How does DNA still work after recombination? If you take two computer programs and randomly swapped pieces from each of them. The result is not going to work. It will just be garbage. If you take two novels and randomly swapped chapters the result will be garbage too.

How is it than DNA (which is infinitely more complicated) can be combined, some from the father and some from the mother and yet it still somehow works?

Can you give a simple example?

One must always be careful not to stretch an analogy further than it can withstand, but since you started these analogies, I will follow up on them and explain the small mistake you've done in their representations.

The two books are not as different as you have in mind. You are not pasting the beginning of Uncle Tom's Cabin with the ending of Harry Potter but only the beginning of Harry Potter with the ending of another Harry Potter in which Ravenclaw is renamed Eagleclaw.

Also, unlike in books, there is no beginning-to-end reading frame for the entire chromosome. There are just genes randomly placed along chromosomes. The reality is that the placing is actually not that random but assuming it is can give you a sense of why it can often be fine to recombine two chromosomes and end up with still functional chromosomes.

For the computer program analogy, it would be like swapping files between branches of the same project (thanks @IronSean for his comment).


How does skin healing work? I stacked my bike and split my head right open.  About three weeks later the scab falls off and the skin is sealed over, like magic!  How does it all work?  How does the brain know that part of the body is injured and needs repair, or does the brain know at all?  What kind of signals between brain/cells/body are involved.

Sorry it's probably a basic question for a biologist, but I come from a different field and have always wondered about this amazing process.  It's also a very hard topic to google about, because most results are about spiritual healing, crystals, prayer and a lot of pseudoscience rubbish.

Healing in the body is normally independent of the brain. Following an injury, a process of inflammation attracts lots of cells to the site of the injury (including platelets, white blood cells, clotting factors). There's also vasoconstriction (tightening of your blood vessels) to reduce blood loss from the injury site. Your skin cells continue to divide rapidly until new skin replaces the damaged one which later falls off. This is a highly simplified version of the process but hope it makes sense. So in summary, healing takes place by cell division (also known as mitosis).


Using evolutionary algorithms in molecular biology? I am currently an MSc student studying molecular biology (on paper I'm a chemist) and soon I have to talk to my supervisor about my future, PhD research topic. Besides molecular biology I'm also interested in machine learning, mostly in evolutionary algorithms (evolutionary strategy alg.s, genetic alg.s) and Bayesian optimization, from both of which I have written multiple, working programs in C# at home. Due to the massive need for people trained in informatics I'd like to convince my supervisor to include this topic into my future research, especially as I have already acquired some basic skills in these areas. However I have only seen research examples that are purely computational and these didn't include any laboratory work. Can you provide me some insight into the use of these techniques in molecular biology and ways of connecting these with laboratory work?

The first thing that springs to mind is modeling and simulating the evolution and specificity determinants in protein - protein binding. You can easily include an experimental  part and make it as big as you like (the bigger, the better). For a useful set of physiologically important protein - protein interactions and background info on the specificity and affinity determinants in those systems, see Ivanov et al., 2017 and Ivanov et al., 2016, and the references therein.


Effect of soap on the survival of non-enveloped viruses As I understand it, non-enveloped viruses are not annihilated by alcohol or have lipid layers to get soluble in soap micelle.
Does soap remove non-enveloped viruses and does hand wash help in their spread?

Yes, hand washing with soap is effective at removing non-enveloped viruses. Here is a study showing that washing with soap is effective at disinfecting norovirus, which is a non-enveloped virus: https://aem.asm.org/content/76/2/394


Is solving cancer required in order to avoid aging? When the telomerase enzyme is not active the telomere shortens every time the cell duplicates leading to a reproductive limit (Hayflicks limit).
On one hand this is a believed reason for aging. On the other hand this makes a mutated cell more difficult to acquire cancer, since in order to become cancerous, it would need to mutate such that the telomere enzyme becomes active.

The telomere enzyme is not active in most human cells.
Therefore activating the telomerase enzyme in somatic (body) cells could theoretically decrease aging but would also increase the risk of cancer.

Am I right to assume that in order to avoid aging of humans one would first need to "solve cancer"?

Interesting question. My answer is no, but it requires a rather science-fiction style answer - at least it's beyond current technology, but here goes:

My Assumptions

I make the simplifying assumption that ageing is only related to telomere length. Thus by "avoid ageing" I assume you mean "avoid telomere shortening". Also to clarify things for others, I'll clear up the role of telomeres in aging and cancer:

Telomeres in cancer - it has been hypothesised that telomeres act as "mitotic clocks" - keeping track of how many times a cell can divide before it stops. This "time limit" is supposed to put a halt to cancerous cells before becoming malignant.

Telomeres in aging - Since telomeres set a limit to the number of times a cell can divide this essentially sets a time limit for the organism as a whole - those cells that divide faster (e.g. hair and skin cells) go out first (grey hair and wrinkles) etc.

Short answer

No.

Long answer

All we need to do is come up with a way to somehow "maintain" average telomere length at some "safe" length, i.e. we keep them at a length that is long enough to prevent us from aging but short enough so that a cancerous cell will not be able to proliferate to dangerous numbers.

For example, every now and then we provide "telomere length booster jabs" (this is some abstract fictional idea of course). This is like adding more time to our lives when we are about to run out: "Oh look, I only have three months left!", "Don't you worry, with our new telomere booster jab you will have an extra 3 months!"...


What if Staphylococcus Aureus are extinct? What if Staphylococcus Aureus are extinct?

Can it be good for human or bad for human?

Thanks for your answer in advance.

It is almost entirely parasitic and has not physiological or ecological effects that could not be replaced easily by another bacterium. It is responsible for immeasurably more infections that protections of humans, therefore it is a disease vector, not a beneficial bacterium.

If it went extinct, humans may suffer from increased population pressure, that would be the only worry.


Corpus luteum during the luteal phase and gonadotropins Does the corpus luteum operate independently of the hypothalamic-hypophyseal-ovarian axis? I know that hCG sustains the corpus luteum in the absence of FSH and LH, but in an ovarian cycle where there is no pregnancy, do FSH and LH affect the corpus luteum? It seems to produce a lot of estrogens and progesterone even when FSH and LH levels are low.

(Online I saw that the corpus luteum degenerates because of low FSH and LH levels. Is this true? Why doesn’t the corpus luteum degenerate immediately after the LH surge, then, whereafter FSH and LH levels are so low? If not, then why does the corpus luteum degenerate?)

Lots of questions, so I'll break them down one at a time:

  Does the corpus luteum operate independently of the hypothalamic-hypophyseal-ovarian axis?

The corpus luteum does depend on intact pituitary signalling.  Hypophysectomy at the beginning of lutenization will result in cessation of corpus luteal growth and subsequent drop in progesterone; in essence, the corpus luteum won't grow and function properly in the absence of pituitary hormones.  In some species, estradiol is needed, so intact gonadal steroidogenesis is also required.

  In an ovarian cycle where there is no pregnancy, do FSH and LH affect the corpus luteum?

Elaborating on the above, yes pulsatile secretion of LH is required to fully develop and maintain the corpus luteum (not so much for FSH).  Other pituitary hormones, such as growth hormone are also involved.  In pregnancy (or pharmacologically), a large dose of hCG can sustain the corpus luteum.  hCG and LH are homologous.  Depending on the species, prolactin and estradiol are also required.

  Is it true that the corpus luteum degenerates because of low FSH and LH levels?

The corpus luteum degenerates (luteolysis) because of prostaglandin produced by the uterus.  In the absence of a uterus (and therefore prostaglandin), luteolysis is delayed.  It is reported that estradiol from the next batch of follicles triggers oxytocin release by the posterior pituitary and subsequent release of prostaglandin and thus is the penultimate cause of luteolysis.

  Why doesn’t the corpus luteum degenerate immediately after the LH surge, then, whereafter FSH and LH levels are so low?

As described above, it is not low FSH and LH that cause luteolysis.

  If not, then why does the corpus luteum degenerate?

Described above.

Source: http://physrev.physiology.org/content/80/1/1.long


What causes anorexia nervorsa? I've heard of anorexia nervosa being a severe loss of appetite. I'm wondering what causes such disease in humans?

