text:
How does the immune system "learn" from a vaccine?
According to Wikipedia:

A vaccine typically contains an agent that resembles a disease-causing
  microorganism, and is often made from weakened or killed forms of the
  microbe, its toxins or one of its surface proteins. The agent
  stimulates the body's immune system to recognize the agent as foreign,
  destroy it, and "remember" it, so that the immune system can more
  easily recognize and destroy any of these microorganisms that it later
  encounters.

Question:  How does the immune system ""remember"" a foreign agent introduced via a vaccine?  And how does it learn how to deal with subsequent encounters?

Thanks for the excellent answers!  (There seems to be a lot I still need to learn)

Vaccines work by introducing an attenuated strain of the pathogen (or alternatively the antigens that are normally present on the pathogens surface) into the body, whereupon the body mounts an immune response.  As this will (hopefully) be the first time that the body has encountered the antigens on the pseudo-pathogen's surface, the response is called the primary response.
This consists of two main divisions: the cell mediated pathway and the humoral pathway.  In vaccination it is the humoral pathway that is important.  This is where a division of white blood cells (B-Cells) produce antibodies that are complementary to the antigens on the pathogen surface, causing a negative effect to the pathogen (death, inability to reproduce, de-activation of toxins, etc.).  However as each B-Cell produces a different antibody, there needs to be a mechanism to select the correct one:

Antigen Presentation (technically part of the cell-mediated-response) - a phagocyte engulfs the pathogen and displays the pathogenic antigens on its own surface.
Clonal Selection - B-Cells that are attracted to the invasion site attempt to bind their antibodies onto the pathogen's antigens.  It takes time for this to occur successfully as you are essentially waiting for the correct mutation to happen.
Clonal Expansion - Once a complementary antibody producing B-Cell has been found it is then activated with the help of a T-Helper cell.  This causes it to divide rapidly whereupon these cloned specific B cells can secrete their antibodies which will cause detriment to the pathogen.

It's at this point that I can start to answer your specific question.  The large clone of B cells will then sub-divide into two types.  Plasma Cells remain in the blood and produce antibodies to fight the infection.  The other type, much smaller in proportion, are called Memory Cells.  These cells have a very long lifetime and move to lymph nodes across the body (including the spleen), where they remain dormant until the same pathogen is found again.
When this is the case, the memory cells are activated by T-helpers so that they can divide into massive numbers of plasma cells to fight the infection the second time.  This secondary response is a much faster as the clonal selection stage does not have to wait for the right mutation - they are already waiting in the lymph nodes.  The response is also much stronger as each memory cell can produce large numbers of plasma cells - i.e. you can start with multiple activated B-cells (as many as you have memory cells) rather than just the one that has mutated into a complementary shape in the primary immune response.
The aim of the vaccine is for the secondary response to be so quick that potentially life threatening symptoms do not occur; the body has time to find and store the correct antigen in a safe environment as the pathogen has been deactivated.

I think there is some misinformation here. As far as I am aware, the point of memory B cells is that they are able to activate without T helper contact, solely based on pathogen contact. Surely if they required T helper contact, the memory response would barely be faster than the initial one.

MBQ and Rory M have already given decent answers on the "hows" of how the vaccine memory is formed. Now, for some twists:
There are three (general) types of vaccine, all of which are meant to make your body "think" its being infected and provoke an immune response, while at the same time not causing active infection. They are:

Live attenuated. These vaccines are made up of living pathogens that have, through a variety of methods, been rendered essentially harmless. Never the less, they are infecting you. It's a bit like getting into a shootout with people carrying Nerf guns. Good news is, the bullets are foam, but they're still shooting you. The advantages to these vaccines are that, generally speaking, they were easier to make, and because you are infected, you can shed the pathogen back into the environment, spreading the vaccine around a bit. The disadvantage? Sometimes the pathogens de-attenuate, and cause disease.
Killed. Dead pathogen - your body responds to the presence of foreign antigens, develops an immune memory, and that's that. You gain safety, but lose the secondary spread of vaccinating attenuated pathogens.
Virus-Like Particles. This is the sexy new class of vaccines, that is both dead and...not real. Synthetically produced, these vaccines (like the HPV vaccine) are both harmless and provoke an immune response, and can be customized - they can have antigens to different strains, etc. that you can't do just with attenuating or killing pathogens in the wild. They're awesome, and brilliant, and expensive as hell to develop and produce.

Once your body "learns" from the vaccine, how well it retains that memory also may vary. Some vaccines provoke a strong immune response, and the pathogen they target is genetically stable enough that you're pretty much set for life. Others, like the chicken pox vaccine, wane over time as your body isn't challenged by new exposures to the pathogen, and needs to be "reupped" now and again by giving you another dose of the vaccine, known as a booster. For some vaccines where your vaccine-triggered immunity may wane over time, we might not bother with a booster because you're now old enough that you're out of danger. The HPV vaccine comes to mind again - we're not sure you're immune for life, but if we can make sure you're immune until say, 65 or 70, it doesn't really matter, because it will take years for cervical cancer from an HPV infection to develop anyway.
Still others target diseases that mutate rapidly enough that your body's memory doesn't last long. The yearly flu vaccine is an example of this. A year after you get your vaccine, you body may "remember" the previous year's strain well enough to fight it off, but that's not the strain of influenza going around that year. This is also a problem for the hypothetical development of an HIV vaccine.

I've never heard of "spreading" a vaccine by shedding live attenuated pathogens into the environment (although the explanation makes sense). Can anyone give more information about how often this occurs and how effective it is?

@adamj537 Best example is live polio vaccines

In short, some of the B-cells (antibody producing lymphocytes) specified to deal with this agent go dormant after the vaccine stimulation -- when the real danger comes, they can proliferate quickly and flood it with new antibodies, also alerting the rest of the immune system.

If you want a shorter version, but with some key terminology in there, here you go:
When the body is exposed to an antigen (a substance that stimulates an immune response), antigen-presenting cells (e.g. macrophages) engulf them and present them on the surface of their cell membrane. Then, T cells bind to it and in short, they eventually get activated. Then activated T cells activate B cells, which then divide by mitosis to form a clone with plasma cells and memory cells. Remember, these plasma cells are specific to that antigen. The memory cells are the one that causes a quicker secondary immune response as it recognises the antigen when the body is exposed to it again and causes a greater number and faster production of antibodies.


text:
Is it correct to regard archeaic humans (i.e.n Neanderthals and Denisovans) as distinct species to Homo sapiens?
There is increasing evidence (e.g. here) that Homo sapiens interbred with contemporary homonins such as Homo neanderthalensis and the "Denisovans". Although these homonins do show differences in their mtDNA, since a species is generally defined as a group of organisms capable of interbreeding and producing viable offspring, should we not regard humans, neanderthals and denisovans as the same species and name them as such?

This question highlights the different species concepts.
If you go by the reproductive species concept (a population of actually or potentially interbreeding organisms), then yes. Apparently, the populations were interbreeding.
If you go by the typological species concept (morphologically distinct), then no. Homo neandertalensis and the "Denosovian" are morphologically distinct enough to be recognized as such.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How are whole Haplotypes for Sequencing isolated?
Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered irradiating sperm and attempting to create haploid females via gynogenesis, but I was wondering if there was a faster and easier method that could utilize gametes directly.

Are you limited to a particular species of fish? Or can you use one of the asexually-reproducing species?

If your aim is to isolate the two haplotypes (chromosomes) maybe you should try flow cytometry. You might read this paper http://www.ncbi.nlm.nih.gov/pubmed/21181533 by Dolezel which is leader in the field, at least for plant chromosomes. I'm pretty sure that the applicability of the method depends on the physical properties of the chromosomes you have (especially their size distribution).

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
What are the limitations to current nucleotide sequencing technologies?
Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with their own distinct advantages, but Illumina seems to be pretty popular for many applications, despite its limitations.
Ideally, we would like a sequencing technology that produces long, error-free reads with high throughput. However, at this point it seems we have to make a choice: throughput or length (and quality). PacBio seems promising, but the last I heard they have still been unable to deliver on their claims.
What are the molecular and biochemical limitations to our current sequencing technologies? Why don't we already have long, error-free reads with high throughput?

I suspect the project triangle is at work here. http://en.wikipedia.org/wiki/Project_triangle

@bobthejoe Ideally, we would like as long as possible, right? :) I consider the upper limit of Sanger read lengths (+/- 1000 bp) to be long, but it would also be nice to know why we can't get longer reads (with or without high throughput, low error rates, so on).

All or most of the limitations you describe can be simply overcome by brute force method. Almost any genome sequenced on any high throughput technology today will be of very high quality if you sequence it 100 times. It's just a matter of time and money. Remember the original human genome was sequenced by many Sanger machines and a lot of cloning.

@yotiao What you're saying is true, but only to a point. My experience is that assemblies and other analysis improve with coverage, but at a certain point adding more data provides only minimal improvements, even if there is a significant addition of new data. And to say that the human genome project was successful primarily because they dedicated a lot of Sanger sequencers to the project ignores the significant differences between the nature and quality of the data produced by the Sanger platform as opposed to today's high-throughput platforms.

@Daniel Yes, you're right in principle. But then if what you require is as-perfect and complete a sequence as possible, then I'd propose that the limitations are the same as they were before: DNA itself, with it's super high repetitive content, poliploidy. Sanger and positional cloning did not manage to solve this problem (hence gaps in finished human genome sequence) and they're regarded as the golden standard (am I that old already?).

