Total dark deprivation at day-neutral plants

I cannot say anything about the general case, or specifically for day-neutral plants. However, Sforza et al. (2012) have studied the effects of light conditions on algae (used for biofuel production), and their results indicate several problems with continuous light. In continuous light conditions they find lower chlorophyll contents and higher carotenoid concentrations in cells, which leads to lower photosynthetic efficiency.

This figure shows chlorophyll contents (black) and chlorophyll/carotenoid ratio (red) under different conditions, with the two treatments to the left representing continuous light. (graph from Plos One)

  Results show that Nannochloropsis can efficiently exploit even very intense light, provided that dark cycles occur to allow for re-oxidation of the electron transporters of the photosynthetic apparatus. If alternation of light and dark is not optimal, algae undergo radiation damage and photosynthetic productivity is greatly reduced.

However, they also experiment with pulsed light, which in some cases lead to even lower rates of photosynthesis:

  However, similar experiments, at different frequencies, also showed that alternating dark and light may be detrimental, as demonstrated by the growth inhibition observed in the 1200-1 and −5 Hz curves. These cells showed a decrease in Fv/Fm values similar to that observed under constant strong light, indicating that the inhibition of growth was due to photoinhibition.

They also find that light pulses can be very short, and still allow for the photosystem to reset:

  The optimal duration of light pulses was found to be around 10 ms, which is consistent with the suggested PSII turnover rate in whole cells [4], [46]. Accordingly, after photon absorption by the photosystem, 1–15 ms are needed to reset the system, before it is ready to receive another photon [22]. If the illumination is this short, most photons are exploited for photosynthesis and do not lead to the formation of ROS which then causes photoinhibition. These results indicate that even strong light does not cause damage if it only lasts a short time. Conversely, longer exposure allows the generation of ROS and damage and, in this case, the abrupt changes in illumination undergone by the cells are as harmful to the photosynthetic apparatus as constant high light.

Different species of plants can have mechanisms to handle light stress in different ways, so the effects on different species and types of plants are likely to differ. However, their results should generalize to some extent/for some plant species.

You may also find this paper by Li et al. (2013) interesting.


So, we typically think about migrating birds as living somewhere (North) and then traveling South for the winter. This way of thinking is actually not accurate according to a number of ornithologists, including many I used to work with/for. Thy suggest that the birds live in the South and migrate North to breed and to avoid overcrowding of Southern locales. (Though see this article that found support for the more often assumed N-to-S direction of migration). If 'South' is in fact their 'home,' then perhaps they will venture there regardless of weather patterns. However, perhaps neither of these thoughts applies to short-range migrators like robins.

Also, many birds migrate during the dark hours of the night, so I wonder if the birds you saw were even migrating, per se, or just moving about regionally.


It's not clear from the question what the biological source of the maltose binding protein (MBP) is. As you may know E. coli MBP is used as a fusion partner in an expression-purification system marketed by New England Biolabs (this becomes relevant below).
My initial thought upon reading your question was to suggest dialysis. However I found some hints online that this might be problematical and eventually found this on a FAQ at the New England Biolabs site. Looks like this may be your answer.

Question: In order to rebind MBP to the column, the maltose must be removed. Can this be done by dialysis?
Dialysis does not work very well to remove maltose from maltose-binding protein. This is a general phenomenon of binding protein/ligand interactions; after the free ligand is gone, ligand that is released from the binding site usually finds another binding site before it encounters the dialysis membrane (28). We have determined empirically that binding the fusion to a chromatography resin and then washing away the maltose is much more effective. We prefer standard chromatography (e.g. DEAE) as the separation step, since it can separate the Factor Xa and MBP from the protein of interest. In case MBP co-elutes with the protein of interest, we include a large volume washing step to remove the maltose before starting the salt gradient. This way, the mixture can be run over an amylose column afterward if necessary.

So, in summary they are suggesting that you bind the protein to an ion exchange column; wash with lots of buffer; then elute the cleaned-up protein (using salt or a change of pH  - you will have to know something about your protein's behaviour on the column to do this).


Part of a fish outside the intestinal sac on the back?

Yes, those are the kidneys. They're quite different from mammalian kidneys.
This is a picture highlighting the kidneys in a salmon dissection from the Pacific Streamkeepers Federation (http://www.pskf.ca/sd/). A very different fish, but similar enough to show the kidneys.

You can also see a dissection of the fish urogenital system here: http://necropsymanual.net/en/teleosts-anatomy/excretory-and-osmo-regulatory-system/, though I can't tell what fish species they're dissecting.


It sounds like you are interested in beta diversity which is the change in taxa composition (i.e., alpha diversity) between plots.  There are a number of approaches to calculating beta diversity and the correct choice generally depends on the question(s) you are trying to answer.  The most common approaches are very well described in this paper:

Anderson, M. J. et al. 2011. Navigating the multiple meanings of Beta diversity: a roadmap for the practicing ecologist. Ecology Letters 14:19-28

P.S. I am not familiar with Disney's index so I cannot comment on its merits.

P.P.S. You may also be interested in this question.


So far as I'm aware, the big distinction right now is whether you want dsDNA or oligos.
If you often want lots of oligos, then getting your own synthesizer likely makes sense. Run the numbers and see what the time for return on investment will be and you'll see if it works for you financially.
If you want gene-scale dsDNA, you're currently generally better off getting a specialist company involved (or a foundry, if you've got one that you can access). Not only do they have economies of scale, but they have a lot of experience figuring out how to handle difficult sequences and assemblies.  If you take it all in house you might appear to save money but actually end up losing significant money and time when you count in the time and frustration that your lab ends up spending to go from oligos to genes.
If you've got particular expertise or highly specialized needs, it's a whole different story, but that doesn't sound like the case based on your question.
Note that there are a number of desktop synthesis companies that are working to make this answer obsolete right now, and it may well change quickly in the future.


Why do dogs come in all shapes, but cats are generally all the same?

Until recently, cats were not extensively selectively bred, but were allowed to roam freely and therefore interbred randomly.  Darwin pointed this out, contrasting cats to species that were routinely "enclosed":

  On the other hand, cats, from their nocturnal rambling habits, can not be easily matched, and, although so much valued by women and children, we rarely see a distinct breed long kept up; such breeds as we do sometimes see are almost always imported from some other country.

In contrast, dogs and some other species were selectively bred for certain characteristics "each good for man in different ways":

  The key is man's power of accumulative selection: nature gives successive variations; man adds them up in certain directions useful to him. In this sense he may be said to have made for himself useful breeds.

Why were cats not selectively bred, while dogs were? This gets to be somewhat speculative, but it's clear from looking at dog breeds that many of the different breed functions need to have a larger animal than a cat, as well as one with different personality: Herding sheep, hunting foxes or badgers, fighting bulls, etc.  Cats' function for humans has traditionally been to hunt mice and rats, a role for which they're already beautifully adapted.

(There are a number of small dog breeds, of course, but these parallel cat breeds in that many are ornamental, or else originated as rat-hunters.)


User friendly phylogenetic tree editing software

Yes, I think that you should consider using MultiSeq which is a package of Visual Molecular Dynamics (VMD). You can use visual molecular dynamics to make phylogenetic trees based on sequence/structural/other statistical means.

If you want to check it out and see if it works for you, then install visual molecular dynamics: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

and try out these tutorials under Bioinformatics from the distributors:

http://www.ks.uiuc.edu/Training/Tutorials/

Note: VMD doesn't work very well in 64-bit Windows operating systems if that's what you use. To get it to work well, I suggest you install virtualbox from Oracle, and install your favorite free open-source Linux operating system into virtualbox or into your guest linux machine on your host machine.

I suggest installing your guest Linux OS on virtualbox with 1/2 the ram of your host physical computer allocated, and like 100 GB of space for when you discover that you love LINUX so much and have lots of information on there.

To full-screen your guest Linux OS, you need to install guest additions.

My favorite Linux OS is Kali Linux.

To install guest additions on Kali Linux and most linux guests on VirtualBox,
you have to do this:

But as I've discovered you have to upgrade Kali Linux to Kali Linux Rolling to get Kali Linux to fullscreen. How you do that is via this:

And you probably shouldn't do your work as user "root" the default user. You have too much power so to increase security create a new user on Kali-Linux:

If you are already using linux, then you won't have any problem with getting VMD to work. But by the way, you have to install VMD from the command terminal in linux and this is how you do it.

The instructions as for how this guy does it (and sorry he doesn't speak English) are in the README file when you download VMD.

Sorry, apparently, I don't have a high enough reputation to cite you all the links. I'm sorry that I had to remove them.


Antibacterial hand soaps (and related products); what are they good for?

This may be related to this question on Skeptics SE:  Does regular handwashing with antibacterial soap prevent disease?  Since it is closely related, I will copy my answer from there to here:
See this related answer.
To answer your specific questions:

Has something changed?

Well, we have access to these products now, whereas we didn't before.

Does this sanitizing really make people healthier?

That is a subject of debate.  While it can prevent rapid spread of some things, keep in mind that anti-bacterial soaps should only have specific uses.
The CDC has concerns about the prevalent use of these products.

Scientists are concerned that the antibacterial agents will select bacteria resistant to them and cross-resistant to antibiotics. Moreover, if they alter a person's microflora, they may negatively affect the normal maturation of the T helper cell response of the immune system to commensal flora antigens; this change could lead to a greater chance of allergies in children. As with antibiotics, prudent use of these products is urged. Their designated purpose is to protect vulnerable patients.

Also, there is some concern as outlined by the hygiene hypothesis (WP).  However, that is mostly associated with childhood immunities and allergies as opposed to the effects on adults.

“The natural immune system does not have as much to do as it did 50 years ago because we’ve increased our efforts to protect our children from dirt and germs,” says McMorris.
“Allergies are on the rise because our society has changed the way we live. As a result, people with allergies are having children with others who have allergies, which in turn creates a natural increase in the prevalence of allergies in our society.