What is anorexia nervosa?

Generally, it is an eating disorder which is characterised by a tremendous fear of food as well as an extreme weight loss.
Patients with anorexia nervosa do not necessarily lose their appetite but rather obsessively control and restrict their food intake.

Anorexia Nervosa as an inherited disease/genetic factors

There has been a lot of research proposing that eating disorders are often biologically inherited and tend to run in families.

  Recent research suggests that inherited biological and genetic factors contribute approximately 56% of the risk for developing an eating disorder. Individuals who have a mother or a sister with anorexia nervosa are approximately twelve times more likely to develop anorexia and four times more likely to develop bulimia than other individuals without a family history of these disorders. Studies of twins have shown a higher rate of eating disorders when they are identical (compared to fraternal twins or other siblings).

The hormone serotonin

There has been found that anorexics have an overproduction of serotonin, which can cause a continual state of acute stress and anxiety.

  Researchers are still puzzled as to why, if anorexics already have high levels of serotonin, then SSRIs (medications like Prozac which raise serotonin levels) are successful treatments for some individuals. These scientists speculate that that there may be different subtypes of this disease, and that different groups of anorexics may have different neurochemical characteristics.

  Researchers have also noted that abnormal eating behaviours and the resulting changes in the body can actually cause a disruption in serotonin levels, thus contributing to an already existing problem. Abnormalities in serotonin levels can lead to depression and anxiety. Studies also suggest that there are genetic predispositions to serotonin disruptions that appear to run in some families.

The hormone dopamine

  Research suggests that women who develop anorexia nervosa may have altered levels of dopamine in their brains. Dopamine disturbances can cause hyperactivity, repetition of behaviour (such as food restriction), and anhedonia (a decreased sense of pleasure). This neurotransmitter also affects reward-motivated behaviour.

The hormone cortisol/hydrocortisone

  Numerous other hormones in the brain have also been linked to eating disorders. Stress triggers the production and release of a hormone called cortisol; chronically elevated cortisol levels have been observed in patients with anorexia. Cortisol can inhibit appetite.

The hormone leptin

  Leptin is a protein hormone produced by the body's adipose tissue. Leptin is regarded as a hormone which can regulate fact storage and appetite. If individuals with anorexia nervosa lose extreme amounts of body fat, their levels of leptin drop which is known as hypoleptinaemia. The side effects of hypoleptinaemia can include amenorrhea, impaired metabolism, and bone loss.

Also, if people receive treatment, their leptin levels do not immediately return to normal. Initially during the treatment, leptin levels rise through the sky, which is also the reason why most patients are most susceptible of relapsing back into an eating order, since very high levels of leptin may cause a weight gain.

Sources:

ENGEL, BRIDGET, NATALIE STAATS REISS, and MARK DOMBECK. "Causes Of Eating Disorders - Biological Factors Continued." Mental Help Causes of Eating Disorders Biological Factors Continued Comments. 2 Feb. 2007
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010958/
http://www.apa.org/monitor/mar02/genetic.aspx


What do "e" "-" "C" and "E" mean in this output? I have given an input of this protein sequence:

MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

from this website  along with the option of COBEpro. Now the output sent by this site to my email is as follows:

Name: temp_prot

Amino Acids:
MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

Predicted Continuous B-cell Epitopes:
MOST LIKELY EPITOPES:
0.82848577 39 TKALGIS CCCCCEE eee-e-e
0.82036375 39 TKALGI CCCCCE eee-e-
0.76503265 38 TTKALGI ECCCCCE eeee-e-
0.73178638 73 TSQPRGDP CCCCCCCC -eeeeeee
…

and a few more. Now can you tell me, if I consider the very first result, I was able to find TKALGIS in the parent sequence but could not find CCCCCEE. What is this CCCCCEE?
And what does this eee-e-e mean?

CCCEEE etc. are the secondary structural elements. In this case, the C refers to non-strand and non-helix regions i.e loop regions rather than a coiled region. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix, however, in the question, it appears that there are no helices. These letters are often different in different software: it's merely a point of semantics between different software.

e or - refers to if the amino acid at that position is exposed or not (- = buried).

For the method, here is the COBEpro paper, although it does seem very technical. The help page has more easily accessible information on the output.


Neomycin resistance gene in E. coli stb3 cells We use a lentivirus packaging vector called pLenti_puro_DEST. We use puromycin to select for the cloned gene in 293T cells. However, the pLenti_Neo_Dest has been discontinued, so I'm cloning a Neomycin resistance gene into the pLenti_Puro_Dest thus replacing Puromycin with Neomycin. I usually just grow up this gene in Stb3 or Stb4 cells from invitrogen. I'm wondering if I can select for cloned pDEST vectors in these cells using Neomycin or G418. According to the G418 manual, you can theoretically use it for bacterial selection, but I think that may be for libraries and not actually growing up the plasmid.

So is it possible to select for my plasmid in these cells by adding a little G418 to the ampicillin plate? Is this common? I can't find anyone selecting bacteria by Neomycin anywhere.

EDIT - The main reason I ask, is that the resistance gene is under a PGK promoter that I have no idea if it works in bacterial cells.

PGK is mammalian (murine) phosphoglycerate kinase promoter. It will therefore not work in bacterial systems. Why don't you select using ampicillin only? You can increase the ampicillin concentration if you want.

Regarding:

  I can't find anyone selecting bacteria by Neomycin anywhere.

Kanamycin is generally used for bacterial selection. The Neomycin resistance gene works on Neomycin, Kanamycin and G418 (a gentamycin variant). The gene basically codes for an aminoglycoside phosphotransferase and different variants of the gene have different affinities for different aminoglycoside substrates. For a basic reference see this.


Why don't raisins lose water when in air? It is common that we soak raisins in water, and they acquire water by endosmosis. That means that the cells are permeable to water, right? Then why don't they lose water when kept in air? Or kept in sugar without any water?

EDIT: Also, take the example of peeled potatoes. Put them in a hypertonic solution, and they lose water, but when kept there, in air, they don't. How come?

That means that the cells are permeable to water, right?

Correct.

  Then why don't they lose water when kept in air?

They do, but it occurs very, very slowly. It might take a few months (or years in some areas), but if you leave raisins exposed to air they will eventually become harder until the water reaches equilibrium with the surrounding air.

This slow process is why there are tips on how to reconstitute raisins that are too hard to make them more moist and plump after getting a bad batch or finding old ones in your kitchen.


Why do different pain killers have different effects on people? I've noticed some pain killers working great for me, while others have no effect.

Works for me

Aspirin
APC †
Naproxen

Doesn't work for me

Paracetamol
Diclofenac
Tramadol

I doubt there is much of a placebo effect at work, since most of these either did or did not work when I first took them, without having expectations either way.

Whenever I have a head ache, I take an APC. I suspect it's actually the aspirin in there that does the job, since when I take just paracetamol, it doesn't do squat. As a kid I got children's aspirin, which worked.

I once had a severe back ache. I was prescribed diclofenac (a heavier variant than the over the counter one), which didn't work. I was then prescribed tramadol — same results. I then tried naproxen, which worked rightaway.

Why do some pain killers work while others don't?

Is there an underlying mechanism, that explains why some of these work while others don't? Does that predict if pain killers that I haven't used yet will work?

Please note that I'm not looking for medical advice on which pain killers to take; I'm just curious about how my body interacts with the various ones.

†: the one consisting of aspirin, paracetamol, and caffeine, not the one containing phenaticin. Think Excedrin.

Short answer: different people have different amount of active receptors.
In treatment, combination scores of Pharmacodynamics and Pharmacokinetics determine the final effect of the drug.
Receptors determine many effects of the drug in many pathways.
Different people also sense pains differently (Psychology).

Review answer

The purpose of treatment is to relieve pain and maintain function.
Your question is biased.
You cannot only concentrate on painkilling in maintaining health.
These both are the reasons for the complains of the patient, not only the pain.

For instance, in rheumatoid arthritis, response to therapy can be quantitated using many measures including American College of Rheumatology system values ACR20, ACR50 and ACR70, which denotes the percentage of patients showing an improvement of 20%, 50% or 70% in a global assessment of signs (maintaining function) and symptoms (pains).

