What are the effects of enzyme exposure to high temperatures?

The answer is that it completely depends on what specific enzyme you're talking about; some of them will and some of them won't. What you wrote is correct, that increasing temperature of most enzymes (although there are exceptions) will increase their activity to a certain point, after which the proteins lose their 3D structure and become unfolded.

Upon cooling, it all depends on whether the enzyme can re-fold by itself or not. Some proteins when heated form aggregates, which are more stable than the original conformation, and so generally won't refold with cooling. Some proteins are able to fold into proper conformation by themselves, while other require assistance from chaperone proteins in order to fold correctly. Many of these chaperones are called heat-shock proteins, which are upregulated in response to thermal stress. That points to the fact that many proteins can't just refold on their own, and require help to regain their original conformation from these HSPs.

So the real answer is that it all depends on the specific protein. It also depends on how much you heat the enzyme, and how much of its 3D structure you affect, if you only partially denature an enzyme, it's more likely to refold than one that's been completely denatured. However, if you want an answer about enzymes in general, I'd say that most enzymes after denaturation aren't able to refold properly and regain their enzymatic activity, so the damage is permanent.


Are freshwater jellyfishes really jellyfishes?

The issue here is simply the meaning of the term "jellyfish" and the term "medusa". The first has no taxonomic value and, as such, can be used the way the book/zoologist/layman/journalist wants, unfortunately. Let's see it:

Cnidarians (Phylum Cnidaria) have two basic morphological types: medusa, or medusoid form, which is free-swimming, and polyp, or polypoid form, which is sessile:

There are Cnidarian species that display only polypoid forms and there are species that display both medusoid and polypoid forms in their life cycles.

Regarding the taxonomy of the most common Classes of Cnidarians, Hydrozoa displays both the polypoid and medusoid forms; Scyphozoa displays both the polypoid and medusoid forms; and finally Anthozoa displays only polypoid forms.

So, we can clearly see that Craspedacusta (an hydrozoan) is a medusa, or, in other words, that it displays the medusoid form in some point of its life cycle. There is no doubt regarding this:

The problem comes when we try to use the term jellyfish.

Again, jellyfish has absolutely no taxonomic value. For instance, my teachers used to call an hydrozoan medusa as a "jellyfish". Some time later, when I started teaching zoology, I used to say to my students that an hydrozoan medusa is a jellyfish... that's not a big deal.

However, some zoologists apply the term jellyfish only to the scyphozoan medusae... in that case, jellyfish does have a taxonomic value. And, because of that, since Craspedacusta belongs to the Class Hydrozoa, its medusoid form cannot be called a jellyfish (again, if we accept the definition of those zoologists).

So, in conclusion, it depends on the book/zoologist: some say that that both Hydrozoan and Schyphozoan medusae can be called jellyfish, while some say that jellyfishes are only the medusoid forms from the Class Schyphozoa. That's the definition used by both the aquaticcommunity.com and the Nature Conservancy articles.

PS: Hydra is a Genus, not a Family. I edited your question just to realize that the mistake is from the original article, not yours.


Shouldn't evolution have taken care of baldness already?

As is typical for questions about fitness, this question has more than one valid answer.

The essential question @AndrewSalmon is answering is the right one:

"If evolution eliminates disadvantages, why can xyz trait still be seen the population?"

Here is a more complete list,

1) The trait is not eliminated by evolution since it is manifested after reproduction.  The classic example of this sort of trait is senescence.  Why do we grow old and die?  Clearly it doesn't stop us from having offspring.  I generally don't find this sort of answer informative. Its not a bad argument for the traits of bipolar and schitzophrenic tendencies which can manifest as a chronic mental condition, often in the 30s after many people have children.
These traits are fairly common (1 in 6) in the population.
It is usually arguable that these traits are of some sort of advantage from some perspective (including my examples).  In this case @Andrew argues this.  I'm not sure I agree, but you can read his post for the argument.

2) Pleiotropy. The idea that the negative trait evidences more than one trait.  In this case one might say that baldness is tied with another trait that is beneficial.  Some say that the cause of male pattern baldness, which is an excess of testosterone, would be tied in with other masculine signals, which can often outweigh disadvantages of being bald and trying to find a mate.  A trait like baldness could also for instance be tied to a desirable trait in women, causing it to persist in men as a result of the advantage of say, less hairy women.  I probably wouldn't take this stand either, though its conceivable.

3) "Neutral variant" The third explanation that I will put out is that baldness simply isn't a trait with enough disadvantage (if any) that it should be removed from the gene pool.  While there is evidence that baldness is a disadvantage come friday night, to say that a trait is disadvantageous we have to see, in the long run - over the lifetime - really is a disadvantage.  I think I would agree with those who say that while some women do not find bald men attractive, its not enough to stop them from having kids, which is all evolution cares about.

And if you happen to be balding probably what you should care about, guys!

If evolution should eliminate male baldness, then why not eliminate sterility, homeliness, impotence, poverty, obesity, being dull, living with your parents and adolescent awkwardness?  These are probably even more important obstacles to finding a mate? All of these traits are beneficial traits that are maladapted to modern life or genetic accidents.  Evolution can't get rid of them at all I think.

For an even more complete discussion of the general subject, see Dawkin's "The Extended Phenotype".  Baldness is not discussed however.


Why do we find some things disgusting and others delicious?

Explaining phenotypic variance

You may want to make sure you have a good understanding of the concepts of the underlying variance of phenotypic variance (discussion linked to the concept of heritability) before reading this answer. In this post, I linked several sources of information on the subject.

Culture (environmental variance)

Variance in food preference is in part (in majority eventually) explained by cultural differences.

Genetic variance

I guess that very few people like the smell of rotten eggs. There is selection on taste and smell preferences. Those who don't like the smell of rotten food increase their chance to suffer from bacterial intoxication and mycotoxins. I remember from my Bachelor degree (can't find the study right now) Nestlé (among others probably) performed a genome-wide association study that showed genetic variance for food preferences.

Adaptation

There are probably many loci that are now fixed (not polymorphic anymore) that were at some point under selection as explaining variance for food preference. In other words, at a given locus there might have no more genetic variance as the current allele is well adapted.

By-products

Also I suppose that a part of the underlying genetic and environmental variance for the variance for food preference might be qualified as by-products. For example, it might be beneficial to appreciate a given smell because the smell when present in the sweat of a partner is associated with greater health. If this odour (or similar odour) happen to be present in food, then we may be indirectly selected to appreciate this food item as a by-product of the selection for recognizing healthy partners.


No, but yes.

Sucrose is a large polar solute.
Because it is polar, it cannot easily pass the hydrophobic core of the membrane.
So, if the lipids of the plasma membrane are mostly impermeable to sucrose, how do cells take in sucrose?

Plants

In biology, membrane-bound proteins are used for efficient transport across the membrane (Brian, 2011 from a review of Suc transport in plant cells).
The specific group of membrane proteins used for sucrose transport are unimaginatively called Suc transporters (SUT).

So in a plant cell, sucrose can be moved across the membrane.

Humans

In mammals, there are no SUTs. Instead, sucrose is broken down into fructose and glucose by the enzyme sucrase.

From there, glucose transporters GLUT proteins carry glucose and fructose across the plasma membrane.


How likely is a lack of DNA match with a distant relative?

First, if you haven't read it already, I highly recommend Carl Zimmer's "She has her mother's laugh." for anyone interested in ancestry/genealogy.
In it, he presents the following figure showing the probability of sharing any autosomal DNA with a given ancestor as a function of the number of generations separating you from that ancestor. (notably, this analysis excludes the very real possibility of intermarriage within a family tree).

So, for example, if you were to look at one single ancestor from 10 generations before you, there's a little less than a 50% chance that you share any of that ancestor's DNA (remember that at 10 generations you have roughly 1,024 ancestors).
So, at 5-7 generations there's still a high probability that you both have at least some genetic material from the same common ancestor(s). But, it's much less likely that you both share the same pieces of that genetic material (probably in the 10-14 range on this graph).
Plus, very few (probably none) of the commercial DNA ancestry sites do full genome sequencing for ancestry comparisons. They look at a limited number of specific regions that can help identify familial relations. So, even if you do share common ancestral DNA, it's less likely that it would be detected without whole genome comparison.
Image Credit: https://gcbias.org/2013/11/11/how-does-your-number-of-genetic-ancestors-grow-back-over-time/
Edit
I just wanted to edit and reference that the above analysis was calculated by Graham Coop and colleagues. I did a little more digging and he's got a blog post (How many genomic blocks do you share with a cousin?) with a more relevant analysis for you're specific question, showing the probability of two "cousins" having zero shared DNA blocks as a function of how many generations back the two shared common ancestors.

Reference: https://gcbias.org/2013/12/02/how-many-genomic-blocks-do-you-share-with-a-cousin/


What are the trajectories of flying insects?

Dickinson (2005) has a good review of insect flight, including behavior, biomechanics, electrophysiology, and neural control with links to more of the primary literature. What follows is a general summary thereof.

The jagged trajectories you mention are called saccades in the insect flight literature. In Drosophila, saccades are ~90° turns accomplished in approximately 50 ms. Because flies can't move their eyes independently of their heads, saccades are though to allow a relatively constant visual field most of the time, interspersed with rapid reorientations during which the fly is "blind."

The actual turn begins with the generation of a torque, which starts the fly turning. Shortly thereafter, the halteres sense this change and a counter-torque is produces, which stops the turn.

Rather than random turns, Drosophila are turning away from visual expansion as they near objects. So as they move closer to an object, it expands in their visual field, and they turn away from it.


How many different smells can a human recognize?