The bottom line on this hypothesis is that more research is required.

He (Richard G. Barbers, M.D., USC professor of medicine at the Keck School) also gives credence to the hygiene hypothesis in that "we may be over-protecting kids, and their immune systems, consequently, do not become well-developed."
Barbers notes that only time and a lot more research will tell whether the hygiene hypothesis is valid, and whether, once again, parents should let their kids play in the dirt.

It is generally understood that interaction with beneficial germs is good for you.  However, normal cleaning will not destroy these germs since they reside within you (unless his germaphobia induces him to take antibiotics).  The human immune response doesn't particularly work that way.

The investigators show that "good" bacteria in the gut keep the immune system primed to more effectively fight infection from invading pathogenic bacteria. Altering the intricate dynamic between resident and foreign bacteria - via antibiotics, for example -- compromises an animal's immune response, specifically, the function of white blood cells called neutrophils.

Using too many anti-bacterial soaps has raised quite a few concerns even still.

Soaps and lotions that include antibacterial agents have no benefit over ordinary soap and water, but more research is needed to allay or substantiate concern that these substances may be leading to increased rates of antibiotic resistance. This is the conclusion of the Food and Drug Administration's Nonprescription Drugs Advisory Committee, which met last month to consider the use of these products outside of the health care setting.
"In the absence of proven benefit, there's no real reason to encourage the use of these products," said Alastair J.J. Wood, MD, committee chair and associate dean at Tennessee's Vanderbilt Medical School.

That is not to say that their use should be discontinued entirely.  Two MDs weigh in and conclude:

Opt for regular soap and water, unless you’re at a hospital or doctor’s office, where it’s best to use antibacterial soap. But if you’re out and about and antibacterial soap is the only kind around, it’s fine to wash with it—and it’s worth keeping in the kitchen to use after handling raw meat.

Hope that helps.


Meaning of "standard reactions" in a DNA extraction procedure description

Is this PCR or just DNA extraction and if so, what is the source material?
If it is just DNA extraction, maybe the standard reaction means to extract some given standard sample DNA (CHO cell genomic DNA?) to optimise the yield and reaction conditions.
You would ideally use these same reaction conditions to extract other genomic DNAs.
Also, is the CHO genomic DNA included in the kit?


Is this statement in agreement with Darwin's theory of evolution?

Short Answer

The statement "The number of offspring is not related to fitness." is wrong! In other words, The number of offspring is related to fitness.

Various definitions of fitness exist depending on the model you want to use but whatever is the model you want to use the number of offspring is always related to fitness. For the purpose of a beginner in evolutionary biology, it is probably enough to assume that the number of offsprings that managed to survive to some adult age and fitness are actually the exact same thing.

Long Answer

Darwin's theory of evolution?

What do you call Darwin's theory of evolution? Do you mean the theory of evolution as it was formulated by Charles Darwin at its time or do you mean the current theory of evolution? Charles Darwin never used the word fitness (if I am not mistaken), so I will talk about the modern theory of evolution only.

Generalities

For most of the purpose it is enough to consider fitness as being the expected number of offsprings that manage to survive to some adult age of an individual given its environment and its genotype. The word "expected" used above refers to the first statistical moment (mean) of the random variable which is the number of offspring of an individual given its genotype and its environment. In other words, the number of offsprings is "related" to fitness.

Absolute versus Relative fitness

In general, we talk about absolute and relative fitness, where the absolute fitness of an individual is its number of offsprings and the relative fitness of an individual is its absolute fitness divided by either the mean fitness of the population or more often divided by the absolute fitness of the fittest individual in the population.

Fitness is a function of fecundity and survival

To be a bit more accurate, fitness is a function of both age-specific survival and age-specific fecundity. A very good measure of fitness is given be the elements of leading eigenvalue of the Leslie matrix $L$ in $\overrightarrow n_{t+1} = L \overrightarrow n_t $ where $\overrightarrow n_t$ is a vector that gives the number of individuals of a given genotype of each age living at time $t$. $\overrightarrow n_t = (n_{1t}, n_{2t}, …, n_{nt})^T$, where $T$ indicates transpose and $n_{xt}$ is the number of individuals of age classe $x$ at time $t$.

Definitions of fitness slightly varies depending on the model you want to use

One may want to use an even more complex definitions of fitness, typically when using models that apply to species that have an alternation of generation. Or when considering, genotypes that have different norms of reactions and considering a changing environment through time.

Anyway, whatever is the model you want to apply, fitness is always related to the expected number of offsprings. It would be wrong though to reduce fitness to the expected number of offsprings only, because a more complex definition might be necessary in some special cases. In any case, fitness is always an index of how much will a variant spread in a population and is therefore closely linked to the number of offsprings.


How to identify the GPD gene when the sequence varies between organisms?

I might be misunderstanding you here, but I take from your links above that you want to match the GPD promoter regions from two (distantly related) fungi Agaricus bisporus and Lentinula edodes, to the GPD promoter of Leishmania major, which belongs to a completely different Kingdom!
Promoter regions tend to be relatively poorly conserved between species compared with protein coding regions, even for closely related species. Given the evolutionary distance between the species you are mentioning, the chance you will find any homology between their promoter regions is probably zero.

Furthermore, how would I identify the GPD gene in another organism if I'm unable to compare it to a known sequence?

What I would do is to take the translated GPD protein sequence, which for Lentinula edodes would be GenBank BAA83550.1. I would then use that to search for protein matches using blastp, specifically subsetting for Leishmania major; and use the result to locate the coding gene in the genome. You can also do this in one single step with tblastn, which looks for matches in a translated nucleotide database (see this tblastn example query).
You can then simply take the 1000 bp or so upstream of the coding region to represent your GPD promoter.


How does the body make sure that Vasoactive Intestinal Protein reaches only the target tissue?

Vasoactive intestinal peptide (VIP) acts in the intestine, brain, kidneys, lungs, heart, blood vessels, etc. (Cardiovasc Res) and its effects all lead to the same goal: to improve the delivery of blood, glucose and oxygen to the tissues, so it's not a problem if it acts on different tissues simultaneously. Specifically, VIP stimulates thirst, water retention and blood flow through the coronary and pulmonary arteries, dilates bronchi and breaks down glycogen to glucose, among other.

VIP can act via the nerves as a neurotransmitter or via the blood as a hormone:

  In research animals and in humans, VIP, administered into the coronary
  artery or intravenously, increases the epicardial coronary artery
  cross-sectional area, decreases coronary vascular resistance, and
  significantly increases coronary artery blood flow. High frequency
  parasympathetic (vagal) nerve stimulation also releases endogenous VIP
  in the coronary vessels and heart and significantly increases coronary
  artery blood flow. (Cardiovasc Res)

In humans, VIP stimulates water retention and thirst:

1) VIP stimulates the secretion of renin:

  VIP has now been shown to produce an increase in renin release in a
  number of species, including humans. (Ann N Y Acad Sci)

The activation of renin-angiotensin-aldosteron system results in water retention.

2) VIP stimulates the secretion of vasopressin (Cardiovascular
Research). Vasopressin stimulates water retention. Since vasopressin (arginin-vasopressin or AVP) is dipsogenic (stimulating thirst):

  given the established dipsogenic effect of AVP in the nonpregnant
  state... (JCI Insight)

and since VIP stimulates the secretion of vasopressin, VIP is also dipsogenic.

Now, there seems to be some conflict in the studies about VIP being dipsogenic or anti-dipsogenic in rats:

  VIP was found to have no effect on drinking when injected centrally
  and peripherally in the eel, although it is dipsogenic in the rat
  after central injection. (ResearchGate)

  Intracerebroventricular administration of vasoactive intestinal
  peptide strongly inhibited drinking in rats deprived of water...
  (Neuropharmacology)

Not to go in the details, but there may be different circumstances, for example, the level of dehydration, in which VIP can act differently...


Genotype:

Simply genotype is the inherited genetic information an individual has, and is conceptually quite easy to grasp. For example, if height is determined by gene $A$ and there are two alleles (variants of the gene, $A_1$ and $A_2$), then the three possible genotypes at that locus are $A_1A_1$, $A_1A_2$, and $A_2A_2$.

Phenotype:

The definition of a phenotype is a little more difficult to grasp, in part because it's so broad. As a quantitative geneticist I would say its any characteristic of an individual that can be measured. There's an enormous variance in the phenotypes that are used, they can be characteristics that are physiological, morphological, behavioural, life-history, even fitness itself. Personally I've used phenotypes from gene expression, which is one of the "lowest" (most close to genotype on the bridge between genotype and phenotype) phenotypic levels, through to lifespan, rates of ageing, and lifetime offspring production. Phenotypes are determined by genotype and/or environment (all non-genetic effects). For example, height may be affected by several genes, but it is also affected by nutrition during development and growth (among other things). As an evolutionary biologist, I feel the need to point out that selection operates on the phenotype, it is because genotype often has some effect on the phenotype that we see evolution by inheritance of genetic information.

Correctness of your statement:

  "Phenotype is the enzyme composition within the cell"

Would be sort of incorrect. It certainly wouldn't be appropriately defining phenotype as a general thing. It would be saying that phenotype means enzyme composition within cells, and the appropriate sentence depends on what you are trying to say. The following would say that, in the discussed case, the enzyme composition of the cell is what you consider to be the phenotype:

  "In this study the enzyme composition within the cell is the phenotype."

Whereas, the following defined the concept of phenotype:

  "Phenotypes are characteristics which could be, in principle, measured, such as the enzyme composition within a cell."

The problem of your statement is it makes it sound like phenotype, as a general thing, is enzyme composition within cells. It's kind of a problem of while enzyme composition of a cell can be a phenotype, not all phenotypes are enzyme compositions of cells. Similarly to all humans are mammals but not all mammals are humans.


Survivorship Curves: Type II curve mortality rate is not constant?