It seems like you answered your own question,the signal from a few molecules running through an enzyme or a polymerase tend to fall out of synch after a few hundred bases.  If an enzyme for sequencing was more rigorously in time step that could help for instance.  The machines read traces in four channels with nice bumps for each base.  See this article for a nice example. You can see that if there are too many of the same base consecutively it gets hard to tell how many bases there are there.  Over time all four traces will start to smear out and you cant tell Adam from Thelma if you take my meaning.
But there are other bottlenecks.
The sequencers currently put out such a high volume of data that the analysis of the meaning of the output data can't be analyzed fast enough.  This follows the trend in biotech over the past 12 years or so - more sequence data, micro array data, more mutation data, more genomes than people who can actually use it to understand the biology.  There is a bit of an analysis bottleneck now.
So some of these sequencers have greater read lengths, which can make it easier to assemble a sequence.  These sequencers generally cost more.  For instance if you have a library to sequence a little fungal or algal genome - you will get the answer back in a day or less now.  In the form of 1 Tb of reads maybe 50 to 200 bp long.  It might take quite a bit of time to put that together into a novel genome sequence, still more to find the genes, build the gene networks from a template of pathways etc.  Just imagine a thousand sequencers pumping out day and night and you get the picture  I'm trying to paint here.
About cost.  Ion Torrent and the new oxford nanopore sequencers are really cheap - \$50k to perhaps \$900 for Oxford Nanopore's USB sequencer.  Most other systems cost hundreds of thousands of dollars.  Ion torrent and Nanopore have more disposables - you throw away a chip or even the entire sequencer - at a cost of hundreds of dollars a sample.

Over the summer I've been to a couple of conferences including a day seminar focused on assembly of 30x coverage genomes from MiSeq data and the biases in the sequencers were creating systematic errors that made some of the data difficult to interpret.  HTS data is not plug and play, even with open source software.  not yet.

Q1) What are the molecular and biochemical limitations to our current sequencing technologies?
A1) AFAIK:
Illumina has hard time producing long reads (although now miseq can generate reads that are 300bp and that can be paired, the so called paired end 2X300) because after a certain number of bases that are synthesized and recorded on camera (Illumina is sequencing by synthesis, basically you add bases and measure fluorescence at each cycle), i.e. after a certain number of "cycles" you can lose syncro, and the quality of bases decreases.
PacBio can generate very long molecules, but they still have big problems with reliability of the reading of the bases (I don't know what's the problem here)
Q2) Why don't we already have long, error-free reads with high throughput?
A2) Because it's hard to do! But we are moving towards this!


text:
Does an annealing temp higher than primer's Tm contribute to primer dimer?
I am attempting to reproduce results from a number of journal articles all referring to the same SNP. In doing this I'm using the same primer set outlined in the articles. When I attempted a run the other day I experienced what I can only assume was primer dimer (~40bp product, bands not visible at expected bps.) While the primers and restriction enzyme were the same among numerous articles, the annealing temperatures in the reaction varied a fair amount (52-59C). All were above the individual Tms of the primers which struck me as odd.
Calculating the Tm via primer blast here are the numbers:
Forward Tm: 50.14  [5'-GCTCTACTTCCTGAAGACCT-3']
Reverse Tm: 51.67  [5'-AGTCTCACTCACCTTTGCAG-3']
Other sites gave slightly higher numbers (54-55) but they are still below the 57C that I used in my reaction. I do not have access to a gradient thermocycler otherwise I would have tried a range myself.
If an annealing temperature is chosen above the individual Tms how do the oligos have a chance to anneal with the template and eventually extend? I remember hearing the Tm calculation is more involved and includes finding where the melting curve changes direction. But on the surfance I would think the primers would never have a chance to anneal at such high temperature? What is wrong about my interpretation?

What kind of polymerase are you using?

Using a Maxime PreMix which includes Intron's i-Taq

I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.
Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using?
Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).
If you start seeing non-specific products at that Tm, I'd do what we call a "Touchdown" PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it "touches down" to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the "restrictiveness" of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.
Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.

"biology is not an exact science" made me chuckle - just don't tell the chemists and physicists or they'll never let us live it down!

@RichardSmith They way I learned it: Me: So, where can I find a volumetric flask? Post-doc: scoffs Who do you think we are? Chemists? :)

Ironically this is one of the few times were I didn't design the primers and used what was mentioned in numerous papers.

@bobtheowl2 Hm.. This may be a last resort thing (and may take a million years) but you can always send an e-mail to the authors of those papers and see if they can help you optimize your reactions or share with you how exactly they did it.

Primer Tm calculations can vary significantly based on the method used. What I can tell you, is that the Tm really depend on the polymerase you are using for the PCR reaction and for each polymerase there is a set of PCR conditions you have to follow.  As I use Phusion® Hot Start High-Fidelity DNA Polymerase from Finnzymes, I will give you an example with it:
First of all, it is suggested to use the Finzymes Tm calculator to determine the Tms of your primers. Usually the Tms are higher than the ones calculated by IDT. Then, according to the length of your primers, different annealing temperature should be set:

for primers > 20nt, anneal for 10 – 30 seconds at a Tm +3°C of the lower Tm primer
for primers ≤ 20nt, use an annealing temperature equal to the Tm of the lower Tm primer

When calculating the Tm of your primers with the calculator:
Fwd primer Tm is 57.27
Rev primer Tm is 60.21
As they are 20bases long, your annealing temperature should be 57 degrees.
You are right that the annealing temperature shouldn't be higher than the Tm of the primers. I think the problem is that different polymerases and different Tm calculators are used in the papers you are referring to. I can discuss other PCR optimizations but let me know first whether the problem is not just the anneaning temperature.

I like your example and calculation. I guess I didn't think Tm was so polymerase specific before. Coincidentally it ends up at the same annealing temperature that I tried though.  Unfortunately the taq I am using gives very little information (and not an online calculator) in regards to choosing temperatures. I am close to ordering a new mastermix anyway, so I will likely try a different brand then. But as for my current problem there are enough variables that I plan to try the same annealing temperature again and if that fails completely then I may look at what @jp89 suggested also.

You can also contact the authors of some the papers you are trying to reproduce and ask them about the specific conditions they used. You shouldn't spend much time troubleshooting this by yourself.

Hey what happened with your experiment?

You can always use a lower Tm, but then you sacrifice specificity. In situations like these, I like using a gradient thermocycler to test a range of annealing temperatures to find the optimum.


text:
What evidence gives clues to the physiological basis for conversion disorder?
Conversion disorder has a set of DSM diagnosis criteria, which, among other things, includes ruling out all neurological disease.
However, as the media has shown us (and one could argue a biased portrayal), many of these young people in Le Roy, NY who were diagnosed with conversion disorder have exhibited tics and starts that are highly reminiscent of Tourette's Syndrome, which is thought to have some basis in pathology of the basal ganglia (and perhaps the thalamus and frontal cortex).
Granted, the issue is being looked into as having an environmental cause, so I can understand how the diagnosis may be reshaped, but I'm more curious about the initial diagnosis of "mass hysteria".
If this syndrome causes real physical symptoms and yet is "psychogenic", through what physiological means is the disease acting?  Why would ruling out a neurological basis be a valid criterion?

It's usually important to rule out other medical conditions when considering many psychiatric diagnoses due to similarities in symptoms between them. There are many examples but I'm not sure if it's appropriate to note them here as a lot of symptoms have to be considered in a clinical context and might be mistaken as medical advice. It's also important to note that concurrent medical and psychiatric conditions frequently occur with individuals diagnosed with conversion disorder.(2).
Conversion disorder was previously combined with somatisation disorder and was known as hysteria.(2). Conversion disorder is a diagnosis of exclusion where the symptoms are not a result of:

neurological or other medical condition;
the effect of a substance; or
cultural behavior or experience.(1).

The key is that these are not intentionally or medically driven symptoms but rather physical manifestations of psychological needs ("unconscious manifestations of emotional conflict"(3)). Psychoanalytic theory suggests that "conversion disorder is caused by repression of unconscious intrapsychic conflict and conversion of anxiety into a physical symptom"(2).
In terms of physiological basis of conversion disorder, it's been suggested that an imbalance in metabolism between the dominant and non-dominant brain hemispheres; and impaired communication between the two may be an issue.(2). There are some other points you can also read at MedScape.

Ferri. Ferri's Clinical Advisor. 2012. Mosby.
Sadock. Kaplan & Sadock's Synopsis of Psychiatry. 10th ed. 2007. Wolters Kluwer.
Jacobson. Psychiatric Secrets. 2nd ed. 2001. Hanley and Belfus.


text:
Why do dendritic cells have CD4/CD8 on their surface?
Why do dendritic cells have CD4 or CD8 antigens on their surface? What is their function without the presence of a T-cell receptor?

There is no direct connection between CD (cluster of differentiation) receptors and T-cell receptor (TCR).
CD-receptors are used to label and distinguish different cells belonging to immune system: macrophages, T- and B-cells etc. Dendtritic cells play a significant role as antigen presenting cells and belong to vertebrate (and human) immune system and thus bear certain CD receptor.
These cells participate in the process of learning a new antigen by the immune system. During the very first phase the antigen is taken up by these cells, cleaved and processed. Depending upon the antigenic properties of the molecule it can be recognized as a valid antigen. In this case dentritic cells participate in the process of antigen presentation, where this new antigen bound to the MHC receptor is expressed on the cell membrane.

TCR is the protein that binds to this complex (MHC + antigen) and as long as this binding takes place the signal about antigen is propagated further to the immune system (leading to formation or augmentation of immune response depending upon the cell type which connects to this complex).

This doesn't answer the question.
The classic explanation for the function of CD4 is that it's a co-receptor for MHC II (along with TCR), and likewise CD8 helps TCR bind to MHC I.
Since DCs don't express TCRs but do express CD4 and CD8, the function of these proteins on DCs is interesting!

