the dna is very low?

Well, in that most changes are neutral, sure.  But EVERY organism on the planet has mutations.  It doesn't matter if the odds are low.  If you have billions of organisms in a square meter of soil, how likely do you think it is that not a single mutation in a single organism will be beneficial in that environment?

Consider a pre-bird without wings, to get wings it has to have
  interstage with some useless pre-wings and then it has to learn how to
  flight.

Ah, another Creationist who thinks that the universe can not possibly contain anything that s/he can not personally imagine.  There might be uses for intermediate structures that you just can't think off off the top of your head  (like gliding).  There might be intermediates paths that you just can't think of.  There might be other structures that worked in concert with the intermediates, and then faded away as things changes, much like you build an arch with a scaffold, and then remove the scaffold.  Just because you personally can't imagine the possibility of a scaffold doesn't mean such things are literally impossible.
Have you even tried googling "bird wing evolution"?

The other thing i am wondering is the smallest living element is the
  cell. How did the first cell evolve?

Come on.  That's a completely different question.  Surely someone who thinks they understand the problems of evolution better than professionals who have studied the data for years know that lipids spontaneously formed closed cells, right?  And knows that RNA can autocatlyze reactions, yes?


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Based on which criteria should i choose the control sample to calculate delta_delta_Ct
I want to calculate the gene expression of an experiment with the Delta delta Ct method.
I have these results from two runs of a real time PCR (one for the GOI(Gene of Interest) and one for the reference gene ($\beta$ actin) )
Samples | GOI CT | reference gene CT |

1         16.52         16.24
2         18.58         18.47
3         14.55         20.56
wt        23.06         24.17

So to calculate the $2^{-\Delta\Delta CT}$ for my GOI I've done this :
1st - Normalize CTs of GOI to CTs of reference gene
$ΔCT = CT_{sample's} - CT_{reference's}$
This new table then occurs:
Samples | ΔCTs

1         0.28
2         0.11
3        -6.01
wt       -1.11

After this i normalize these ΔCTs to a control sample. And here is where the question was born. On which criteria should i choose the control sample ?
What i've done was to choose the sample with the bigest CT from the first table. And that was the sample No. 2.
2nd - Normalizing all samples to the control sample
$\Delta\Delta CT = \Delta CT_{sample} - \Delta CT_{control}$
and the final results are
Samples | ΔΔCTs

1         0.17
2         0
3        -6.12
wt       -3.08

Is that method correct ? If yes, let me write once more the question.
On which criteria should i choose the control sample for the last normalization ? Should i choose the sample with the highest Ct or the lowest one ? And why ?
I hope now be more clear.
Question edited to be more clear.

What do you mean by calibrator sample? Standard curve??
See these posts- 1 and 2

No. I don't mean standard curve. In the video above, they choose a calibrator sample from target gene samples to normalize later on the ΔCT to it. Here is the video link: http://youtu.be/tgp4bbnj-ng?t=34s

But what do you mean by calibrator sample.. I have never heard this term.. You have a reference gene which is $\beta$-actin in your case.

In the video they use the term calibrator sample to mean control case. Nobody uses the term calibrator. Follow good references. Check the link to a paper on RTPCR analysis, provided in the posts that I mentioned in previous comments.

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DNA is charged negative. Where is all the positive charge in my body?
DNA is charged negative because of its phosphate backbone. Since charges need to be balanced (so that there are no charges building up somewhere), what is the positive charge which neutralizes this negative charge?

It would be great if you state the context of the question to allow a more constructive response. Many ions such as Na+ and Mg2+ are positively charged.

There is no noteworthy context. I'm a physicist, just saw the structure formula of DNA and was wondering about this.

@Bez The question is short and it is ok to ask it out of curiosity.

Another point to be noted is that isoelectric pH of DNA is close to 7 (6.7) [Ref].

The charge on dna is balanced by the histone protein which is composed of basic amino acid...so ultimately histone is positive chargee

DNA in the body is not available as a free molecule, it is organized around DNA binding proteins, mostly the histone octamers. These proteins carry positive charges (mostly from lysine side chains) which interact with the phosphate backbone of the DNA. It is like in the figure below, the charges play an important role in the tight packaging. See here for more details.

The charge (or the temporary neutralization at some points of the DNA) is also important for the regulation of the DNA. Acetylation neutralizes the histone tail and loosens the DNA-protein structure (see here for more information).
Positively charged ions don't play a role in neutralizing the DNA charge in living cells (this is different for precipitations), as both are solubilized and split into ions. The concentration of positively charged ions like sodium and potassium are tightly controlled by the cells, as they are important for the function of transporters (for example the sodium-glucose transporters and others) or for keeping up membrane potentials. Moving the ions, which have to neutralize the DNA charge around would lead to a polarized nucleus.

Your cells have a high concentration of sodium ions that are positive. Other important cations are potassium and calcium. Additionally, many amino acids are positively charged at physiological pH. DNA is not the only source of negative charge in your body, other amino acids are negative, and most cell surfaces are negative as well. The interactions between charged species play an important role in many biochemical processes, but at the end of the day, and for the whole organism, the charges are all pretty much balanced out.

Could you please provide a reference regarding the statement "the charges are all pretty much balanced out"? I could be wrong but the resting membrane potential for example in neurone is -70mV so that doesn't sound like balanced!

That's charge of inside vs outside of cell. If your whole body had a significant net charge, you'd be constantly affected by static cling, or sparking static electricity all the time, or electrostatically repelled from other living things. Based on my observations, these things don't happen.

I agree! but at a single cell level cells can have a charge so perhaps it would be best if you edited your response slightly to clarify the last sentence.

Made an edit to clarify the statement is about the whole animal.

The negative charge in DNA is localized to individual oxygen atoms in DNA. This negative charge is balanced by positive ions in the body.
In the case of a magnet or molecules with a dipole, negative and positive magnetic field lines align to produce an overall magnetic field. DNA has many small dipole moments but none across the entire molecule.
In the case of a neuron, an excess of negative charge inside the cell and positive charge outside the cell is maintained by the diffusion gradient of potassium and sodium across a membrane. An overall electric potential is not created with DNA.

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How to measure trajectory regularity?
I have two animal running trajectories. A regular one with repeated back and forth running between point A and B, like the one on top in the figure. The other one is very irregular, animal paused and turned around a lot in the middle. Is there any algorithm to measure the regularity of a trajectory, like repeated activity on the top? And compare the extend of regularity between the two trajectories? Thanks in advance.

are you trying to see if an animal runs in the same pattern over and over again? I know there are computer programs that use a camera to watch a mouse and plot its movement over time. This is used to measure mouse activity when you can't have a human watch it 24/7. You might be able to overlay the paths and get an average and standard deviation, but I don't really know much about it.

In the world of physics, you can distinguish between random motion (e.g. thermal Brownian walk) and directed motion (called ballistic: think of a cannon ball) by studying the mean square displacement of the object: you'll be able to fit this displacement as a function of time by a linear law if it is random, and by a quadratic one if it is directed. Exponents in between will give you an indication of the degree of randomness. The advantage of this (even if it is not specialized for your case) is that there's a large body of work using this, including for living organisms.
Note also that if your motion is as in the first case above, you'll have ballistic motion for times smaller than the travel time from left to right, and diffusive (random) for times larger than that. This has been used e.g. to analyse the run-and-tumble motion of bacteria who have a short-time ballistic motion and then after some time tumble to explore another randomly-chosen direction.
Example of this type of coexistence of two regimes:

In the field of biophysics, much of this was initiated by Howard Berg and coworkers
In your first case, you'll have an initial ballistic regime and then something that plateaus (because you stay between A and B). The transition time-lag will be the travel time between A and B.
In your second case, you'll be able to characterize the random walk: if the animal is aiming at going from A to B but randomly errs for short times, you'll have a short-time diffusive behaviour, and an intermediate time ballistic one. (And then again a plateau, as in the first case and for the same reasons). If the animal reaches B by mere chance, on the contrary, you'll have a diffusive regime only before this plateau.

I guess what you suggested is more applicable in 2-D situations. In my case, displacement in Y-axis is very small most of the time.

@sgyf: It is valid in any dimension. Use only the x-direction displacement if y-direction is irrelevant.


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Books for biology,popular but rigorous?
There are very goods in physics and mathematics (like Feynman lectures for exemple) that give an elementry but but broad view of their,therefore I'd like for help to find help to find a biology book that:
-Covers a variety of subject in an elementary fashion.
-Is written for the non-specialist.

Wikipedia is fairly decent :P

Where I studied, every undergrad read Campbell Biology. You can start it as a non-specialist but you will not be one at the end..

Such a good book.