$r$ is the individual mortality rate per time step. Survivorship curves (plotted on a log scale) show the proportion of individuals surviving with time, and with a Type II curve a constant proportion is dying at each time step (constant mortality with age, $r$). When the model is expressed as $y$ you are looking at the number of individuals surviving to a time step, which is an negative exponential for Type II, since a smaller and smaller proportion of the population remains at each time step. Therefore $y'$ is the change (slope) in the number of individuals surviving over time. This can be seen as a rate, but it is not the mortality rate of individuals, and it is not accurate to describe it as the "..real mortality rate..".

For an introduction to survivorship curves you can also look at "Survivorship Curves" from Nature Education


The other answer is a bit misleading.

  "Another cause is the the intracellular K+ concentration"

No, this is exactly the same cause, the differing concentrations is what causes the equilibrium potential. You can think of the equilibrium potential for one ion as "how much voltage does there need to be to prevent this ion from flowing down its concentration gradient." The Nernst equation gives you the equilibrium potential for any one ion. The equilibrium potential is also known as the "reversal potential" because if the voltage exceeds the equilibrium potential, ions will flow the opposite way, against their concentration gradient.

  Don't get confused by the resting potential, because it is only a potential that the cell arranges for itself to maintain a stable environment. This cost a lot of energy and attention in form of protein synthesis to keep this potential. This mechanism is achieved by the Na+-K+ ion-pump

The resting potential is not to "maintain a stable environment" or anything like that. The resting potential is the net potential that a cell reaches due to all of the conductances of various ions and the flowing current of each ion governed by its own equilibrium potential.

  This mechanism is achieved by the Na+-K+ ion-pump, which exchanges those two ions

This is partly true, but again, misleading. The Na+/K+ pump establishes the relative concentration of ions, which only leads to a certain resting potential because the conductances of different ions vary at rest. Because the conductance of K+ is higher at rest than the conductance of Na+, the resting potential is closer to the equilibrium potential for K+. If the Na+/K+ pump was functioning exactly as it does, pumping Na+ out and K+ in, but the membrane was more permeable to Na+, then the resting potential would be positive rather than negative. All that matters for resting potential is relative ion concentrations and conductivity. The Goldman equation is the way to calculate this resting potential.

What is happening to K+ when a cell has a resting potential of -70mV but a K+ equilibrium of -90mV?

Because you need -90mV to 'hold in' the potassium against it's concentration gradient, at -70mV K+ will flow out of the cell. However, by definition, resting potential is the potential at which the net current will be zero. That means that, yes, other ions have to be involved. This is where the Goldman equation is very useful.

Although K+ may be the ion with the highest membrane conductance, there will also always be some leak of Na+ and Cl- ions (usually others ions are ignored because these three are the major players; other ions can be important in some situations). Therefore, if -70mV is rest, there must be at least as many Na+ ions flowing in or Cl- ions flowing out as there are K+ ions flowing out.

You can calculate these currents if you know the conductance of each ion and the equilibrium potential for each ion using Ohm's Law: I = V/R, where R is 1/conductance and V is the difference between the current voltage and the equilibrium potential. Try it out with the Goldman equation! If you use the voltage the Goldman equation gives you (the resting potential) you will find that the net current is zero!

Okay, so far we've answered your questions (1) and (2). Now (3): you state "Otherwise it is not clear why K+ should stop leaving the cell at any moment". It is important to note that equilibrium potential doesn't mean no ions are moving: it means the voltage isn't changing. If you just left the cell at -70mV and waited some time, eventually the concentrations of the different ions would change. This is where the Na+/K+ pump comes in: this ATPase is constantly pumping some K+ out and Na+ in to counteract the leak that occurs at resting potential. Cl- ions move, too, but mostly passively. It's also important to note that very few ions have to move for the potential to change on the order of millivolts. -70mV might sound like a lot, but electrical forces are very powerful, so very few ions relative to all the ions available have to move.

I don't quite understand what you are asking with (4) but if you can edit the question I will try my best to answer that as well. It's possible I already answered your question by talking about what "equilibrium potential" means for one ion. For a Cl- ion, if the equilibrium potential for Cl- is -65mV, then Cl- will flow into the cell when the membrane voltage is -60mV (tending to make the cell closer to -65mV), and it will flow out of the cell when the membrane voltage is -70mV (still tending to make the cell closer to -65mV).


Unable to identify a muscle of the anterior thorax

This appears to be the sternalis muscle. The reason it is not mentioned may because it is not present in all individuals, and is therefore relatively poorly characterised.

The image is from An Atlas of anatomy by regions by John Charles Boileau Grant.

Another image of the muscle can be found in Pocket Atlas of Human Anatomy by Thieme:


Why does ammonium oxalate cause swelling of RBCs?

After a lot of search I think the following seems a satisfactory answer.

You are correct in thinking that outside the RBC, $\ce{NH_4^+}$ converts to $\ce{NH_3}$ and once inside the RBC, it again converts to $\ce{NH_4^+}$. But this does not explain how $\ce{NH_4^+}$ swells up the RBCs. For that, let us look at the process from the beginning.

As described by Hemker et al, 2003, an important part of this process is the enzyme carbonic anhydrase (an absolutely important constituent of RBCs). Hemker et al, while studying how the Rh complex in RBCs exports $\ce{NH_4^+}$ ions out of the cell (although they used $\ce{NH_4Cl}$ in their study, it doesn't matter since blood already contains enough $\ce{Cl^-}$) they came up with the following scenario:

$\ce{NH_4^+}$ breaks into $\ce{NH_3}$ and $\ce{H^+}$ and enters inside the RBC. $\ce{H^+}$ combines with $\ce{OH^-}$ (coming from $\ce{HCO_3^}-$, we'll talk about this later) to give $\ce{H_2O}$.
Due to increased osmotic pressure (by $\ce{NH_3}$), $\ce{H_2O}$ enters inside the RBC where it is again broken into $\ce{H^+}$ and $\ce{OH^-}$. $\ce{NH_3}$ combines with $\ce{H^+}$ to give $\ce{NH_4^+}$ again (and we're done with $\ce{NH_4^+}$ here, though Hemker et al took this further).
The $\ce{OH^-}$ (from water) combines with $\ce{CO_2}$ (via carbonic anhydrase) to give $\ce{HCO_3^-}$. This $\ce{HCO_3^-}$, via Hamburger shift, is exchanged with a $\ce{Cl^-}$ while the $\ce{HCO_3^-}$ outside converts into $\ce{H^+}$, $\ce{OH^-}$ and $\ce{CO_2}$ (providing $\ce{OH^-}$ to $\ce{NH_4^+}$). See the diagram below for visual representation:

So, where does the swelling effect come in? It turns out, it is due to the increasing concentration of $\ce{NH_4^+}$ and $\ce{Cl^}-$ inside the RBC which keeps on generating higher and higher osmotic pressure. Hemker et al also found that Rhnull RBCs (lacking Rh complex) became victims to osmolysis much faster than the normal RBCs, suggesting that increased concentration of intracellular $\ce{NH_4^+}$ is the main cause of swelling and osmolysis of RBCs (in their research, they concluded that Rh factor indeed exports $\ce{NH_4^+}$ outside the RBCs).

Reference: Hemker, M. B., Cheroutre, G., Van Zwieten, R., Maaskant-van Wijk, P. A., Roos, D., Loos, J. A., Van Der Schoot, C. E. and Von Dem Borne, A. E. G. Kr. (2003), The Rh complex exports ammonium from human red blood cells. British Journal of Haematology, 122: 333–340. doi:10.1046/j.1365-2141.2003.04425.x


Does "RT-PCR" denote "real-time PCR" or "reverse transcription PCR"?

Real-time PCR is used to quantify a PCR target by measuring some indicator of target amplification in real time after each amplification cycle, thus it is sometimes(often) called quantitative PCR (qPCR). The key to distinguishing between reverse transcription PCR and real-time PCR in the context of a paper or protocol is to look at the starting material being used and the data output.
If the source material is RNA, it needs to be reverse-transcribed into cDNA before PCR amplification. And if they're showing quantification of a specific target, it's likely a real-time PCR of some sort. Quantification of a gene target from normal DNA is likely a standard real-time PCR (aka qPCR). Quantification of an RNA target (like gene expression from mRNA), is likely quantitative reverse transcription PCR (RT-qPCR). The same goes for if the starting material is cDNA (end product of an RNA reverse transcription reaction). Lastly, any mention of Ct or Cq values (or delta-Ct, or delta-delta-Ct) generally indicates a real-time quantitative methodology.
If they are citing the use of RT-PCR to simply confirm the presence or absence of a target (sometimes called endpoint PCR) or to amplify it for downstream applications like sequencing, with no mention of specific target quantification, it's likely a standard reverse-transcription PCR.
There are exceptions to some of these rules, but it should help get you through most literature with some idea of what methods are being used.
Edit: In the past few days, I've seen multiple papers using "RT-PCR" as shorthand (I guess) when they were talking about RT-qPCR or rRT-PCR. Like I said, always exceptions to the rule. But as long as you read the methods it should be simple enough to figure out.


What is happening physically when I get sleepy and when I wake up?

During sleep the cerebrospinal fluid clears out the waste products of brains cells. Sleep fragmentation or sleep deprivation can prevent this process, or reduce its efficiency. So I think the accumulation of waste products cause that you have to sleep more after sleep deprivation and extreme sleep deprivation (e.g. by fatal insomnia) can cause death. Low quality sleep and sleep deprivation can cause or worsen both neural (e.g. Alzheimer's disease),  and metabolic diseases (e.g. diabetes mellitus, etc...), so you should avoid it, if you can (I cannot :D).

Daily sleep is regulated by the circadian clock. Many hormones can affect that clock, e.g. melatonin (dependent on blue light), insulin, etc...