As nobody is suggesting an answer I'll give my guess that I already discussed in the comments and give some extra details about ongoing debates on the subject.

We'll start with the sense of color sight in order to make easier. One can argue that we see in 3 dimensions because we use three cells which level of activation inform the brain of the color. I guess that the whole 3D space delimited by the maximum level of activation of each three receptors can be used. Therefore, it is nothing else than the number of receptor that determine the number of dimensions in which we can sense. Now it is assuming that each receptor can send signal of different strength information of the intensity of the light or smell.

According to wikipedia. Mammals have about thousands of genes that code for olfactory receptors. Moreover, the question of how these receptors work is still debated

  In mammals, each olfactory receptor neuron expresses only one functional odor receptor. Odor receptor nerve cells function like a key-lock system: If the airborne molecules of a certain chemical can fit into the lock, the nerve cell will respond. There are, at present, a number of competing theories regarding the mechanism of odor coding and perception. According to the shape theory, each receptor detects a feature of the odor molecule. Weak-shape theory, known as odotope theory, suggests that different receptors detect only small pieces of molecules, and these minimal inputs are combined to form a larger olfactory perception (similar to the way visual perception is built up of smaller, information-poor sensations, combined and refined to create a detailed overall perception).[citation needed] An alternative theory, the vibration theory proposed by Luca Turin, posits that odor receptors detect the frequencies of vibrations of odor molecules in the infrared range by electron tunnelling. However, the behavioral predictions of this theory have been called into question. There is no theory yet that explains olfactory perception completely.

Note: the two competing theories for color sights: Opponent process and Trichromacy

Hope this helps!

I think this question would also be a good fit for cognitive science beta.


Are there neurons that can sense light shining in your ears?

There is no known mechanism for light detection through the ears in humans, as far as I know. It is certainly true that the pineal gland is part of the system that regulates the circadian rhythm (briefly, the daily sleep-wake cycle). However, while the pineal gland in birds and other non-mammalian vertebrates is directly sensitive to light, the mammalian pineal gland is not (see, for review, Doyle and Menaker, 2007 and Csernus, 2006).

In all animals, the circadian rhythm is regulated by a photoperiod cue and therefore requires light detection. In mammals, the light sensors are found exclusively in the retina, the sensory portion of the eye. There are two classes of light detecting cells in the retina. First, rod and cone photoreceptors mediate vision in the usual sense of the word. These cells contain proteins called opsins that absorb photons of light and thereby excite the photoreceptors that contain them, informing the brain that light was detected.

A second class of photosenstive cells in the retina are called intrinsically photosensitive retinal ganglion cells (ipRGCs) (see Do and Yau, 2010 for review). These cells mediate "non-image-forming" vision and are an important part of the circadian rhythm pathway. They also contain an opsin called melanopsin which is a photosensitive pigment. This is not to be confused with melatonin, which is the sleep hormone released by the pineal gland. The ipRGCs in the retina send the photoperiod cue to a brain area called the suprachiasmatic nucleus (SCN). The SCN then signals to the pineal gland.

If we are generous and assume that these light-emitting headphones are the result of misunderstandings, we can guess that the confusion arises from (1) the fact that some animals have a directly photosensitive pineal gland, but not mammals and (2) that the pineal gland secretes melatonin but not the photosensitive pigment melanopsin.

Update: From a bit of research, it turns out that the company selling the headphones is not "confused" as I politely offered. I don't think this site is the appropriate forum to refute their research or claims. Suffice to say that the retina is the only part of the human brain shown to be photosensitive.


What is the shortest mRNA the ribosome can read to produce a peptide?

Reading the paper linked by @canadianer and its references was pretty illuminating. It's a straightforward paper except for its conclusions, and the most convincing part is the evidence of actual translation. There's some evidence that transcription start sites are used as a regulatory mechanism by displacing other things that might otherwise bind. An unknown fraction, but most(90%+), very short bioinformatically detected ORFs are not translated.

Some, however, are. See this table for the experimentally verified translated micropeptides. The shortest is a nearly unbelievable 6 peptides long.


Opposite results between Blomberg's K and phylogenetic signal in Phylocom (AOT)

I think I figured. Someone told me that the above results are the same. The absolute value of K = 0.29 indicates the magnitude of the signal is less than expected under a Brownian motion process, but it’s still more than random expectation (according to the P-value,P = 0.001). So both methods suggest that treewise phylogenetic conservatism is significantly greater than random expectations.

Actually the meanings of K statistic and P-value were clearly stated in the original paper (Blomberg et al. 2003). I should have looked at it first... but anyway, I think it is solved now.


I don't know any-such continuous-membrane-material that can do so. But yes certain membrane-transport-proteins can do so.

Carrier proteins are normally highly specific about in which-direction to transport which molecule; and in general,  they are classified as uniporters, symporters and antiporters.  *

So an uniporter would be an accurate example of situation you are asking about.

Carrier proteins those utilize ATP for pumping (those shows "primary active transport"), are also normally highly specific to direction. For example the Na+-K+pump and the H+ pump.

Channel proteins too, sometimes show directionality, for example certain K+ channels ** such as inward-rectifying potassium channel

A potassium channel diagram showing the selectivity filter (diagram from The cell/ Cooper **, slightly edited: Na+ filter-out not shown, and the term 'selectivity filter' is labelled in image ).

KcsA potassium channel diagram from wikipedia. In its open-conformation out of the following;

i.e. the third one, can conduct the K+ ion in a specific direction, because the pore-region is very specific- it allows K+ ion only to enter in the cell.

  Reference:

  * Plant biochemistry by Hans Walter Heldt, 3rd edition, Academic Press-Elsevier, Paperback edition.
  ** The Cell, a molecular approach/ Cooper/ Sinauer and ASM press.
  Harper's illustrated Biochemistry/ Murray, Bender, Botham, Rodwell, Well/ Lange and McGraw Hill.
  Wikipedia.


There are several papers that use alkaline hydrolysis to delipidate or "detoxify" the endotoxin for use as a vaccine (1, 2, 3). The point of many of these papers is to develop a detoxified LPS (dLPS) vaccine to protect against sepsis in the pathogenesis and treatment of gram-negative infections. The detoxification is important, as the lipid-A portion of the LPS contributes significantly to sepsis. In this case you would be targeting the O-antigen or core oligosaccharide.

So one of the problems that I can see is that there are many bacterial serotypes, comprised of many different O- and core groups. I'm not aware of any vaccines with that sort of breadth. Issue two is you get an infection and you need to administer these vaccines quite fast, if not prophylactically, as adaptive immunity takes a number of days to come to speed.

It's also not clear to me whether a prophylactic vaccine to E. coli is useful to the populace at large, epidemiologically (just as an example).

The field also seems to lack clinical data on tolerability and efficacy, which is what I'd be more interested in, e.g. is it safe for humans and does it work?


Does the Urea Cycle exist in invertebrates?

Perhaps worth adding that the role of the urea cycle in terrestrial vertebrates is the disposal of excess N derived from protein metabolism. Such animals are ureotelic. Arthropods, in contrast, are uricotelic, using uric acid for N disposal, so it would make no sense for them to have a functional urea cycle. (Nematodes - I don't know.)

The importance of avoiding having a urea cycle when it is not needed is illustrated by the situation in yeast (Saccharomyces cerevisiae). In yeast some of the enzymes that would be part of the urea cycle are used in degrading arginine, while others are used in the biosynthesis of arginine. Yeast cells will carry out one or the other of these processes depending upon their metabolic status. If both processes were to be active at the same time this would result in a urea cycle that would waste ATP. This is avoided by having a multienzyme complex consisting of arginase and ornithine transcarbamoylase (in the degradative and biosynthetic pathways respectively), allowing reciprocal regulation so that only one of these is active at any time.


What is the reason for 'microcytic' anaemia?

The reduced iron availability affects the red cell size during differentiation.

  The presence of red cells with reduced mean corpuscular volume (MCV) reflects reduced hemoglobin synthesis, which can have several causes. It can result from defects either in iron acquisition or availability, or in heme or globin synthesis. Experimental data in mouse demonstrated that early mitotic divisions are accompanied with no reduction of MCV, whereas during differentiation mitotic events are associated with a substantial reduction of MCV[1]

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649346/

Coopersmith A, Ingram M. Red cell volumes and erythropoiesis. II. Age: density: volume relationships of macrocytes. Am J Physiol. 1969;216:473–82.


Check the parameters that go into the Goldman equation... it shows that permeability of ions is as important as their concentrations. If the permeability is zero, there is no potential. Because other conductances are mostly closed at rest, the leak channels are almost entirely responsible for the resting membrane potential (there is a minor component, a couple mV, supplied by the sodium-potassium pump itself, that is missed by the Goldman equation). If there were no leak channels, there would be effectively no resting potential, and certainly no useful one.
Additionally, there would be no return to "baseline" after a signalling event.
Leak channels are entirely integral to nervous system functioning (and the function of other excitable cells, including muscles and immune cells) - a system without them would be nothing at all like what we actually observe in any biological nervous system. The membrane potential massively amplifies the concentration differences into an electrical signal, such that large changes in voltage occur merely by opening and closing channels: very few ions need to move for this to happen, making a very efficient signalling system, requiring only the maintenance of ion concentration gradients (which change very slowly).
I would say it's correct to say that the role of leak channels is quite diminished during an action potential, since voltage-gated conductances ultimately overwhelm the leak conductance. You can see this from the Goldman equation, too. But they are quite important in setting threshold itself, and in returning to rest after an action potential. However, even during an action potential there is very little actual ion flux. Electrical forces are very strong, so not many ions need to move (see again the answer I linked above).


Are there natural selection experiments that quantitatively agree with theoretical modeling?