The Campbell Biology is a good very introductory book to biology. It is popular book but a very standard text book. I am not aware of any popular and introductory book that are broad enough to encompass all of biology.
I would suggest that you get the campbell and in parallel you can follow free online courseware. There are lots of them. Starting with KhanAcademy is maybe a good solution. It gives some introductory courses to a bunch of disciplines. ItunesU is also a good solution to search for further introductory courses given by the best universities such as Berkeley and the MIT typically.

I would suggest something like "The Selfish Gene" by Richard Dawkins. It covers many examples or organisms and how their behaviour at a molecular level is ultimately selfish in order to ensure survival by passing their genes, which is perhaps the most important biological function of any living organism. However, as pointed in comments below, this book primarily concentrates on evolutionary biology and little else (at least in any noticeable depth) and puts forward many philosophical arguments regarding survival and passing your genes but doesn't talk about proteins or mRNA. "The Extended Phenotype" by Richard Dawkins again is an evolutionary biology book but it does talk about protein synthesis and the idea of phenotype and how genotype effects this and how the genotype of an organism can affect the environment!
Books by Richard Dawkins tends to give examples of whole organisms and in a sense the bigger picture to make his points about elementary concepts which allow life and its propagation and how it shapes the environment but doesn't go too much into details in order to keep the attention of the reader and keep it interesting to the lay audience. [for the lay audience] It is much easier to imagine a bird and its mating habits and how genes control this than knowing the molecular mechanism behind the signalling pathway responsible! However since the question is slightly subjective, my response tends to reflect a subjective response.

The Selfish Gene is indeed a very popular book but it talk exclusively about evolutionary biology and about nothing else. One that reads the selfish gene will probably not have any clue about how mitosis works, about the chemistry of life (proteins, mRNA,..) or about cytology! Also the Selfish Gene gets into some philosophical and epistemiological issues in biology. I don't this is what the OP is looking for.

indeed. I agree! I shall edit my response to clarify this point. thanks.

I am a Richard Dawkins fan too !

Alongwith campbell ,look up some "advanced" books - like  Bruce Alberts molecular biology of The Cell , Lehninger, etc. It is not necessary to read everything in those books. Read whichever topics interest you the most.
There is also a very good site : ibiomagazine.org which has videos of some of the big shots of biology.
And remember, most important is to keep all your senses open always. There is so much biology going around. Observing and thinking about it can teach you things which 100 textbooks can't !


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naturally occuring fatty acids
The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance of cis double bond in naturally occurring fatty acids? Why the naturally occurring fatty acids don't have double bond in trans configuration?

Trans double bonds in fatty acids may disrupt cellular membranes because of their shape. Normally the fatty acid tails on phospholipids are kind of lined up, allowing them to form a double layer. You can imagine them being more or less rectanglular, and 2 layers of these rectangles form the membrane, with fatty acid tails pointing in. Since cis double bonds don't disrupt the shape, they fit in ok. Trans double bonds kink the tail, and make the membrane less ordered. This is pure speculation, so I'm leaving it as comment.

@user137.. you are correct.. But it is not about kinking.. trans-fatty acids make the membrane rigid because they pack closely.

The diversity of fatty acids produced by an organism is limited by the diversity of enzymes which synthesize them. Unsaturated fatty acids contain carbon-carbon double bonds which do not isomerize. The capacity for humans to produce cis fatty acids is probably selected for because of their lower melting point which prevents arterial clogging. Cold blooded animals utilize cholesterol to increase membrane fluidity when their body temperature is low.


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Why don't animals produce alcohol
As I understand during anaerobic respiration, the electrons received from the decomposition of glucose are transferred to nicotinamide adenine dinucleotide and flavin adenine dinucleotide. As there is no oxygen the electrons are then transferred to something else, either Lactic Acid or Ethanol (in the case of yeast).
So why do animals produce Lactic Acid and not Ethanol?
Also, (I know this is silly, but) what would happen if they did?

exact answer: https://in.answers.yahoo.com/question/index?qid=20110227125518AAh0WrC

@DevashishDas. I dont think that link answers the question. Also, I am not sure what OP intends to ask- a. How is it that alcohol is not produced in animals b. Why (or for what greater reason) is it not produced. Answer to a. is trivial: animals don't have that enzyme.

@WYSIWYG: It was the first result on google to similar to the question.

Consider this from the point of view of integrating whole body metabolism.
The body operates on a fuel economy built around glucose. Active muscle produces lactate (C3) which is exported to the liver through the bloodstream. Liver converts lactate to glucose (C6) which is then exported to the tissues.
What if muscle produced ethanol (C2)? Liver metabolises this to acetate. This could be converted to acetyl CoA and so on to fatty acids, but there is no way to achieve net synthesis of glucose from acetate. Muscle can of course use fatty acids, so you could conceive of an alternative system based upon this. It may be that this is less efficent from the point of view of energy useage - I haven't checked this because there is a more compelling argument against using ethanol.
According to this paper, lactate levels in the bloodstream can reach 15 - 25 mM during exercise. If muscle exported ethanol instead of lactate then blood alcohol content (BAC) would reach the same levels.
The middle of that range, 20 mM ethanol, is equivalent to a BAC of 0.076% which is just below the legal limit for driving in the USA and the UK, and above the legal limit in many European countries. This BAC is associated with effects upon reasoning, depth perception and peripheral vision. So, from an evolutionary position it really wouldn't make sense to have a metabolic system based around sending this much ethanol through the blood.

Our metabolic system would be different if this would be our way...

yeah I agree with Chris totally

But the question wasn't about a hypothetical alternative metabolic system, it was about the existing one using lactate and not ethanol as an end product of fermentation. So yes, if our metabolic sytem was constructed differently it would be ... different.


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How are HSPs identified in UCLUST
I am new in Bioinformatics and recently studying UCLUST algorithm by Robert Edgar(2010). It is a fast sequence searching and clustering algorithm. The algorithm is heuristic based. I studied that first, this algorithm finds unique common words(k-mers) between a query sequence and a target sequence.(one of the sequences from sequence database). If there are enough common k-mers between a target sequence and a database sequence then it is selected for the alignment in the next step, otherwise skipped. All such sequences having enough common k-mers are selected. Target sequences are compared in order of decreasing common k-mers.
In next step, HSPs (High Scoring Segment Pairs) are identified. For this purpose, exact matching words between a query sequence and a target sequence (one of the sequences selected in the previous step) are found. I AM CONFUSED AT THIS POINT. Is it necessary that these matching words(between the query sequence and the target sequence) be at same positions ?
Kindly if some one explains with an example, will be very help full.
Any guidance will highly be appreciated.


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Why doesn't the human skin grow back exactly how it was before being damaged?
Very simple: Why (and how) is regenerated skin different from original ?
As we know we lose skin cells that becomes the dust in out homes and it always grows back to full thickness right ? So when I have a cut, I imagined it to heal provisionally with whatever possible and then after some time to replace itself with the normal skin that is coded in my chromosomes. So why doesn't it do that ? Scars remain and the color is always different from the neighbor parts.
Update:

Why we get scars?
What about skin transplants ?
Why doesn't skin actually grow/replace itself?

Update 2:

(I've been thinking) Skin has lots of different layers, right ? So when an area is damaged does it regenerate all layers or just one for being simple and efficient (in "hope" the subject will take precautions not to damage this part of body again, so that regenerating everything back to 100% would be overkill) ?
I'm not a scientist, I have only the basics from school, so I'll probably not understand most of the technical terms
also I'm more interested about an explanation that goes towards the "survival of the fittest" rule, and not so much about the biochemical reactions in our bodies (because it was just some random mutation that turned out to be the better choice for us → why?)

This is a very large topic regarding wound healing (http://en.wikipedia.org/wiki/Wound_healing) and the scaring is primarily caused by inflammatory factors, which are important in initiating wound healing response, leading to a trade of!

I totally agree with Bez with this. And you if you are asking about scars specifically,this might help http://en.wikipedia.org/wiki/Scar

There are other reasons for scars.. If the underlying collagen fibers are damaged then the new ones dont get incorporated in the exact same orientation.. You dont get scars that easily.. You can also refer any book on clinical anatomy..

Is that a lie scientist are telling us ?... What sort of a statement is this? Scientists don't lie, governments and profiteers do.

@WYSIWYG It is not a statement but a question. In general now I wonder why this site is trying to exist. If all I need is to open Wikipedia or buy a book ... (which both I wouldn't understand I guess)

@Leck.. 1. you are not supposed to attach your social assumptions when asking a scientific question. 2. This site is not your school classroom where the TA is supposed to teach you. If something is already there in wikipedia then why are you asking it- why dont you simply read it from there. If you can't understand what is written there then ask your professor or a friend. Though it is allowed here to ask something that you don't understand but all that is expected is that you make an effort. Nobody is obliged to teach you.

And I didn't vote to close the question, I just asked you to refine your language.