Each patient has own health, different from one another.
Our body adapts to the environment and individual conditions of the body to maintain homeostasis.
Receptors adapt for instance.
They can be active or inactive - in short-run and long-run - again depending on the conditions at hand.

Painkillers i.e. analgesics have different properties:

anti-inflammatory effect - acute and chronic conditions (inflammation is the major mechanism under many pathologies) e.g. nonsteiroidal anti-inflammatory drugs (NSAIDs, please, see this answer about the particular mechanisms and how different people have different effects from NSAID painkillers) and glucocorticoids (most)
symptoms relieving specific drugs e.g. disease-modifying antirheumatic drugs (DMARDs)
anti-platelet effect - e.g. the older you get, the more platelets stick together.
anti-pyretic effect
...

which all can be toxic.
Note that many drugs alone or/and as combination can work as painkillers i.e. pain relievers.
Aspirin for instance has both anti-inflammatory and anti-platelet properties.
However, it is rarely anymore used as anti-inflammatory.
The anti-platelet property is dependent on the exact dosage of the administration.
Aspirin's mechanism of action is to inhibit platelet COX which antiplatelet effect lasts 8-10 days (life of the platelet).
In other tissues, synthesis of new COX replaces the inactivated enzyme so that ordinary doses have a duration of 6-12 hours.
Please, review any Pharmacology -textbook for more info about aspirin.

Each these drug has own Pharmacodynamics and Pharmacokinetics

Pharmacodynamics answers to the question What drug does to the body? It stimulates some receptors, activates some pathways, ...
Pharmacokinetics - What does body do to the drug? It metabolises it (enzymes, receptors). It distributes it. It excretes it (kidneys, feaces).

In treatment, you consider what is the target organ.
You need to think what is causing the dysfunction and the pain.
You try to restore the function and relieve pain.
The component of drug needs to reach the target tissue e.g. your pancreas' beta cells do no produce insulin so your blood glucose is high.
Complications of this are polyuria and eventually exodus if untreated.
Insulin is injected into the fatty tissue.
We do not have long-term acting insulin administered orally - our metabolism start to break the drug so it does not have wanted treatment.
If insulin administered to the muscle, the time of action is too times less, again because muscle is metabolising the insulin i.e. a chain of peptides (protein).

No all symptoms and diseases have painkillers.
For instance, prehemorrhoid and some types of itching related to  posthemorrhoids.
However, for both, there are some special salvas for proplylaxis but they are not complete.

Now, you can start to read something in SuperBest's answer about host's physiological variables and addiction/tolerance which alters the mechanisms (receptors) of pathways in Pharmacodynamics and Pharmacokinetics.

Sources

Basic and Clinical Pharmacology, 11th edition, 2009, Bertram Katzung.
My notes in Pharmacology classes during 2014.


Do immortal organisms exist? Do organisms exist that are able to live indefinitely if they are not killed by external factors?

Under external factors I would consider things like predators and natural disaster but not illness by bacteria for example.

I now found this Wikipedia article on biological immortality. It's pretty much what I was looking for.

Wikipedia describes the phenomenon as follows:

  Biological immortality refers to a stable or decreasing rate of
  mortality from cellular senescence as a function of chronological age.
  Various unicellular and multicellular species may achieve this state
  either throughout their existence or after living long enough. A
  biologically immortal living thing can still die from means other than
  senescence, such as through injury or disease.

It has a list of such organisms as well, consisting of

tardigrades
hydras
turritopsis nutricula, some sort of jellyfish
lobsters*
planarian flatworms

Addendum: This blog post takes a good look into the myth of lobster immortality. It seems to be as much a myth as the result of any substantial observation.


White blood cells after dealing with an infection I just have a quick question. If there was an infection of a tissue within the body, white blood cells would leave the capillaries around the tissue and enter the tissues to help cure the infection. How would these cells leave the tissue after that? Would the white blood cells be broken down or would they manage to find their way back into the capillary that they came from?

White blood cells, especially neutrophils, rapidly leave the blood and migrate in tissues toward infections (or other forms of stimulations). Many of them do die at the location of an infection, but they can also migrate back. The simplest route for this is to follow lymph flow. Lymphatic fluid is picked up by lymphatic vessels, which work in parallel to blood vessels, and from there can move back into blood. Just as an example of migration through lymphatics

  Thus, we provide in vivo evidence that neutrophils, like DCs or inflammatory monocytes, migrate via afferent lymphatics to lymphoid tissue and can shuttle live microorganisms.

--Neutrophils rapidly migrate via lymphatics after Mycobacterium bovis BCG intradermal vaccination and shuttle live bacilli to the draining lymph nodes


Why does a high osmotic pressure pull water in, yet a high hydrostatic pressure pushes water out? When I normally think of high pressure, I think of it as pushing something away from the zone of high pressure.

Yet for a high osmotic pressure, water is pulled IN to this high osmotic pressure region.

Why is this the case?

Great question, the answer has to do with the definition of osmotic pressure and the difference between this pressure and "hydrostatic pressure" which is the water pressure you are thinking of.

Here is the definition of "osmotic pressure" given by Google:

  the pressure that would have to be applied to a pure solvent to prevent it from passing into a given solution by osmosis, often used to express the concentration of the solution.

Osmotic pressure in this definition is best illustrated by the commonly used tool to show osmotic pressure, often seen in a textbook as something like this:

In this picture, osmotic pressure is roughly how hard do you have to push down on the water on the right to make the levels the same on the left and right, despite the difference in concentrations. Osmotic pressure is not a pressure of water, as your question seems to imply, it is a pressure of the solutes in the water.

If it helps, I think it would be appropriate to think of this as sort of a "suction" on the water. Net flow of water stops when:

osmotic pressure - hydrostatic pressure = 0

...on the right side of the diagram.


Blood acidity and bones By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?

I ask this because i recently discovered bone is a base, as its chemical formula is approximated as Ca10(PO4)6(OH)2 where the (OH)2 suggests bone is basic and thus prone to a neutralisation reaction with acidic blood. If so, what salt would be produced?

Short Answer: As the comments mention, this is a hot topic for pseudoscientists to use as a selling point for their supplements. There is limited evidence that dietary acid intake significantly alters bone resorption, especially in the setting of normal renal function. This paper should answer all of your questions (emphasis mine):

  Frassetto, Banerjee, Powe, Sebastian. Acid Balance, Dietary Acid Load, and Bone Effects—A Controversial Subject. Nutrients. 2018. 10(4),517.

    Abstract: Modern Western diets, with higher contents of animal compared to fruits and vegetable products, have a greater content of acid precursors vs. base precursors, which results in a net acid load to the body. To prevent inexorable accumulation of acid in the body and progressively increasing degrees of metabolic acidosis, the body has multiple systems to buffer and titrate acid, including bone which contains large quantities of alkaline salts of calcium. Both in vitro and in vivo studies in animals and humans suggest that bone base helps neutralize part of the dietary net acid load. This raises the question of whether decades of eating a high acid diet might contribute to the loss of bone mass in osteoporosis. If this idea is true, then additional alkali ingestion in the form of net base-producing foods or alkalinizing salts could potentially prevent this acid-related loss of bone. Presently, data exists that support both the proponents as well as the opponents of this hypothesis. Recent literature reviews have tended to support either one side or the other. Assuming that the data cited by both sides is correct, we suggest a way to reconcile the discordant findings. This overview will first discuss dietary acids and bases and the idea of changes in acid balance with increasing age, then review the evidence for and against the usefulness of alkali therapy as a treatment for osteoporosis, and finally suggest a way of reconciling these two opposing points of view.

This paper is open-access and I recommend you read it, but the conclusions summarize their findings nicely:

  7. Synthesis

    We suggest the way to put all of this information together is to agree...that bone alone cannot buffer the positive acid balance that one can calculate from measures of acid production and acid excretion. In addition, endogenous acid production goes up and down in an attempt to maintain systemic blood pH...