I think the closest example to this is Greg Lang's work at Princeton. His work will take a population of yeast and let it grow for 1000 generations. At each generation a sample will be kept allowing sequencing of the population at each generation.
His website is available here: http://www.genomics.princeton.edu/glang/

And some of his work has already been published here: http://www.genomics.princeton.edu/glang/papers.htm


DNA methylation and the validity of the definition of epigenetics

A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).


Why do adults lose hearing at high frequencies?

Hearing declines with age and, typically, high frequencies are affected first. Age-related hearing loss (or presbyacusis (Kujawa & Liberman, 2006)) is progressive and starts at the highest frequencies and as a person ages the lower frequencies are affected. The reduction in hearing sensitivity is caused by the loss of hair cells. Hair cells are sensory cells in the inner ear that convert acoustic vibrations into electrical signals. These signals are transmitted to the brain via the auditory nerve.

Because of the tonotopic organization of the inner ear (the cochlea) one can conclude that presbyacusis develops from the basal to apical region. The following schematic of the cochlea from Encyclopædia Britannica, Inc. nicely shows the cochlear tonotopy (i.e., high frequencies in the base, low frequencies in the apex);

As to your question why the basal region is more sensitive to aging - that is a very good and interesting question that has not been answered, as far as I am aware. What is known, however, is that the basal regions of the cochlea are also more sensitive to the damaging effects of ototoxic antibiotics such as kanamycin (Stronks et al., 2011) and other aminoglycosides, and some chemotherapeutics such as cisplatin (Schacht et al., 2012). In low doses these compounds specifically target the basal regions over the apical ones (at high doses the whole cochlea is affected).

Perhaps the specific anatomy and circulation causes the basal region to be affected more by these chemicals. For example, blood flow may be enhanced basally whereby environmental and food-based chemicals may enter the basal region more readily (educated guesses, I can dig up references of authors posing these possibilities if necessary). This scenario may also contribute to presbyacusis, since it is quite imaginable that years of exposure to various substances may cause accumulation damage specifically to the basal parts of the cochlea.

In addition, since high frequencies are coded in the basal region, and given that sound enters the cochlea in the basal region (see picture below), all sounds, including damaging loud low-frequency stimuli first travel to the base on their way to their point of processing.

Because sound is analyzed as a travelling wave, sound travel stops at that point where the frequency matches the cochlear characteristic frequency. There the wave quickly dies out due to cochlear filtering (Mather, 2006); see the first picture above. In effect, more apical parts of the cochlea are exposed less frequently to (damaging) sound stimuli, while the base of the cochlea is exposed to all sounds entering the inner ear.

Hence, chemical exposure and acoustic wear and tear may be more prominent in the cochlear base, which can explain why presbyacusis starts at the very high frequencies and progresses to low frequencies (upward in the cochlea) from there.

References
- Encyclopedia Brittanica* The-analysis-of-sound-frequencies-by-the-basilar-membrane
- Kujawa & Liberman, J Neurosci 2006; 26:2115-23
- Mather, Foundations of Perception, 2009
- Schacht et al, Anat Rec Hoboken 2013; 295:1837-50
- Stronks et al, Hear Res 2011; 272:95-107


Does photosynthesis begin instantly when a plant is exposed to light?

This is a really interesting question! It gets to the heart of how photosynthesis works.

First, note that whether or not the plant will immediately start producing glucose depends on a variety of factors (what type of plant, what type of light). For example, many succulents undergo CAM photosynthesis (Crassulacean Acid Metabolism) in which light capture and CO2 fixation are temporally separated (the former during daylight hours and the latter at night). Additionally, artificial light comes with different wavelength compositions (ratio of red to far-red light  can differ) and photosynthesis rates will change accordingly read more here.

But I haven't yet addressed the heart of your question: how long does it take for a plant to start photosynthesizing once it is exposed to light? To think about this, consider what is actually happening when light hits a leaf. Light energy is absorbed by pigments in the chloroplasts, which transfer energy to neighboring pigments until an electron is transferred to a reaction center. From here, "light reactions" of photosynthesis continue and usable chemical energy is obtained. From there, the CBB cycle (sometimes called the Calvin Cycle, Calvin-Benson, or "dark" reaction) continues, which is where the CO2 from your question comes into play, and 6-carbon sugars are produced. It isn't a matter of "ramping up", so much as completing this series of chemical reactions.

So now, it is time to consider your thought experiment. Let's say that you have a bean plant in your kitchen (C3 photosynthesizer), and you conduct your experiment shining a white-light lamp on the plant with the experimental conditions as described. I believe that you would produce roughly the same amount of sugars in each because glucose synthesis occurs on the order of seconds (~30s). If you exposed your bean plant to white light for only 5-second increments, there would not be time to produce the energy needed to complete the CBB cycle.

Aside: the experiments that first elucidated the CBB cycle were conducted by exposing cyanobacteria (a photosynthetic bacteria) to labeled (heavy) carbon, and exposing it to light for a few seconds, and characterizing which compounds were produced from that heavy carbon within that few-second time frame. Read more about that experiment in the previous link. It sounds like Calvin himself wondered the same thing you did!

For further reading on the basics of plant physiology, including photosynthesis, I always recommend the plant bio "bible": Plant Physiology and Development by Taiz L., Zeiger E., 2010. I still consult it often.

Hope this helps. Stay inquisitive!


What causes the opaque green colour in Lepidoptera?

According to this paper, green pigments are found in lepidoptera. The study focused on Geometridae, and found that the primary pigment in emerald moths, such as Hemistola chrysoprasaria is also found as secondary pigment in Pseudoips prasinana. The authors dubbed the substance 'Geoverdin' and suggest it may be a derivative of chlorophyll consumed during the larval stage. I cannot find any further studies mentioning 'geoverdin' or its chemical identity.


How does the ideal free distribution work?

The order of settling depends on the resource availability in different patches (in your case the difference between high and low quality habitat), but generally speaking, the pattern you observe conforms to the ideal free distribution.

The key factor in the ideal free distribution is that habitat patches are filled according to the current resource availablity (~per capita resource access), given the current density of individuals in the patch (so the marginal resource availability). If the high quality patch has much higher resource levels than the low quality patch, this means that many individuals can settle in the high quality patch before the marginal resource availability becomes equal to the resource availability in the low quality patch, at which point individuals will start settling in both patches. Therefore, the two observations you make; 1) lower overall density in low quality habitat and 2) the high quality patch being settled first, both agree with the ideal free distribution.

This graph (from wikipedia.org) illustrates this pattern nicely, for the standard version of the ideal free distribution:

Here, the marginal, apparent value of a patch is shown on the y-axis and the number of individuals in the patch on the x-axis, and the numbers refer to the order that individuals will settle in the two patches (so the first 6 settle in the high-quality Patch B, ind. 7-9 in Patch A, ind. 10 in Patch B etc).

However, I encourage you to read about other theories on habitat choice, and the pattern you describe can probably be explained by other processes as well. The ideal free distribution also has some rather restrictive assumptions (e.g. equal quality of individuals and no dominance/territorial/interference behaviours among individuals), which you have have to consider.


Immediate cause of death due to dehydration

The simple answer is dehydration kills you by causing the blood flow to become completely ineffective.

Dehydration limits the amount of water in the bloodstream causing an increase in blood viscosity, and thereby an increase in blood pressure.  As this process gets more extreme the body has a difficult time getting the blood to the places it needs to be, and will limit blood flow to non-essential organs (kind of similar to what happens when it's cold outside and your fingers go numb).  At the same time waste is beginning to build up as the kidneys cannot filter the blood effectively, and the internal temperature rises because of the lack of sweating.  This process gets more extreme until one of your essential organs cannot take it anymore and shuts down, likely the liver first.

Most everything I got for this answer was from a PopSci Article. Although there is also a nice 1935 study with many measurements from real people.


Can coding DNA be used for DNA fingerprinting?

When selecting sequences to use for DNA fingerprinting, you have to use sequences that are highly variable within the population.  Coding sequences mostly aren't, and they aren't going to vary much in size, the way tandem repeat sections do.


Since Eumelanin is the protective form of melanin and there is some research available that Pheomelanin contributes to the generation of reactive oxygen species which are harmful to the cell (see reference 1, which contains a lot of further references on this topic), I don't see any reason to do so, but ok. Additionally removing Eumelanin from your skin will lead to a higher risk for skin cancers as Melanoma. Let's think through this:

If we look at the biosynthesis pathway of the Melanins, they both start with the same two reactions (see the figure from here):

The routs parts at the DOPAquinone, which in the presence of Gluthathione or Cysteine goes into the pheomelanin direction. The concentration of Cysteine available to the cell needs to be higher than 0,76 µM (see references 2 and 3 for details), otherwise the reaction goes exclusively into the Eumelanin direction.

There are some skin whitening (or better lightening) products available which contain L-Cysteine or GSH. This will work to some extend, but once the level drops enough, the ratio will shift back to the more natural ratio between Eumelanin and Pheomelanin. There is also no data available on the risks of doing this, so I would strongly advocate against it. See the review in reference 4 for details and additional references on this topic.

If you now think, ok, taking some pills is enough, I would call this a false hope, since this process is highly regulated. This happens on one part through external signaling through the MC1R receptor (which as you already mentioned is of importance here) and also through the availability of key enzymes in the process as well as stability of them and their regulation.

Signaling through the MC1R receptor is highly important for pigmentation and also the amount of enzymes available (the transcription factor MITF is regulated by it). If the signaling is strong, the cysteine storage is soon depleted bringing on the production of Eumelanin. If this signaling is weak
this will not happen and the production of pheomelanin is favoured. Mutations in MC1R are the reason for people having red hair and and fair skin. See reference 5 and 6.