@WYSIWYG You've been rude here. I was reading this before I commented (AND I answered the "I wonder why" by myself if you read what's in the brackets). And I also can't see the close votes because I'm too low on rep (don't really care). If I find no answer here then I'll keep it as one of those life's mysteries that make my life worthwhile. Bye!

Is it better Now?

@Leck there are different kinds of scars (scaring) caused by different kinds of insults and treatments.  In a healthy individual, your skin is constantly growing and replacing itself.  It dies and sloughs off as new skin is formed under it.  I'm still not sure what your question is asking for beyond the wiki link.  After you've read some more (or perhaps now) please take another stab at wording your question, and we'll see if we can't get on the same page.

scar tissue evolved long before humans, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057359/#:~:text=Animals%20respond%20to%20traumatic%20organ,reproduction%20of%20the%20missing%20tissue.

Human skin is made up of three layers [1]:

Epidermis; it contains no blood vessels; it has 5 cellular layers (starting from surface):

stratum corneum
stratum lucidum
stratum granulosum
stratum spinosum
stratum germinativum

Dermis; it is separated from the above by the basal membrane; made up of connective tissue (with blood vessels and nerve endings)
Hypodermis - it is not even considered part of the skin

"Gray940". Licensed under Public domain via Wikimedia Commons.

Why (and how) is regenerated skin different from original ?

Why? Skin is a very important organ. It protects from pathogens, it maintains body temperature, it keeps body water [1], etc. How? That depends on what causes the regeneration. I've emphasized two terms in the above list.

Stratum corneum represents the "skin cells that becomes the dust in our homes and it always grows back to full thickness". It is lost during a physiological process called desquamation [2]. The cells that are lost are non living corneocytes. Their only purpose is to from a protection barrier [3].
Basement membrane holds the germinativum layer of the epidermis. Injuries that do not affect it are repaired by complete regeneration of all destroyed layers. However, if the injury destroys membrane continuity, the germinative cells on the edges will fail to "reconnect" with each other, thus the layers derived from them will follow the same rule. A process of fibrosis is triggered. The result of  extensive fibrosis is a scar, containing collagen secreted by the granulation tissue with dermal origins. Yet, the germinative layer tends to join back together [6], but probably the excess collagen production, without the limiting basement membrane, bulges into the epidermis and limits germinative layer extension. That's why keeping the edges of the tissue close to each other reduces excessive fibrosis and allows germinative layer regeneration, thus resulting in none to small, barely visible scars.

How deep should an injury be in order not to affect basement membrane? No more than 0.06 to 0.08 mm [5].

What about skin transplants ?

Skin grafts contain at least a part of dermis [4], which will allow granulation tissue formation thus permitting revascularisation and making the graft stick. Otherwise it would fall off and/or be lost by necrosis.

References:

Wikipedia contributors, "Skin," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Skin&oldid=619454074 (accessed August 4, 2014).
Wikipedia contributors, "Desquamation," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Desquamation&oldid=614028888 (accessed August 4, 2014).
Wikipedia contributors, "Stratum corneum," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Stratum_corneum&oldid=615247326 (accessed August 4, 2014).
Wikipedia contributors, "Skin grafting," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Skin_grafting&oldid=603324006 (accessed August 4, 2014).
Sandby-Møller J, Poulsen T, Wulf HC. Epidermal thickness at different body sites: relationship to age, gender, pigmentation, blood content, skin type and smoking habits. Acta Derm. Venereol. 2003;83(6):410-3. doi: 10.1080/00015550310015419. PubMed PMID: 14690333.
Dawn A. Tamarkin, Ph.D. Repair of skin. 2011 STCC Foundation Press. Available from http://faculty.stcc.edu/AandP/AP/AP1pages/Units1to4/skin/repairof.htm (accessed 04.08.2014)

You're confusing an emergent system with a determined system. Your cells have programming which emerges as the form you see. You are using determinism to decide what your form should be. Determinism gives one reaction for every action. Biology is emergent, not deterministic. The biological mechanisms which are responsible for healing exist in a different information space, with different evolutionary pressures from those which generated your form. The close approximation of scar tissue to undamaged flesh is an emergent property of these two instructions sharing the same physical location. There is no communication between the information which patterned your form and the information which heals your body.

This is a good explinaion

I don't understand q_q. Or explain the information space you're referencing. Are chromosomes the deterministic information space ? What is the "different information space" ?

Genes are the buildings blocks of biological information. Different genes are selected for and against and the fact that you can differentially regulate them is what separates them into their own information space. What you look like comes in large part from hox genes which have very different evolutionary pressures from genes regulating collagen production during healing.


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Cicada Killer Behavior
I've had a giant wasp hanging around outside my window the past few days, so I've resolved to learn more about it. I believe it is a male Cicada Killer, because it displays the following behavior:

During the day, it is extremely localized in a region less than a square meter.
It lands or hovers in the same grassy area all day, and occasionally chases off other wasps that come near it.

First question: Am I correct that this is a male? The females should be off burrowing or catching Cicadas, right? He is quite large (2 inches?), but I don't have a female for comparison in terms of morphology.
Second question: Where does this guy go at night? He leaves before sunset (~5 pm) and shows up again in the morning (~10 am).
Third: If he's around, I should be able to find some female burrows in the area as well, right? Where should I look for these for confirmation?
The question is admittedly a little vague since I am just trying to confirm I understand the behavior I am observing, but I've tried to isolate the specific questions I want answered.
EDIT: Finally got some pictures, only these two came out.

Can you post any images?

Yes, it's a male.
http://bugmugs.org/wordpress/wp-content/uploads/2012/08/cicada_killer_pair_00052.jpg
Source: http://bugmugs.org/2012/08/cicada-killer-pair/
Update:
Wasps are in general very territorial. Even a paper bag can scare them as they take it as enemy hive. More on this: Do fake wasp nests actually fool wasps?

Where does this guy go at night?

Wasps are known to be lazy(less active) at night. Probably they go to the nearby mud nest.

If he's around, I should be able to find some female burrows in the area as well, right?

yes, there are chances of finding a female burrow near by, as they rarely fly away farther than the nest. Otherwise, there main food(cicada) is very heavy for them to carry to the nest.
follow this if you want to find it's borrow: http://www.wikihow.com/Get-Rid-of-Ground-Digger-Wasps-(Cicada-Killers)-from-Your-Lawn

It is extremely difficult to get close to this guy to check, but 1) I don't see a stinger, 2) cannot confirm or deny spurs, and 3) doesn't appear to have the "fuzzy" thorax. But man this guy is big - does the extremely territorial behavior match the female?


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Why do humans seem so much more prone to disease than animals?
It seems like when we observe animals in the wild, the occurrence of noticeable disease in adult individuals is much lower than in humans. Why?
There are a number of reasons that this could happen, but I want to know which reasons contribute the most, or what other reasons I haven't thought of could be involved. So, here's my list of theories:
1) Animals that are prone to disease usually die when very young, while humans in developed countries are given vaccinations/medical attention and have a much greater chance to live to adulthood and advanced age. However, even taking this into consideration, it seems like human populations in third-world countries with little or no access to medicine are much, much more riddled with disease than animal populations appear to be. (Or do they only look that way because that's what we see the most of in the news?)
2) The animals that we see in documentaries are generally purposely selected for viewing as being healthy individuals or a mostly healthy group. This doesn't account for YouTube's many amateur safari videos and pictures, however, where it still seems like animals die much more from territorial disputes or preying than of disease. Safari-goers aren't likely to sit around filming diseased animals, but it still seems like animals 'in the background' and in herds appear to generally be very healthy when it'd be pretty easy to notice a somehow diseased or disabled person in an equivalently large group on the sidewalk.
3) Most humans don't know what common wildlife diseases look or sound like, and at a distance they all appear healthy to us even if there is a roughly equivalent percentage of disease among adult animals as among adult humans.
3a) Animals are much better at concealing the symptoms of their common diseases than the average human, as a defense mechanism from predators. (I know that cats are particularly good at not showing that they're in pain, but I'm not sure how many other animals behave this way.)
4) While most modern humans go out of their way to do every possible thing they can to make sure an infant survives, animal parents purposely kill, abandon or even eat young that they can sense are diseased or disabled in some way. I saw an example of this on a youtube video where a lion cub was gored by a cape buffalo and its back legs were paralyzed. After numerous failed attempts to nudge the cub into standing or walking properly, the mother purposely killed the cub with a suffocating bite and ate it. (Did/do humans practice this to any significant extent? I once read about a culture, can't remember which, that didn't consider an infant viable enough to even name until it was at least 3 months old. I also read that either the ancient Greeks or the Romans would bathe a newborn in wine, and if it survived, it was deemed strong enough to deserve a chance at life. I don't know how true either of these claims are, though. But that's kind of a different question, so consider it optional 'bonus points' to answer.)
5) Diseased and disabled animals are killed off by predators or rivals quickly enough that the populations we see are filled with healthy animals just because the infirm are constantly weeded out. This doesn't address animals that have few/no natural predators or rivals, such as in the case of areas that have so many deer with no natural predators that human hunters must cull them to keep them from reproducing out of control. Are these populations more prone to adulthood diseases than populations that have natural predators?
6) At about seven billion, humans are easily the most populous species that is the size of humans. Other animals with larger populations are much smaller than humans. Compared to other animals of our size or larger, we are intensely overcrowded, leading to lots of people coming in contact with lots of other people all the time, frequently on an international scale as thousands of planes and ships travel around the world on a daily basis. This only covers contagious diseases, though. Even the most isolated hermit could die from a genetic condition that he had since before he was born.
7) Stress. Animals live what we would consider to be a very high-stress life, but they experience their stress in short, intense bursts. Humans, even (especially!) those who live in first-world countries with lots of information to learn and lots of things to do, often get to the point where they can't figure out where the 'off' switch for their stress is. Stress is a silent, gradual killer, and it's possible that minor genetic conditions that may have otherwise been fairly benign or unnoticed turn ugly as a person ages through a life where stress is constant.
8) Diet. It's no secret that there's a lot of heart disease and other diet-related issues in the modern world, but I don't know if that covers ancient humans, and there seems to have been plenty of disease to go around in the olden days even when people ate purely natural foods.
I can't think of any other theories at the moment. One way I thought of to possibly help answer this question was to take into consideration domestic animals - how many diseases do veterinarians have to treat compared to how many diseases human doctors have to treat? This line of thought is rather tainted by the fact that domestic animals are often given vaccinations of their own, though, but it doesn't seem like they receive nearly as many as humans do.
This is my first time asking a question on stackexchange, so I hope I've given you plenty of meat to chew on with this post. I look forward to the replies!