    Diets high in acid precursors add to the body’s acid burden. For the majority of people eating typical western diets with acid loads of ≤1 mmol/kg, whose renal function and acid excretory ability is normal, dietary acid loads would not be a readily detectable factor in altering bone mineral density leading to the development of osteoporosis. Other factors such as age, gender, race, and immobility are quantitatively more major factors in determining bone mass and bone breakdown.

    However, body retention of only 1 or 2 mEq of acid each day, barely detectable by current measurement techniques, buffered by muscle and kidney and titrated by skeletal base over decades, could potentially result in major depletion of bone mineral. Thus, we suggest that those older subjects with diminished renal function, decreased renal acid excretory ability, and lower buffering capacity due to lower muscle and/or bone mass, whose diets contain high net acid loads could potentially benefit the most from alkali therapies.

Long Answer: Although there's a wealth of pseudoscience on the internet relating to acidemia and bone composition, there is some truth to the idea that bone can be affected by pH. An excellent model to explore this concept is chronic kidney disease, as impaired renal function causes decreased H+ secretion, which results in a chronic metabolic acidosis:

  Kopple, Kalantar-Zadeh, Mehrotra. Risks of chronic metabolic acidosis in patients with chronic kidney disease. Kidney International. 2005. 67(95),S21-27.

    Metabolic Acidosis

      Severe chronic metabolic acidosis (i.e., the presence of excess hydrogen ions in blood) has two well-recognized major systemic consequences. First, metabolic acidosis, or acidemia, induces increased protein catabolism, decreased protein synthesis, and negative nitrogen and total body protein balance, which improve upon bicarbonate supplementation. Second, metabolic acidosis causes physicochemical dissolution of bone and cell-mediated bone resorption (inhibition of osteoblast and stimulation of osteoclast function).

    Metabolic Acidosis and Bone Disease

      Metabolic acidosis exerts multiple effects on bone. It causes the physicochemical dissolution of bone and cell-mediated bone resorption through the inhibition of osteoblast activity and stimulation of osteoclast function. These events are associated with a loss of calcium and phosphorus from the bone. Metabolic acidosis stimulates osteoblasts to release prostaglandins. This stimulates osteoclast function and inhibits osteoblast activity. Glucocorticoids can inhibit the production of prostaglandins by osteoblasts.

      Metabolic acidosis is also associated with a decrease in the content of bone bicarbonate. Additionally, bicarbonate supplementation in postmenopausal women is associated with decreases in urinary calcium, phosphorus, and increased osteocalcin levels, indicating a beneficial effect. Figure 4 shows the mechanisms relating metabolic acidosis with bone disease3. These observations suggest that uncorrected metabolic acidosis has adverse consequences on bone anatomy and physiology.

      Figure 4. The various mechanisms by which metabolic acidosis may contribute to bone disease. (From3).

From here, your questions can be answered:

Q: By consuming acidic foods, could one cause their blood to become acidic and therefore cause an acid+base reaction between their blood and bone?

A: Maybe. It is possible to induce a metabolic acidosis with diet:

  Adeva, Souto. Diet-induced metabolic acidosis. Clinical Nutrition. 2011. 30(4),416-21.

    The modern Western-type diet is deficient in fruits and vegetables and contains excessive animal products, generating the accumulation of non-metabolizable anions and a lifespan state of overlooked metabolic acidosis, whose magnitude increases progressively with aging due to the physiological decline in kidney function. In response to this state of diet-derived metabolic acidosis, the kidney implements compensating mechanisms aimed to restore the acid-base balance, such as the removal of the non-metabolizable anions, the conservation of citrate, and the enhancement of kidney ammoniagenesis and urinary excretion of ammonium ions. These adaptive processes lower the urine pH and induce an extensive change in urine composition, including hypocitraturia, hypercalciuria, and nitrogen and phosphate wasting.

And there is existing research on short-term effects of altered diet on blood and urine pH and composition, but the clinical relevance of these values is indeterminate:

  Buclin, Cosma, Appenzeller, Jacquet, Décosterd, Biollaz, Burckhardt. Diet Acids and Alkalis Influence Calcium Retention in Bone. Osteoporosis International. 2001. 12(6),493-99.

    The urine-acidifying properties of food constituents depend on their content of non-oxidizable acids or precursors. Acidifying constituents such as animal proteins may negatively affect calcium metabolism and accelerate bone resorption, thus representing an aggravating factor for osteoporosis...acid-forming diet increased urinary calcium excretion by 74% when compared with the base-forming diet (p50.0001), both at baseline and after the oral calcium load, and C-telopeptide excretion by 19% (p=0.01), suggesting a skeletal origin for the excess calcium output. This observation confirms that renally excreted acids derived from food influence calcium metabolism, and that alkalizing nutrients inhibit bone resorption. Further studies are needed to determine the clinical impact of dietary counseling for avoiding diet acids as a preventive measure against osteoporosis.

But best recent evidence does not support the idea that significant changes in bone composition could be induced by diet alone (see my "Short Answer" above).

Q: ...what salt would be produced?

There are many metabolic acids, but for simplicity, we'll consider H+. Bone bases are stored as alkaline salts (e.g. calcium carbonate, CaCO3, which is really Ca2+ and CO32-). So, if H+ comes into contact with calcium carbonate, you'll make carbonic acid (with H+ displacing Ca2+ to produce H2CO3 – you excrete the Ca2+, resulting in the hypercalcuria described above). Through the bicarbonate buffer system,  that H2CO3 will be converted into carbon dioxide and water, which you excrete from your body via respiration.


Are alleles passed down and shuffled randomly to the offspring during meiosis or fertilization? If it does occur during meiosis, are the alleles switched over from one sister chromatid to the other during the crossing over process in Prophase I?

Crossing over/synapsis in Prophase I of Meiosis I is when alleles are switched over from one non-sister homologous chromatid to another non-sister homologous chromatid. This happens before fertilization ever happens. Meiosis occurs even before birth in females in order to make gametes in the form of oocytes. In contrast, this frequently occurs in men who continue to produce gametes in the form of spermatocytes throughout their lifetime. Fertilization simply refers to the fusion of two gametes-- a spermatocyte and oocyte combining together-- and does not involve meiosis.

Here's a short and straightforward Youtube video about Meiosis.


Understanding entropy and the second law of thermodynamics as involved in metabolic processes My AP biology textbook, (the 10th edition of Campbell Biology) states entropy as being the disorder or randomness of the atoms involved in any matter, but Khan Academy says that this example isn't quite right, and is too simplistic of a way of explaining the concept. And the TedED video I watched goes on talking about quanta and stuff ...

The online definition I was able to find of entropy on Wikipedia states the "The entropy of an object is a measure of the amount of energy which is unavailable to do work. Entropy is also a measure of the number of possible arrangements the atoms in a system can have. "

I'm confused how it's both at the same time and how they're related. And how does this even relate back to Biology again???

2nd law of thermodynamics states that the overall entropy of the universe cannot decrease at any time. This can also be stated as the fact that the universe naturally falls towards the lowest energy state, or equilibrium. This becomes important in metabolic reactions. Reactions which seem to increase the state of energy, or perhaps the 'order' of the universe, have done so at the expense of another part of the universe, usually through the conversion of energy from molecules such as ATP or NADPH.

Think of the ATP Synthase on the cell membrane. It is creating ATP (Adenine tri-phosphate) molecules from ADP (adenine di-phosphate) and a phosphate group. This too seems like a system changing molecules from a low energy state to a high energy state. It is, but it can only do so by the natural flow of H+ ions which have accumulated on one side of the cell membrane and naturally flow from their high concentration to their low concentration on the other side. So while the ATP synthase molecule is making higher energy molecules (decreasing entropy) it is doing so as H+ naturally flows towards equilibrium, which increases the overall entropy in the universe.

In essence: things are always going towards a low energy state, i.e. equilibrium, i.e. maximum entropy. If any system goes against this, it does so via an outside energy source which has increased the entropy of the universe somewhere else.


Why is an HIV infection considered "incurable"? My biology teacher told me that if one caught HIV, they cannot be cured because it was near to impossible to be completely virus-free. She said this was because HIV keeps on changing its glycoprotein coat.

Can someone please explain what she meant by "keeps on changing its glycoprotein coat" to me?