  The conservation of sleep across all animal species suggests that
  sleep serves a vital function. We here report that sleep has a
  critical function in ensuring metabolic homeostasis. Using real-time
  assessments of tetramethylammonium diffusion and two-photon imaging in
  live mice, we show that natural sleep or anesthesia are associated
  with a 60% increase in the interstitial space, resulting in a striking
  increase in convective exchange of cerebrospinal fluid with
  interstitial fluid. In turn, convective fluxes of interstitial fluid
  increased the rate of β-amyloid clearance during sleep. Thus, the
  restorative function of sleep may be a consequence of the enhanced
  removal of potentially neurotoxic waste products that accumulate in
  the awake central nervous system.

2013 - Sleep Drives Metabolite Clearance from the Adult Brain
2013 - Sleep Facilitates Clearance of Metabolites from the Brain: Glymphatic Function in Aging and Neurodegenerative Diseases

  According to the traditional understanding of cerebrospinal fluid
  (CSF) physiology, the majority of CSF is produced by the choroid
  plexus, circulates through the ventricles, the cisterns, and the
  subarachnoid space to be absorbed into the blood by the arachnoid
  villi. This review surveys key developments leading to the traditional
  concept. Challenging this concept are novel insights utilizing
  molecular and cellular biology as well as neuroimaging, which indicate
  that CSF physiology may be much more complex than previously believed.
  The CSF circulation comprises not only a directed flow of CSF, but in
  addition a pulsatile to and fro movement throughout the entire brain
  with local fluid exchange between blood, interstitial fluid, and CSF.
  Astrocytes, aquaporins, and other membrane transporters are key
  elements in brain water and CSF homeostasis. A continuous
  bidirectional fluid exchange at the blood brain barrier produces flow
  rates, which exceed the choroidal CSF production rate by far. The CSF
  circulation around blood vessels penetrating from the subarachnoid
  space into the Virchow Robin spaces provides both a drainage pathway
  for the clearance of waste molecules from the brain and a site for the
  interaction of the systemic immune system with that of the brain.
  Important physiological functions, for example the regeneration of the
  brain during sleep, may depend on CSF circulation.

2014 - A new look at cerebrospinal fluid circulation

  Sleep fragmentation is present in numerous sleep pathologies and
  constitutes a major feature of patients with obstructive sleep apnea.
  A prevalence of metabolic syndrome, diabetes and obesity has been
  shown to be associated to obstructive sleep apnea. While sleep
  fragmentation has been shown to impact sleep homeostasis, its specific
  effects on metabolic variables are only beginning to emerge. In this
  context, it is important to develop realistic animal models that would
  account for chronic metabolic effects of sleep fragmentation. We
  developed a 14-day model of instrumental sleep fragmentation in mice,
  and show an impact on both brain-specific and general metabolism. We
  first report that sleep fragmentation increases food intake without
  affecting body weight. This imbalance was accompanied by the inability
  to adequately decrease brain temperature during fragmented sleep. In
  addition, we report that sleep-fragmented mice develop glucose
  intolerance. We also observe that sleep fragmentation slightly
  increases the circadian peak level of glucocorticoids, a factor that
  may be involved in the observed metabolic effects. Our results confirm
  that poor-quality sleep with sustained sleep fragmentation has similar
  effects on general metabolism as actual sleep loss. Altogether, these
  results strongly suggest that sleep fragmentation is an aggravating
  factor for the development of metabolic dysfunctions that may be
  relevant for sleep disorders such as obstructive sleep apnea.

2012 - Sustained sleep fragmentation affects brain temperature, food intake and glucose tolerance in mice
2014 - Sirtuin 3: A Molecular Pathway Linking Sleep Deprivation to Neurological Diseases

  Inadequate sleep simultaneously modulates the levels of multiple
  hormones that govern metabolism, In general, with sleep deprivation,
  the following hormones are decreased: insulin, growth hormone (GH),
  growth hormone releasing hormone (GHRH), and leptin levels. In
  contrast, ghrelin and somatostatin are increased. Essentially,
  hormones that signal that the body has plenty of energy are decreased,
  while those that signal energy need are increased. Experiments
  utilizing knockout animals as well as pharmacological agonists,
  antagonists, and immunodepletion of the proteins, illustrate that
  these hormones affect sleep regulation. Diabetic rats have decreased
  sleep time and consolidation while replacement of insulin increases
  increases slow-wave sleep.

2013 - The Genetic Basis of Sleep and Sleep Disorders (book)

  In humans, melatonin is produced by the pineal gland, a small
  endocrine gland[26] located in the center of the brain but outside the
  blood–brain barrier. The melatonin signal forms part of the system
  that regulates the sleep–wake cycle by chemically causing drowsiness
  and lowering the body temperature, but it is the central nervous
  system (specifically the suprachiasmatic nuclei, or SCN)[26] that
  controls the daily cycle in most components of the paracrine and
  endocrine systems[27][28] rather than the melatonin signal (as was
  once postulated).

wikipedia - melatonin


I have not found texts relevant to your question and related to the spread of SARS-CoV-2.  However, here is a publication that discusses the utility of contact duration data when constructing infection models, in the general case --
Simulation of an SEIR infectious disease model on the dynamic contact network of conference attendees
Methods
At a conference, 405 attendees volunteered to wear RFID tags. Over two days, the time and duration of 28,540 face-to-face interactions between these individuals were recorded, with a temporal resolution of 20 seconds. Note the spatial limits of the RFID data:

RFID devices engage in bidirectional radio communication at multiple power levels, exchanging packets that contain a device-specific identifier. At low power level, packets can only be exchanged between tags within a radius of 1 to 2 meters.

From these data, three networks were constructed:

dynamic network (DYN) -- this network preserves the sequence and duration of contacts between individuals.  Using the language of graph theory, this is a directed network with weighted edges.
So, if individual A comes into contact with individuals B and C, and individual B is infectious, individual A must contact individual B before individual C in order to have a chance of A → C transmission.  Causality constrains the chain of transmission.
heterogenous network (HET) -- this network preserves the duration of contacts between individuals but disregards the sequence of contacts. The graph of this network is weighted but undirected. Adopting the previous example, B can infect C via A regardless of the relative order of the A ↔ B and A ↔ C interactions.  Causality is suspended, and the probability of transmission depends on the number and duration of contacts.
homogenous network (HOM) -- this network inherits the topology of HET, but ignores the duration of contacts.  The graph of this network is unweighted and undirected. Each contact event carries an equal probability of resulting in transmission, so the probability of transmission depends solely on the number of contacts.

To simulate the spread of an infectious disease over realistic time-scales, each network was longitudinally extended using three procedures:

repetition (REP) -- the recorded contacts are repeated with the same duration and order.
random shuffling (RAND-SH) -- the structure of the network is preserved, but the IDs associated with the nodes in the network are shuffled between iterations.
constrained shuffling (CONSTR-SH) -- same as RAND-SH, but the reordering of IDs is constrained to preserve individual social activity (i.e. IDs with many contacts are not assigned to a low-contact node in the network) and repeated contacts.  This procedure rectifies the oversimplifications of REP and RAND-SH by acknowledging that people tend to interact with the same people day-to-day, with occasional contacts with strangers.

The authors applied a SEIR epidemic model (Susceptible, Exposed, Infectious, or Recovered).  For each network-procedure pair, they considered two disease scenarios with different assumed values of mean latency period (σ -1), mean infectious period (ν -1), and transmission rate (β):

very short incubation and infectious periods

σ -1 = 1 day
ν -1 = 2 days
β = 3.10 -4/s

short incubation and infectious periods

σ -1 = 2 days
ν -1 = 4 days
β = 15.10 -5/s

A note from the authors on why these values were chosen:

These sets of parameter values were chosen to maintain the same value of β/ν, which is the biologic factor responsible for the rate of increase of cases during the epidemic outbreak, while changing the global timescales of incubation and infectious periods, and assessing the role played by the social factors embedded in the contact patterns.

Results
Epidemic outbreaks in the three networks across the three data-extension procedures were compared by computing the mean R0, defined by the authors as the mean, over all iterations, of the number of secondary cases from the single initial randomly chosen infectious individual.
Considering the simplified REP procedure, higher values of R0 were observed in the HOM network compared to the HET and DYN networks, for all scenarios.  The authors explain this observation by noting that the probability of rapid extinction of the pathogen was smallest for the HOM network; indeed, this held true independent of procedure.
In terms of the final number of cases (R∞) and the rate of spread, the HET and DYN networks were similar for both disease scenarios.  The peak of the epidemic was reached first in the HOM network, on average, consistent with the reduced probability of extinction.
In the RAND-SH procedure, spread was slower but lasted longer, leading to a larger R∞ for all networks.  In general, greater shuffling of ID tags led to more efficient disease spread, such that R∞(RAND-SH) > R∞(CONSTR-SH) > R∞(REP) for all networks and scenarios.  The interaction of more efficient disease spread in the RAND-SH procedure with increased values of σ -1 and ν -1 in the "short" scenario seems to produce consistently higher R0 values across networks (see Figure 3), though high variance in R0 means the effect of this interaction is not significant.
Conclusions
By comparing the different network types across all procedures and scenarios, it was shown that ignoring the direction and duration of contacts overestimates both the rate at which a disease spreads and the total number of individuals infected.  Additionally, shuffling individual positions in contact networks while preserving network topology increases disease spread when compared to a static model, though this effect is buffered by the "realistic" inclusion of preserved sub-networks of repeated contacts.
While this publication does not directly integrate factors for the duration and rate of contacts into the SEIR model, as suggested by Hans-Peter Stricker, the authors are able to show that mapping such a model to networks in which the direction and duration of contacts are encoded as edge weights leads to different measured outcomes (R0, R∞, time to peak) when compared to topologically identical networks lacking these encodings.


What vitamins exist for other animals but not humans?

The best example I can think of is taurine, which is a non-proteinogenic amino acid.

Taurine is "conditionally essential" for humans1, but essential for cats2,3.

References:

1: Stapleton, P. P., Charles, R. P., Redmond, H. P., & Bouchier-Hayes, D. J. (1997). Taurine and human nutrition. Clinical nutrition, 16(3), 103-108.