This is a totally legitimate question I myself have wondered about many times; I would have very much liked to see it answered in more detail.  Even if most animals (silently) suffer more than, say, my neighbours, this is far from a fair comparison, which would need to hold at least some factors equal by assuming the human is in a laissez-faire, sink-or-swim environment as opposed to being ridiculously cared for and which the current answer does not do.  The question as I see it still stands.

How in the world is this opinion-based?

I'd have closed it for a number of reasons.  The top being overly broad.  @KevinKrumwiede the question itself is an opinion.  There's no mention of research linked showing that animals are less prone to disease than humans. The entire question, though the ample theories are interesting, is based on an opinion.

@Nathan The idea that animals are more prone to disease is not an opinion.  It is either right or wrong.  (Or more precisely, likely to be right or wrong, as with all empirical knowledge.)  The question could certainly be improved by adding references for its premise, but the lack thereof does not make it an opinion.  That's simply not what an opinion is.

Many examples of animals which have more difficulty maintaining their population size than humans exist. This is partially why some species go extinct. The Tasmanian Devil is at high risk for extinction from a genetic predisposition for cancer onset by infection. Your premise that humans are unhealthy is not sound. Humans are long lived, genetically diverse animals which reproduce exceptionally. We are among the most successful species.

What do you mean by "the most successful"?

Biological success is an encapsulation of various quantifiable elements like: genetic diversity, lifespan, reproductive efficiency, and more. I used the word "success" to refer these items as a whole.

I thought that the population bottleneck from the Toba eruption made humans have fairly low diversity and that humans were very inefficient at reproduction, both due to their lengthy developmental periods and their relatively low birth rates from birth control. I predict that some sort of widespread invasive tree is the most successful based off of the criteria you gave.

You should investigate then, ask another biology stack question about comparing mammalian genetic diversity and what it means.

This answer seems to suggest that humans are actually less prone to disease than other animals, and that our diverse genetic pool is the reason why. Let's see some references, this is more or less stated as fact without much to back it up.


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What is the specific use of a capsule in E.coli?
In evolutionary terms, will the capsule cease to exist someday or will it improve ? Does it provide any boost to the organism in any way which harms us ? Can't we remove capsules or engineer E.coli without capsule ?

According to wikipedia, the capsule contains tightly packed polysaccharides that preform several functions including keeping bacteriophages out, blocking recognition by macrophages, and holding water during dessication. Given the wide diversity of bacteria with capsules, it's probably been around for a long time, which implies it isn't going away any time soon.
If the capsule prevents the E. coli from being taken up by macrophages, then yes, it could allow the bacteria to harm us more effectively. This is one form of a virulence factor.
With proper conditions we probably could develop a bacteria with little to no capsule. We have developed L-form bacteria, which don't have peptidoglycan cell walls. It would seem to me that the cell wall is more important than the capsule, but L-form bacteria are very fragile. I don't know what advantage would be gained by producing capsule free bacteria. There would probably be more to gain from making bacteria with different capsules, perhaps carrying proteins that recognize certain substances and produce a signal, allowing the bacteria to be used as a biosensor, or to accumulate toxic compounds for bioremediation.
references: http://en.wikipedia.org/wiki/Bacterial_capsule http://en.wikipedia.org/wiki/L-form_bacteria

Is there any other organic compound known to gain competency without capsule ?


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Is there an evolutionary purpose to armpit perspiration?
Given that most Americans seem to do fine using anti-perspirant, it got me wondering: is there an evolutionary purpose to underarm perspiration?  I can't imagine it acts to attract the opposite sex.
Or is it just likely an unfortunate side effect of whole-body evaporative cooling via sweat?

some hidden hints: http://biology.stackexchange.com/questions/5217/what-is-the-armpit-hair-for

There may be an evolutionary purpose to underarm perspiration, as alluded to in the "hidden hint" link of @DevashishDas, and also hinted at by the answer by @Chris. The apocrine sweat glands of our armpits produce steroids. One group of steroids secreted by the axillary apocrine glands are sex pheromones.  Although we may not consciously notice the chemical odors of sex pheromones, they do likely affect our behaviors.
For example, Wedekind et al. showed that females showed distinct preferences for certain male odors. Women tended to prefer the odors of males that were genetically different at the major histocompatibility complex (MHC) loci, a group of genes associated with our immune response system. Greater genetic variation of MHC genes generally translates to greater ability to combat disease.  Females that select males that are genetically different at the MHC would produce offspring with greater genetic variability at the complex, and therefore more likely to have greater resistance to disease or ability to fight disease.
These results suggest that the pheromones secreted in underarm perspiration is a sexually selected trait in humans. If so, underarm perspiration would have an evolutionary (fitness) advantage.

First: Not everything what happens in biology is necessarily directly selected for. Sweating is of course selected for, so our body can maintain its normal body temperature in hot climates.
There is a difference between sweat glands under our armpits and for example on the forearm. Under our armpits we have the so called "apocrine sweat glands" while most of the rest of our body is covered with "eccrine sweat glands". They are not only different in size, but produce different types of sweat. Eccrine sweat glands produce sweat, that is made mostly of water and salt, while the apocrine sweat glands sweat contains additionally lipids, proteins and also steroids. Decomposition of the sweat by bacteria which live on our skin produces the typical sweaty odor. The sweat glands also differ in their activation (see here for more details), so can the apocrine glands be triggered by stress.
According to this source ("A short history of sweat gland biology") is roughly comparable, although the total numbers vary quite a lot between the single studies. Assuming that the amount of sweat is comparable, than another factor comes into play: The different evaporation from our arms and from under our armpits. The last form a kind of cavity where the sweat can not easily evaporate and will then stay. It might also play a role, that they can be activated by stress, which will happen in situations which are uncomfortable for us and make the situation worse.
A paper which also looks very interesting in this context (to which I unfortunately have no access) is: "The evolution of sweat glands."

Armpit sweat does not have a strong intrinsic odor. What you smell is the waste of the microorganisms which colonize your armpits. It is a similar mechanism responsible for foot odor and bad breath. All external bodily surfaces have particular microbes which prefer different areas. This also includes the intestinal, oral and nasal regions.
If you charted these microbes on our body, their colonies would read like a map of microbial nations. Different lipids, sugars, proteins on individuals promote different types of microbes and different metabolic pathways giving individuals different scents.
Our ability to perceive a wide range of microbial odors might have an evolutionary pressure given the importance of detecting microbes in spoiled food, etc. I hypothesize our ability to detect body odor is inherited from detecting microorganisms in general.
Surely as our olfactory sense has diminished over evolution, these microbial odors are being taken out of some ancient context.


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Leaves not liked by herbivores
I at times have many goats grazing in our locality. Recently a few cows were seen too. I just offered one of the cows a few leaves from Jasminum sambac plant growing in our garden. The cow smelled and left those leaves untouched. However on being given mango leaves, not a bit of it remained. The same situation did I observe with goats.I have the following questions:
What is the difference between leaves of others and leaves of Jasminum sambac?
Why do herbivores avoid consumption of these leaves?
Does it happen with other leaves too?