The reasons why HIV is "incurable" (a misnomer) are legion:

HIV is a retrovirus, which means it inserts its own genome into the host cell's genome.  You must therefore kill each and every infected cell to rid the body of the virus.
HIV is a lentivirus, which means it has a long incubation period, so it can "lay low" before symptoms are readily detected.
HIV infects CD4+ helper T-cells, macrophages, and dendritic cells, which are responsible for mediating the host immune response.  Thus, it infects specifically the cells we need to fight an infection.
HIV drastically reduces the number of CD4+ T-cells.
HIV has a number of viral proteins that prevent some of the body's antiviral mechanisms
HIV can infect via cell-free (large number of particles, low infection rate) or cell-to-cell (low number of particles, high infection rate) routes.
HIV is wildly variable.  It has a small RNA genome (about 10kb) that mutates very rapidly.  Given the number of viral particles produced each day during infection — well over 1 billion — every single base is mutated every day.

I'm simplifying matters a bit — you should just read the en.Wikipedia article for your own research — but that's a rundown of some of the reasons why.


Can dietary monosodium glutamate intake induce restlestness? The question is all in the title.

More context:

I like phở soup. I have noticed that I get restless after eating the phở soup at some restaurants. The effects are similar to the ones resulting from caffeine intake. (Ingesting a cup of Turkish coffee or a couple of espressos results in my hands shaking badly.)

The phở soups which I think trigger the reaction appear to be the most savory ones. Given that:

Monosodium glutamate (MSG) is a common ingredient in phở
MSG has flavor enhancing properties
Glutamate is a neurotransmitter

I thought there was possibly a connection. (Or perhaps not. Or perhaps it's the intake of MSG together with the consumption of an herb containing caffeine or another psychoactive drug. Phở contains herbs in large quantities.)

I found this paper which states the effects of caffeine result from an increase of glutamic acid (GA) in the posterior hypothalamus which in turns triggers wakefulness.

Thus I guess what I am asking is: does dietary intake of MSG increase blood serum levels of GA and does an increase of GA blood serum level result in an increase of GA in the brain (or in some parts of the brain)?

There is no strong evidence for MSG having any kind of neurotoxic/neuromodulatory effect.

However, A 2010 article says that, in a double blind trial, it was found that the people who consumed MSG containing soda, reported headache in significantly more numbers compared to the placebo subjects [1]. The concentration of MSG used in this study was 75-150 mg/kg. Assuming that one serving of soda would be 300ml i.e 300g, the amount of MSG consumed would be maximally 45mg, which is much less than glutamate concentration in some natural food stuffs such as tomatoes (~2000mg/kg [2,3]; a tomato that weighs 6oz/~170g contains ~340mg of glutamate). Therefore, I would doubt the findings of this article. The results could have possibly been observed because of some hidden dependent variable (such as the soda formulation).

In general, the USFDA considers MSG as GRAS (generally regarded as safe) [4].

Finally, a 2014 article concludes that dietary MSG would not lead to increase in either blood or brain levels of glutamate [5].

From the Abstract:

  The sodium salt of glutamate (monosodium glutamate; MSG) imparts a
  savory/meaty taste to foods, and has been used as a flavoring agent
  for millennia. Past research on MSG/glutamate has evaluated its
  physiologic, metabolic and behavioral actions, and its safety.
  Ingested MSG has been found to be safe, and to produce no remarkable
  effects, except on taste. However, some recent epidemiologic and
  animal studies have associated MSG use with obesity and aberrations in
  fat metabolism. Reported effects are usually attributed to direct
  actions of ingested MSG in brain. As these observations conflict with
  past MSG research findings, a symposium was convened at the 13th
  International Congress on Amino Acids, Peptides and Proteins to
  discuss them. The principal conclusions were: (1) the proposed link
  between MSG intake and weight gain is likely explained by co-varying
  environmental factors (e.g., diet, physical activity) linked to the
  "nutrition transition" in developing Asian countries. (2) Controlled
  intervention studies adding MSG to the diet of animals and humans show
  no effect on body weight. (3) Hypotheses positing dietary MSG effects
  on body weight involve results from rodent MSG injection studies that
  link MSG to actions in brain not applicable to MSG ingestion studies.
  The fundamental reason is that glutamate is metabolically
  compartmentalized in the body, and generally does not passively cross
  biologic membranes. Hence, almost no ingested glutamate/MSG passes
  from gut into blood, and essentially none transits placenta from
  maternal to fetal circulation, or crosses the blood-brain barrier.
  Dietary MSG, therefore, does not gain access to brain. Overall, it
  appears that normal dietary MSG use is unlikely to influence energy
  intake, body weight or fat metabolism.


Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods? Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some CRISPR-like tools? I guess, that extensive databases of already performed experiments are available and human mind is required to select candidate genes for experiments. But maybe there are some methods, that allow computational select, planning of experiment, e.g. using: 1) already known biological pathways for different biological processes or incomplete pathways for the process under consideration; 2) protein-protein interaction models to predict some pathways and to select genes from them. Etc.

I am complete novice for this field, coming from computer science and only starting to read books about molecular cell biology, epigenetics and protein-protein interaction. Maybe there are special terms that allow me to Google for the subject of this question

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work with CRISPR-CAS9 is still limited to model organisms and tissue cultures.

Are you referring to Adiposis Dolorosa?  Apparently the cause is not actually known yet. It's thought to be heritable, but it isn't known to be associated with a single gene or family of genes. The most common technique for analyzing what genes and gene mutations cause disease is Genome Wide Association Studies (GWAS), so you might use that as a staring point for your searches.

There are several computer programs that try to model what pathological effects a given mutation will have, but these are pure research at this point, and typically require extensive training for each gene or protein product. Try searching for "sequence based pathology prediction". However you may not find much related to Adiposis Dolorosa since the causative genes are apparently not known yet.


Conversion of ATP to NADH without creating a proton motive force? Is it possible to convert ATP into NADH and vice versa without first creating a proton motive force? If so by what mechanism is it done?

I am not aware of any enzymes that both oxidize NADH and generate ATP.

However, in the absence of oxygen, many bacteria ferment ethanol and acetate (among other products) to oxidize NADH and produce ATP. ATP is produced by acetate kinase and NADH is consumed by dehydrogenases in the parallel ethanol secretion pathway. Together, these pathways consume (or more accurately, recycle) NADH and generate ATP.

http://mmbr.asm.org/content/69/1/124/F6.expansion.html


Why does the formula for blood velocity hold true? v = Q/A
where
v = velocity (cm/s)
Q = blood flow (ml/s)
A = cross sectional area (cm2)
So the greater the cros sectional area, the lower the velocity, assuming that the cardiac output is a constant for a individual.
But i dont understand the formula content wise, why do you get the velocity by dividing Q by A? I do understand that the units are correct, and you get cm/s as final unit.
Can anyone explain this, perhaps graphically?

In the capillaries the A must be extremely low, yet why is the velocity so small? My book says that you have to add all capillaries up, but you cant do that, since you would get the velocity of an extremely big pipe, which isnt that of a capillary?
Thanks in advance for answering.

The trick here is that 1 mL = 1 cm3 (or cc).  So if you divide cm3/s by cm2 the result will be in cm/s.  What that means is that the blood volume has three dimensions - if you picture the vessel as a simple "box", then it has widths in two dimensions, which define a cross-sectional area, and then the third dimension is the distance that the blood has moved past, through the vessel, in order to define the three-dimensional "box" of blood that has moved past as the blood moved that distance.
The principle should be familiar from the phrase "still waters run deep".  A stream that flows rapidly in a shallow cascade over rocks can abruptly become quite slow at a deep hole, as a great depth and breadth of water is sharing the work of moving forward.


Some trophoblast excreting digestive enzymes in implantation I found this paragraph in my study materials about implantation

Original

  Simplest trophoblast excretes trypsin related substances and embedding consists of 3 stages:

  The blastocyst (composed of cytotrophoblast and embryoblast) stick to the uterine wall
  Enzymes digest nische (little hole in the endometrium) to the functional layer and the blastocyst deepens in it. The nische is a closed and destroyed functional layer, in it tissue and blood is used for trophic (called a nischtrophic way of feeding)
  Implantation ends in 13½ day when the functional layer covers the blastocyst.
  Implantation normally takes place in anterior and posterior wall of uterus, sometimes in superior or fundus wall.