I believe rather than canonical involvement in T cell activation the question was what role does CD4 and CD8 have in a non-T cell population. Here is an article that provides some interesting insight:
CD4 and CD8: an inside-out coreceptor model for innate immune cells
http://www.jleukbio.org/content/86/2/251.full

While the linked article may be useful, you should add some explanation in your answer rather than just providing a link.


text:
At what stage of meiosis does "first meiotic arrest of oogenesis" occur?
An exam question asked what stage of meiosis corresponds with "first meiotic arrest of oogenesis". I can't work out the answer from the wiki page - can anyone explain which step this refers to?

Prophase of first division. Check Wikipedia.

Well, the answer in one line is....... Diplotene of meiosis 1......or simply prophase 1

@JasjeetSingh I think Jasjeet's answer is very good because it is answering exactly what I am asking for. I do not agree with the decision to move his answer to a comment here. - - You should at least offer him a reason why you did the change. He is new here, and the more important, it is. - - Again, I really like his answer with open perspective indicated by ... in the topic because it is open.

When females are in their mother's womb all their Oogonium (plural Oogonia) are being made, they they undergo mitotic divisions to become a primary oocyte. Then, the primary oocytes start to undergo meiosis I -  but meiosis I is arrested. This is the first meiotic arrest. Meiosis I continues when a female hits puberty, every month one or more primary oocytes undergo meiosis I and create secondary oocytes. These secondary oocytes will then  start the second meiotic division, but this second meiotic division is arrested as well. It is arrested for about 24 hours, waiting for a sperm to fertilise it in the Fallopian tubes. The only time an egg (or in medical terms - secondary oocyte) will complete meiosis II is if a sperm penetrates the egg, and then it is called an ovum, which develops into a zygote and a then foetus.
Therefore, the answer to your question will be - the first meiotic arrest in oogenesis will occur from the time the primary oocytes are created in the womb, until a female reaches  puberty. starting puberty until menopause every month one or more primary oocytes will mature and complete the first meiotic division.

Could you recommend a book that explains oogenesis in human beings in details?

Meiosis consists of two divisions. Both are somehow similar to "ordinary" type of cell division - mitosis, but there is no DNA replication between them. As mitosis, each of two meiosis divisions might be divided into 5 stages:

Profaze (condensation of chromosomes, formation of microtubular spindle apparatus between two centrosomes)
Prometaphase (the nuclear membrane desintegrate and chromosomes and microtubules attach to kinetochores of chromosomes)
Metaphase (The chromosomes align at the metaphase plate)
Anaphase (segregation of chromosomes)
Telophase (restoration of nuclear membrane, cytokinesis)

The first division is crucial for reducing number of chromosomes. The prophase is subdivided to following stages:

Leptotene (condensation of chromosomes)
Zygotene (homologous chromosomes form tetrads )
Pachytene (crossing over)
Diplotene (chromosomes separate a little, sister chromosomes remain bounded in chiasmata)
Diakinesis (futher condensation of chromosomes, the nuclear membrane desintegrates)

In animals the function of meiosis is producing gametes. In case of oogenesis (in human) this process starts during prenatal development. Between 12-th and 25-th week of female fetus development cells called oogonia become primary oocytes and enter meiosis, but become arrested in stage of dictyotene, which is prolonged diplotene of prophase of first division. Then they wait 12 up to 50 years (too long waiting increase risk of chromosomal disjunction disorders such as Down syndrome in children of old mothers), covered by a layer of cells - primordial follicle. At the beginning of each menstruation cycle one or a few of the follicles become growing (the follicle cells divide, but oocyte is still waiting). At the stage of Graafian follicle the follicle is about 75 times bigger and there is a cavity full of liquid between oocyte and surrounding cells. The hormone signal - LH from pituitary gland - brakes the meiosis block, the primary oocyte divide into secondary oocyte and small first polar body (which quickly degenerates). At this time the follicle breaks - its ovulation. The oocyte starts second division, but stops at the metaphase. This second arrest ends when sperm cell penetrates into oocyte. The second, small polar cell is released and haploid nuclei of ovum and spermatozoon fuse together.
more:
http://www.ncbi.nlm.nih.gov/books/NBK10008/

very well written, I was confused by the subphase of prophase. Need to study them to undertand wiki better. Thank you!

Lol, I just noticed that Graafian follicle is also arrested in stage of dictyotene that is subphase of prohpase II. So the stage of meiosis of Graafian follicle is prohpase II. - It seems that similar analogy works in different arrested stages: always being in the accumulating stage i.e. prophase.

@Masi, Graafian follicle is just next stage of development of primordial follicle.

You jump a bit. After primordial follicle comes Primary follicle, then secondary follicle and finally Graafian follicle. So the next stage of development of primordial follicle is Primary follicle in my opinion.


text:
How exactly does long-term tension (over months) build up in the ligaments, tendons, muscles?
And is there any basis for believing that massage relieves that tension?

Can you explain a little more? What do you mean by "tension"?

Hm, here's the thing: I'm not even sure what that type of tension means. It's just what massage practitioners say when they massage one's sore muscles and tendons (and it works, at least temporarily).

So, do I understand right that you mean massage by "tension"? Not static tension or something similar?

oh, i mean, the type of tension that massage relieves.

Related: What is the difference between muscle tension and muscle tightness?

Tension is not a quantifiable thing, rather an abstract concept to describe feelings of stress in muscles.  I think I see what you are getting at but I would separate it into two questions.
"Is massage provably beneficial to muscles under physically induced stress?"
Emphatically yes, however there are so many different types of massage, some are more medically viable than others.  Most massage stimulates muscles to encourage a release of tightening, much like exercise does, though I would assume that there's also a psychosomatic that plays a significant role as well due to human contact.
The other question, more the point "Are massage therapist's claims about relief true?"
Some are and some aren't.  Unless it's by a medical professional (prescribed physical therapy for instance) they can claim whatever they like.  "Reiki contributes to your body balance and wellness by attuning your energy"  This can not be proven, but not really disproven either, so they can claim it all they want though it's purely anecdotal (if not outright fabrication on the part of less ethical individuals.)
In summary: Massage has tangible benefits, but if the claims of the therapist sound too good to be true, they probably are.

Thanks for the reply. Hmm, how exactly is "tightening" measured? And what is biologically involved in "tightening"?

@InquilineKea Have you found any information regarding your question on tightness measurement? I was wondering the same: How can I quantify muscle tightness?


text:
How do caspase proteins kill a cell?
Wikipedia just says...

The active effector caspases then proteolytically degrade a host of
  intracellular proteins to carry out the cell death program.

Okay, but what parts of the cell do they cleave up? And what happens to the rest of the cells' internal components, especially the parts that don't get cleaved up?

Caspase do not directly kill the cell, but rather activate a process known as apoptosis, or programmed cell death. The programmed part is there to distinguish it from other types of cell death, such as necrosis, which are more aspecific death processes.
Coming back to caspases, they are a series of proteasis, that can activate in cascade in response to a pro-apoptotic signal.
To simplify matters a lot, the pro-apoptotic signal first activates initiator caspases, such as caspase 8, 9, 10 (plus a series of other proteins).
These, in turn, cleave other effector caspases, which are the ones who effectively do the dirty job: caspase 3, 6, and 7.
Now there are many things happening at the same time (see this PDF from AbCam to get an idea of the complexity of the system).
At the nuclear level you have, for instance:

activation of DNA cleaving enzymes, such as CAD (caspase-activable DNAse), which is normally inactive, due to binding to its inhibitor I-CAD. The latter is a target of effector caspases and its degradation causes CAD to go in the nucleus and starting fragmenting DNA.
cleavage of PARP (Poly(ADP-ribose) polymerase), a nuclear enzyme involved in finding and repairing single-strand breaks on DNA.
cleavage of lamins (by effector caspases + other proteases), proteins that are important for the formation of nuclear lamina, and stability of the cell nucleus
cleavage of U1, a nuclear protein necessary for processing of mRNA.

Very complex events also happen at the mitochondria level: here you have a series of protein, which belong to the Bcl-2 family that control apoptosis mostly by regulating the levels of Ca2+ in the cell. There are 25 members of this family, that can be divided into two "sides": pro-apoptotic proteins such as Bax, Bak, and BAD and anti-apoptotic proteins such as Bcl-2, Bcl-xL, and Bcl-w.
The functioning of the Blc-2 proteins is very complex and I am not up-to-date with the last literature but to simplify, essentially what happens is that when the balance between anti-apoptotic and pro-apoptotic proteins is shifted towards the pro-, there is:

liberation of cytochrome c from the mytochondria into the cytoplasm, which can activate effector caspases.
induction of MPTPs (Mitochondrial Permeability Transition Pores), proteins which increases mitochondrial permeability which causes all sorts of trouble, eventually leading to swelling of mitochondria and loss of their function

Different events also bring to an increase in cytoplasmic calcium concentration, which can, for instance, induce the activity of calcium-activated endonuclease or other pro-apoptotic calcium-dependent proteins.
This is far from being an exaustive list of what happens, but it gives you the idea of the complexity of the system.


text:
Why isn't the p16-INK4a gene involved in apoptosis expressed in heart or liver tissues?
New York Times article explains how killing p16-INK4a positive senescent cells can help keep the surrounding cells vigorous.
So here's my question: why is p16-INK4a expressed in most cells other than heart and liver cells? What would happen if we knocked it out everywhere?

do you have a reference for CDKN2A (p16-INK4a) not being expressed in heart/liver tissues? On GeneCards it looks to me like it has been found to be expressed there.