Interfering with the signaling cascade which is activated by MC1R is certainly not a good idea either, since this will interfere with other processes in the cell as well. These pathways are also disregulated in cancers, so I would not touch these.

Summarizing I think there will only be a way of influencing this by taking some supplements, but how safe this is, is unknown. All the other possible ways are certainly more dangerous.

References:

How does pheomelanin synthesis contribute to melanomagenesis?: Two
distinct mechanisms could explain the carcinogenicity of pheomelanin
synthesis.
Rate constants for the first two chemical steps of eumelanogenesis.
Chemistry of mixed melanogenesis--pivotal roles of dopaquinone.
Systemic skin whitening/lightening agents: What is the evidence?
UV signaling pathways within the skin
The melanocortin-1 receptor: red hair and beyond.


Protein binding to DNA is not bivalent. ChIP is enriching for DNA to which your protein of interest is bound, but that protein may bind certain sites throughout the genome more strongly and frequently than others. Stochiometric effects play a role, as do the strength of the binding motifs.

Some proteins bind very specifically to a given sequence, but most allow for some degeneracy in their binding sites. A strong site will be bound more frequently (and thus more highly enriched during ChIP) than a weaker site. Not just the presence, but the frequency of binding is what ChIP really measures.


Enzymes vary in substrate specificity

This is covered in most textbooks of biochemistry, but you can find explanations on the web, e.g. here. As far as ribonucleases are concerned, there can be high specificity (e.g. recognition of a RNA with a specific base sequence), lower specificity (3′- or 5′-exonucleases — act from these respective ends) or specificity limited to the particular bond to be broken (e.g. pancreatic ribonuclease digests any RNA phosphodiester bond — but not DNA). (There is also specificity of strandedness—  between double- and single-stranded RNA.)

What determines this varying specificity?

Evidently, the substrate specificity is determined by the extent of the structure of the substrate that the enzyme has to recognize — i.e. bind to like a ‘lock and key’, refered to in the question. This requires familiarity with the chemistry of the substrate, in this case RNA:

In the diagram above (modified from Berg et al.) the phosphodiester bond which must be cleaved is highlighted. We can deduce from this diagram that in order to be specific for RNA — but no more — a ribonuclease needs to be able to recognize the ribose 2′OH (i.e. distinguish it from 2′-deoxyribose) as well as recognizing the phosphodiester bond. There is no need to recognize the bases.

The mechanism of action of bovine pancreatic ribonuclease

The mechanism of pancreatic RNase was established in the 1960s, long before any RNase that recognized particular sequences, although it has been refined subsequently. A diagram from the paper by Roberts et al. (1969) is shown below.

The diagram does show a ‘pocket’ for one of the bases adjacent to the phosphodiester bond, but this need only be generally hydrophobic, able to accomodate any of the four bases.

To study the interaction of the bases with RNAase one has to obtain crystal structures of RNAase complexed to pseudo-substrates or inhibitors (the true substrate hydrolyses, of course). The literature here is complex, and I am unable to provide a convenient review of the topic. It does appear that the binding of RNA is stabilized by the interaction of particular bases with the protein, but the key point is that any such interactions are not a requisite for the binding of the substrate. As a starting point to the literature I suggest the Protopedia page on RNase A, and a paper by Birdsall and McPherson.


How do I find the number of child terms associated with a specific GO term?

I don't think it's possible to do this via QuickGO. You can, however, do it from GO's website, using their GOOSE tool. This offers an interface to the GO SQL database and lets you run queries. It also offers example searches, one of which ("Find descendants of the node 'nucleus'") can easily be modified to return what you are asking for:

SELECT COUNT(*)
FROM
 term
 INNER JOIN graph_path ON (term.id=graph_path.term1_id)
 INNER JOIN term AS descendant ON (descendant.id=graph_path.term2_id)
WHERE term.name='heart development' AND distance = 1 ;

In the query above, I modified the example and changed 'nucleus' to 'heart development' (GO:0007507) and changed distance <> 0 to distance = 1 to make it list only direct descendants. Finally, I also changed SELECT DISTINCT descendant.acc, descendant.name, descendant.term_type to simply SELECT COUNT(*) since all we are interested in is the number of descendants. If you also want their names, leave the SELECT line as is. That will show both the list of names and the total in the output.

The modified query shows us that this term has 30 descendants:


Will eukaryotic RNA fold in the same way in prokaryotes?

As you have mentioned ions and temperature affect RNA structure. There are also different types of RNA structures and their dependence on ions are different. Mg2+, as Mad Scientist mentioned, stabilizes duplexes; so do monovalent cations like K+ and Na+. However, Mg2+ favors duplex over quadruplex if the same RNA can adopt both these conformations.
Dependence on temperature is a trivial case.

Ions and temperature should be more or less same for prokaryotes and eukaryotes unless we are talking about extremophiles.

Apart from these factors I can think of two other factors that can cause difference in RNA structure between prokaryotes and eukaryotes:

Osmolytes
RNA binding proteins/chaperones (Already mentioned in comments by Mad Scientist)

Osmolytes

It has been shown that TMAO (Trimethylamine N-oxide) stabilizes RNA secondary structures. The metabolism of TMAO is different in prokaryotes and eukaryotes.

From this paper:

  Although eukaryototes can endogenously produce L-carnitine, only
  prokaryotic organisms can catabolize L-carnitine11. A role for
  intestinal microbiota in TMAO production from dietary carnitine was
  first suggested by studies in rats; moreover, while TMAO production
  from alternative dietary trimethylamines has been suggested in humans,
  a role for microbiota in production of TMAO from dietary L-carnitine
  in humans had not yet been demonstrated30-32. The present studies
  reveal an obligatory role of gut microbiota in the production of TMAO
  from ingested L-carnitine in humans (Fig. 6c)

I cannot ascertain that this will affect RNA folding but is possible.

RBP

This is something that you can be certain about. Some RNAs require protein counterparts to adopt a functionally capable structure. In the absence of the protein they may not form the relevant structure. So if an RNA needs Hfq then you have to express it in the eukaryotic system where you want to use the RNA (and converse).


Protein folding, extra dimensions and bio-mathematics

Short Answer

What mathematical work is currently being done in this area?

A... lot?
Longer Answer
The "n-dimensional slope" thing that you're talking about shows up in the modern theory of protein dynamics as the "landscapes" concept. There's no truly standardized form for the theory, so it goes by many names. Try googling folding funnel, energy landscape, probability landscape, free energy surface, etc.
adendum
Oh, and also the current consensus is that the "quantum leap"-style effects that you were talking a little bit about don't play a large role in folding, at least in the initial stages. The current thinking is that most (not all!) of the dynamics of protein folding can be modeled using classical physics. Quantum effects can't come into play until the atoms of a protein are closely smooshed together (ie after the initial "collapse" phase of protein folding has finished).


Good question. The answer really depends. There is a normal range of plasma sodium concentration that ranges from about 135 to 145 mM. You body has multiple endocrinologic and neurological mechanisms to closely regulate this concentration. So even if you went out and ate a ton of salty snacks, your body would still keep your plasma sodium concentration within this range. A salt concentration much lower or greater than this can start to cause problems depending on how fast it happens and how far from the normal value. Brain surgery patient are often given lots of extra salt to keep their brains "salty" as this protects from cerebral edema and counteracts salt wasting that often occurs with brain injury. However, the opposite or very high sodium concentrations are also not good. As you said, a diet high in salt can lead to high blood pressure and chronic high blood pressure can cause damage the small blood vessels in the brain and cause small strokes over time or very high blood pressure can cause larger bleeds. Usually we see this in patients with very high uncontrolled blood pressures in the 170-200s systolic range. I'm kind of pulling those numbers out of my memory and you would have to check the literature to verify.


It looks like a unicornfish (genus Naso), maybe Naso vlamingii, the Bignose Unicornfish. They're Acanthurids, related to surgeonfishes and tangs.

These are mainly found in Indo-Pacific ocean around the depth of 50 mts from surface. Coral reefs are their main habitat and destruction of coral reefs is their current biggest threat alongside trading by fisheries. A good source of information for this species is available here.

A copy of this fish.

Picture credits: UM Rosenstiel School


Since you asked three questions, I'll answer them one by one.

Are glycoproteins and glycolipids present only on the cell surface membrane?

No, glycoproteins have many functions and are certainly not restricted to cell membranes.

Some examples of glycoproteins in blood include fibrinogen, antibodies, miraculin, etc. See this:

  Fibrinogen (factor I) is a glycoprotein in vertebrates that helps in the formation of blood clots.

For a more detailed list of glycoproteins, see this wikipedia article.

On the other hand, glycolipids are found only on cell membranes. See this:

  Glycolipids are lipids with a carbohydrate attached by a glycosidic bond. Their role is to maintain stability of the membrane and to facilitate cellular recognition. The carbohydrates are found on the outer surface of all eukaryotic cell membranes.

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.

Glycoproteins, or any proteins, after they are completely processed , don't just float around in the cell and reach their appropriate place. Its obviously not that proteins 'know' where to go, but they are actually taken to their appropriate places. This is known as protein targeting. See this:

  Protein targeting or protein sorting is the biological mechanism by which proteins are transported to the appropriate destinations in the cell or outside of it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases.

There are differences between cell membrane and organelle membrane, which makes them distinguishable for targeting factors.

Why would there not be glycosylation enzymes on the cytosolic side?

Glycosylation is a post-translational modification or proteins.

  Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Only certain proteins require glycosylation, that is why they are translated by ribosomes connected to golgi apparatus or endoplasmic reticulum. If glycosylation enzymes are present everywhere in the cell, then every protein that encounters them would get modified and, possibly, non-functional. Thus, there are special compartments in the cell for such purposes.