My suggestion for corrections

  Syncitiotrophoblast excretes Digestive Enzymes and embedding consists of 3 stages:

  The blastocyst (composed of cytotrophoblast and embryoblast) stick to the uterine wall
  Syncytiotrophoblast expresses digestive enzymes which dig a little hole (nische) into endometrium. The hole is usually filled with maternal tissue (so closed) and blood used by the conceptus for histotrophic feeding (nischtrophic way of feeding)
  Implantation should end in 13½ day when the endometrium covers the blastocyst.
  Implantation normally takes place in anterior and posterior wall of uterus between glands of the hypertrophic endometrium, sometimes in superior or fundus wall.

I cannot accept the phrase simplest trophoblast and the use of the words trypsin related substances. Really, how can you get trypsin without pancreas? I would not use the word trypsin although the enzymes may have some structural similarities.

How would you reformulate the paragraph?

I have no idea what is meant by 'the simplest trophoblast'. I did, however, find this review, pointing to a role of proteases in the implantation process:

  Salamonsen L.A. Salamonsen and Nie, G. (2002) Proteases at the Endometrial–Trophoblast Interface: Their Role in Implantation. Reviews in Endocrine and Metabolic Disorders, 3:133-143

which discusses the roles in implantation of three classes of proteases : matrix metalloproteinases, serine proteinases and cystein proteinases. The reference to 'trypsin-like' presumably relates to the serine proteases. The review reports the results of a number of gene knockout experiments in mice in which genes for individual proteases have been disrupted which indicate that no single enzyme is identified as being essential.

Referring to

  Afonso S et al (1997) The expression and function of cystatin C and cathepsin B and cathepsin L during mouse embryo implantation and placentation. Development 124:3415-3425.

the authors of the review state that:

  [they] demonstrated that cysteine proteases play a critical role in implantation. Cathepsin B mRNA was expressed by mouse trophoblast throughout the invasive period (days 5.5±10.5) while the proteins for cathepsins B and L were localized to the mature invasive trophoblast giant cells; activity of these enzymes was also demonstrated. Cathepsin L was also present within the stroma particularly in the lateral decidualizing zone. Cystatin C, the major inhibitor of cathepsins, was shown to be a major product of the adjacent decidualizing stroma close to the embryo, suggesting a restraining role. After the completion of placental trophoblast invasion (day 11.5) the trophoblast cells express high levels of cystatin C, probably in association with a switch from an invasive cell type to one providing nutrients to the conceptus [35]. In addition, treatment of pregnant mice with E-64, a synthetic cysteine protease inhibitor, resulted in failure of implantation and normal uterine decidualization.


When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres? I've heard that part of cognitive processing is information passing between left and right cerebral hemispheres.

  This is what happens in the Cerebral Cortex which is divided into two hemispheres,
  left brain and right brain connected by a thick layer of nerve fibers called the corpus callosum. These nerve fibers allow messages to pass between the left and right brain
  hemispheres

My question is When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?

Assumptions:

I'm making a big leap from 'electronic impulses of neurons' to 'thoughts'.

Neuroscience doesn't really have a clear model for what a "thought" consists of exactly. Certain processes that are involved in thought have begun to be mapped--for example, this recent paper talks about a model for how the brain associates location in space with it's own mental map (http://www.ncbi.nlm.nih.gov/pubmed/24462102, I'll try to find something related that's not behind a paywall...). This one doesn't address your particular problem though, they only measured activity on one side of the brain. So basically, it might be possible to partially answer your question for more specific brain processes, but different kinds of "thoughts" are processed in different ways.

And of course I am also conflating impulses crossing the corpus callosum with the thoughts themselves, but I don't think this is really accurate. The most popular models in the labs I'm familiar with suggest that a "thought" is composed of a bunch of neural activity taken together rather than the activities of a few neurons on their own. But that might ultimately just be arguing semantics.


When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then? I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and Zinc finger nucleases.

I understand that there may be a few metrics used for analyzing any genome editing system.  One is the efficiency, which could be measured perhaps in edits per time or edits per molecule.  Another metric might be error-rate.  What is the probability that a genome is altered in something other than the intended way?  Another metric might be the length of the genome that may be edited at once.

I've also read that CRISPR/Cas9 evolved in bacteria.  When did CRISPR/Cas9 evolve in the history of life on earth?

If CRISPR/Cas9 evolved in bacteria, and before other evolutionary advances, including some of those that may have enabled certain multiceullar forms of life, I have to wonder if other systems like CRISPR/Cas9 but superior to it in some metric evolved as well.

How does recombination in sexual reproduction work?  Might it involve biomolecular machinery like that of CRISPR/Cas9?

How does the adaptive immune system work?  How does VDJ recombination work?  Does it involve an advanced (relative to CRISPR/Cas9) genome editing system?

How might one estimate the probability that a system superior to CRISPR/Cas9 exists already?

Lots of interesting questions! Let me try to address a few of them as I don't think I am qualified to answer them all but hopefully I can get this thread started. I am a graduate student in the biophysical chemistry field and have been following a little bit of the Crispr Cas9 craze in the last couple of years. So I am not an expert on Cas9 by any means but I do find it interesting.

Many speculate that as long as their have been cellular life, viruses or some obligate parasites have existed as well. This stems from the idea that viruses perhaps are not "non-self" but rather are parts of the host that happen to become inanimate particles that escape the cell and then find another suitable host. Some viruses have co-evolved with the host, perhaps to prevent other viruses from invading its "home/birth mother". Again, much of this paragraph is just speculation, but it is likely that CRISPR systems, or an adaptive immune systems like it have existed as long as viruses/obligate parasites have.

Error rates, you can look at some of the papers that have come out recently but the idea is that there are a lot of error rates, especially if the RNA is constitutively transcribed from a plasmid. Some people have suggested delivering, not the plasmids for the guide RNAs and the Cas9 protein, but instead, the Cas9 protein complexed to the RNA itself. Other ways to control the amount you deliver to a cell include delivering the RNA for the Cas9 protein so it is eventually degraded. This avoids the complication of delivering DNA which can be transcribed multiple times potentially flooding your cell with cas9 protein or guide RNAs, increasing the likelihood of off target effects. Or you can have the cas9 protein and the guide RNA plasmids under inducible promoters, so you only get expression say if you introduce a small molecule to your cultured organism and limit the amount you deliver of it.

As to if there are other systems "superior" to it, and by superior you mean more efficient, and has less off targeting effects? Sure those things may very well exist, since we haven't sequenced the entire planet yet! All joking aside, maybe start looking around at research groups that do adaptive immunity in prokaryotes, you might find some interesting ideas...

VDJ is a very cool system that I know only a little about but this review might be worth checking out:

"Mechanism and Control of V(D)J Recombination versus ClassSwitch Recombination: Similarities and Differences", which can be found here.

Also recombination in meiotic versus mitotic replication is covered in this review: "Meiotic versus Mitotic Recombination: Two Different Routes for Double-Strand Break Repair", which is available here.

So to answer your question, I will have to defer to someone else!

My question to you is what is "advanced"? Life as we understand it has been evolving for about 3-4 billion years. "Advanced" suggests that one organism has evolved better or faster. I don't know if I would call anything more advanced per se, but maybe more complicated and more capable of rapidly adapting to new environmental pressures? Bacteria have us trumped if there were rapid changes to the environment, global warming, asteroids careening into the planet etc.