That's a good question. The Nature paper referenced in the NYT article says it, but with no citation, and their tissue work backs it up. The GeneCard data does run counter to that, though. I'd add the caveat that the Nature paper is talking about mice, and mice handle senescence differently than humans do. For one thing, they don't turn off their telomerase.

p16-INK4a is a part of a very important checkpoint mechanism. It's the "bad guy" in the context of aging because it induces senescence, and too much senescence leads to aging-related  tissue degradation.
But senescence is important. It's one of the responses cells take when something goes wrong-- DNA damage, viral infection, telomere depletion, that sort of thing. Senescent cells have stopped proliferating. We have a word for cells that don't stop proliferating, and that word is "cancer". So, p16-INK4a is a major tumor suppressor. A universal p16-INK4a knockout would have a much harder time shutting down the proliferation of cells that had undergone DNA damage, and would therefore be much more prone to cancer. You'd have very young-looking tissues filled with tumors.
So, the headline question is why INK4a is not expressed in the heart or liver if it's so important. This is speculation on my part, but I think it's because those tissues are especially prone to being damaged by fibrosis, and a build-up of senescent cells would lead to increased fibrosis. Senescence is just one possible response to DNA damage, though. Another is apoptosis. If the senescence-induction pathways aren't active in heart and lung tissue, I'd expect the apoptosis-induction pathways to be pretty active.

nice answer; care to elaborate/speculate further on why senescence in favourable over apoptosis in other tissues? Or could the removal of senescent cells simply be an un-selected-for trait (by this I mean that reproduction has generally happened prior to the buildup of senescent cells)

Yeah, that's an interesting question. I'd say main advantage of senescence in most tissues is that the cell gets to hang around and do its job. If it goes through apoptosis, it's going to need to be replaced. Senescence as a strategy, then, would keep overall proliferation rates lower in the tissue as a whole, which could have upsides, like limiting the potential for errors to creep in. Which one gets selected for in which tissue could definitely be influenced by the balance of those factors compared to reproduction time.


text:
Why are beta-galactosidase proteins overexpressed in senescent cells?
Wikipedia explains that it's a hypothetical hydrolase enzyme that catalyzes the hydrolysis of β-galactosides into monosaccharides only in senescent cells.
I'm just wondering - what causes it to be overexpressed in senescent cells - to the point that it often becomes a biomarker of senescence? And what exactly happens to the particular cell when you catalyze the hydrolysis of more β-galactosides (like lactose) into monosaccharides?

Looking at the articles referenced in the Wikipedia article, there's probably no direct physiological link between senescence and beta-galactosides. Lee et al (2006) and others before them have shown that the "hypothetical" protein is just regular lysosomal beta-galactosidase, which is present in higher concentrations in aging and stressed cells because the number of lysosomes increase under those conditions. There's a collection of references in the Discussion section of the Lee paper that delves deeper into the aging-lysosome connection.
I'm well out of my depth by this point, but if I were going to take a wild guess I'd suggest that lysosomal upregulation could be part of a stress response involving autophagy (i.e. the cell breaking down and recycling intracellular materials to meet critical demands), though I don't know the specific connection to aging. As far as beta-galactosides go: if you have any hanging around, you get to eat them, is all, I bet. I bet the references in Lee would tell you if I'm on track or not.


text:
How long will a vegetable live for after being harvested?
I understand this might depend on the types of vegetables, but is there an average or studied specifics? Does it die immediately? Is there a way to precisely diagnose death in plants? If so, what are the conditions for it?

Great question :-)

The short answer is that as long as the vegetable/fruit is fresh looking - i.e. the cells have not disintegrated - they will be respiring, many cells will be functioning quite normally, and the plant is still technically alive. In cases where the part of the plant we treat as a vegetable is a part intended for reproduction (e.g. a seed, or a tuber like a potato) the plant will keep growing.
The point at which the plant dies is not clearly defined like it is in animals, but generally if you can still eat it, it's still alive.
Death in plants is quite different from that in animals - we refer to it as senescence. The key difference is that it happens to tissues and organs which can die and separate from the organism. Individual leaves can die without the plant's health being affected. Once this has happened to all the parts, the organism is considered dead, but if there is any respiring tissue left, it's still alive.

Thank you for the answer. As a followup question: when you say " the cells have not disintegrated - they will be respiring, many cells will be functioning quite normally, and the plant is still technically alive", how dos this differ from animals? Is it the case that supplies for plants are distributed to cells in a different way, in such a way that if the animal's death occur, no nutrients will reach the cells and therefore they will all die together with the animal?

@Hector That's exactly right: animals generally rely on the coordination of their processes by a central system, involving for example the nervous system and the circulatory system. Those systems are vulnerable to interruption, and that's what we call death in animals. Plants on the other hand do not have their essential processes coordinated centrally; they are controlled by environmental forces (gravity, thermodynamics, etc.) which generally are not subject to sudden termination.

To continue..  Because plants grow iteratively, by repeatedly generating similar parts, there is no individual organ which is essential to the functioning of the rest. Contrast that with the determined growth of animals, where there is one head and if the head is removed, nothing else can happen. The growth pattern and the control system are interrelated.

Very interesting. Thank you again for answering.

@Richard Smith, that is a very good answer, and I would vote it up, but unfortunately, I used all of my votes for today. Is the fleshy part of fruit alive?

@jmusser thanks! Yes, the fleshy part is alive, i.e. respiring until it starts to look necrotic or rotten.


text:
Is it the case that all changes in phenotype during life are not inheritable?
This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.
Regarding Evolution, nothing, absolutely nothing, that a person does to herself in life can be genetically inherited. It does not matter how much this person drinks, the changes they do to their body,  how dark their skin gets over life etc. Such changes can not be transmitted to their offspring in any way, correct?
*Summary:*Is the assertion "You can not change in life what will be genetically inherited in any possible way" true?

Yes, short of drinking mutagens every day to deliberately induce mutations

The assertion "You cannot change in life what will be genetically inherited in any possible way" is true, as you cannot (healthily) change the DNA in your germ cells.
However, the assertion "You cannot change in life what will be inherited in any possible way" is wrong, because of epigenetics. Parts of your DNA are marked (in different ways), and this can be inherited and have an effect. E.g. the only causal difference between these two mice is the diet of their mothers:

Image source and a further explanation: Nutrition and the epigenome.

–1, the paper didn’t actually provide evidence of epigenetic inheritance in any meaningful sense of the word, as is the more general conclusion: so far as we know, there is no single naturally occurring case of passing on of acquired traits. This isn’t unthinkable (see Prader-Willi syndrome), but remains yet to be demonstrated. I’ve written my take on the subject on Skeptics.SE: http://skeptics.stackexchange.com/a/7338/82

In general, Darwin's theory has been supported over and over again by experiments - our modern understanding of evolution is fundamentally what Darwin suggested. However, apart from appreciating many more details than Darwin ever could have, we also now know that Lamarck may not have been so crazy as he was later portrayed.
Inheritance in the Darwinian sense involves the digital information of DNA, i.e the sequence of bases. But we also know that DNA can be altered structurally - i.e. in the way it folds, or whether bases are methylated - and that these structural alterations can affect the expression of genes. In some cases, these epigenetic modifications can be trans-generational; they can be passed on to offspring.
Here are the mechanisms that I know of (perhaps others can expand on this):

X-chromosome inactivation (XCI): this is when one of two copies of the X-chromosome in females is completely inactivated by being packed into heterochromatin, preventing the DNA from being transcribed. Which chromosome (the maternal or paternal) is deactivated initially is random, but the decision can be inherited by all daughter cells. Skewed x-inactivation is when a cell very early in the cell line passes on its XCI decision, and can result in a particular phenotype being activated in a whole organ or tissue (such as patches in tortoiseshell cats). It has been shown that in mice and in humans, the somatic cells can sometimes have their XCI decision influenced by the mother, and that this can lead to early skewing of the XCI in the offspring, thereby passing on a decision about which alleles are present without affecting the DNA sequence.
Parental imprinting: in this case, individual alleles derived from one parent are preferentially activated or deactivated by methylation or histone modification. This change is passed on to the zygote, and alters expression in the offspring. Several human heritable diseases are associated with this kind of modification, such as Prader-Willi Syndrome.
Paramutation: first discovered in maize, this is when the presence of one allele in a genome can affect another allele in a heritable way. I.e. if allele A is present in the same genome as allele B for a single generation, allele A is permanently inactivated so that if you breed out allele B, allele A will not be active in the offspring.

Finally, there is also a phenomenon called structural inheritance, whereby a structural feature of an organism is inherited in a non-genetic way. There is less written about this, so the mechanism is not entirely clear as far as I know, but an example is that the 'handedness' of the spiral pattern on the shell of a protozoan Tetrahymena is inherited without any genetic change (Nelsen et al., 1989).
References:
Nelsen, E.M., Frankel, J. & Jenkins, L.M. (1989) Non-genic inheritance of cellular handedness. Development (Cambridge, England). 105 (3), 447–456.

Is the assertion "You can not change in life what will be genetically inherited in any possible way" true?
  No. Does not seems the case, as other people already replied.

Here, I just want to point to two recent research articles showing evidence against your assertion.
The first, published in Cell in 2010, is from Dr Oliver Rando, and suggests that you are what your father ate, too.

The second, published in Nature in 2011, is from Dr Anne Brunet, and argues that worms can inherit a 'memory of longevity' from long-lived parents.

That last paragraph is completely unnecessary. Anyone who knows what is going on would know this.