No idea why the cow hate it. Its a rabbit safe plant: http://wabbitwiki.com/wiki/Vegetables

I havent ever experimented with rabbits. However this is a practical situation in case of cows and goats. I have observed this a number of times, since I was small

Some animals don't like any unusual smelling or textured foliage. I've noticed that deer will avoid many non-toxic plants that rabbits enjoy. I've noted that deer avoid aromatic, slimy, prickly, hairy, spicy, etc, and prefer plants like hostas, which taste similar to lettuce.

what about regular herbivores...cows and goats??

Goats will eat almost anything, including the canvass on your convertible mustang :(.

Goats will eat bark off a full grown oak tree.

We havent got oaks growing here...yes, I have seen goats eating leaves of different types...but I wanted to know, why they do not like the above mentioned!!!

I have noticed goats eating film posters and banners stuck on walls but yes I do remember them avoiding certain leaves. Could be just like some of us hate some food items while other might hate it.. They have their preferences. Might be that the leaf you offered   could have been eaten by another cow.

I have seen cattle eat the flowers off thistles if they get hungry enough, they wrap their tongue around the back of the flower and pull it off. The rest of the plant is too thorny. But about herbivores avoiding some plants, many plants have defensive mechanisms such as raphides, tiny needles of calcium oxalate which are extremely irritating to the tissues in the mouth and esophagus and can create holes in cells that allow toxic plant proteins inside. Maybe some of these plants have raphides.

Cattles actually hate shrubs which are very tough to break and tasteless(for a cow). Some plants they won't touch are:

Lantana urticoides (West Indian shrub verbena),
Malvaviscus arboreus var.drummondii (wax mallow)
Rhus copallinum (winged sumac)
Viburnum acerifolium (mapleleaf viburnum).
Morella cerifera (wax myrtle)
Ilex vomitoria (yaupon).

Source:
https://www.wildflower.org/expert/show.php?id=2108

Lantana urticoides
http://www.wellgrowhorti.com/Pictures/Landscape%20Plants/Shrubs/Web%20Pictures1/M/Malvaviscus%20Arboreus.jpg
Malvaviscus Arboreus
http://www.floridata.com/wallpaper/jpg/Rhus_copallinum_frt800.jpg
Rhus copallinum

(source: naturallandscapesnursery.com)
Viburnum acerifolium

Morella cerifera

Ilex vomitoria

Also see 'Is there a grassy plant that's unattractive to livestock without being poisonous?' and 'What kind of landscaping plants do livestock avoid eating and need minimal attention?'

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


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What is a "scutella of reindeer"?
In the film "The Perfect Human Diet" at 32:36, a scientist points to animal remains and states "we've got a scutella of reindeer there."  What is scutella in this context?

Scutella refers to shield or plate-like structure on animals (dictionary.com), such as the scutes of a turtle shell.  I have never seen reference to scutes or scutella or anything similar on any type of deer, including reindeer.
I have not seen the movie so I do not know the context of usage. My gut reaction is the person was trying to make something sound important or "scientific" when a much simpler (and perhaps more accurate) word would have sufficed.


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Is this pCAMBIA co-transformation possible?
I would like to know whether the pCAMBIA1200 and pCAMBIA0380 be used for co-transformation of rice using Agrobacterium LBA4404.They probably have the same ori site so they belong to the same incompatibility group.So will they co-exist in one Agrobacterium strain and be transferred to the rice plant?
Please let me know.

It would be good if you include the plasmid map.

Please check and tell me and how do I go about the co-transformation of rice using Agrobacterium starting from E.coli


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What is the biological principle of this "holotropic breathwork" technique?
Holotropic breathwork is a non-drug technique developed by Stanislav Grof used in psychotherapy. The therapy as a whole is usually called holotropic breathwork (at least by Grof himself) and will most probably rely on a range of effects. However, I am mainly concerned about the core technique, which leads to hallucination and a changed state of conciousness (i.e. being half concious and having a distorted perception of time).
As quick googling does not reveal any specific information of the technique, I will describe a demonstration of an amateur enactment of something which was stated to be based on the same principle as holotropic breathwork. (I consider the respective people very irresponsible to have done this without trained assistance, it is probably very dangerous, do NOT try at home!)
A person squats curled near a wall and breaths as quickly and as heavily as possible for a few minutes. After that they quickly stand up in front of the wall and another person pushes them quickly in the chest and presses them strongly against the wall behind them. The pushed person collapses completely, their muscles relaxed, they even don't have the time to close eyes and you can see their eyeballs rolling around freely. They are in this state for about 15 seconds and then wake up reporting vivid hallucinations. Some of the people said that their perception e.g. of sources of light and surfaces were altered for another several hours.
So, what is the biological basis of this collapse and hallucinations? (It would be perhaps good to also comment on the possible risks.)

I think this is mostly caused by hyperventilation. The excessive breathing disturbs the balance between CO$_{2}$ and oxygen in our lungs. This will cause respiratory alkalosis (the blood pH, which is normally strictly regulated, gets higher), which can cause dizziness, headaches and fainting.
The shift in pH can also disturb the eclectrolyte balance, especially the concentration of the free dissolved calcium, as it binds to negatively charged plasma proteins (which release protons into the blood due to the higher pH). This can lead to craps and spasms.
I would be very careful not playing around here, as this can have some severe consequences.

It makes sense that the high levels of oxygen may cause fainting, but what is the mechanism of the hallucinations? Somebody told me that the procedure causes a sudden peak of adrenaline which overwhelms the receptors, but I cannot find any reference.

Pressing on the chest changes the concentration of dissolved gasses in the blood stream. Your brain reacts due to excessive oxygen in the blood. This is oxygen toxicity.
Why the brain generates vivid imagery when unconscious is a big topic. There's a theory that correlates dreams with a lack of cognitive stimulation. This is called autostimulation and may function as pseudo-learning when external stimulation is low. For children it's thought this helps them learn when they can't communicate. We may dream less as we age because adults are highly stimulated.
I hypothesize dreaming while knocked unconscious has side effects which mimic dreaming.


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Are there any arboreal mammals which eat leeches?
Are there any tree-dwelling mammals which might be found taking a living leech and eating it?
(And do any hollow-dwelling birds of prey eat leeches?)

I'm not an ecologist, but doesn't arboreal mean they live in trees? Since leeches are found in water, where would an arboreal mammal find a leech? There are grub eating mammals in trees, and I assume if they found a leech they could eat it. And how are birds involved in this question?

I guess they could meet in the water? Even koalas are known to drink from streams or lakes. I was going to say that leeches are also known to climb trees to drop on their victims but apparently that's a myth.

Arboreals are known to have food that is easily available near their habitats...trees...leeches if available for consumption up there, would obviously be consumed!

First I'd like to point out that there are over 500 species of leeches. Most of them live in fresh water (nearly 90%), and so most tree-living animals would not come into contact with these leeches. Because of this a leech's biggest predator would be fish.

According to The New World Encyclopaedia the predators of leeches are fish, crayfish, turtles, birds, frogs, dragonflies, and damselflies. It states that many of their predators have also been their prey. Ecospark also adds snails and other insects to the list. Biokids also points out that leeches will eat other leeches.
Britannica cautions humans about swimming and drinking water with leeches in it. They can attach to internal cavities - such as the nose and throat and then the leeches can drop into the lungs and cause suffocation. In Asia, it is common for a domesticated animal to die in this fashion.
According to Animals.mom.me monkeys and other omnivorous animals will eat leeches that live on land, but land leeches aren't very common. After over an hour of searching various websites and information about leeches, there is no other source stating that mammals eat leeches.
However, it is possible to eat leeches. They did it on a television show called Fear Factor (video of the leeches being eaten linked). Before you go eating leeches though, remember these people were monitored both during and after ingestion of the leeches.
Short answer: There are no recorded mammals as predators to leeches, but it is known that pets have eaten leeches (as well as breathed them in). And humans are also able to eat leeches. It's all about if the leech is within grabbing distance when the mammal is hungry.


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Where does extra blood come from to fill your muscles during exercise?
Let's say I go to the gym and lift some weights an hour.  During this time my arms will grow due to the "pump" -- the extra blood rushing in to feed the muscles.  For example, I've measured about 2-3 centimeters increase just in the diameter of the upper arm (bicep+tricep).
But where did this blood come from?  Also, if my arms got bigger, since I'm the same weight that means some part of my body must have gotten smaller, right?

Did you also drink water or a protein shake around the time of the workout?

It happens even if you don't drink anything beforehand.