EDIT: To answer the questions you asked in comments:

are there any glycoproteins found elsewhere inside the cell? For example in the mitochondria?

We aren't sure about that yet. There have been a couple of studies to find out whether there could be glycoproteins in mitochondria, one of which is this:

  Isolated intact mitochondria selectively incorporate monosaccharides from nucleotide diphosphate monosaccharides into protein. Fucose, mannose, glucose, and galactose were incorporated by the mitochondria into glycoprotein; xylose was not. Structural integrity of the mitochondria was not necessary for the incorporation of monosaccharide into glycoprotein; mitochondria broken by homogenization also incorporated monosaccharide. The monosaccharides incorporated into glycoprotein were localized in the inner mitochondrial membranes, the same membranes which contain the protein into which leucine is incorporated by the isolated mitochondria.

If there are glycoproteins in mitochondria, they could be at many other places too inside a cell.

does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm?

Glycoproteins are not required inside cell (I, or maybe nobody, knows why). Their main function is as receptors or secreted products, thus they are not found inside a cell. However, glycosyltransferases can behave as dynamic glycoproteins and hence are found inside cells. See this:

  Glycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based.


Is there a difference between "Alpha Helix" and "Alpha subunit"?

These terms are completely unrelated. Alpha-subunit is an arbitrary name for a protein subunit in a multi-subunit protein complex (one having a quaternary structure like haemoglobin or G-protein etc).

Alpha-helix is a type of secondary structure.

Addition by David:

For those who may be unfamiliar with this, alpha, beta, gamma etc. are Greek letters of the alphabet (equivalent to English a, b, c) — also written α, β, γ. They are sometimes used in science to enumerate or differentiate between a series of related things — proteins, small molecules etc.


How do big cats perceive objects, specifically vehicles?

It's basically the same as humans, they include higher predatory associations and less logical and word associations. The neural circuits study all the images received from the eye and compare new objects to previously learnt categories: Bird/Log/Horn/flailing upside down limb/face/car/rhino... You can feel your own neural networks at work when you focus on an unidentified detail (bird/branch/rock) and class them into right and wrong results. Moving objects occupy a moving class of their own, i.e. in your garden, they are a potential threat or a prey.
When the truck is rolling along normally, the cat has extensively studied this kind of object already and has made these associations: Glass windows he can't get into, faces inside glasses, rubber tires, slight smell of humans, major smell of petrol and artificial stuff, indestructible, square and round bits, sees it every day from all angles and has interacted with trucks plenty of times. He rarely gets any food from safari trucks, they all look a bit the same. A truck occupy the same prey opportunity as birds in trees which can just fly away.
The brain behaves differently towards known objects and movements and new, unknown animate objects, the unknown animate things result in: the capture of attention.
When there is an arm waving out of the window, the cat's brain is receiving an unidentified living thing attached to the truck, perhaps some kind of living meat! A living thing, a prey. Is it a leg of lamb? is it inside or behind the box? Can he get into this truck? Is it a bird? The cat will be interested in the unidentified, new kind of living thing until he has figured it out.
general reading.
visual cortex of monkeys and cats.
Activation of the hypothalamic feeding centre upon visual prey detection
other research.


Can bacteria only thrive in agar solution?

You seem to have some misconceptions about growing bacteria. These are cultivated using specific media, for E.coli this is usually LB Medium which contains the following ingredients per liter:

10g Bacto-tryptone
5g yeast extract
10g NaCl

This is dissolved in water and subsequently sterilized by autoclaving. Note that there are much more medium recipes for different strains and different culturing conditions.

Bacteria can then be grown either in suspension (shaking in an Erlenmeyer bottle in the liquid media) or on the surface of plates. To produce these plates, you need an agent, which solidifies the medium without having any effect on the growth of the bacteria or the medium. And this is where the Agarose is used. It can be heated up with the medium during sterilization, does not interact with the medium and bacteria do not metabolize it. If you cultivate bacteria, which produce agarase (which is an enzyme to break down agarose), you need to use a different agent to solidify your medium. And you will use a different medium anyways.
They simply grow on the surface of the solified medium and can easily be picked for further analysis or the inoculation of (bigger) liquid cultures.


In many cases cell division depends on the stage of development an organism is in. The rate of cell division is obviously much faster in a developing organism and from what I understand fully differentiated cells such as neuron and those in skeletal muscles don't divide (correct me if I'm wrong here).

In early development totipotent cells (stem cells that can become anything) begin to differentiate dependent on environmental factors, turning into multipotent (partially differentiated) cells that can only lead to certain cell types. For example: mesodermal precursors can differentiate to myoblasts, which can go on to differentiate into myotubes, later forming muscles.

Epithelial and and blood cells are the two of the main types of cells that need to be constantly replaced in developed organisms. As far as I know cells lining the gut epithelium are fastest to divide. They are created from stem cells in 'crypts' (pockets) in the lining and are pushed outwards, where they are later broken down (by what I would assume would be abrasion and intestinal juices). My book gives them a lifespan of 3-5 days. External skin cells are much slower to divide (though I'n not sure by exactly how much).

Red blood cells have have a lifespan of approximately 120 days. They are replenished by stem cells in the marrow of certain bones (e.g. a femur). Neutrophils are the next most common blood cell, with a circulating life of 8 hours (but lifespan may be a few days). Per day, roughly equal numbers of RBCs and neutrophils are created and are most numerous new cells created per day. Lymphocytes, another white blood cell, are responsible for immune 'memory' can persist for years. The fastest recorded mitotic cycle for a mammalian cell (in culture) is ~8-10hrs.


Why does white light viewed through optical chopper appear purple/blue?

I totally wasn't expecting to immediately duplicate this with a fidget spinner and the fluorescent light in my office.  What a neat effect!

My technique: I hold the spinner quite close to my eye, so that it occupies nearly all of my field of view, and look through the spinning part at my ceiling light.  If the spinner is very fast or very slow, I don't see any change in the hue of the light.  However there's an intermediate rate where the back part of the fluorescent lamp takes on a patchy blue tint with colored edges. The tinted region is irregular and unpredictable in the same way as a pressure phosphene, if you're familiar with that better-documented effect, and has kind of the same "feel" to it.

Trying to photograph the effect just gives the rolling shutter problem, so that's no use.  (No color change in the photo, either.)

At the rotational speed where the color change effect is the most pronounced, I estimate the frequency at which the spinner blocks nearly all of the light to be 10-20 Hz.  (How? I let the thing hit a fingernail and listened to it tap; it sounds like thirty-second notes, four to a click, at a good presto tempo.)  I've read elsewhere that the human eye can process images at 10-15 Hz. So some sort of biological stroboscopic effect, where the eye has just enough time to begin to respond to the reduced light before the light returns, seems plausible to me.


Why is the heart adversely impacted by chronic psychological stress, yet it benefits from routine physical exercise?

From the perspective of sympathetic nervous system

Exercise induced adaptations of heart

A common phenomenon in endurance athletes is the athlete's heart /athletic heart syndrome

Once athletes stop training, the heart returns to its normal size.

You must understand why this type of adaptation is happening in them:
Firstly the athletes train to produce work output at near maximal levels/ sub maximal levels of work done which cannot be physiologically achieved in a day.So the increased heart rate generated by the sympathetic stimulation is sufficient to fulfill oxygen demand of the body only at certain levels of work done by raising the heart rate
As the grade of work done nears submaximal level the oxygen demand increases in the body and the increased sympathetic stimulation (which also restricts the cardiac muscle efficiency by decreasing diastolic time,coronary blood flow) is no longer able to suffice it.Such high oxygen demand is responsible for the useful adaptations of the heart in the form of athlete's heart.Athlete's heart reduces the need for sympathetic stimulation to increase cardiac output .

During intensive prolonged endurance or strength training, the body signals the heart to pump more blood through the body to counteract the oxygen deficit building in the skeletal muscles. Enlargement of the heart is a natural physical adaptation of the body to deal with the high pressures and large amounts of blood that can affect the heart during these periods of time.

Comparison with chronic psychological stress

During stress the body may or may not have high oxygen demand (the principal stimulus for adaptation) because the sympathetic stimulation is psychological and not in response to physiological work.So the heart instead of adaptating gets afflicted with detrimental pathophysiological effects of prolonged sympathetic stimulation.

stressors’ contributions to diverse pathophysiological changes including sudden death, myocardial infarction, myocardial ischemia, and wall motion abnormalities, as well as to alterations in cardiac regulation as indexed by changes in sympathetic nervous system activity and hemostasis.

From the perspective of cortisol (stress hormone)

Effect of psychological stress on athletes

When we are talking about the detrimental effects of psychic stress it is important to note that it may override the cardiac adaptations and severely affect performance like,for example high cortisol levels in blood released in response to stress (physical/ psychological).Although cortisol levels in the blood observe a circadian rhythm in normal healthy indivituals, some reports claim that exercise reduces detrimental effects of high cortisol levels on the heart.However,stress may override exercise induced effects in athletes but this is a prospective study, subject to greater research

A prospective study found a clinically significant increase in overnight urinary cortisol:cortisone ratio during a high training load period in triathletes, who subsequently underperformed and reported fatigue

REFERENCE TEXTBOOKS:

Exercise Physiology And Ergonomics (An Introduction) Asis Goswami Academic Publishers.Pg-39 to 57

Essentials Of Exercise Physiology (4th Ed.) Victor L.Katch,William D.McArdle,Frank I.Katch pg-302-333


Help identifying an insect (I think it was an insect)

This is not easy to answer without a picture. However, if it was unsegmented, it was definitely not an insect (which have a segmented body plan, both as larvae/nymph and adult). Your description also sounds nothing like an insect. However, the overall description fits fairly well with a flatworm (Phyluym: Plathelminthes), see e.g. Geoplanidae. They can resemble slugs or leeches, but both lack segmentation and antenna. Finding one inside your house sounds a bit strange though, as they generally prefer moist habitats.