The purpose of peer review is not to detect fraud, so the peer review process did not fail 24 times for the same researcher. It's just that a researcher falsified his results. Unfortunately in science, as in all things, people can be deceiving. I don't think it's a reason to be any more skeptical about scientific papers than about anything else, and indeed scientific papers have other characteristics that make them, generally, the most reliable source of information we have.

Infections by a retro-virus (such as HIV) can, at least in principle, be inherited.
These viruses integrate their genome into the host's DNA, and these changes pass to next generations as the cells split. So if a germ cell is infected, all the cells in the child would be.
The question is whether there's a retro-virus that infects germ cells. I don't think HIV does (it can certainly pass from mother to child, but as a "normal" infection, not through the DNA).

There's a related review paper: "Beyond DNA: integrating inclusive inheritance into an extended theory of evolution" (PDF)

Very interesting, although this answer looks more like a comment to me.


text:
What is a good non-fluorescent DNA dye?
Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak signal, even a low emission would disturb the reading.

I don't understand why you want to dye the DNA at the same time as performing the Raman spectroscopy, anything else you put in your sample will interfere in some way during your measurements, I assume. Does the dye need to be specific for DNA, or is a general nucleic acid dye enough? Should it be a non-covalent dye or something your want to specifically attach to a certain position in your DNA?

The Dye is needed to know where to aim. The Signal form the dye can be subtracted by measuring it without DNA. The main thing of importance is that the Signal is not so strong that it overshadows the DNA signal.

One option is to use biotin labelling. Most molecular biology supply companies do kits for this, and supply biotinylated nucleotides.

I accepted your answer, but I don't really know how well it would have worked, as the experiments were never performed after all. (It was a colleagues project, not mine)

Methylene blue? Certainly not as sensitive or specific as other options but it's cheap and does not fluoresce.


text:
What cells would have the CD3 marker on them (other than T-cells)
Do you know of any peripheral blood mononuclear cells that would express any amount (beit low or high) of CD3 on their surface (other than T-cells)?

CD3 is initially expressed in the cytoplasm of pro-thymocytes, the
  stem cells from which T-cells arise in the thymus. The pro-thymocytes
  differentiate into common thymocytes, and then into medullary
  thymocytes, and it is at this latter stage that CD3 antigen begins to
  migrate to the cell membrane. The antigen is found bound to the
  membranes of all mature T cells, and in virtually no other cell type,
  although it does appear to be present in small amounts in Purkinje
  cells. This high specificity, combined with the presence of CD3 at
  all stages of T cell development, makes it a useful
  immunohistochemical marker for T cells in tissue sections. The antigen
  remains present in almost all T-cell lymphomas and leukaemias, and can
  therefore be used to distinguish them from superficially similar
  B-cell and myeloid neoplasms.

Source: http://en.wikipedia.org/wiki/CD3_(immunology)

Purkinje cells are neurons rather than peripheral blood cells

As you know CD3 is

a protein complex and is composed of four distinct chains. In mammals, the complex contains a CD3γ chain, a CD3δ chain, and two CD3ε chains.

Natural Killer (NK) cells have been shown to express CD3 epsilon proteins, but not CD3 delta or gamma.
Also on a side note, there are several other non peripheral mononucleated cells besides Purkinje cells that can express CD3, but mostly in pathological circumstances. For instance Warthin-Finkeldey cells, also known as polykaryocyes, display CD3, although the origin of these cells is not certain (they might be multinucleated T-cells).
(PS: If you want more information on CD3, I found this site very interesting.)


text:
How do you turn a minimal CIF description into a complete one?
I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition.  This page provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.
Maddeningly, I see in my project job history a couple "dictionary" jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):

When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF ("mmCIF") file, nothing happens.
Also under the sketcher, I can severely abuse the "Load Monomer from Library" and it looks like I get the right thing:

However, when setting up the above, it throws "Error: can't read "monomer_lib(code,n..." warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.

If there are other solutions, I'd be interested as well.  I've used PRODRG to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.

Not quite as ideal as I had hoped, but it works:

Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere.  Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return

If it complains it's not found, the CCP4 bin directory may not be in your PATH environment variable.  You can get around this by specifing the full path to the program, e.g.: c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe (may vary with version)

Say "Y" or "A" at the _DOC: prompt for some more files, "N" if you don't care (I generally don't)
At the --> prompts, specify:

the input file, e.g.: file_l: ABC.cif
the monomer: mon: ABC
output file name: file_o: ABC_out

Leave a prompt blank and hit return to start processing.

If it runs successfully it might look something like this:
C:\Users\Nick>libcheck

  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/

  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: libcheck.bat
 _DOC:n

 #
 #      Keywords:
 #
 #FILE_L:   < >  - additional library, " " means without this file
 #MON:      < >  - give info about this monomer
 ... (shortened) ...
 #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
 #                 (only with NODIST = N)

 #---  type "keyword   parameters" and/or ---
 #---  press key "CR" to run program      ---
 -->file_l: ABC.cif
 -->mon: ABC
 -->file_o: ABC_out
 -->
 MON   : ABC
 -------------
 Output file   :ABC_comp
 Input user lib:ABC.cif
 _chem_comp.name "DRUG INTERMEDIATE"

          17          55
 "DRUG INTERMEDIATE"

 -------------
 Keywords:
 HFLAG : Y
 COOR  : N
 LCOOR : Y
 SRCH  : 0
 REF   : Y
 NODIST: Y
 ERROR ==> In the loop containing the item_chem_comp.three_letter_code
 ERROR ==> The number of expected items and the number existing items do not match
 ERROR ==> The number of expected items is    7
  NUMBER OF MONOMERS IN THE LIBRARY          :     1
                with complete description    :     0
  NUMBER OF MODIFICATIONS                    :     0
  NUMBER OF LINKS                            :     0
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  I am reading library. Please wait.
      - monomer"s description
  WARNING : monomer:ABC      - has the minimal description.
  now monomer:ABC      - has complete description.
  I will check it.
 * CIFile  : ABC_out_ABC.cif
 * PDBfile : ABC_out_ABC.pdb
 * Plotfile: ABC_out_ABC.ps
  I am writing new description to
  file: ABC_out.lib

C:\Users\Nick>

It yields the following output files:

(file_o): looks like a CIF file with lots of whitespace and records stripped out
(file_o).lib: the desired, complete definition file
(file_o)_(mon).cif: an even more minimal CIF file with only XYZ coords
(file_o)_(mon).pdb: a PDB file
(file_o)_(mon).ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes.  Can convert it to the easier-to-use PDF format using this http://www.ps2pdf.com/convert.htm, or other tools.


text:
Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?
[Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe.  I'm not interested in debating creationism.]
According to Wikipedia[1]:

In Darwin’s Black Box (Behe 1996) I claimed that the bacterial
  flagellum was irreducibly complex and so required deliberate
  intelligent design. The flip side of this claim is that the flagellum
  can’t be produced by natural selection acting on random mutation, or
  any other unintelligent process. To falsify such a claim, a scientist
  could go into the laboratory, place a bacterial species lacking a
  flagellum under some selective pressure (for mobility, say), grow it
  for ten thousand generations, and see if a flagellum--or any equally
  complex system--was produced. If that happened, my claims would be
  neatly disproven.

[emphasis mine.]
As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications).  [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity[2].]  This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).

Question: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?

Experiments reproducing steps in evolution seem to turn out much easier than I would have expected a priori, e.g. reproductive isolation of fruit flies[3], experimental evolution of multicellularity[4], so perhaps Behe's experiment would also be surprisingly easy to implement.
References:

Wikipedia: Michael Behe
 Blocker A, Komoriya K, Aizawa S-I. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.
 Dodd DMB. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.
 Ratcliff WC, Denison RF, Borrello M, Travisano M. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.

Behe has no concept of the time scales involved: (Douglas Adams, replace space with time)Space is big. You just won't believe how vastly, hugely, mind- bogglingly big it is. I mean, you may think it's a long way down the road to the chemist's, but that's just peanuts to space.

still thanks for asking this question! its the sort of mental exercise that should be done more often.

The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and that it could not have arisen by natural selection. This is theoretically falsifiable, but the experiment he proposed does not provide a good dichotomy - there is a very large chance that he is wrong but over the experimental term of 10,000 or 10,000,000 generations, the flagellum might not arise.
The absence of the flagellum in the experiment is the most likely scenario, and doesn't either support or falsify his claim. It took evolutionary time, something on the order of 1010+ generations, to arise the first time (according to the consensus claim); we could not expect similar complexity to arise for the same purpose under conditions of directed evolution. That's a terrible experimental design: huge resource input, huge likelihood of no result.
To be clear: it is technically feasible, but not a good experiment. He proposed it because he knew that nobody would do it (because it's a bad idea).

Hmm... yes, if we replayed the tape of life, we would see a lot of generations, but (I would expect that) most of them did not contribute towards the evolution of the flagellum (nor its precursors).  Through artificial selection, the number of generations required in the lab should be far less than in nature.  [PS. I don't mean to sound unappreciative of your answer.]

It's true that directed evolution, by definition, is supposed to take a shortcut. But the likelihood of achieving the desired outcome is miniscule in this case, precisely because of the complexity of the organ. And whilst we might skip some of the non-contributory generations, we are talking many orders of magnitude difference between a human lifetime and evolutionary time. Previous directed evolution experiments have never achieved this. By a random evolutionary walk, we might see a simpler solution or none at all in human timescales in the lab.

On the other hand people who have tried looking for complex phenotypes have found interesting results.  These folks got a primitive multicelluar phenotype in about a month.  http://www.pnas.org/content/109/5/1595.long  It would not kill anyone to try a month long experiment for a few liters of culture.  While it would probably not produce a flagellum, its hard to believe that something would not happen.  Negative thinking never discovered anything. This one does not have to be expensive and could be done as a high school science project or in someone's basement.