The blood comes from the body's reservoirs:

spleen (mostly erythrocytes) [1]
liver [2]
veins (probably the most important blood resevoir as they contain 50-60 % of the volume) [3]

In pathological situations, if hypovolemia occurs, blood can also come from:

splachnic vascular bed [5]

But what attracts the blood into the muscle? The phenomenon is called active hyperemia:

Active hyperemia is the increase in organ blood flow (hyperemia) that is associated with increased metabolic activity of an organ or tissue. An example of active hyperemia is the increase in blood flow that accompanies muscle contraction, which is also called exercise or functional hyperemia in skeletal muscle. Blood flow increases because the increased oxygen consumption of during muscle contraction stimulates the production of vasoactive substances that dilate the resistance vessels in the skeletal muscle [4].

References:

The human spleen as an erythrocyte reservoir in diving-related interventions. Kurt Espersen, Hans Frandsen, Torben Lorentzen, Inge-Lis Kanstrup, Niels J. Christensen. Journal of Applied PhysiologyMay 2002,92(5)2071-2079;DOI: 10.1152/japplphysiol.00055.2001
Lautt WW, Greenway CV. Hepatic venous compliance and role of liver as a blood reservoir. Am. J. Physiol. 1976 Aug;231(2):292-5. PubMed PMID: 961879.
Michael J. Gregory, Ph.D. The Circulatory System. Licensed under CC-BY-NC-SA-3.0
Richard E. Klabunde, PhD. Cardiovascular Physiology Concepts. Active Hyperemia. Available from http://www.cvphysiology.com/Blood%20Flow/BF005.htm (accessed 03.08.2014)
Blaber AP, Hinghofer-Szalkay H, Goswami N. Blood volume redistribution during hypovolemia. Aviat Space Environ Med. 2013 Jan;84(1):59-64. PubMed PMID: 23305001.

But veins also bulge and get bigger when you exercise; do you mean that if I exercise my arms it draws blood from the veins of my legs?

@CaptainCodeman the veins that bulge on the surface of the body part you are exercising are superficial veins. Because muscle contracts, profound veins are getting flat and the only way for blood to return to the heart is the superficial colateral venous system. And yes, it will draw also blood from your legs, from the abdominal veins etc.

How does extra blood come from to fill your muscles during exercise?
Blood pumps (blood) and sucks (lymph).
There are many pumps in our body

thoracic pump
smooth musculature
respiratory pump

which work together to provide the blood to the peripheral circulation.
These pumps provide us Pulse, Vasomotor tone and Respiratory waves which when act together can lead to local hyperemia or congestion; see my answer only about these waves here in the thread What does irregular heartbeat mean in simple language.
By Starling law, anything that goes inside the heart goes out from there.
See this answer about elevated position on the venous return which is similar to the the exercise on the venous return.
Smooth musculature accommodates blood to the venous return.
Why your muscle gets bigger during exercise?
There are many reasons which can be explained by Frank-Starling principle and Fick's law.
They lead either to

hyperemia (increased local blood flow) or
congestion

because of

protein intake before the exercise
increased sympaticus (decreased parasympaticus; yes, sympathetic tone in digestive truct and some other systems is down-regulated) and blood flow through the muscle (see the above thread)
unstretched muscle can have congestion during exercise which is felt as hard muscle, also long after the training
too regular exercising without rest can also lead to congestion

in the spaces described in my earlier answers like here about What can cause the swelling in high protein diet of Whey proteins:

where explanations in my earlier answer.
Where does the extra blood come from to fill your muscles during exercise?
From your body (See Cornelius' answer for specific locations)

veins 50-60%
spleen
liver

under physiologic fine regulation where heart is the main pump (positive gradient) while its sucking effect (negative gradient; lymph) keeps homeostasis stable for exercising muscles to maintain hyperemia supported by rapid adaptive smooth musculature, vasomotor tone and respiratory pumps (three types of waves).

If you stand up too quickly, you get a head rush. One way to counteract the symptoms of the head rush is to contract your leg muscles really intensely. This forces blood out of your legs and into the rest of your circulation, including your head. This is actually a tip my family doctor told me that I've always remembered.
As mentioned in the links below working out a muscle group causes excess blood flow to these areas which could cause the blood vessels to dilate, causing the muscles in these areas to swell and appear larger. I now realize this has nothing to do with the head rush item I mentioned above, but still may be a useful piece of advice if you every get a head rush!
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479005/
http://www.livestrong.com/article/75670-swell-after-workout/

Can you add some references?

Why would pushing blood to your legs and away from your head help with the head rush(orthostatic hypotension)? The dizziness and other symptoms are caused by blood leaving your head. In the short term, flexing drives blood from the muscle group, and opens blood vessels to increase later blood supply to the muscle group.(see also Hick maneuver, a similar leg/torso flex to keep blood in the head for fighter pilots)

thank you I realized I said this wrong, fixing my answer now.


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Which species were first described by Charles Darwin?
There are many plants and animals named for the naturalist Charles Darwin, such as Darwin's Frog (Rhinoderma darwinii), but which were named by him? I'm finding it difficult to find such a list.

I haven't found a list of species named by him, but an article of species named after him. They list some 301 different animals in it. A few where probably named after him for findeing them (he collected vast numbers of them and sent them back to London) but others where named to honor him. You can find the list here.

Darwin described adaptive radiation by describing small, dark birds in Australia. Those birds are known as Darwin's finches.

Lets not forget the Galapagos Finches and other species described in "Voyage of the Beagle".

I've discovered that searching for Darwin on the Encyclopedia of Life (EOL) appears to prioritise in its search results those species named by Darwin rather than for him. The first page of results includes many barnacle species (as noted by 3cat). The first five species are:

Amphibalanus amphitrite (Striped Barnacle)
Megabalanus coccopoma (Titan Acorn Barnacle)
Balanus glandula (Acorn Barnacle)
Elminius modestus (New Zealand Barnacle)
Balanus nubilus (Giant Barnacle)
...

There are 370 results, but some of them are not species level (e.g. Chthamalidae), and some other entries are mixed in (e.g. S.C. Darwin and S.P.Darwin), and later results include, for example, Nemoria darwiniata, so it's hard to quantify the results.
I might try writing an SQL query for the downloaded Catalogue of Life, as its online interface doesn't seem to allow the relevant query.
EDIT:

The complete list: Species described by Charles Darwin (EOL), listing 81 species. (Pointed out in comments. Thanks 3Cat)

Nice initiative. I followed your link and browsed through it. I clicked on one of the species (a bird, described in 1839) and discovered that it belonged to a collection called "Species described by Charles Darwin." (http://eol.org/collections/12085). It lists 81 species.

@3cat Perfect! I feel like a fool for missing that. I wish I could award the "answered" tick to your comment.

A 'correctly' formatted scientific name will usually have an author citation and date, (http://en.wikipedia.org/wiki/Author_citation_(zoology)), as you can see on the EOL page.

@Qubei - it was your answer that sparked my comment. You set me on the right trail. If you want, add my comment to your answer and accept yours.

I don't know if these are his earliest descriptions but Darwin did describe several species of Planaria, such as Planaria vaginuloides, P. oceania, plus a new genus, Diplanaria in 1844.
Darwin, C. R. 1844. Brief descriptions of several terrestrial planariæ, and of some remarkable marine species, with an account of their habits. Annals and Magazine of Natural History 14 (October): 241-251, 1 plate.
Perhaps his best known taxonomic work is on barnacles (Cirripedia). He described several species in his monograph first monograph on the group.
Darwin, C. R. 1851 [=1852]. A monograph of the sub-class Cirripedia, with figures of all the species. The Lepadidæ; or, pedunculated cirripedes.. London: The Ray Society. Volume 1
The first monograph was followed by three other monographs on living and fossil Cirripedia.
I believe that most of his writings after publication of On the Origin of Species focused on expanding his evolutionary ideas rather than on descriptions of new species.
You can read nearly all of Darwin's writings online at http://darwin-online.org.uk. With careful searching you can find all (or nearly all) species descriptions.

Thanks for the reply. I'm surprised there isn't simply a list somewhere though. His publications after Origin weren't all expanding on the theory—His last scientific book was The Formation of Vegetable Mould through the Action of Worms, with Observations on their Habits, not really about natural selection.

I'm not aware of any lists. Perhaps something has been compiled in a biography. I suspect that his work on natural selection (and related) has overshadowed all of his other important contributions, at least for most science historians. Perhaps you'll pull together such a list! Please feel free to accept my answer it is, well, acceptable to you.


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Extinction of species
I barely know anything about biology and realize that this might be a stupid question, but I'll ask anyway! I know that species "transform" into other species through the process of evolution. Many species around today still co-exist with the species in which they evolved from, right? Actually, is it correct to say that all species coexist with some common ancestor?
Anyway, my question is; if the monkeys that we evolved from are still around today, then where are all the in-between species. Are there still early humans, like Neanderthal's or Hominids or what have you still roaming around some where?
If all early forms of humans are gone, is it because the more modern humans had a greater evolutionary advantage? But wouldn't these less modernized humans have those same advantages over the less evolved monkeys?

This 'missing link' question has been posed many times here. I think a reading list is the best response and should be posted in context of closure process.