2: Knopf, K., Sturman, J. A., Armstrong, M., & Hayes, K. C. (1978). Taurine: an essential nutrient for the cat. The Journal of nutrition, 108(5), 773-778.

3: Markwell, P. J., & Earle, K. E. (1995). Taurine: an essential nutrient for the cat. A brief review of the biochemistry of its requirement and the clinical consequences of deficiency. Nutrition research, 15(1), 53-58.


Why Isn't mineral transport in xylem multi-directional?

Movement through the xylem is powered by transpiration of water through stomata in leaves and a sustained tension in the xylem itself due to water's cohesive properties.  See: https://en.wikipedia.org/wiki/Xylem#Cohesion-tension_theory

The "multi-directional" transport you are talking about does not actually occur in the xylem.  Minerals have to be transported OUT of the xylem before they can move other ways.  Transport THROUGH the xylem is uni-directional; transport OUTSIDE of the xylem can be multi-directional.


An extensive collection of the various mutation rates (from which you could reverse-engineer their fraction on the total share of mutations):

http://www.bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=mutations&org=&rpp=100


Making penicillin using animals - specifically, a goat

Here is a link to a survivalist blog with a protocol for making penicillin. (I'm not recommending this by the way.)

Is it possible that the reference to the goat in Lucifer's Hammer is for the extraction of insulin (from the pancreas)? Have a look at the Wikipedia entry for Eva Saxl - in Shanghai during WWII her husband kept her alive with insulin extracted from water buffalo pancreas.


Lab marker for labelling cell culture plastics?

This is hardcore going to come across as a SPAM answer, but I simply did a Google search:

Laboratory Marking Pens from Ted Pella

Statmark Pen™: resistant to formalin, ethanol isopropanol and xylene

Secureline® Marker: water resistant; autoclavable; not suitable below 0°C (32°F)

Secureline® II / Superfrost: resistant to xylene, ethanol, acetone and formalin; service temperature -15°C to 100°C (5°F to 212°F)

You can try a Sample Pack of all 3 for $8 USD to see which you like the best.


Evolution: How could all useful traits evolve simultaneously?

Has anyone calculated or simulated how the adaptation for many different traits can happen simultaneously?

There are a lots of studies on the subject but I don't fully understand what is your issue. So I'll try to give some words hoping that helps a bit but it is possible that I'll totally miss the point you want to make.

The mutation rate in humans is around $1.25 \cdot 10^{-8}$ per base pair per individual per generation. The human genome contains about 3400 Mpb, meaning that you probably carry $1.25 \cdot 10^{-8} * 3.4*10^9 = 42.5$ mutations that none of your parents had in their genome. Now if you consider the population size, you'll see that a fairly big amount of mutations occurs each generation in the human population. So mutations are not that rare! It might unfair to take human as an example though as human's population size is very big. Anyway, the great majority of mutations are deleterious. In consequence, you are right, probably not many beneficial mutations will occur in a given population at one given generation and especially not in the same individual (except if you think of viruses!).

Now, depending on how beneficial is the mutation you are considering (selection coefficient), depending on its dominance, depending on the (effective) population size, your new mutations might take quite a bit of generations before reaching fixation in the population. In this time other mutations might occur. And then, the question is very interesting. Imagine a population of asexual individuals where two beneficial mutations exist (at two different loci [=position on a chromosome]). Because there is no recombination (by definition of what is an asexual population) never these two mutations will be found in the same individuals and in consequence if one mutation reaches fixation, it necessarily mean that the other mutation would have disappear. In sexual population it is different. Recombination allow that the two mutations, once they reaches a sufficient frequency will probably be found in the same organism and therefore, the two mutations can reach fixation.

Hope that helped a bit


The rate is determined by the size and complexity of the sequence. Short, non-repetitive sequences should re-associate (at a given r.t.p.) faster than longer, repetitive DNA.

I'm guessing that that is what this question is getting at.


Any latest edition or successor of "Invertebrate zoology" by Ruppert & Barnes 2003?

A worthy successor to this book series is "Invertebrates" by Richard C. Brusca et al. The latest edition being from 2016, so exactly what I was looking for.

https://www.amazon.com/gp/product/1605353752/ref=pe_353720_261047730_em_sp_C_1p_1_ti


Does becoming martyr have an evolutionary advantage?

There isn an effect called "Indirect reciprocity" where individuals just give to everyone they meet without direct requirement of reciprocity.

This sort of benefit to others is common - hospitality to strangers, general politeness, good customer service all fall along these lines.  You hope they will come back and benefit you again, but maybe they will tell someone else who will know you are a good community member.

It is only sustainable in a system where the cost/benefit ratio is less than the reputation benefit of the act.  It sounds as if this is only good for public acts but if the benefit is transferred to a social entity that outlasts the individual (like your children, a relative's children, a religion or a corporation say), the result could still hold.

If you think about typical morality/ethics really it still makes sense to think that what we call altruism must still have a net positive benefit.  If there is no benefit long term or to anyone, it really isn't useful or even good, its random.  What we usually call altruism is usually some sort of reciprocal cooperation.

A soldier who dies in combat or someone who dies for their beliefs but everyone knows about it as a public statement benefits from their act indirectly.  I don't think its altruism in the pure sense of the word. Defending the nation, ones' beliefs or whatever is, in its sense its own reward.  Veterans come back from a war are hopefully respected for their work.  Having a purple heart can be a good thing to show people.  I'm not saying these people are adequately compensated for what they have been through, but just trying to draw a distinction between pure biological altruism and 'indirect reciprocity'.

Examples of Indirect reciprocity might be the use of tax money to build highways and build power and water infrastructure.  Its important - its the glue that holds a nation or a group together.  If you got punished for doing these things we wouldn't be hanging as a nation very long!

A martyr with no family at all who would benefit would still count as an altruism I think, but most acts of public piety and sacrifice do benefit the individual by reputation. Something to think about.


The methods that come immediately to mind are mostly related to next-generation sequencing. You can do deep sequencing on your sample, which is just increasing the coverage as much as possible to find rare events. You can do RNA-seq to look at the transcriptome, ChIP-seq to look at chromatin modifications, and single-cell sequencing (a form of deep sequencing operating on individual cells) to get truly cell-by-cell data, either from the genome (DNA) or transcriptome (RNA).

If you are purely looking at phenotypes, flow cytometry is quite useful for analyzing relative expression levels of proteins, using both extracellular and intracellular markers and stains. FACS is an extension of flow cytometry that allows for the sorting of various cell populations into separate containers. These "purified" samples can then be used in any of the methods listed above.


Why don't mammals have more than 4 limbs?

Number of legs in terrestrial vertebrates

Not only do mammals have four legs but actually all terrestrial vertebrates (which include mammals) have four legs. There are slight exceptions though as some lineages have lost their legs. Typically snakes have no legs anymore. Apesteguia and Zaher (2006) discuss the evolution of snakes legs reduction and report a fossil of snakes with a robust sacrum. Cetaecea (whales and friends) have lost their hind legs but we can still spot them on the skeleton. See for example the orca (killer whale, easily recognizable to its teeth) on the picture below. Pay attention to the small bones below its vertebral column at the level on the left side of the picture.

I also want to draw attention to the importance of the definition of legs. I guess that we would call something a pair of legs if it is constructed using a similar developmental pathway than current existing legs. If we are using some broader definition, then a prehensile tail as found in some new world monkeys, for example, could be considered as a leg (but only a single leg, not a pair of legs obviously). A list of animals having a prehensile tail can be found here (Wikipedia).

Did you say Natural Selection?

I think (might be wrong) that you have too selectionist a view of evolution. What I mean is that you are wondering why mammals have four legs and you're looking for an explanation of the kind "because mammal have this kind of need of locomotion and for this purpose four is the most optimal number of legs". Consider the following sentence: "If there is a need, natural selection will find a way!". This sentence is wrong! Evolution is not that easy. This false view of evolution is sometimes referred to as panselectionist.

The reality is that it is not easy to evolve such a developmental pathway as drastic as having an extra pair of legs that are well integrated into the body of the carrier of this new trait. Such an individual would need a brain, a nerve code, a heart and some other features that are adapted to have extra legs. Also, assuming such a thing came to existence it is rather complicated to imagine how it could be selected for. To go slightly further, you have to realize that there are many stochastic processes in evolution (including mutation and random variation in reproductive success) and an organism is a piece of complex machinery and is not necessarily easily transformable to some other form that would be more efficient (have higher reproductive success). Often going from one form to another may involve a "valley crossing" meaning that if several mutations are needed, intermediate forms may have low reproductive success and therefore a high amount of genetic drift (stochasticity in reproductive success) to cross such valley of low reproductive success. See shifting balance theory. Finally, even if there is selection for another trait, it may take time for the mean trait in the population to shift especially if there is only little genetic variance. A complete discussion on why the sentence "If there is a need, natural selection will find a way!" is wrong would fill up a whole book.

Gould (1979) is a classic article on the subject and is very easy to read even for a layperson.

Why 4 legs?

Terrestrial vertebrates have four legs because they evolved from a fish ancestor that had four members that were not too far from actual legs (members that could "easily" evolve into legs). This is what we call a phylogenetic signal. The explanation is as simple and basic as that. You can have a look at the diversity of terrestrial vertebrates here (click on the branches).

Number of legs in invertebrates

Arthropoda (Spiders (and other chelicerata), insects (and other hexapods), crustaceans (crabs, shrimps…) and Myriapoda (millipedes) and Trilobite as well)) evolved from a common ancestor who had a highly segmented body. From this ancestor, many groups have fused some segments. In these taxa, each pair of legs is attached to a particular segment (I don't think the segments are still visible in spiders today). In insects, for example, all 6 legs are attached to the thorax but to 3 different segments of the thorax, the pro- meso and meta-thorax (see below).