You may be interested in this paper and a video that summarizes it. It seems to be made quite clear that 1) effectively all of the parts of the flagellum are not original to it, and 2) there is a reasonable evolutionary path (one involving only increment/refine steps) that could have been responsible for it.
The video mentions but doesn't describe experiments that were in support of the proposed model. I assume they might involve refinement or statistical issues of the environment, not the  whole-thing-at-once as Behe outlines. Obviously, if you can show that each step is independently adaptive, then the whole chain is shown to be possible evolutionarily, without trying to set up an experiment where you win the lottery n times simultaneously.
Personally I think the fact that the most awesome thing about the flagellum -- the rotation -- already exists in ATP synthase steals a lot of the flagellum's thunder. :)
Edit (Douglas S. Stones):  Following the above references led me to this paper:

M.J. Pallen, N.J. Matzke "From The Origin of Species to the origin of bacterial flagella" Nature Reviews Microbiology 4 (2006), 784-790. (pdf)

In this article the authors discuss the possibility of designing a lab experiment to reproduce (steps of) the evolution of the flagellum.

Scott Minnich speculated in his testimony that studies on flagellar
evolution need not be restricted to sequence analysis or theoretical
models, but that instead this topic could become the subject of
laboratory-based experimental studies. But obviously, one cannot
model millions of years of evolution in a few weeks or months.
So how
might such studies be conducted? One option might be to look back in
time. It is feasible to use phylogenetic analyses to reconstruct
plausible ancestral sequences of modern-day proteins, and then
synthesize and investigate these ancestral proteins. Proof of
principle for this approach has already been demonstrated on several
NF proteins[69–75]. Similar studies could recreate plausible ancestors
for various flagellar components (for example, the common ancestor of
flagellins and HAP3 proteins). These proteins could then be reproduced
in the laboratory in order to examine their properties (for example,
how well they self-assemble into filaments and what those filaments
look like).
An alternative, more radical, option would be to model
flagellar evolution prospectively, for example, by creating random or
minimally constrained libraries and then iteratively selecting
proteins that assemble into ever more sophisticated artificial
analogues of the flagellar filament.
Another experimental option might
be to investigate the environmental conditions that favour or
disfavour bacterial motility. The fundamental physics involved
(diffusion due to Brownian motion) is mathematically tractable, and
has already been used to predict, for example, that powered motility
is useless in very small bacteria[76,77].

[For readability, I've added some line breaks to the above.  There's too many cited references to list them all.]

[I'm answering my own question, but this seems too important not to include as an answer.]
A long-term E. coli evolution experiment (Wikipedia) was begun in February 1988 by Richard Lenski.  He took 12 initially identical populations of Escherichia coli, and let them grow, having now completed over 50,000 generations.
One striking observation made through this research, is that one sample of E. coli evolved the ability to metabolise citrate, which took over 30,000 generations (see Blount, Borland, Lenski, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli" PNAS (2008)).  This evolutionary step was achieved in a glucose-limited medium, thereby adding evolutionary pressure.  Moreover, their results suggest that a necessary "potentiating change" occurred at around 20,000 generations.
These results demonstrate that significant evolutionary change is possible to observe in the laboratory, and gives a feel for how long it might take for something as complicated as the flagellum.


text:
Do insects' muscles become stronger with exercise?
I am curious to know if insect muscles become stronger with exercise, because I have seen many insects get tired out, but I have never seen one get stronger. They always seem to become permanently weakened from excessive exercise. Do they get stronger like people do?

Would be interested to know how you might "see" one get stronger. As is the case with most wild animals, generally existing (scavenging, hunting, browsing, etc) requires exercise, and barring illness or old age, most animals are likely to be fit, but not fitter than necessary - building muscles becomes a waste of time after a certain point.

There are instances of insect muscle growth in response to increased use. The flight muscles of the tsetse fly (Glossina morsitans) have been observed to grow at a faster rate when subjected to enforced exercise (Anderson and Finlayson, 1976). Also larger mandibular adductor muscles (which power the feeding apparatus), and associated head capsule have been noted for caterpillars and grasshoppers feeding on particularly hard grasses (Bernays, 1986). However these examples occur immediately post-eclosion (i.e. after emergence as adults), and during immature stages respectively. Insect muscle typically grows during larval/nymphal (immature) stages, and often for a brief period at the start of adulthood - known as the teneral period. During immature stages, insects typically have a flexible membrane to allow for tissue growth and expansion, this can also be the case during the teneral period, before the inflexible exoskeleton has fully hardened. However at full maturity, insect growth is limited by the rigidity of their exoskeleton.
As far as excessive exercise is concerned, that some insects may be weakened permanently may be more to do with the fact that their life strategy is different to ours. Due to the vast number of offspring per adult, and subsequent low survival chance of any given individual, there could be an evolutionary advantage for individuals pushing themselves to possibly deadly extremes. This could lead to many deaths, whilst retaining a viable population and thus accelerate the emergence of a population of fitter individuals.
References

Anderson, M. & Finlayson, L.H., 1976. The effect of exercise on the growth of mitochondria and myofibrils in the flight muscles of the tsetse fly, Glossina morsitans. Journal of Morphology, 150(2), pp.321-326.
Bernays, E.A., 1986. Diet-Induced Head Allometry among Foliage-Chewing Insects and its Importance for Graminivores. Science, 231(4737), pp.495-497.

What about the butterfly ripping out from the chrysalis?


text:
What effect does ambient temperature have on the cardiovascular system?
I am sorry if this is not appropriate for this site, but I think it fits so I am asking it here:
I went for a run yesterday, and it was about -8⁰C.  I was wearing a couple pairs of shorts, a t-shirt and a long sleeved shirt, which is not that much, so I went with the idea that I would warm up a lot while running.  After running for a while, I found that I was tired and out of breath much earlier on then I would normally be.  It raised the question:

How does decreasing the ambient temperature affect the cardiovascular system?

There were two things I could think of that might directly affect it.  (1) The fact that my body's metabolism has to work to heat itself, and this takes energy.  However I am not sure how much of a role this plays since running warms you up anyway.  (2) The air being so cold, and entering the lungs, I imagine my body has to work much harder in some way to deal with it.  What exactly happens here, and how is the process different from breathing at 25⁰C?
Also, how much faster would we expect a runner to be able to finish a 10km run when it is 25⁰C outside versus -5⁰C outside?

This question is somewhere between Fitness and Biology. If you're interested in a biological answer maybe you could focus the question more on that. If you want a more fitness-oriented answer I can migrate the question to our [Fitness.SE] site.

@MadScientist: A more biological answer would be better

Your question mismatches your description: as long as you weren't jogging naked outside your body wasn't actually exposed to cold (and provided good warmth insulation by your clothes there wasn't need for excessive heat production). So, are you interested in considering your personal case or an abstract case of people running naked in cold environment? :)

@AlexanderGalkin:  I guess I would be most interested in how breathing changes, and how much work it takes for your body to breath in the cold air.

In relation to the cardio vascular system a combination of adrenaline from exercise and the bodies natural response to the cold causes constriction of blood vessels in the skin and extremities. This helps to reduce heat loss.
The movement from running increases the amount of cold air that runs across your body and into your lungs, which would offset the effect of heat generated from running. According to the article about Thermoregulation in cold conditions on Wikipedia, the offset is great enough to make shivering while standing still a better way to keep warm.

I think you are correct to discount your first point as the cellular respiration proceeding to supply your muscles with ATP when running will produce heat anyway, as you say.
As to the lungs having to work harder in cold conditions, its an interesting proposition.  I would hypothesise that this may indeed be the case:
Gas exchange across the lungs occurs by diffusion.  Fick's law (simplified) states that the rate of diffusion is proportional to the difference in concentrations multiplied by the surface area along which diffusion is occurring, all divided by the length of the diffusion pathway:
$V_d=k\frac{\large a.([C_2]-[C_1])}{\large l}$
In the situation of the diffusion of O2 and CO2 across the alveolar membrane, k is dependent solely on the temperature of the diffusing particles. Therefore the rate of diffusion will almost certainly be reduced in lower temperatures.
The slower rate of diffusion will mean that the body will indeed have to 'work harder' to expel CO2 and take up O2.  This would be achieved by increasing both the hearts stroke rate and the ventilation rate.  This holds true in theory, however I can not say for certain if it would occur in reality as I do not know how greatly Vd (diffusion rate) would be affected by the change in temperature and also crucially how much of a decrease in Vd would be sufficient to initiate the homeostatic responses mentioned above.


text:
How does water buffer a sudden drop in temperature?
A property of water is that it is slow to heat and cool. According to my biology book, some energy from an increase in temperature would spent breaking hydrogen bonds, so that temperature does not rise too fast - helping a cell to maintain homeostasis.
As far as I can tell, this answer does not explain how a drop in temperature would be slowed down by water in a cell. How does water slow down heat loss? Is it just because it is difficult for the heat that is already inside the cell to leave?

This question is about physics rather than biology or biochemistry.

I agree with Marta, this belongs on the Physics SE.

Speaking as a Physics.SE mod I'm sufficiently at sea to not know if this is a good question for our site. Ultimate Gobblement, could you clarify the question a bit?

Are you wanting more than the high specific heat capacity of water meaning that it is a good store of energy, which it releases to keep cooling objects warm (as your question suggests) as a result of thermodynamics?

I know this is probably more a physics question, but I think it is related to biology. If someone would like to move the question, then feel free to. I have edited it so hopefully my question makes more sense now.