I disagree about this question being off topic.  The help center specifically states that "general questions about biological concepts" are suitable. This question addresses common misconceptions about the evolutionary process. Of course, I'm new here but I wanted to share my opinion.

I too do not see how this question is off topic. If it is a duplicate, then you could perhaps link it, or perhaps suggest a source in which I could find it? I have found some of the answers here helpful

This is a common misconception about evolution, many skeptics ask something along the lines of "If humans evolved from monkeys, why are there still monkeys?" The answer is that evolution is not a linear process of one species becoming the next species becoming the next. Species branch off much more like a tree. At some point in the past the last common ancestor of humans and monkeys split into two directions, one that became the apes including humans, and one that became modern monkeys. Evolution did not stop for either branch, but only our branch became humans, after several more branchings. Sometimes species adapt and evolve without major changes in morphology, for example modern turtles look a lot like turtles from 100 million years ago, but this doesn't mean they haven't evolved.
The intermediate species are often lost with time as environmental conditions and competition changes. For example, if one early human group found itself competing with a slightly more advanced human group with better tools, the more primitive group would have trouble getting enough food and eventually die off, leaving the more advanced group to pass its genes on.
Now, if those more primitive humans were more suited to a particular niche, they could survive there. Lets say they could climb trees better ( assume REALLY primitive ancestors, barely out of the forest ), they might survive in the forested areas while the more advanced groups become dominant in the grasslands. Something like this is why our ancestors didn't totally displace monkeys, the monkeys were better suited for their forested ecosystem. If those same monkeys had to live on dry savannas we would have eaten them all long ago.

Cool, thank you for your answer. I agree completely that it makes perfect sense why there are still monkey's around today. So I think what you're saying is that I can (vaguely!) think of it like this:

At the branching point between the common ancestor of modern monkeys and modern humans, there were sort of two scenarios which evolution acted on, one in which the "to be monkeys" were better suited and the other "to be humans." In the former, the monkeys won and still strive in those areas today. In the later, the "to be humans" won. But in this setting, the modern humans were just evolutionary superior, and so the in between species of human eventually died out?

Worth noting that they took a fairly long time to die out everywhere. The Denisovans(Siberia), the Neanderthals(Europe), and probably some others all stuck around for thousands of years after modern humans evolved and spread out of Africa. As these 'more human' hominids shared ecological niches(bipedal, relatively smart, thumbs) with early humans, we outcompeted them for resources(small game, territory) while we don't compete as much with say, orangutans. They live in trees and eat leaves and fruit, but we need protein and fat for brain-making.

I think other answers have explained natural selection, but I think it is also important to note that species boundaries are applied in retrospect. This sounds blindingly obvious, but when presented by skulls from two species, such as Homo erectus and Homo sapiens, many will then ask where the evidence is for the species that came between those two.
There are several reasons why you can't see all of these in-between forms:

The fossil record is imperfect. Although there are no longer any "missing links" in the fossil record for the evolution of humans from our most recent common ancestor with chimpanzees, not every change in skeleton shape has been preserved for us to look at.
Species boundaries are applied retrospectively. This means that when we find a new set of bones that seem to be in-between two species, we give these bones a new species name, because they clearly don't belong to the other species we've already identified. The bones actually represent one of the "in-between" forms that people are asking about, but we can't just label it "intermediate" or "missing link". It has to be categorised as a new species or sub-species.
You're not technically looking for an "intermediate". It's not that chimpanzees are an "intermediate" between humans and some ancestral species. It's that humans and chimpanzees share a common ancestor. When you see a pictures of a neanderthal, they might superficially look like an intermediate between humans and chimpanzees, a sort of hybrid between the two, but that's not quite right. It's not that chimpanzees eventually became neanderthals, which eventually became modern humans. It's actually that humans and neanderthals share a common ancestor and that ancestor is no longer around for reasons given in other answers. Similarly, neanderthals and chimpanzees share a common ancestor that is now extinct. My point is that if you're looking for something like a "crocatoo" that's a hybrid between a crocodile and cockatoo, you won't find it. Yes, crocodiles and cockatoos share a common ancestor somewhere in their family trees, but there's no reason that it will look half like one species and half like the other! It might look nothing like either of them!

If you're looking for more information on evolution, I'd highly recommend "The Greatest Show on Earth" by Richard Dawkins. If you want citations for the points I make, you'll find all of it in there. It explains this stuff quite clearly, with ample evidence to back it up (assuming you can put up with his occasional rants about young earth creationists...)

If all early forms of humans are gone, is it because the more modern
  humans had a greater evolutionary advantage?

If you take an environment where species dwell, three things could have happened:

The population got smaller and smaller, in a given environment, and then bam the last ones disappeared without producing any offspring. This is because population as a whole wasn't  reproducing as fast as they disappeared, for a variety of reasons. By disappeared I mean: went away to other environment or died out.
In another environment, so much changes had spread through the population that at one time the new offspring was born with their genotype now "too much" different and thus incompatible. By "too much" I mean this: they could still mate with both partners from their population and with "less changed" neighboring populations, but they could only produce a fertile offspring with former but not with the latter. We nowadays refer to such situation as "they became new species". From this point they obviously couldn't spread "their" genetic changes anymore to other environments via reproduction (spreading parts of genotypes). Their offspring would be infertile. They only could spread "their" genetic changes by sending whole groups of folks (complete genotypes) to other environment to try and cope there. And sometimes to kill others interfering, because, hey, that's what living creatures sometimes just do.
The population lived without "too much" change in the genotype and still exists today in the given environment. Without "too much" change means they were unchanged or rather changed slow enough that at any given time they could leak their changes to other populated environments via reproduction (they kept being the same species as their neighbors).

I have written about genetic "changes". You call these "advantages" and even "modernizations", but for the sake of argument it just doesn't matter (and only blurs the picture with the unnecessary concept of "superiority"). Advantages in one environment are disadvantages in another.
I use "environment" here for simplicity, but a more proper term would be a "habitat".

We don't observe any early humans today. It seems that all their populations have met one of these two former fates.
Also, you tend to overuse high-level abstract terms that distract you from thinking what have actually happened at low level. "Evolution" does not "act" on any "scenario". This is just a bit too much of anthropomorphism.

It would be fantastic if you included some references in your response!

I know that species "transform" into other species through the process
  of evolution.

I don't think you are thinking about that right.
We have a population of organisms that are breeding together.  We humans label that a 'species'.  That population has descendants, and over time, the population changes, and when we humans think that the new population look sufficiently different from the old, we label them a new species.

Many species around today still co-exist with the species in which
  they evolved from, right?

You might have founder situations, where a small sub population breaks off and inhabits a new environment, and changes a great deal more over time than the original population does, such that we continue to label the original population the same species, while we label the offshoot a different species.  But I think what happens more often is that the alleles that cause humans to label a population a distinct 'species' dwindle to nothing in the descendants, and then we say that the original species is extinct, replaced by the new one.  but that's a matter of labels: there is continuity in that the new 'species' is just the descendants of the older one.

Actually, is it correct to say that all species coexist with some
  common ancestor?

No.  Can you even name any examples where you think this is true?

if the monkeys that we evolved from are still around today,

What on earth makes you think that's remotely true?  For one thing we aren't descended from monkeys.  We are descended from primates that were more like apes, not monkeys.  There is no living population of primates that we would categorize as being the same species as that non-homo sapiens ancestor population.

Are there still early humans, like Neanderthal's or Hominids or what
  have you still roaming around some where?

I'm confused how you think an organism or a population existing in the 21st century could be "early". All the hominids walking around today are members of homo sapiens sapiens.


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Is it true that viruses cannot be seen with phase-contrast microscopy?
There appears to be a lot of material on the internet claiming that viruses can be only seen with electron microscopes, and not with light microscopes. To the contrary, for example this old paper published in Nature states that viruses can be seen using phase-contrast (light) microscopy. Who's correct? What is the smallest thing I can see using a phase-contrast microscope?

It is true for most viruses. They have a size of roughly 1/100 of bacteria (or smaller), so they are too small to be seen in light microscopy. According to Wikipedia the maximum limit with light microscopy is around 1500x magnification (or making structures, which are at least around 200nm in size visible).
A lot of viruses are smaller, for example the influenza A virus is around 80-120nm, the HIV virus around 120nm and the rhinovirus which causes the common cold around 30nm. They would only be visible in electon microscopy. The measles virus on the other hand has between 350 and 400nm and should be visible in light microscopy. However, since you are very close to the region where you reach the diffraction limit for visible light, it is usually not used very much.

What does diffraction limit has to do with with this thing?