Estimating this probability requires knowing how large the entire sequence space of the Earth is, some have estimated 5-50 million eukaryotic species but depends on what metric you would use to define a new species. It is unknown for prokaryotes. My guess is that you have 100's of millions of different organisms that are capable of having some type of adaptive immune system that may be inherently different from CRISPR/Cas9 system but still use some similar elements, like nucleic acid complementation, as a mode of defending against obligate parasites. Then the questions are how many of those organisms have we sequenced and how many proteins do we have any idea how they function based on sequence similarities to other proteins? Or if we have directly characterized their 3D structure based on Cryogenic Transmission Electron Microscopy (Cryo EM), NMR or X-ray crystallography. So, I imagine we have just hit the tip of the iceberg in finding natural enzymes that can function as gene editing and gene locating tools. Plus, we may start designing our own enzymes like what Professor David Baker at UW works on. Huge ocean to go exploring, bring a molecular fishing pole :-)


If someone were to die on the moon, would their body decay? I heard that the footprints of Neil Armstrong are still there, so I was wondering if someone were to die there, would they remain preserved, too?

If not how long would it take for them to decay?

I am assuming in spacesuit here, on the face (lit side) of the moon. Bodily degradation involves much more than external fungi and bacteria.

Cells that receive no oxygen or nutrients die. We talk of such tissue death as dry gangrene when it affects extremities, such as fingers, feet, etc. However, we also recognize gangrenous bowel, etc. which results in tissue necrosis.

Such necrotic cell death is the consequence of acute disruption of cellular metabolism, leading to ATP depletion, ion dysregulation, mitochondrial and cellular swelling, activation of degradative enzymes, plasma membrane failure and cell lysis [1]

Lysis is messy and wet. Combined with the fluids in our bodies, what one would end up with is a mushy, smelly degraded body, not a preserved body. For a while, anaerobic bowel bacteria would flourish (which smell terrible).

Add to this the extremes of temperature (253° F in the sun and -243° F in the dark.) The suit would have lost it's heating and cooling mechanisms, so the body would alternately spend 14 days in the heat and 14 days in the freezing cold depending exactly where it was (lets say the equator of the moon.) These freeze/bake cycles would further contribute to degradation through ice crystal formation and thawing.

Eventually, because there was no new substrate, degradation would come to a halt, but I'm not sure at what stage this would be. I assume, though, there would be a vast difference between a mummified body (done by dehydration) and a body left to degrade in a spacesuit.

[1] The mitochondrial permeability transition in cell death: a common mechanism in necrosis, apoptosis and autophagy, John J. Lemasters et. al, Biochimica et Biophysica Acta 1366 (1998) 177-196


Why does protein kinase C activated by different means have different effects? I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it just phosphorylated differently or what?

You probably remember correctly — at least in part. The part that is missing is that protein kinase C isn't just one enzyme, but perhaps a dozen different isoforms that fall into three different classes, differing, among other things in their requirements for activation (e.g. whether they require calcium ions as well as diacylglycerol). It would be theoretically possible for protein kinase C activated by one pathway to have different effects from that activated by another if the different isoforms involved had different properties. This has indeed been suggested, although it has been difficult to establish experimentally.

The following two reviews that deal with this are about 20 years old, but may allow easier general access (and are easier to read):

Dekker, L.V. and Parker, P.J. (1994) Trends in Biochemical Sciences vol 19 pp 73–77.

Jaken, S. (1996) Current Opinion in Cell Biology, vol 8, pp 168–173.

The following quotation from the summary of a more recent and more extensive review article (Steinberg, S.F. [2008] Physiol. Review. vol. 88 pp. 1341–1378) may be pertinent:

  "There is growing evidence that individual PKC isoforms subserve unique (and in some cases opposing) functions in cells, at least in part as a result of isoform-specific subcellular compartmentalization patterns, protein-protein interactions, and post-translational modifications that influence catalytic function."

One other feature of protein kinase C is relevant to this question. Most other protein kinases (which tend not to have multiple isoforms) have a more or less restricted substrate specificity determined by residues of a particular type at particular positions with respect to the phosphorylation target residue (Ser, Thr or Tyr). This limits the proteins the kinases act on to specific targets. In contrast, protein kinase C can phosphorylate target residues in a wide variety of contexts. The current model (above) allows specificity of protein kinase C for target proteins to be obtained in a different way — by the specific proteins that each activated isoform binds to, i.e. by protein–protein interaction rather than target-site context.


Have Polyphyodonts ever evolved from Diphyodonts? The Wikipedia article for polyphyodont says this:

  Although most extant mammals are not polyphyodont, mammalian ancestors were. During the evolution of Therapsida, there was a period during which mammals were so small and short-lived that wear on the teeth yielded no significant selection pressure to constantly replace them.

...which was a bit surprising at first, but makes sense. So I'm wondering - have any species evolved in the opposite direction? In other words, have there been any non-polyphyodont species which have teeth, and evolved into polyphyodonts?

Not true polydonty, True polydonty is an animals that grows endless numbers of teeth like reptiles and fish do.  Elephants, kangaroos, and manatees are sometimes called polydont but they are doing something very different, they still only grow a set number of teeth, but instead of growing them in two sets they spread them out growing them a few at a time. the total number of teeth is still the same as other mammals and once that last tooth falls out they can't make anymore. It is worth noting the teeth migrate forward in the jaw as they wear out unlike true polydont in which new teeth grow from below endlessly.In essence they are rationing that limited number of teeth.

True polydonty has never evolved from a non-polydont ancestor.


Number of families in Animal kingdom I found this question about how many taxonomic families there are. That made me wonder how many are just in the animal kingdom alone. I want to know about families not species. Now the linked question was three years ago, so there should be some new information and numbers. A good answer would preferably include a breakdown of the phyla.

The Integrated Taxonomic Information System (ITIS) is maintained regularly by a consortium of North American governmental agencies, and will give you a list of all the classes, orders, families or genera in any of seven kingdoms they recognize. It might be biased towards North American taxa, but it might be quicker to get a list from then rather than extracting them from Wikipedia.

To help you further, user Rozenn Keribin used an awk script to summarize the number of families per phylum at https://justpaste.it/163c6.

Phylum:  Myxozoa -- 4
Phylum:  Chordata -- 1049
Phylum:  Echinodermata -- 139
Phylum:  Hemichordata -- 7
Phylum:  Xenacoelomorpha -- 9
Phylum:  Chaetognatha -- 9
Phylum:  Arthropoda -- 2504
Phylum:  Kinorhyncha -- 10
Phylum:  Loricifera -- 2
Phylum:  Nematoda -- 192
Phylum:  Nematomorpha -- 3
Phylum:  Onychophora -- 2
Phylum:  Priapulida -- 3
Phylum:  Tardigrada -- 20
Phylum:  Annelida -- 142
Phylum:  Brachiopoda -- 21
Phylum:  Bryozoa -- 133
Phylum:  Kamptozoa -- 5
Phylum:  Mollusca -- 581
Phylum:  Nemertea -- 20
Phylum:  Phoronida -- 0
Phylum:  Sipuncula -- 6
Phylum:  Acanthocephala -- 26
Phylum:  Gastrotricha -- 13
Phylum:  Gnathostomulida -- 12
Phylum:  Micrognathozoa -- 1
Phylum:  Orthonectida -- 2
Phylum:  Platyhelminthes -- 321
Phylum:  Rhombozoa -- 3
Phylum:  Rotifera -- 34
Phylum:  Cnidaria -- 269
Phylum:  Ctenophora -- 19
Phylum:  Placozoa -- 0
Phylum:  Porifera -- 142
Total -- 5703


Why are these nesting magpies building another nest Pair if eurasian magpies occupy a nest visible from my balcony. It's the nesting season for them here, and I assumed they have laid eggs. I can't see the eggs directly, but one of the magpies has been regularly sitting inside the nest (at least for last two or three weeks) and they always attack other birds that come too close.

Today, they've started building a new nest on another tree. It's pretty close, the nests are about 20 meters apart. They still visit their original nest.

What does it mean? Is it a sign of nesting failure? Does it mean their original nest is no longer sufficient?

I found an article that explains secondary nests as backups in case of nest usurpation by other birds:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858914/
This is for black sparrowhawks losing nests to Egyptian geese around Cape Town. They measured number of nests built per breeding pair of sparrowhawks and found it to correlate with number of Egyptian geese present and especially their nest usurpation behaviour.