Terrestial flatworms are relatively mobile and most are predators or scavengers

Example pictures:


Which is more important for protein expression mRNA structure or codon optimization?

This is an excellent question! To my knowledge, there hasn't been a definite answer yet. Recently, I did tons of research on which factors influence protein expression and you should definitely check out the following questions which I asked:

What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?
What determines a successful protein expression in E. coli?

I answered my second question by posting a concise version of a paper from DNA2.0 (a gene synthesis company) that discusses the protein expression. It summarizes all the important factors (RBS site, codon frequency match, 5' mRNA secondary structure), but it doesn't discuss the extend to which they influence expression.

There is a nature paper from Voigt lab about RBS calculator, which takes into account only the 5' mRNA secondary structure and it doesn't discuss at all the codon-optimization. The calculator was good, but far away from perfect: there is a 50% chance of predicting an expression level within a 2-fold range of the target one.

On the other hand, an older paper from DNA2.0 argues that the mRNA is covered with ribosomes practically all the time, so the secondary structure of the mRNA should have little effect. Besides, an actively translating ribosome can break up stem-loop structures.

In my opinion, we are still far off from predicting RNA secondary structure formation, although it might be highly implicated in protein expression. From what I read, I think that it is equally crucial that there is no strong secondary structure at the 5' end of the mRNA, the RBS sequence is close to the consensus one and it it appropriately spaced upstream of the start codon, and the first 60-100 codon frequencies match the frequency of your heterologous host.


Is Pork more prone to carrying higher loads of parasites than Beef?

Trichenellosis from pork occurs in about about 5 people per year since the 1980's in the US. it has a 0.2% mortality rate there. We can say that 1 American/ 1 European dies from pig meat every 20 years. That's a fair concession. Worldwide the death rate is in the 100ds per year from pork, compared to 3 million who die from the fat in beef and chicken and lamb and excess sugars, and 1.35 million attributed to cars.
The other pork parasites are less dangerous and have less than a 90 cases per year in the USA, mostly people coming from epidemic areas. https://www.oie.int/doc/ged/d9157.pdf
Beef can transmit tuberculosis, E-Coli, BSE/CJD and sarcosystosis. E-Coli from unsanitized beef kills many times more people than pork born diseases, i.e. 100 times more people in the US die from E coli from beef, it is one of the main vectors and a lot more difficult to control than via pork. E-Coli is uncommon from pork. Worldwide many thousands of people die of E-Coli from beef every year.
There were an estimated 147 000 new cases of zoonotic tuberculosis and some 12 500 people died of the disease in 2016. Beef are the main causal agent. All animals have tape worms and other worms.
Beef, Lamb, Pork, chicken, and milk all increase the risk of heart attacks and strokes because animal fat can increase cholesterol dramatically, and eating beef from one region can make you more susceptible to heart attacks than pork from another region, because the fat content can vary a lot. Far more people die of heart attacks than animal parasites these days, about 1 million times more rich people die from animal fat and sugar related disease than from pork parasites.

No pork parasites are counted on this list of parasite deaths, globally it's perhaps 50-350 per year.

About 99.999 percent of people that die from meat, die from the fat and other high sugar diets, and it doesn't matter if it's pork or beef. (source WHO)... 5 million people die every year from tobacco, and 2.5 million die every year from Alcohol, especially in very poor countries.
The income levels of people that die from parasites and alcohol are very low, something like 99.9% of parasite deaths are poor people and 90% of alcohol deaths.
So you can concede that alcohol kills many poor people, but that animal parasites from pigs kill 10,000 times less people than alcohol. Pork kills a million times less people in the west than cars or fatty foods.
Details:
There are three important parasites found in pigs which pose
a risk to humans who ingest raw or undercooked pork
products. These parasites are Trichinella spiralis, a nematode
or roundworm, Taenia solium, a tapeworm, and Toxoplasma
gondii,


Could we transmit smells electronically?

There are only three kinds of optical receptors in the eye, but more than 900 kinds of olfactory receptors. Thus you can encode pictures with the three primary colors, but there is no small set of primary scents.

To transmit a smell via "primary scents", you'd have to create an artificial nose that monitors the response of each of the olfactory receptors, and then at the other end release a chemical mixture that has the exact same response pattern. (You won't find a one-to-one mapping of chemical compound to receptor.)


What regulates the timing of the motion of molecular machines during DNA Replication?

That's a pretty neat video, I'll just give you some background information first. It's an illustration of the "trombone model" of DNA replication. The darker blue molecule is helicase, it unwinds the DNA and facilitates translocation (this is an ATP dependent process). The dark purple molecules are DNA polymerase, they catalyze DNA strand synthesis (an NTP dependent process) using an ssDNA template and 3'-OH primer (the primer:template junction). The green circular molecules are sliding clamps, they increase the processivity of DNA polymerase. The light purple molecule is the sliding clamp loader, unsurprisingly it loads the sliding clamp onto the DNA (ATP dependent). The light blue molecule is a flexible linker that connects everything together. The other green molecule (the one that contacts helicase) is primase, it synthesizes RNA primers (which contains the 3'-OH initially used by DNA polymerase).

Certainly intermolecular forces play a significant role in this (and every) biochemical process, but I'm not really sure what you're talking about when you're describing electric forces and Brownian motion.

Anyways, the answer to your question is no, Okazaki fragments do not have a fixed length. DNA synthesis, as mentioned above, occurs only by adding NTPs to a 3'-OH primer. Thus the length of Okazaki fragments is dependent on the spacing between primers on the lagging strand. This is dependent on when primase binds which in turn is dependent on primase concentration as well as its binding affinity with DNA and other replication fork proteins (especially helicase). High concentration and/or high affinity leads to a higher binding frequency and therefore shorter Okazaki fragments. The opposite is true for low concentration and/or low affinity. Note that most (or all?) primases have some degree of sequence specificity which means that specific DNA motifs will increase binding affinity. For example, Escherichia coli primase (DnaG) recognizes the trimer GTA.

This process also requires some degree of coordination between leading and lagging strand synthesis. Primer synthesis and DNA polymerase recycling on the lagging strand is much slower than the continuous synthesis on the leading strand. It has been suggested that primase acts as a "molecular brake" by halting the replication fork during primer synthesis to prevent the leading strand polymerase from rapidly outpacing those on the lagging strand (Lee JB, Hite RK, Hamdan SM, Xie XS, Richardson CC, van Oijen AM. 2006. DNA primase actas as a molecular brake in DNA replication. Nature. 439(7076):621-624.).


Can "red" cone cells actually see much red light?

This is a good question. The first  thing to note is that human colour vision is very complex and still poorly understood. If you visit the wikipedia page on RGB,  you will find that this correctly mentions that the S, M and L cones are most responsive to violet, green and yellow wavelengths respectively (which answers your first question - calling the cones red, green and blue is primarily for historical reasons, because there aren't any real wavelengths that only activate a single cone, it's hard to say what colour a cone 'is'). So why do we use red, green and blue phosphors? A practical answer can be found by looking at the CIE 1931 colour space: this was essentially an attempt to find how one could add together different amounts of a small number of wavelengths to make the result indistinguishable from any desired wavelength (read the linked page if you want more information, also have a look here). The result found was that the colour matching functions should look like the following graph (what this is showing is how much of a red, green and blue light are required to simulate a wavelength):

You can see that this is similar to the responses of the cones except for the peak in the red (which corresponds to violet looking like red-blue):

To answer the question in your title, red cells do see the most red light of any cone, but that is not where they see the most light. Here is an example set of spectra of the red, green and blue phosphors in a CRT:

To answer your question about why we use red, green and blue in the first place (rather than yellow-green-blue or red-green-violet), it's good to understand why the CIE 1931 functions are that shape in the first place. The wikipedia RGB page mentions that:

  ...good primaries are stimuli that maximize the difference between the responses of the cone cells of the human retina to light of different wavelengths, and that thereby make a large color triangle.

This gets at the fundamental reason, which is that it is generally believed that we do not perceive colours in terms of the activities of each cone, but in terms of the differences between those signals (as it says here), an opponent process. The following image illustrates a simplified version of how the opponent signals in colour vision processing are thought to function, so that the resulting signals are a black-white, a yellow-blue and a red-green axis:

This image shows the theorized shapes of the response curves of these opponent functions (see here for an interesting historical paper on this theory and here for more details and some predictions of the theory):

It is possibly apparent from the last graph why the CIE 1931 colour graph is the shape that it is, since we see red as a bimodal distribution with a distribution of green in between, and a large distribution of blue at short wavelengths and yellow is red + green. (Incidentally this also explains why we also perceive yellow as a primary colour - see the 4 highlighted points R, Y, G and B where one curve passes through 0). Additional information on the neurological and psychological correlates of colour vision can be found here and here and more technical theoretical details here.

The upshot of all of this is that red, green and blue are the best 3 colours to use as the basis for additive colour mixing, but not because they are what L, M and S cones are most sensitive to. Rather it is because it has been shown that these particular colours fall where there is maximal difference between the cone signals and because they can accurately represent all of the colours in our colour space as illustrated by CIE 1931 (due to being widely spaced and all perceived easily as you have mentioned in points 2 and 3 of your question). Effectively, the reasons are complicated and to do with the neurological processing of the colour signals and the differences between the signals rather than the straightforward signals themselves.