As a side note, it is interesting to know that the wings in insects did not evolve from the legs (as it is the case in birds and bats). There are two competing hypotheses for the origin of insect wings. Wings either developed from gills or from sclerite (chitine plate, the hard part of the insect). When insect first wings, they actually evolved three pairs of wings (one on each segment of the thorax). At least one pair has then been lost in all modern species. In the diptera, a second pair of wings have been lost and are replaced by halteres, particularly easy to spot in craneflies (see below picture). In millipedes, the link between segmentation and legs is even more obvious (see picture below). You can have a look at the diversity of Arthropoda here (click on the branches).

Pictures

Update 1

Asking how likely it is for a given population to evolve a given trait is extremely hard to answer. There are two main issues: 1) a definition of the question issue and 2) a knowledge issue. When asking for a probability one always needs to state the a priori knowledge. If everything is known a priori, then there is nothing stochastic (outside quantum physics). So to answer the question one has to decide what we take for granted and what we don't. The second issue is a knowledge issue. We are far from having enough knowledge in protein biophysics (and many other fields)  to answer that question. There are so many parameters to take into account. I would expect that creating a third pair of legs would need major changes and therefore one mutation will never be enough in order to develop a third pair of legs. But, no I cannot cite you any reference for this, I am just guessing!

Following the wings example in insects. Insects have had three pairs of wings. While some mutation(s) prevented the expression of the third (the first actually) pair many of the genetic information for this third pair remain in the genotype of insects as they still use it for the two other pairs. Taking advantage of that, Membracidae (treehoppers) developed some features using a similar biochemical pathway than the one used to develop wings. Those structures are used as protection or batesian mimicry.

Update 2

Let's imagine that an extremely unlikely series of mutations occur that create some rodent with 6-legs. Let's imagine this rodent with six legs has a larger heart in order to pump blood to these extra legs and it has a brain that is adapted to using six legs and some changes in its nerve cord so that it can control its 3rd pair of legs. Will this rodent have higher reproductive success than other individuals in the population? Well… let's imagine that with its six legs, it can run faster or whatever and has a very high fitness. How would the offspring of a six-leg mother (or father) and a four-leg father (or mother) look like? Will it be able to reproduce? See the issue is that it is hard for such trait to come to existence because 1) it needs many steps (mutations) and 2) it is hard to imagine how it could be selected for. For those reasons, there exist no vertebrates with 6 fully functional legs.

Well, let's assume it does and in consequence, after 200 generations or so, the whole population is only made of 6-legged individuals. Maybe the species got extinct then and no fossil record has ever been found. This is possible. It is not because something has existed that we necessarily find something in the fossil record.


How does evolution get around the combinatorial problem?

No, with some caveats. First, about the actual value of the ratio: it's probably tiny, with almost all possible genetic sequences failing to lead to living organisms.

Why does this not make evolution impossible? Each sequence can have billions* of neighbors in sequence space. If even a very small number of those are functional, evolution can proceed. More importantly, the functional sequences are clustered in sequence space. If you pick 3 billion nucleotides randomly, you'll get nonsense, but if you mutate a single nucleotide in a human you'll most likely get a perfectly good human.

There are interesting open questions here, though, especially regarding the origin of life, and whether natural selection tends to drive populations to regions of sequence space that are especially dense with functional sequences.

*Just looking at point mutations. Including the full mutational spectrum gives many more.


Define a "Hit" (based on some cutoff- evalue, score etc)
Get output in the tabular format
Count number of hits per query — it is usually given in the header; if you want to look for some selected hits (based on some cutoff, then you can parse the file and find out)

Example file (header):

# BLASTN 2.2.27+
# Query: TCONS_00036712 gene=XLOC_017996
# Database: ../nt_db/nt
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1014 hits found

If you want to parse the header to look for number of hits then you can run this command in the terminal (if you have awk — there by default in linux and other unix based systems. For windows install gnuwin32).

awk -v OFS="\t" '/^# Query/{q=$3 FS $4} /^# .* hits found/{h[q]=$2} END{for(i in h){print i,h[i]}}' blastoutput.txt

To get the number of hits for a given criterion (for e.g. I just defined bitscore [12th column] to be >400)

awk -F "\t" '!/^#/ && $12>400{a[$1]++} END{for(i in a){print i,a[i]}}' blastoutput.txt


How do people actually find codons in a DNA transcript just by looking at it?

Codons refer to sequences of nucleotide triplets that translate to amino acids. As you know, polypeptides are translated at the ribosome using a messenger RNA (mRNA) blueprint produced by RNA polymerases from the DNA.

DNA consists of four nucleotides: adenine, guanine, cytosine and thymine. Thus, DNA sequences read, for example, ATAAGC. RNA, however, replaces thymine with uracil. So to transcribe the above DNA nucleotide sequence into mRNA would result in UAUUCG.

The mRNA may also get spliced into various isoforms coming from the same gene. In short, it may be difficult to determine the gene product from the DNA sequence.

Does that make sense?


I believe you're talking of the members of the families Unionidae and Margaritiferidae, which have a larval stage called glochidium. From the Wikipedia page linked here:

  This larva form has hooks, which enable it to attach itself to fish (for example to the gills of a fish host species) for a period before it detaches and falls to the substrate and takes on the typical form of a juvenile mussel. Since a fish is active and free-swimming, this process helps distribute the mussel species to potential areas of habitat that it could not reach any other way.

This interesting study about phylogeny of these species shows that lures mimics mainly fish, but also different prey species such as insect larvae. Some species display an aspecific lure, while others show fine mimicking in order to attract a precise set of host fish species.

As to how luring evolved:

  What drives the evolution of luring? Very little is known about what drives the evolution and diversification of luring, which has evolved independently multiple times. In Lampsilini mussels, luring appears to have arisen early, and the complexity of the lure has increased through the lineage. It is likely that diverse selection pressures govern the evolution of luring. One hypothesis is that luring increases the rate of prey encounter without incurring the metabolic costs associated with active search and pursuit. Alternatively, luring may present predators with an opportunity to exert control over a prey’s movement, reducing the risk of injury when hunting. Luring systems present a unique opportunity to understand signal design and evolution.

Do oysters need to see in order to evolve the lure?

No. Evolution of a body part does not require sight or will. From this blog post:

  Note that [...] the mussel can’t see the fish it’s parasitizing.  In this case natural selection is literally blind. Those mutations in the mussel that make its brood pouch look more fishlike will give it a reproductive advantage over its confrères, even if it can’t see the fish it’s deceiving. Note as well that selection has “acted” (I’m anthropomorphizing here: selection doesn’t really “act”, for it’s not an external force but a process of gene sorting) not just on the appearance of the mussel, but on its behavior.  It has genes that make it wiggle its brood pouch in a fishlike manner.

The mechanism is all here:

1st step: mutations that modify the coupling of fish bites and glochidia release/mantle shape/the movement of the mantle arise.
2nd step: The bearers of favourable mutations will have more progeny and the population will have more and more bearers as generations pass.

No need of being conscious about anything. :)


What placement of plasmid parts makes the most sense?

The relative placement of genes on a plasmid should not affect their expression.

Both will be expressed and to what extent is dependent on the strength of the promoters and a few other factors like codon availability.

However where you ultimately plan to express these genes can be an important consideration in plasmid design. For example, if you are designing a binary vector for agrobacterium mediated transformation of plants then positioning the plant resistance cassette next to the left border is a sensible move.


Each cell will indeed have the same DNA sequences and ability to produce any given protein. However, there are certain factors (transcription factors) and cellular conditions within a cell that dictate which proteins are produced. If the conditions are right then only certain proteins will be produced depending on what type of cell it is. This process by which a cell continues to express selected proteins and becomes specialized for a specific function, is called differentiation. Expression of proteins that are not required can be prevented by transcriptional repressors (or by epigenetic mechanisms such as methylation of DNA sequences). So to answer your question, while cells contain the instructions (DNA sequences) to produce potentially any protein, not every type of protein will always be produced.

Keep in mind that my answer is very basic; the answer isn't as simplistic as I'm making it out to be.


It depends how you define it. Many early cell lines (as well as some modern ones) were derived from tumors. Tumors are spontaneously immortalized cells which became immortalized in vivo. If you're asking how often researchers collect primary cells (non immortalized) and grow them with the hopes they will become immortal the answer is pretty much never.


First, there are inaccuracies and misconceptions in the article you quote, which also relates to obese people with insulin-resistance (pre type II diabetics) rather than normal people. These are:

I’m not sure what a “low glucose state” is supposed to mean, but the tissues of the organism co-operate to ensure that the blood glucose concentration normally never falls below about 4 mM, with a range of approx. 4–8 mM. Thus, glucose is available in the blood for tissues that can take it up in a particular circumstance. These are not “paltry levels”, as quoted.
The body’s metabolism cannot predict the future. The scientific credentials of anyone who writes “the body senses that dietary glucose might not be coming anytime soon” are hardly to be trusted. (I don't think much of his literary style either.)
In short-term starvation, when the blood glucose concentration falls towards the lower end of its range, insulin resistance is not triggered. Insulin secretion from the pancreas stops (and glucagon secretion starts).
The brain is not sensitive to insulin (i.e. its glucose
transporter(s) is not), whereas the muscle is. This is what allows the brain continued access to glucose.

Some of this is elaborated in my answers to: “What is the purpose of gluconeogenesis?”,  “How do muscle cells synthesize glycogen?” and “During starvation, does the human body do anything to prioritize which organs receive nutrients?”. A section from Berg et al. may also be of interest.

Answer

Lactate can (and must) be generated by non-aerobic muscle metabolism (i.e. in muscle lacking mitochondria) during exercise because anaerobic glycolysis, with conversion of pyruvate to lactate, is the only way the muscle can obtain ATP to power its contraction. The source of this is the glycogen stores laid down in the muscle after a meal, and glucose taken up from the blood.