I think the updated question is a much better fit for this site, as you put it in a biological context. I think Rory's answer is the right one, perhaps he could expand it into a full answer?

Maybe you want to ask about frost resistance?

Biologists should still know about statistical thermodynamics.

From pure biophysical viewpoint the question
"Why does water buffer sudden temperature changes?" can be answered in the following way:
Water has relatively high specific heat capacity. This is the measure of the energy required to raise the temperature of one kilogram of a substance by one kelvin without a change of state occurring. "Relatively high" means that water can absorb more energy without noticeable (for the cell) increase in temperature.
Here are some heat capacity values from the above-linked Wikipedia article:

Animal (incl. human) tissue   3500 Jkg-1
  Water at 25 °C    liquid  4181.3 Jkg-1
  Methanol  liquid  2597 Jkg-1
  Ethanol       liquid  2440 Jkg-1
  Paraffin  wax solid   2500 Jkg-1
  Graphite  solid   710 Jkg-1

Water has relatively high thermal conductivity. This means that the absorbed heat is quickly distributed over the complete cell volume, leveling down the focal temperature increases in cell. Here are again some values for comparison:

Water 0.6 Wm-1K-1
  Wood 0.2  Wm-1K-1
  Paper 0.05  Wm-1K-1
  Glycerol 0.3 Wm-1K-1

The follow-up questions:
"Why does water have relatively high heat capacity?" and "Why does water have relatively high thermal conductances?" are not within the scope of this site. However, here exactly comes your explanation with hydrogen bonds in play (from Wikipedia):

Hydrogen-containing polar molecules like ethanol, ammonia, and water
  have powerful, intermolecular hydrogen bonds when in their liquid
  phase. These bonds provide another place where heat may be stored as
  potential energy of vibration, even at comparatively low temperatures.
  Hydrogen bonds account for the fact that liquid water stores nearly
  the theoretical limit of 3 R per mole of atoms, even at relatively low
  temperatures (i.e. near the freezing point of water).


text:
How do I clean phenol contaminated RNA without losing any of the sample?
I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went into obtaining them (harvesting thousands of miniscule leaves, one from each plant, to get the required mass).
I extracted the RNA with TRIzol and chloroform. Nanodrop showed excellent yield as you would expect for actively growing young tissue, but some of the samples had really low 260/230 ratios. I know this suggests phenol or salt contamination, but what can I do to clean the samples without losing any of the precious RNA? And how can I avoid the contamination in the future?

You can clean up phenol by washing with choloroform, and then doing an isopropanol precipitation followed by a 75% EtOH wash (let me know if you'd like an exact protocol).
To avoid contamination (and sample loss), you have to be meticulous in your pipetting (which you'll get better with practice). You can always use those phase-lock tubes which basically jams a solid gel between the aqueous and organic phases so it's a lot easier to pipette.

Which bit of pipetting is the crucial part? Is it the removal of the clear upper phase after centrifugation? If so - do most people leave a bit of the upper phase behind so as to avoid contamination? I was trying to get every last drop!

@RichardSmith Yeah the pipetting of the organic/aqueous phase is crucial. It depends on (1) how good you are at pipetting, and (2) how "precious" your samples are. Of course, if you're more meticulous about getting as much sample you can get, there's a tradeoff between yield vs. purity. If I can spare some sample, I usually leave just a tiny bit to spare myself from touching the junk in the interphase between the two layers.

I must not be as good at pipetting as I thought! Thanks very much for your answer. I'll make sure I get better at pipetting and in the meantime I'll leave a safe amount of the aqueous phase behind.

@RichardSmith It might've not been completely your fault. The standard procedure is to clean up the RNA with isopropanol and Ethanol, which it didn't seem like you did. Once you do that, you should get super clean RNA even if there was a bump in your pipetting.

I did clean with isopropanol and Ethanol, and then Nanodropped afterwards. I take full responsibility!

@jp89, From what I understand the IPA and Ethanol cleans only effectively take care of the salts. The Phenol Choloroform extraction does a much better job with the removal of proteins. Possibly you could take some of the interphase and clean again. The phenol will affect your columns and affect your yields.

Also to get rid of all traces of phenol, try extracting with ether.

An ethanol precipitation should work. But I have had great success using the Qiagen RNA cleanup columns, which are in my opinion easier.  Here is a URL to see the RNA cleanup columns Qiagen offers:  http://www.qiagen.com/products/rnacleanupconcentration/default.aspx
Also in the future you should consider using PhaseLock tubes:
http://www.5prime.com/products/nucleic-acid-purification/organic-nucleic-acid-extraction/phase-lock-gel-.aspx
That saved me from having your exact problem many times over.

Thanks very much for the answer and the links. I'll keep the PhaseLock tubes in mind - I take it with the PhaseLock I don't need the cleanup kit?

Oh, and welcome to biology.SE :)

Thanks. Just started on the Home Brewing.SE and saw there was a biology one as well. Seems like a good idea. ;-)


text:
What's a good reference for choosing histological staining chemicals?
It's often difficult to find the appropriate or best stain to use when I want to examine a new type of tissue. I think that's partly because many histological techniques were developed a long time ago, so the papers don't turn up in Google Scholar. Is there a standard reference which links tissues, cell types or states and their corresponding best stain?
I'm mostly interested in a reference text or website covering plant histology, but general references are welcome too.

Did you try the websites of vendors? They usually want this kind of info front and center so people buy from them.

Vendors tend to expect you to already know what chemicals you want. I'm looking for something which covers modern (e.g. fluoro) histology as well as traditional (e.g. nuclear stains, differential stains).

If you want to go way back, google books has Methods in Plant Histology (Chamberlin, 1905) with a PDF. It details stains and the tissues they are used for and even has a section titled "Selection of a Stain."


text:
Why do some plant species have lobed leaves, while similar species in the same habitat don't?
Some plants have lobed leaves, like the English oak (Quercus robur), while other plants growing the same deciduous woodland habitats, and very often growing alongside oaks, such as the European beech (Fagus sylvaticus) don't have lobes. Here are two two leaves side by side for comparison:

These two species should be subject to most of the same evolutionary pressures. Why would one evolve lobed leaves, whilst the other has only tiny serrations?

Could I interpret this question as asking what is the function of lobes on a leaf?

The answer to that question could constitute part of the answer to mine, but a good answer will also explain why it might arise in one species and not in another, despite them both having similar evolutionary pressures.

This is a question for which, I think at the moment, we don't have a clear answer.
It is important to bear in mind that the leaf plays a number of important roles in the plant (photosynthesis, thermoregulation etc.) so leaf shapes probably evolved through a process of successive trade-offs. This may make it difficult to identify the exact selection processes operating on any one species. In contrast, something like the eye has a well-defined single function, which in principle at least, makes it easier to understand the link between form and function.
From Niklas (1988):

Life history and optimisation theory suggest that the number of
  phenotypic solutions that allow for different equally successful trait
  combinations increases as the number of trade-offs increases – a
  conclusion that applies to traits within the leaf (e.g. for shape) as
  well as to leaf–branch relationships.

However, there are a  number of ideas to explain leaf shape diversity which include:

Thermoregulation

It has been shown that by adding lobes to leaves, the rate of heat transfer across a leaf is greater than that of an unlobed leaf of the same area (e.g. Gurevitch and Schuepp 1990). So, lobed leaves may be selected for under certain environmental conditions.

hydromechanical constraints

Lobed leaves may have greater hydraulic efficiency. For smaller veins, hydraulic pressure increases as they present an increased resistance to water flow. This places stress on the deliate outer leaf tissues. If  lobed leaves have relatively less mesophyll tissue than large, highly conductive veins, they may have reduced hydraulic resistance compared  unlobed leaves (Sack and Tyree 2005).

optimization for photosynthesis
adaptations against herbivorous animals
random (non-selected) variation. This is a possibility, although probably unlikely due to the importance of the leaf in plants.

So, some or all of the above possibilities (which are not necessarily mutually exclusive) may shape the leaves of species which may appear to have undergone very similar selective pressures.
This is a good read by Nicotra et al. (2011) which summarizes the state of play.
Gurevitch J, Schuepp PH (1990) Boundary layer properties of highly dissected leaves – an investigation using an electrochemical fluid tunnel. Plant, Cell & Environment 13, 783–792. doi:10.1111/j.1365- 3040.1990.tb01094.x
Nicotra et al., The evolution and functional significance of leaf shape
in the angiosperms, Functional Plant Biology, 2011, 38, 535–552
Niklas KJ (1988) The role of phyllotactic pattern as a developmental constraint on the interception of light by leaf surfaces. Evolution 42, 1–16. doi:10.2307/2409111
Sack L, Tyree MT (2005) Leaf hydraulics and its implications in plant structure and function. In ‘Vascular transport in plants.’ (Eds NM Holbrook, MA Zwieniecki) pp. 93–114. (Elsevier Academic Press: Burlington, MA, USA)


text:
Does cooking ginger reduce its anti-nausea effect?
There seems to be strong evidence to support the hypothesis that eating ginger helps reduce nausea e.g. during pregnancy (e.g. Vutyavanich et al.).  It seems that gingerol is the active ingredient in preventing nausea (cf. Qian et al.).  Wikipedia writes: "Cooking ginger transforms gingerol into zingerone...".  Presumably, zingerone does not affect nausea.
Question: Does cooking ginger reduce its anti-nausea effect?
A Google search will reveal numerous suggestions for giving ginger tea to pregnant women to help with morning sickness.  But boiling the ginger could conceivably defeat the purpose of taking the ginger in the first place (and any effects are primarily due to the placebo).
There's an article (Basirat et al.) which describes an experiment in which biscuits with ginger were given to patients (instead of ginger tablets), although their results alone have not convinced me one way or the other.  The authors conclude that their results indicate an anti-nausea effect, but some of their tests do not match that conclusion (i.e. a placebo was comparably effective).  Also, the group given the ginger biscuits started off with worse conditions on average.