Effective population size when the population sizes varies from season to season

This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is:

$H_t = \left(1 - \frac{1}{2N}\right)^tH_0$

When $N$ varies between generations you use the product of this formula:

$H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - \frac{1}{2N_1}\right)...\left(1 - \frac{1}{2N_{t-1}}\right)H_0 = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)H_0$

To get the overall $N_e$ you need to find the population size that gives the corresponding decrease in heterozygocity over t generations i.e:

$\left(1 - \frac{1}{2N_{e}}\right)^t = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)$

Rearranging gives:

$N_e = \frac{1}{2\left[1-\left[\prod_{i=0}^{t-1}\left(1 -\frac{1}{2N_{i}}\right)\right]^{1/t}\right]}$

This expression can be approximated by the harmonic mean, which is easy to verify with some toy data (you get small deviations if yearly population sizes are very small). The explanation given above can also be found in Hedrick (2009, p217ff), along with some nice examples that integrates the effects on effective population size from several factors.


How do B memory cells provide immunological memory? Do they differentiate into plasma cells?

This 2005 review in the Annual Review of Immunology entitled "Antigen-specific memory B cell development" would be a great first resource in answering your question in great detail. Briefly, memory B cells (MBC), upon re-exposure to the same antigen, very rapidly expand and differentiate into antibody-producing plasma cells (PC), with the help of memory T helper cells (Th). However, more MBC are still produced by this reaction, so that a second challenge with antigen doesn't deplete the memory population.

PC are geared towards producing gobs of antibody, and not much else. Upon stimulation with antigen, MBC will produce some cytokines to attract the Th cells that are required for costimulation and regulation, but to my understanding it is the Th cells that manage the whole response, activating effector T cells ("killer" T cells), NK cells, dendritic cells, etc., and not the MBC themselves.


Can a viable embryo develop from the fusion of two egg cells?

Yes, it is possible to make a zygote from two ovules. Other more complex scenarios are possible as well. You might want to read this cbc article. If the two ovules came from the same organism, then the baby will very likely suffer from a number of diseases due to very low heterozygosity (same mechanism that is causing inbreeding depression and problems of consanguinity).

It is likely not possible to get a zygote from two spermatozoids though because you would lack mitochondrial DNA (mtDNA). There is a little bit of mtDNA in spermatozoids but they are generally not transmitted. Through experimental setup I imagine it might be possible. Also, spermatozoids are very small and would lack many of the ressources necessary to start a zygote.


This post goes over what MuTec requires as input. mark duplicates and indel realignment will probably have to be done on bam file to use it as input. BQSR is optional and does not change the quality too much. HaplotypeCaller is used for germline not somatic variant calling.

If you have followup bioinformatics questions, you might be able to find answers more quickly on biostars or GATK forums


Relation between trigeminal and facial nerve in sympathetic response

Certain parts of the facial nerve cooperatively share structure of trigeminal nerve. For example, to reach the sublingual gland, the chorda tympani of the facial nerve joins the mandibular branch of the lingual nerve. Additionally, to reach the lacrimal gland of the eye, the greater petrosal nerve branch of the facial nerve joins the structure of the maximallary branch of the trigeminal nerve.

For a pictorial demonstration of this, please refer to page 1069 of Clinically Oriented Anatomy 7th edition by Moore.


Why do some people find vegetables so repellent when evolutionarily they should find them an attractive and thus tasty food?

Evolution is not that simple. There is no selective pressure for a feature if it does not ultimately in some way benefit reproduction or the offspring. Vegetables are healthy for us now because we live much longer than we used to in an environment not dominated by us, and they contain many nutrients which help to sustain a healthy body beyond, say, 50.

However, if you imagine an average life span of around 30, it becomes clearer why evolution would favour foods high in energy over foods containing high amounts of micronutrients. Over such a time span, the long-term effects of a diet rich in fat and sugar do not develop significantly, but the energy supply is exactly what is needed to sustain bare life to the reproductive age.


The classic analogy here is that of a blueprint. For example this one I found here which is kind of relevant:

If you use the blueprint above to make yourself a little sister and later change the blueprint, the sister you built will not be affected.

That is only part of the story though, the analogy can only go so far. DNA is constantly "read", what this means is that genes are transcribed to RNA which in turn is translated into proteins. To use a horrible simplification, genes are the blueprints for proteins. Therefore, if you change the gene, and the cell then reads from it to create a protein, it will indeed create a different protein than what the original gene would have coded for.

The point I am trying to make is that depending on which genes are changed, you can either have no effect or a huge one. Some genes are only read once when the cells are reproducing, others are read constantly as the proteins they code for are used up and then produced anew. So, if the gene you change is one that will be read again during the cell's lifetime, then you will see a change. A classic example of this is cancer. If, on the other hand, it is a gene that will not be read again, then the changes will not have any effect.


Does cartilage connect to other cartilage?

A ligament can connect two bones:

Picture 1: Knee joint ligaments (source: Wikipedia, Creative Commons license)

A ligament can connect two cartilages or a bone and a cartilage:

Picture 2: Larynx ligaments (source: Wikipedia, Creative Commons license)

Ligaments can also connect internal organs:

Picture 3: Ligaments connecting abdominal organs (source: Wikipedia, Creative Commons license)


OK, let us start from the beginning. We know what makes one cell type different from another cell type is its expression - i.e. what genes are actually being transcribed into RNA. Therefore, there should be certain RNA in one cell type that should not exit in another cell type. If you isolate RNA from a certain cell type, say a neuron and you want to show that your sample RNA contains only neuronal RNA, than you have to prove 2 things:

That your sample contains certain RNA sequences that are known to be in neurons
That your sample does NOT contain certain RNA sequences that are known NOT to be in neurons

There are several lab procedures for identifying the presence/absence of certain RNA sequences in a sample, your chosen technique is qPCR. Here is a brief explanation of how qPCR works.

You put your RNA sample along with a sequence specific primer in the qPCR machine. The primer will bind to a specific sequence and then that strand will be replicated. This will keep on repeating, cycle after cycle. So if you start with 1 sequence of say sequenceA, after cycle 1, you will end up with 2, then 4, then 8 and so on.

Anyways, if your goal is to use qPCR to prove your RNA sample comes from a neuron then you must find some sequences that are known to be specific to neurons. Then find primers for these sequences. Then use these primers to amplify some RNA from your sample. If you get amplification, then you must have had that sequence in your RNA sample. To further support yourself, you may also want to look up a few sequences that are known NOT to be expressed in neurons and using the same principle prove that these sequences are NOT in your sample.

The above will give you qualitative data, it will simply tell you if a certain sequence exits or does not exist in your RNA sample. Since you are only interested in the presence or absence of markers, this should be sufficient. Howver, if you would like to quantify your data, i.e. find out how much a certain sequence is expressed then read on.

You can also get quantitative data from qPCR (after all qPCR stands for quantitative PCR). The number of copies of an RNA sequence after a certain number of cycles is proportional to the initial number of copies of that sequence in your sample. In other words, if your initial RNA sample has a lot of sequenceA and a little sequenceB, then at any cycle, you should see more sequenceA.

We can take advantage of this relationship. There are two general methods you can use to quantify your results. One is called Absolute quantification and the other Relative quantification.

The idea behind absolute quantification is that you run two qPCRs. In one, you do your RNA sample. In the second, you run a standard sample, for which a standard curve is available. You can then compare your RNA sample results with the standard's results to get an idea of the number of copies in your sample.

The idea behind relative quantification is that you compare the qPCR results for your sequence of interest with the qPCR results of a refrence gene. This will only give you an idea of how many times more or less your sequence of interest if expressed than the reference gene. Since you do not have a refrence gene you cannot use this method, but you can use the absolute quantification method explained in the paragraph above!

Here are very useful links on quantifying using qPCR:
http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction#Quantification_of_gene_expression

http://relative.gene-quantification.info/

Let me know if you need further clarifications.


This is a tussock moth caterpillar in the Lymantriidae family.

The image is not clear enough for a definitive ID, but it appears you have some species in the genus Orgyia.

Likely, this is a white-marked tussock moth caterpillar (Orgyia leucostigma).

From Auburn University:

  The full-grown larva (Photo 2) is around 35 mm long. The head and shield on the segment behind the head are red. There are two long black pencils of hairs on the first segment of the thorax that project forward. A single black hair “pencil” arises from the eighth abdominal segment and projects upward and rearward. The back is mostly black and the sides yellow, cream, or grayish. There is an erect brushlike tuft of white or yellowish hairs on each of the first four abdominal segments, and a conspicuous red dot on segments six and seven.

Range: Entire eastern U.S. and west to Minnesota and Texas. [source].


Rationale behind washing off unbound protein antigen in indirect ELISA

The method is based on the principle that the amount of antigen bound to the plastic will be proportional to the concentration in the sample being tested. And of course an ELISA will usually be run with a calibration in parallel so that the signal from your sample is compared to that from standards.

The wells will be rinsed anyway in subsequent steps to remove unbound antibody molecules: if you didn't wash off unbound antigen it would simply compete for binding the antibody then disappear later in the procedure.


Stabbing muscles when flexed and when relaxed

Well, if we look in very basic detail at how muscle contraction works within a myofibril of the sarcomere:

N.b. this isn't on a loop and only plays through seven times

The red lines represent actin filaments whilst the blue lines represent myosin filaments.  During muscle contraction the filaments move over each other:

As shown in the above diagrams the "more contracted" a muscle is then the smaller the size of the H zone (the area where there are just myosin filaments).

So if we consider a penetrating impact that went through a plethora of identically aligned sarcomeres (obviously this is not the case in nature) then we could presume that (et ceteris paribus) the object would not penetrate as deeply into a contracted muscle as it will hit more tissue on its route than in a relaxed muscle.