I don’t know anything about low-carb diets, but I assume they include protein, so that some of the amino acids from this can be converted to glucose by the liver (glucogenic amino acids) as well as those that cannot (the ketogenic ones that can give rise to ketone bodies). Even if the blood glucose is at the lower end of its range, in the non-starved state the muscle can take it up from the blood. (The blood glucose will be restored by the so-called Cori Cycle.) Even in starvation, if the muscle is working there will be a concentration difference between blood and muscle glucose that will allow uptake.

I think that this question is provoked by the feeling that the existence of ketosis means that glucose is not available to cells. This, as I hope I have explained, is a misconception, perhaps arising from confusion with the different situation of ketosis in long-term starvation.

Finally, there are other sources of lactate besides muscle, regardless of diet. One is the erythrocytes which lack mitochondria and therefore can only use anaerobic glycolysis to produce the ATP they need for active cation transport etc.


Is fat distributed proportionally around the body?

@fileunderwater's suggestion to use a scale is probably the best answer you could get, but looking at this broadly, the answer is no.  The oft-referenced apple and pear shapes are indeed very real and have medical consequences.  One of the issues is that there are sex differences in fat distribution.  There is no evidence I can find that finger fat is a good correlate of overall body fat, although admittedly yours could be.  It is also likely a function of how much overweight you were when you began the "experiment" i.e. the relationship probably isn't linear.

That being said, in men the ratio of the length of the second and fourth digits are otherwise meaningful.


What's the evolutionary reason behind feeling 'sorrow'?

I‘ll answer from a perspective I‘ve been studying in Psychology, but can‘t provide sources. If this is not within the scope of this SE, I‘d kindly ask to either add appropriate sources to my answer or close it.

Sorrow is an emotion that has specific cues and expressions like tears, distinct micro-facial cues (which are stable over practically all cultures according to studies of Paul Ekman et al.), a general tendency to withdraw from social settings.

This can be understood as communicating to other members of your group the need for consolation and social closeness, which would count as an evolutional gain.

Update:
I found an extensive article on the subject: http://www-personal.umich.edu/~nesse/Articles/Nesse-EvolutionBereavement-2005.pdf


Is there a link between digestion and nightmares?

A nightmare is basically an alarm; typically your subconcious mind trying to wake you. Nightmares often occur when you are experiencing pain or discomfort (like needing to use the bathroom).

Dreams are a way of sorting through questions in a "what if" sort of way. When it comes to a nightmare, you are in a panic-situation, often without a solution, or where a "logical" solution is unsuccessful.


Both Nearsightedness and farsightedness are inheritable.

According to Citizen Scientists Look into Nearsightedness, 23andme blog:

  Nearsightedness, a condition in which far-away objects look blurry, is
  a problem of endemic proportions — approximately 30-40 percent of
  adults in the United States are nearsighted.  And, as computers and
  cellphones (which train our eyes to focus on short distances) play an
  ever-increasing role in our lives, we can only expect that this number
  will grow. One study in the United States highlights the rising rates
  of nearsightedness. These researchers found that in the early 1970’s,
  approximately 25 percent of Americans between the ages of 12 and 54
  were nearsighted, but thirty years later that number had skyrocketed
  to 42 percent. While it’s been clear that genetics play an important
  role in nearsightedness, until this month relatively little was known
  about which genes are involved. Two large studies on nearsightedness,
  however, have recently shed light on the subject. One of these studies
  was conducted by the 23andMe research team under the leadership of Amy
  Kiefer and Nick Eriksson.

  Read more at
  http://blog.23andme.com/23andme-research/citizen-scientists-look-into-nearsightedness/#ijOHfuvePBSFOm4A.99

Which types of eye disease are inherited?

Genetic factors play a role in many kinds of eye disease, including those diseases that are the leading cause of blindness among infants, children and adults.

More than 60 percent of cases of blindness among infants are caused by inherited eye diseases such as congenital (present at birth) cataracts, congenital glaucoma, retinal degeneration, optic atrophy and eye malformations. Up to 40% of patients with certain types of strabismus (ocular misalignment) have a family history of the disease and efforts are currently under way to identify the responsible genes.

In adults, glaucoma and age-related macular degeneration are two of the leading causes of blindness, and both appear to be inherited in a large portion of cases. Researchers have mapped several genes for glaucoma and are starting to identify genes involved in macular degeneration. They also are making very significant progress in identifying the genes that cause retinitis pigmentosa, a degenerative disease of the retina that causes night blindness and gradual vision loss.

Can common vision problems be inherited?

Genetics also play a role in vision problems that occur in otherwise healthy eyes. Genetic ophthalmologic researchers now have evidence that the most common vision problems among children and adults are genetically determined. The list includes strabismus (cross-eyes), amblyopia (lazy eye) and refraction errors such as myopia (nearsightedness), hyperopia (farsightedness) and astigmatism.

Can inherited eye diseases be corrected if an early diagnosis is made?

YES

Source: http://my.clevelandclinic.org/disorders/inherited_eye_disease/default.aspx

This Table gives a better insight on Causes of Myopia:


Reeve and Keller in the first chapter of Levels of Selection in Evolution (Princeton Univ. Press,1999) seem to address this question in the second item in the following paragraph.

  The purpose of this volume is to sample current theoretical and empirical research on (1) how natural selection among lower-level biological units (e.g., organisms) creates higher-level units (e.g., societies), and (2) given that multiple levels exist, how natural selection at one biological level affects selection at lower or higher levels [boldface added]. These two problems together constitute what Leigh (chap. 2) calls the "fundamental problem of ethology." Indeed, as Leigh further suggests, they could be viewed jointly as the "fundamental problem of biology," when genes and organisms are also included as adjacent levels in the biological hierarchy. This generalization has the desirable property of immediately removing the long-standing conceptual chasm between organismal and molecular biologists.

The authors suggest definitions of fitness that account for hierarchical relationships (the level of selection problem) by considering the effect of a trait (nepotism among social insects) on "adjacent" biological levels, such as individual and colony.

By measuring what they call 'absolute fitness force' they propose to eclipse what they see as spurious debate over the fundamental level of selection (genes vs. individuals, say).

A somewhat surprising aspect of their discussion emerges here:

"It is still embarrassingly common to read inaccurate statements...that frogs have to produce many eggs to ensure the survival of the species because tadpoles suffer extremely high rates of predation, or that wolves have evolved ritualized displays to establish dominance hierarchies because physical combats would be too disadvantageous for the species. These naive statements betray a widespread and persistent misunderstanding of the level at which natural selection most commonly operates."

Their point is that such statements focus on the wrong level of selection (group), and that stronger selection may occur at the individual level; their overall argument being that both levels should be factored in.

I cannot present this as a 'community definition' but it may be a representative example.


That jumping spider is a Jumping Spider! (That is, family Salticidae, commonly called Jumping Spiders).

There's a lot of diversity in the family, but your pictures look similar to the Zebra Jumping Spider.


Absolutely, humans belong to the superclass Gnathostomata. It's simply the class of jawed vertebrates, and includes 99% of vertebrates.  It also includes the class Mammalia, which includes humans.

For basic and fairly light reading, check out Wikipedia on Gnathostomata and Mammalia.


Why is it good to use Glycerol as carbon source to produce intermediates in pharmaceuticals?

First, glycerol is economically and environmentally interesting as a substrate. It is a side product of first generation biodiesel production, which has been increasing in the past years. So large amounts of glycerol are being accumulated, while we make little use of it. Therefore it has become a necessity to develop glycerol utilizing industries. Another consequence is that glycerol is now a cheap and abundant substrate.

The metabolism of glycerol is quite complex and has many end products that are of industrial relevance. For example, 1,3-propanediol and succinic acid have commercial applications and can be produced directly from glycerol by some microorganisms. So depending on the strain you use, you may not need heavy metabolic engineering.

Here is an article that might help you.


What is this small tissue structure found in kidney?

This is a slice of an adrenal gland:

Source (Creative Commons Attribution-Noncommercial-Share Alike 3.0 License): http://histology.medicine.umich.edu/resources/endocrine-system

These glands sit on top of the kidneys, typically under adipose tissue (which can also be seen in both your image and the image I included here). The most identifying feature of the adrenal gland is its clear separation into two parts: the outer "cortex" and inner "medulla", as labeled on the image.

The two parts have different endocrine functions: the cortex primarily produces steroid hormones, like aldosterone and cortisol, whereas the medulla makes catecholamines epinephrine and norepinephrine (also called adrenaline and noradrenaline). I believe the inset in your image is of the medulla.


Any simulations of four-winged dinosaur flight? (microraptors)

Note nowhere in the article does it mention the rear wings flapping. The rear wings do not provide lift, they are acting as control surfaces to improve stability and maneuverability. (think of the tail of a plane).earlier/proto flies have far more demand for control surfaces than developed/derived fliers due to lacking more precise control of flight surfaces.

They basically take off just like any other bird, if they could fly. Flight in dinosaurs likely did not even evolve from gliding as we commonly think of it but instead from raptorian pouncing, the sprawled posture of microraptor you sometimes see, with its hind legs spread wide, is anatomically impossible, you literally have to dislocate both legs to do it. Dinosaur hip joints do not allow for much lateral extension unlike mammalian or varanid ones, more like a hinge than a ball and socket.

The animal in flight would have looked like this.

Hall, Justin, et al. "A new model for hindwing function in the four-winged theropod dinosaur Microraptor gui." JOURNAL OF VERTEBRATE PALEONTOLOGY. Vol. 32. 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA: TAYLOR & FRANCIS INC, 2012.


Could someone entirely absorb smells by smelling?