Good news! Some Australians have published on the stability of aqueous gingerol at elevated temperatures: http://onlinelibrary.wiley.com/doi/10.1002/jps.1116/full
Gingerol turns out to be stable enough to make a cup of tea with at neutral pH. They also note that gingerol and its primary decomposition product form a 50-50 mixture that doesn't degrade further over shortish time periods, and that the decomposition product is probably restored to gingerol in the stomach's acidic pH -- so you're good to make your tea, and probably to hold on to it for at least a few days.

Excellent!  That certainly answers my question.

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


text:
If I put a cup over a spider, and leave it there for a day, will the spider survive?
Will it travel more slowly since it hasn't had food for a day?
What if I left the cup there for longer?

Just solely in terms of not having food (ignoring the importance of O2 that Ramkryp has pointed out), spiders don't necessarily have to feed on a daily basis anyway.  It's not the same species of spider as you ask about in your question, but consider:

The metabolic and water evaporation strategies in spiders may be part of a set of physiological adaptations to tolerate low or unpredictable food availability, buffering spiders against environmental fluctuations such as those of the high mountains of the central Andes. The aim of this study is to analyze experimentally the variations in metabolic rate and the rate of evaporative water with food and/or water restriction in a high mountain mygalomorph spider population (Paraphysa sp.). We found that the low metabolism of this spider was not affected by water restriction, but its metabolism was depressed after 3 weeks of food deprivation.

from Canals M, Figueroa D, et al (2011). Effects of diet and water supply on energy intake and water loss in a mygalomorph spider in a fluctuating environment of the central Andes. J. Insect Physiol, 57(11), 1489-94.
The biochemical makeup of the spider may be radically different than most other animals, and breaking down energy stores must take place over a longer timecourse.

To answer the first part of your question: it is extremely unlikely that the spider will die or be weakened after just one day.
Wolf spiders (Lycosids) are all predators. Due to variations in prey populations, and low efficiency of consumption at higher trophic levels, they are subject to inconsistent and unpredictable food supply (Greenstone and Bennett, 1980). They are very well adapted to this lifestyle and consequently, long periods of starvation often yield no behavioural changes (Persons, 1999). It is highly unlikely that the spider will die after just one day: Anderson, (1974) observed no changes in activity after starving Lycosa lenta (a species of wolf spider) for 30 days; and Tanaka and Itô, (1982) observed Pardosa astrigera (another species of wolf spider) living for up to 54 days of starvation. Age and sex of the spider are more likely to affect its behaviour and performance than food or oxygen availability (Persons, 1999).
As for oxygen consumption, Greenstone and Bennett, (1980) measure an oxygen consumption of 100µL/hr for wolf spiders. Assuming that your cup is of the size of the unit of volume of the same name, the cup (~0.237L), a small calculation (see figure) shows that there will be enough oxygen for the spider to survive for over 98 days. The oxygen concentration within the cup may decrease as it is used by the spider, however this is likely to have a minimal effect as a cup placed on a surface is unlikely to be hermetically sealed.

In short, oxygen availability is unlikely to have an effect on the spider before other limitations (such as food) are reached. However neither of these effects are likely to cause behavioural changes during the first month.
References

Anderson, J.F., 1974. Responses to Starvation in the Spiders Lycosa Lenta Hentz and Filistata Hibernalis (Hentz). Ecology, 55(3), pp.576-585.
Greenstone, M.H. & Bennett, A.F., 1980. Foraging Strategy and Metabolic Rate in Spiders. Ecology, 61(5), pp.1255-1259.
Persons, M.H., 1999. Hunger effects on foraging responses to perceptual cues in immature and adult wolf spiders (Lycosidae). Animal Behaviour, 57(1), pp.81-88.
Tanaka, K. & Itô, Y., 1982. Decrease in respiratory rate in a wolf spider, Pardosa astrigera (L. Koch), under starvation. Researches on Population Ecology, 24(2), pp.360-374.

Your assertion may be true but the cup contains only about 20% oxygen at sea level. You have to throw in a factor of 0.2, right? That's only about 19 days...

different but related: How much energy does a small spider expend per day just waiting for its web to vibrate? in that there may be at least a rough relationship between the rate of conversion of O2 to CO2 and caloric consumption.

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


text:
How do you see the stage of the second meiotic arrest in oogenesis in the given video?
My old question raised this new question. After reading this page I can say now that metaphase is the stage in which the second meiotic arrest occurs within oogenesis:

The oocyte is arrested again in the metaphase of the second meiotic
  division.

It is difficult to visualize the thing in my head. I could not find a video of specifically for oogenesis but probably the general model for meiosis holds true. The problem I am having is that I cannot see the arresting steps in this general meiosis video.
How do you see the second meiotic arrest of oogenesis in the above video?
I cannot even see clearly the first meiotic arrest. I only know that it is in prophase for the first and metaphase for the second.

I seem to understand the thing now.
The video is utterly simplified for animal cell meiosis I and II.
In oogenesis, you get after every anaphase one cell with very little cytoplasm, polar body, and another cell with much cytoplasm. In the video, the amount of cytoplasm is equal so the thing is idealized.
The video is better to explain male gametogenesis: spermatogenesis, since the amount of cytoplasm does not differ after each anaphase.
The video is too going too fast to teach you oogenesis, since in reality the things are arrested rather long time. The second meiotic arrest in oogenesis can lasts 12 - 50 years starting after puberty. The rupturing secondary oocytes lasts then again less in the second meiotic arrest of oogenesis, since they start to develop into ovum after the monthly release.


text:
Why does scar tissue change color?
I was wondering why, when you are cold, scar tissue turns bluish or purple while original skin stays the same color.
The only thing I can think of, is that maybe scar tissue gets less circulation than regular skin, so when it gets cold it restricts circulation.

The main mechanism behind the scar changing its color is the dilation of blood vessels within the scar tissue. The dilated vessels lead to the congestion of blood flow. The red blood cells moving more slowly leave more oxygen due to its diffusion to the tissue and the hemoglobin -- the oxygen holding protein -- changes its color from scarlet (bound to oxygen) to cyan (released/bound to CO2). Since scars are not covered by skin, the blood vessels are clearly visible here and you see this characteristic color.
The triggering mechanism here is cold that increases the energy barrier for many biochemical reactions, first of all those required for smooth muscle contraction.
Cold-induced vessel dilation (that can be seen, for example, on cheeks and extremities) with mild circulatory disturbances ultimately undergoes into so-called cold vessel paralysis when smooth muscles of blood vessel walls completely loose their ability to contract and are maximally dilated. The cyan color of the scar is usually seen at the very last stage, that can occur unexpectedly quickly because scars do not have any warmth insulation layer compared to the regions covered by skin.

Why does dilation of blood vessels cause congestion of blood flow? Should not a bigger cross section ease the blood flow? This seems contradictory to me.


text:
Harmless virus?
Is it possible for a virus to live symbiotically with its host?
Is the human body plagued with viral infections that do negligible harm, or even serve a beneficial role?

It is possible for viruses to live in mutualistic relationships with their hosts, these associations are often overlooked due to the devastating effect that many viruses can have.
To give an example in humans, when HIV-1-infected patients are also infected with hepatitis G virus, progression to AIDS is slowed significantly (Heringlake et al., 1998; Tillmann et al., 2001). Also hepatitis A infection can surpress hepatitis C infection (Deterding et al., 2006).
There are many other notable examples within plants, fungi, insects, and other animals, reviewed by Shen (2009), and Roossinck (2011), in two excellent papers.
The table below, summarises some beneficial viruses across all organisms, and is taken from Roossinck (2011).

References

Deterding, K. et al., 2006. Hepatitis A virus infection suppresses hepatitis C virus replication and may lead to clearance of HCV. Journal of Hepatology, 45(6), pp.770-778.
Heringlake, S. et al., 1998. GB Virus C/Hepatitis G Virus Infection: A Favorable Prognostic Factor in Human Immunodeficiency Virus-Infected Patients? Journal of Infectious Diseases, 177(6), pp.1723 -1726.
Roossinck, M.J., 2011. The good viruses: viral mutualistic symbioses. Nature Reviews Microbiology, 9(2), pp.99–108.
Shen, H.-H., 2009. The challenge of discovering beneficial viruses. Journal of Medical Microbiology, 58(4), pp.531 -532.
Tillmann, H.L. et al., 2001. Infection with GB Virus C and Reduced Mortality among HIV-Infected Patients. New England Journal of Medicine, 345(10), pp.715-724.

That aphids require a particular virus to be present in order to develop wings, is one of the most amazing things I've ever learned in biology.

I have asked about Herpes virus suppressing HIV here: http://biology.stackexchange.com/q/1365/238

As mentioned in this question , Adeno-associated virus is often used for gene therapy.  This is due largely to its predictability when injecting genes (1), however it is also used as it is not implicated in any human pathology. As it is a replication deficient/helper dependent virus, natural infection is much less likely.
The human immune system does mount an immune response against wild-type AAV, as Alexander Galkin discusses regarding an engineered AAV here. Despite this, I think that AAV does meet your criteria for a 'harmless virus' , even if it is unlikely to infect without human encouragement.

(1)  Kotin RM, Siniscalco M, Samulski RJ, et al. (1 March 1990). "Site-specific integration by adeno-associated virus" . doi:10.1073/pnas.87.6.2211 .