Is it necessary to conduct a power analysis before beginning an experiment?

You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.

Yes

It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you should do in collaboration with the person who is going to be helping you analyze your data. To address a couple points:

You'll see all kinds of researchers doing all manner of sloppy things when it comes to statistics and data analysis. Reading some journals makes me groan. You won't necessarily find it a problem for your field, but one should ask oneself if the goal is merely not to get called out by your peers, or to actually run a well designed experiment.
The consequences to the validity of your results lie in an increased risk of Type II error - the incorrect failure to reject the null hypothesis, or in slightly clearer English, finding no effect when an effect exists in reality. Which means, if you run an under powered study, you run the risk of doing the entire experiment, finding nothing, and being wrong. The consequences of that are myriad - first, it likely harms your chances to get published, as null results are often quite difficult to get into press. Second, if it does get into press, you've managed to get an incorrect finding into the literature, which will then be propagated in meta-analysis, reviews, and the minds of impressionable future readers. And then there's the chance you'll abandon a potentially productive line of inquiry because you couldn't be bothered to do power analysis.
One thing to also consider is that not having conducted power analysis somewhat limits your ability to chase after interesting sub-findings. If you've built your experiment on a shaky foundation, and then want to do a second analysis on a sub-set of your results, you almost certainly don't have the power for it.
There are times when you'll be required to do power analysis. If you do research that's clinically relevant, and you ever want it to appear in one of those journals, you may very well be required to show you had a properly powered experiment. And many grant applications require you do so. Even if they don't require it, some people will do a napkin math estimation of your power if they don't see it appearing in your application anywhere.

sjcockell is partially correct. To do power analysis, you at least need to have some notion of the effect measure you're likely to see. And these are indeed just estimations of what you'll see. But in nearly all circumstances, you'll likely have some ideas already. Are there similar experiments you can draw from? Your own pilot studies? A "feel" born of experience in your particular system?

It's also trivially easy to calculate power under a number of difference scenarios, to ensure your experiment is sufficiently powered if things go considerably worse than expected. For example, in a study I once did the power calculations for, we weren't sure what the ratio of exposed to unexposed subjects would be. So I ran it over a large range:

Which left me with the confidence that even if I was in my "worst case" scenario, I'd have reasonably good power at realistic effect sizes.

That's the true strength of power calculations. They'll tell you things about your study. What you need. What doesn't matter. Whether or not before you spend time and money pursuing an idea if you have a reasonable chance at success. Sit down with someone, take an hour or two (at most for a simple experiment) and do it right. Or ask CrossValidated for advice.


Is it possible to have life that feeds on thermal energy

It is theoretically possible but no known organisms does it. The problem is you need a pretty strong and persistent temprature gradient to generate usable work out of it, and those are not that common in nature.


The "hollow" i.e. the neural canal develops into the ventricles, the cerebral aqueduct and the spinal canal (Wikipedia; also see this site).

For a more authoritative reference, see this book by Haines and Ard† (page 82 onwards in google books; google book links are apparently transient and they expire; therefore I didn't provide one).

† Haines, Duane E., and M. D. Ard. Fundamental neuroscience for basic and clinical applications. Philadelphia, PA: Elsevier/Saunders, 2013. ISBN: 9781437702941


What is the medical definition of death?

Ok. So when a doctor declares a person dead, it is when their heart or brain is totally not working, and won't start working no matter what they do.

This is legal death.

If your heart stops cold, you are clinically dead. This is reversible, if you are lucky. This definition basically only exists so people can say they "died". It has no real biological significance, except for the fact that your heart is not pumping blood and providing you with oxygen. This will cause...

Biological death:
Within 5-10 minutes at room temp you have reached the event horizon of biological death. Biological death is real death.

Once this time threshold is crossed, there is almost always no going back.
This is because Cells in the brain are destroyed by oncosis, and other mechanisms and forces far beyond me.


Differences between comatosed states and brain death

I'd recommend reading a review paper on disorders of consciousness, which cover the spectrum of minimally conscious states, vegetative states, and coma. Brain death is outside the context of disorders of consciousness, but is often discussed for comparison. Nico Schiff is one expert in the area; I've attached a reference to a review he coauthored at the bottom and I'll draw mostly from that review in this answer.
Schiff and Fins write, with some bolded emphasis by me:

At present, brain death is diagnosed if clinical evidence of the complete loss of brainstem function is present at the bedside and the patient demonstrates a failure of ventilatory drive in the setting of documented hypercapnia (significant elevation of blood partial pressure of carbon dioxide over a chosen threshold) — the ‘apnea test’. Fulfillment of these criteria should invariably associate with an ‘empty skull’: no sign of any metabolic activity or blood flow measured by positron emission tomography, a ground truth linking the biological model to the clinical assessments

The first two statements are most relevant clinically; PET is not commonly used except in research and rare cases of uncertainty. Biologically, brain death is when the brain is...dead. There is no recoverable neural function. The signs are a lack of any brainstem reflexes, including lack of respiratory drive. Additionally, other potential causes of these symptoms (such as pharmacological causes) must be ruled out.

Coma is a state of unconsciousness, but some brain functions are preserved. Again from Schiff and Fins:

Both comatose and vegetative state patients are unresponsive to environmental stimuli, although reflex movements may be present; in neither condition are goal-directed behaviors initiated. Comatose patients lack state variations and typically remain in a closed-eyes state that is unchanging even when presented with the most vigorous stimulation.

Comatose patients do not meet the criteria for brain death described above, but do have a complete inability to respond to stimuli and do not make purposeful movements besides reflexes. Schiff and Fins (and others) compare this state to deep anesthesia. Though your question posits that there should be some distinction between medically-induced and one that is not, there is really no functional difference. The possibility of recovery is tricky to assess, but generally patients who spend a long time in coma have a worse prognosis than those that do.
The clinical approach is different. A brain dead patient is dead. Nothing can be done to recover function; potential for organ donation can be considered, but there is nothing medically to do for the individual. For a comatose patient, it's more complex, and decisions need to be made regarding the level of medical support to provide given expected prognosis in both probability and extent of recovery.

In brain death, the neurons are dead. The lack of electrical activity is not because they are in some quiescent state, it's because they are dead. With coma, it's less clear except that there are signs that some neural function remains. Coma is really a clinical state, not a biological one. It's not always possible to determine the level of irreversible damage in a comatose patient, nor the extent of possible recovery.

Schiff, N. D., & Fins, J. J. (2016). Brain death and disorders of consciousness. Current biology, 26(13), R572-R576.


Does drying meat in the sun make digesting it easier?

Various food processing methods, such as cooking, can make meat easier, that is faster, to digest. The purpose of drying meat is to extend its shelf life, not to make it more digestible. Drying removes water from the meat and somewhat physically (but not really chemically) change it.

The amount of calories used for digestion is not that high; probably less than 100 Calories per day, so meat prepared in different ways does not likely significantly affect the amount of calories burnt.


The principle of targeting cancers with high intensity radiation is already in use. For example:

http://www.mayoclinic.org/tests-procedures/gamma-knife-radiosurgery/basics/definition/prc-20014760


Osmotic pressure and turgor pressure details

when we talk about external force applied in this case we talk about a setup that is made by us. like a U tube experiment that is filled with water and separates both the hands of the tube via semipermiable membrane and we add solute one side and due to this water starts to rise in that hand of the tube to avoid this rise in water level an external pressure is applied tht prevents this water rise and this pressure is termed as osmotic pressure. THIS IS THE CASE OF A ENVIROMENT WHERE EXTERNALFORCES CAN BE APPLIED BY US AND IT IS VERY MUCH DIFFERENT FROM THAT OF THE CELL WORLD.
in case of cells osmotic pressure is directly proportional to the concentration of the solution i.e more the solute more the OP and visa versa. in cells osmotic pressure are internal force that is caused due to  difference in concentration of the solutions.
and as we know water move from low osmotic pressure to high osmotic pressure
{ from less concentrated to more concentrated solution} thus cell swells up because of entering of water when cell is placed in pure water or hypotonic solution.
CONCLUSION : CELL DO NOT SHRINK BECAUSE NO EXTERNAL FORCE IS APPLIED BY US THE DEFINATION U GAVE IS CORRECT BUT IT IS NOT APPLIED IN CELL WORLD. IN CELL WORLD OP IS A PRESSURE DEVELOPED DUE TO DIFFERENCE IN CONCENTRATION OF SOLUTIONS AND THIS PRESSURE IS CREATED INORDER TO EQUAL THE CONCENTRATION OF SOLVENT (WATER) IN BOTH THE SOLUTIONS.


Can I tell my antioxidants intake based on nutrition facts labels?

Well yes, you could get this information from food labels, since the recommended daily intake of vitamins is well established. But there is really no need to worry about dietary "antioxidants" (usually vitamins A, C and E, and carotenoids). If you eat a reasonably balanced diet, you are getting all the vitamins you need. Thankfully, vitamin deficiency is very rare in the western world today.

There is a lot of hype around "antioxidant" dietary supplements, but there is no convincing evidence that high levels of these vitamins in your diet has any beneficial effect at all. Randomized clinical trials have failed to show any effects whatsoever of antioxidant supplements on chronic diseases, and excess intake may even increase overall mortality.

Non-vitamin compounds like carnitine are not necessary in the diet at all, since they can be synthesized by the body in sufficient amounts. In general, the fact that a compound is a "major player" in cellular metabolism (in oxidative defense or other wise) does not mean that you have to consume it. For example, the TCA cycle intermediates are arguably the biggest "players" in human metabolism, but none of them are necessary in the diet.