On the contrary, your olfactory epithelium - the bit that does the smelling up at the top of your nasal cavity - doesn't absorb smells. The olfactory receptors bind small molecules reversibly.
However, the olfactory epithelium has a coating of mucus, and so small molecules dissolve in the mucus in order to meet the receptors. Molecules will also evaporate off this mucus, but some vanishingly small fraction of the odorant in a room may stay in the mucus of the nose and the upper respiratory tract long enough to be moved by cilia to the stomach.
I think that for water-soluble molecules, the surface area of mucus lining the airways that odorant can reach is a more relevant factor than the number of a particular receptor (which is very low); but depleting a room of an odorant (which is concentrated enough for you to sense in the first place) by breathing would surely take an extremely long time; as the concentration dropped the remaining molecules would become 'harder to catch', and you'd suffocate first in this enclosed space.
Interestingly, hydrophobic molecules that do not readily dissolve in mucus may be bound by soluble 'shuttle'-like proteins which bridge the gap to the receptors: http://www.ncbi.nlm.nih.gov/pubmed/12044155
These odorant-binding-proteins probably contribute to the diversity of molecules we can smell, and presumably also bind odorants reversibly and may release them back in to the nasal cavity.


In what two ways is ATP used in coupled reactions?

A coupled reaction is where a catabolic reaction drives an anabolic reaction, usually with ATP as an intermediary. The energy released from the first reaction allows for the formation of ATP from ADP and P. The second reaction is then driven by the hydrolysis (breakdown) of ATP, which releases energy.

So the answer to your question is: In a coupled reaction, ATP is first used to store energy from a catabolic reaction and then used to release energy for an anabolic reaction.


Why people like to see pornographic scenes, but do not feel the same about eating scenes?

For these two phenomena to create the same feelings all of the time, the physiology that engenders these feelings would have to be the same.  All I can do is point out that these have been separate and distinct even in yeast and bacteria and invoke a likelihood argument.

The impulse for hunger is almost as old as living things.  In bacteria, cyclic Adenosine mono phosphate (cAMP) mediates hunger, though this does not appear to be universal.

Sexual reproduction appeared much later - in the single celled eukaryotes mating factors for instance are mediated by the MATa/alpha receptors.

In animals like C elegans the differences persist (hunger, mating).  This is not a precise argument, but there is the entropy argument - the odds of these 2 signals evolving together biochemically or genetically is quite unlikely given how separate they have always been.

That's not to say that eating food can't create a sexual arousal, but it does not do so all the time.  The sexual response appears to be plastic and adaptable to nearly any sort of stimulus.  The fact that in primates and many other animals, the pleasure stimulus is related to both mating and eating might make them seem like similar impulses, but when you go deeper it doesn't seem plausible.  So the two could hypothetically create the same feeling, but if you are asking why doesn't it usually... then there are lots of reasons why.

I find it helpful to reverse the question and ask - what would happen to a species where you could suppress the mating impulse by eating?  Probably not an adaptation that would survive long.


Water-bird that can take off vertically from the water?

Yes. A duck can be observed taking off near-vertically from the water's surface in this video. Watch the first duck to take off (from about 0:08). Immediately after take-off, the duck has a very low horizontal speed, and works to gain speed by a combination of flapping and vertically beating its tail. The full process is as follows:

Beat 1: The duck gives a sudden start. Both wings are beaten once on the water's surface to take advantage of the extra resistance the water provides, compared to air. The duck presumably also pushes down on the water with its feet below the surface in order to gain extra lift, but this is not visible.

Beat 2: By the start of the second downbeat, the duck's body is clear of the water, but the feet are obscured by spray.

Beat 3: The whole duck is clear of the water, and is gaining some horizontal speed. This wingbeat is accompanied by a clear vertical flap of the tail.

Beats 4 onwards: The duck continues to accelerate horizontally, remaining clear of the water.

Because the duck comes near-vertically off the water's surface, and remains airborne thereafter, I'd define the take-off as vertical, and the subsequent flight as transitioning into a duck's normal near-horizontal flight. Similar take-offs by terns can be seen in this video (but starting from a dive under the water's surface, see from about 1:02).

More generally, many waterbirds can take-off vertically from the water's surface, without requiring a run-up. All that is generally necessary is to face into the wind, and spread their wings. If the sea-surface is basically stationary, but there is wind, then any difference in speed between the air and the water can be exploited to generate lift.

If there is no effective wind (i.e., the water and the air are moving at the same speed), then the birds have to generate the lift for take-off by expending energy. Some species can do this, but it gets harder with increasing body-mass and wing-loading. I have personally observed a juvenile frigatebird (a species that generally weighs around 1 kg, but with very low wing-loading) lifting off vertically from the water's surface on a windless day. Note that frigatebirds would not normally land on the water (their feathers are not waterproof), and trying out a water landing seems to have been a play behaviour on the part of the juvenile.


Does Pseudomonas aeruginosa have any common name at all?

I think there's a difference between a vernacular or common name ("tiger", "cat", "pigeon", "elm", "pine") and a pet name or nickname as you use it here. The former are names in human languages for a particular kind of animal or plant, while the latter are a colloquial name used by professionals to refer to a particular species, often based on its scientific name.

I can't think of many micro-organisms that have a true vernacular name -- most micro-organisms were given fancy scientific names, and those were used consistently thereafter. The only proper microscopic common name I can think of is "slipper animalcules" -- but I'd be happy to be proved wrong!

Lots of micro-organisms have pet-names -- E. coli, C. diff., "smallpox", "Ebola", "white nose", even Pelagibacter ubique -- but they're either based on the scientific name or on the disease the organisms cause. AFAIK (and based on the comments), Pseudomonas aeruginosa doesn't have one. However, of the list of species you list, only H. sapiens has a vernacular name, while the others only have nicknames based on their scientific name, so I'm not sure it's that surprising! IMO it's mostly macro-organisms that get vernacular names.


Which animal that lives in the forest makes this noise?

It is a bird sound and most probaby a young bird of prey. It might be a young buzzard. Or, if it's in the eveving or night it might be the sound of a young owl.


Distribution of genotypes after adverse selection

If you distribute the 0.12 equally to the two other genotypes you change the relative frequencies. You have to withdraw 0.12 to 0.48 and then set the three frequencies so that they sum up to 1. Therefore, the correct calculation is the following:

If we set $fAA = 0.36$, $fAa = 0.48$ and $faa = 0.16$ and then simulate the death of 25% of the Aa individuals, the same variables at the next time step (without reproduction) will be...

$$faa = \frac{0.16}{0.36 + 0.36 + 0.16} ≈ 0.1818$$

$$fAa = \frac{0.36}{0.36 + 0.36 + 0.16} ≈ 0.4091$$

$$fAA = \frac{0.36}{0.36 + 0.36 + 0.16} ≈ 0.4091$$


Question on kilobase - packaging of genomic material in viruses

This value is only true for linear DNA. However, DNA in cells is not linear, it is folded, which makes it ways more compact (otherwise the DNA in our own cells would be around 2 meters long).

See the figure from reference 1 for a schematic view how this works in higher cells:

The table below (from reference 2, either klick on the picture or the link below for a bigger version) shows how the length of a piece of DNA is influenced by packaging:

There is another caveat in this question, Corona viruses (as the SARS virus) are singlestranded RNA viruses. The RNA of viruses contains packaging signal sequences, where special proteins bind, before the virus is assembled around the bound genetic information. See reference 3 for a general overview and reference 4 for the packaging of the SARS virus in special.

DNA Packaging: Nucleosomes and Chromatin
DNA, chromatin and genome numbers
Genome packaging in viruses.
Assembly of severe acute respiratory syndrome coronavirus RNA
packaging signal into virus-like particles is nucleocapsid
dependent.


Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?

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).


Which literature/study/myth spurred the idea that urine is sterile?

But why does this mantra persist; where does it come from?

Behind this line of inquiry is a fascinating observation about the disconnect between the laboratory and the clinic. The basic answer, from my perspective, goes like this:

It is doctors who talk with people about their urine, and any testing thereof;
for doctors, urine is practically1 sterile; and
among those who are aware of the microbiologic reality, doctors inevitably gloss details when explaining laboratory results to patients.

The average clinician learns most of what he knows about his patients' urine from urinalyses. Most clinical urinalysis assays show negative nitrites and negative leukocyte esterase in normal people. A glance at the reference ranges for a clinical assay will demonstrate this. (See also the clinical review below.)

Ideally, urinalyses should not be performed in patients without relevant symptoms, but they are sent anyway, and they're mostly negative.2  Even in people who have symptoms possibly suggesting a UTI they're frequently negative.  Furthermore, urine cultures from properly collected specimens grown on the media used in clinical laboratories mostly return at 72 hours: "no growth". This point is emphasized in the abstract by Hilt et. al. linked in the question. Of the cultures that grew in their "expanded quantitative urine culture" protocol,

  90% of these specimens were deemed "No Growth" by the standard urine culture technique, highlighting its limitations.

The last phrase "highlighting its limitations" is an interesting one. It appears to me to be yet to be proven that this is a clinically meaningful "limitation" of such assays. Without attempting to refute these data  — fortunately this question doesn't require me to do so — I will note that the two linked studies aimed to show that people with overactive bladder are characterized by increased urinary flora. The explicitly stated hypothesis is that this may contribute to symptoms. Even in this study demonstrating the existence of such a micro-biome even in normal people, then, it is understood as a potentially pathologic state.

The reason this "mantra persists", then, is that it remains true for clinical purposes. In contrast to most (all?) other bodily discharges, urine is not packed with bacteria, and the commonly used assays reflect this fact.  Medicine and laboratory science have different "modes of discourse", each calibrated to convey levels of precision that are appropriate to the outcomes of interest.

Notes

1. In American English at least, that adverb is ambiguous, meaning either "for practical purposes" or (idiomatically) "almost". Both senses are intended here.

2. Of course, there are plenty of data in various populations demonstrating that some substantial minority of urinalyses among asymptomatic people return positive, "proving" that we shouldn't be checking them (amen!). But this is not the point. The gestalt remains: normal = negative.

3. The nitrite parameter in particular is not especially sensitive. It is, however, quite specific (92-100%), meaning it reliably returns negative in people without infection. (See review, below.) Of course, negative nitrites does not mean sterile in the sense that the OP has used it; see "modes of discourse", above.

Reference

Simerville JA, et al. Urinalysis: A Comprehensive Review. Am Fam Physician. 2005 Mar;71(6):1153-1162.