It is true generally but it's not an absolutely truth.
There is a group of giant viruses which can be seen under the traditional light microscope - such as the pandoravirous - which its size is about 1000 nano-meters.
Sources:

An academical lecture of virologist (see here: 39:33, but I recommend you to start from 35:35) that answers directly your answer.
Live science-Largest Viruses Ever Revealed

Viruses are usually too small to be seen at the light microscope level. However: large virus conglomerates within cells can be seen under a light microscope. In that case they're called "inclusion bodies". These have diagnostic value. For example in the case of rabies, were those so-called "Negri-bodies" provide the beyond-any-doubt post mortem diagnosis of rabies.


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Can butterflies still fly after their wings are touched?
When I was a kid, I was told not to ever touch a butterflies wing, as it would lose its ability to fly. This was because of some dust which was supposed to be in place on the wings and when disturbed it had the described consequences. I doubt at least the story about the dust, which sounds a bit too much like "fairy dust", but am I right?
What damage will be done by touching a butterfly?

So basically the question could be rephrased as: Can butterflies still flight after being touched by humans? What kind of damages do human fingers usually cause to butterflies? Is it correct?

Yes, this would be a shorter version of my question. And probably more precise :-)

I've heard the same about moths which seem to be more "dusty"

Both the Forewing as well as the Hindwing of Butterflies are made of thin chitin structures which are pretty thin and sensitive. If you touch the wing with to much force, it may break.
Then the upper side of the butterfly wing is covered with small scales - what you called the "dust". This can be seen in this figure (from here):

and also in this electron microscopy image (from the Wikipedia):

The scales have a number of functions, they are responsible for the butterflies color and pattern (which are important for finding mating partners as well as for camouflage) and they also seem to play a role in insulation and thermo regulation (see here for more details).
The scales play also a role in making the wings stronger and help improving the flight characteristics. When flying upwards the get pressed to the wing and act aerodynamically, what the wings are in downward motion, they help stabilizing the flight. See here for more details: "Butterfly wing scales : pigmentation and structural properties".
Some of the scales get lost during flying and collecting nectar, so taken together, loss of a big number of them will influence the flight characteristics of a butterfly. However, I think it is much more likely that such a rude treatment will damage the wings, which is obviously more harmful. So light touches will not do harm, more severe will.

I happened to be watching a nat geo documentary last night about butterflies, and it claimed several times that the activity of the scales also helped to provide feedback to the animal while in flight.

Can they still fly beautifully if one of their wings is half cut?


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Why Did 6 Great Ape Species Survive But Only 1 Hominid Species?
My dad asked this question when I explained some circumstances surrounding Homo sapiens survival against all odds.
We know there is only one hominid species left in the world, Homo sapiens. We also know that there are only 6 other species of great apes left: 2 species of chimpanzees, 2 species of gorillas, and 2 species of orangutans. These 7 species are the last remaining in the family Hominidae.
All the other hominids besides Homo sapiens died out tens of thousands of years ago, and we believe the reason our ancestors survived is because we were more "adaptable", meaning we were not restricted to a single environment but could survive in many others. This is the reason we later spread out all over the world, and probably why we gained "sapience" and are able to contemplate these grim circumstances.
At one point, following the eruption of the Toba volcano 70,000 years ago, there were between 1,000 and 10,000 mating pairs of Homo sapiens left, though there may have been other hominid species alive at the time. My dad asked, if the hominids faced such grueling environments and all but a few died, why did the great apes fare any better? Why are there 6 extant non-human Hominidae species left, but only 1 hominid species?

Good question and a great answer below. I think that there are a couple of issues with the question, however: 1) apples and oranges comparison - a monophyletic group (Homo) with a paraphyletic group ('all of the other great apes besides Homo'). 2) taxonomic / taphonomic bias - less effort is put into finding and naming extinct non-human great ape species, and because of their habitats, they also just might not fossilize very well (apparently the first chimpanzee fossil was only discovered in 2005!)

My dad actually asked it when I explained some of this to him. I'm open to suggestions of how to explain it better here and may make an attempt when I get time from work this week/end. Wait, are you saying the first chimp fossil ever found was found in 2005? That's strangely late.

Determining why one species (or group of species survived) while others did not can be difficult to answer, but I can offer one possible explanation for the genus Homo: competition. Competition between similar species is one possibility. Consider for example gorillas or chimps. The two species of gorillas occupy different habitats so they rarely compete with each other for resources (food, water, shelter, etc.). The two species of chimpanzees have non-overlapping ranges (or minimally so) so again they do not compete for resources.
Chimps and gorillas do overlap with each other for parts of their range and even potentially use the same resources, although no competition for resources has been observed (see this primate factsheet and McNeilage 2001). The same applies for the orangutans, which lives on two different southeast Asian islands.
The genus Homo is an entirely different story. As you may know, Homo first evolved in east central Africa. The first species to leave Africa and disperse across Europe and Asia was Homo erectus. This migration out of Africa happened as early as aout 1.8 million years ago. Homo sapiens had not yet evolved. However, while H. erectus was establishing itself across Europe and Asia, populations still in Africa continued to evolve.
Modern Homo sapiens evolved in central Africa perhaps about 250-200,000 years ago and dispersed out of Africa about 100,000 years ago. Homo sapiens also dispersed across Europe and Asia. Both H. erectus and H. sapiens co-occurred across parts of their range. Some have argued (Stringer and Andrews, among others, I believe but I'll have to be at work before I can verify ths reference) that H. sapiens outcompeted H. erectus, leading to its eventual extinction by competition. They occurred together and used the same resources, so H. sapiens could have caused the extinction of H. erectus. This has been called the replacement hypothesis. The later evolving species (H. sapiens) replaced the earlier evolving H. erectus.
However, Templeton (2002) has argued that the two species interbred so the species became integrated rather replaced (if I am interpreting him correctly).  While I don't dispute the possibility of interbreeding, I am skeptical of Templeton's complete dismissal of replacement.
Complicating the picture is H. neanderthalensis. Genetic evidence published by Green et al. (2010) suggests that Neanderthals diverged from H. sapiens (in central Africa) between 800,000-500,000 years ago and also dispersed out of Africa.  They also provided evidence of interbreeding between H. sapiens and H. neanderthalensis in Europe.  Modern H. sapiens may also have outcompeted H. neanderthals.
All of this was occurring during the Pleistocene ice age. Europe was experiencing repeated bouts of extensive glaciation. Thus, it is also possible that climate change caused or contributed to the extinction of H. erectus, H. neanderthalensis, or both.
In summary, the processes that led to the extinction of other species of Homo are complex and likey interactive. Competetion among species is, in my view, well within the realm of possibility but would be extremely difficult (if not impossible) to test. Climate change is also a very likely contributing factor. There are several other hypotheses but I have tried to hit the major highlights.  The debate is certainly not settled.
McNeilage A. 2001. Diet and habitat use of two mountain gorilla groups in contrasting habitats in the Virungas. In: Robbins MM, Sicotte P, Stewart KJ, editors. Mountain gorillas: three decades of research at Karisoke. Cambridge (England): Cambridge University Press. p 265

This is a good answer


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How to selectively download 3 fields from every record in UniProtKB?
I want to download a comprehensive table of protein names from uniprot.org.
More precisely, I want to generate a tab-delimited table consisting of the id (accession), entry name, and protein names "columns" from the UniProtKB database.
I want to get these three columns/fields for all 80M records in UniProtKB, and I don't want to specify all those Uniprot IDs through, e.g., a bazillion URL-encoded queries.  Also, I need to do this from a host that I can access only through a text interface, which basically rules out browser-based solutions.
I just spent a couple of hours going back-and-forth over the Uniprot site's docs, and I can find nothing useful.  The Perl example given there1 shows how to download full records, but downloading every full record from UniProtKB would be too slow and onerous to be considered2.
Does anyone know how to modify the Perl example (or any other way) to download only the three desired columns from UniProtKB?

1 You need to click on the phrase "Perl example" to see the code.
2 I downloaded a small test sample of 1000 full records, I found that the size of the information I actually want from those records is only 0.2% of the total.  IOW, downloading the full records would take up ~500x as long as downloading only the desired information.

I have never worked with perl and I'm unsure of its commands but by the sound of it you need to specify the columns using regular expressions in the download command lines (e.g. in the R language you use commands such as grep or regexpr). Hope this hint helps!

did Biomart work ?

@WYSIWYG: Thanks for the suggestion, but I had used Biomart before and found it difficult to work with, so I basically ruled it out as an option for this.  I was looking for answers based directly on an API published by Uniprot.org.

BioMart is connected to UniProt (it is basically an ENSEMBL resource to connect with all EBI/EMBL databases).. If you install biomart then you can easily pass commands to download specific data. It is quite convenient; they have improvised it as well; so you can have a look at it again.

Use BioMart. It retrieves UniProt information and you can select the features that you want. These files wont be that huge. So  you can download it in your PC and SFTP to wherever you are doing your analysis. A better way is to install BioMart in your workstation. See the BioMart documentation.