That article mentions brood parasitism (e.g. cuckoos) as another possibility for other birds, and I've seen references to duplicate nests with eggs in each. ( https://www.tandfonline.com/doi/pdf/10.1071/MU939286a )


What are these curious cetaceans? At the beginning of the superb documentary film “Un jardin d’Eden sous les mers” (“A garden of Eden under the seas”) [1], we see a group of curious cetaceans. At about 1 min.

What are these cetaceans?

I think that they are odontocetes. But what species are they? This is a mystery.

[1] Documentary film “Un jardin d’Eden sous les mers” (“A garden of Eden under the seas”). It will be rebroadcasted on Arte on 2016‑04‑01 at 7:45 Paris time. You can watch it on-line here.

Thank you.

I am completely shooting in the dark here, but do you mean the ones between 1:06 - 1:13 minutes in the video? (After Hammerhead and before Baby and Mama white Shark :) )

SPECIES IDENTIFIED: Pseudorca crassidens (False Killer Whale)

Matching image from the internet (used for identification):

Courtsey: UAE Dolphin Project

PS: Images are screenshot from the video Documentary film “Un Jardin d’Eden sous les mers” (“A garden of Eden under the seas”) are completly owned by the owner of the video and "arte HD" channel.

PPS: Anyone reading this, if you haven't already, then please watch the video. Though it is completely in french, the videography is amazing.

References:

Pacific Islands Cetaceans
Other Whales


Count colonies in the right way I use Rose bengal agar cloramfenicol for search yeast and molds for inclusion in petri plat. Which is the method correct for count? I'm not sure if i count everything or only the bigger one?

Yes, you have to count every individual colony.

However, in practice the question is more, what is deemed a countable plate and how important is it. In many laboratories you will find that technicians and scientists won't bother to count each and every colony on the plate if you have a visibly high number of colonies. They will for example simply say (with a bit of experience), the count for this plate is greater than 300 (write >300).

Nevertheless, you will of course still need a count, so it is common practice to do one of the following:

Split your plate into sectors of equal size (you can draw lines on the bottom of the plate), count all colonies in one sector and then multiply this number by the number of sectors you have divided in. So, say, you have split your plate into 4 sectors (quadrants) by drawing a big cross on it, you would count the colonies in one quadrant and then multiply by 4. This is obviously an extrapolation.
The other option, is to dilute your sample until you get it within countable range. So you could do a serial dilution, put it onto plates and then once your organisms have grown you can count the entire plate and then multiply by the dilution factor. So, say, for example you have your sample in an enrichment broth and do two 1/10 dilutions (1/100) and then plate out 0.1mL (counts as 1/10), you have a final dilution factor of 1000. So you would need to multiply the count that you get on this imaginary plate by 1000.

In your sample you obviously have a variety of different organisms. It is probably advisable to check official methods for what they recommend. Here is an excerpt from the official BAM method for Yeasts, Molds and Mycotoxins:

  Count plates after 5 days of incubation. If there is no growth at 5 days, re-incubate for another 48 h. Do not count colonies before the end of the incubation period because handling of plates could result in secondary growth from dislodged spores, making final counts invalid. Count plates containing 10-150 colonies. If mainly yeasts are present, plates with 150 colonies are usually countable. However, if substantial amounts of mold are present, depending on the type of mold, the upper countable limit may have to be lowered at the discretion of the analyst. Report results in colony forming units (CFU)/g or CFU/ml based on average count of triplicate set. Round off counts to two significant figures. If third digit is 6 or above, round off to digit above (e.g., 456 = 460); if 4 or below, round off to digit below (e.g., 454 = 450). If third digit is 5, round off to digit below if first 2 digits are an even number (e.g., 445 = 440); round off to digit above if first 2 digits are an odd number (e.g., 455 = 460). When plates from all dilutions have no colonies, report mold and yeast counts (MYC) as less than 1 times the lowest dilution used. Isolate individual colonies on PDA or MA, if further analysis and species identification is necessary.

Please see link here.


Is it possible to contract the plague by kissing a wild chipmunk?" I watched  this cute video and I came to conclusion that the lady in the video is putting her life in danger. She kisses a wild chipmunk.

As I know, they have fleas, and fleas have a black plague. Am I right? But maybe the risk of infection in contact with just one chipmunk is low?

How dangerous is such behaviour?

The causative agent of the plague, Yersinia pestis, can be indirectly (via a flea vector) or directly (via exposure to infectious fluid or a bite) transmitted by rodents. In the western United States in particular, Y. pestis is endemic, and ground squirrels, prairie dogs, chipmunks, and woodrats are important reservoirs (see Cecil Medicine Ch. 320). US National parks have signs warning against feeding squirrels and chipmunks for this reason. You can read more about it in a national park brochure . Chipmunks and squirrels indirectly and directly transmit a variety of other diseases as well, including Tularemia (Cecil Ch 319) and various tick and flea borne encephalitides.


Which part of the reflex arc takes the longest time? The reflex arc is composed of 5 parts:

sensory receptors, afferent neuron(s), synapses within the central integrating station, efferent neuron(s) and the effector (includes transmission across the neuro-muscular junction and contractile mechanism - Assuming this is a myotatic reflex).

Which part takes the longest time & why?

The answer to this question depends which reflex arc was activated, without knowing the exact reflex arc one should assume the answer as multifactorial and relate to this (or similar) table:

(Source: Fundamental Neuroscience for Basic and Clinical Applications,  by Duane E. Haines)


Can a non-response to a vaccine be tested? The BioNTech/Pfizer vaccine against SARS-CoV-2 is said to be 90% effective.
Is there a test to establish the (degree of) success in individuals of a vaccine at provoking the desired immune response? Or will we all have to hope for the best?

You can test for antibody titers (and also connected memory) for the persons who got the vaccine and then decide, if these antibody levels are protective or not. Problem with this method is, that it is not clear, what levels are protective. There is still no experience with it for SARS-CoV-2, this is routinely done for other diseases.
According to clinicaltrials.gov, the study design is a placebo controlled trial triple blinded (Participant, Care Provider, Investigator) which enables the direct comparision of the vaccine arm with the placebo arm. Here you analyze the difference between these arms. If the vaccine delivers a sufficient protection, less (or ideally no) people in the vaccine arm get sick - which is exactly what was observed.
A last possibility would be to challenge people, who received the test vaccine with the virus and see, if they develop the disease. However, this approach is highly unethical since you possibly infect a large number of people with a potentially deadly virus, when the vaccine does not work. I doubt that a researcher who wants to do this will get clearance for these experiments by the internal review boards involved in these trials.
This is done in earlier stages in animal experiments, to challenge the immune response.


Finding DNA from Amino Acid sequence problem My attempt: First I took the single letter AA codes and made them amino acids.  So, the first one is Trp which is 5'-UGG-3'.   From this I got the DNA sequence 3'-CCA-5'.  However, the correct answer (shown in red) doesn't have this sequence.  What did i do wrong?

Your approach to translate the AA sequence, codon by codon, was correct. This was a bit of a trick question because to recognize it, you had to read the sequence backwards.

UGG-CAA-GGT-CAC etc is read directly off of the 3'->5' strand of the circled answer, reading from right to left.

The bottom left is a red herring because it starts with a start codon, ATG, but reading beyond the start codon, the sequence wouldn't match.


What are the side-effects of long-term liquid breathing? I just saw a recent Physics question that mentioned liquid breathing (which I had never heard of before) and I started to wonder about its long-term effects. Let's imagine a person underwent liquid breathing for some wacky reason - see the Wikipedia page for some starters - for a long time, maybe a month. What would begin to happen to them? Would any effects be reversible?

Overview.

This is a very interesting question. The ideas behind this have been around for a while and the methods are covered in great detail elsewhere.

The overall answer to the hypothetical question is rather surprising. There may be actually potential benefits to perpetual liquid ventilation for people with certain diseases. Trials so far have not found side effects in fluorocarbon liquid breathing.

So lets talk about the history of liquid breathing and case studies, then we will move onto the hypothetical situation of liquid breathing indefinitely.

A great review (Shaffer et al, 1992) covers the field in great depth.

@MCM pointed out in the comments that my original answer did no emphasise that animal diaphragms are not powerful enough to move the liquid in and out of the lungs. I should mention now that the below cases all use ventilators to pump the fluid into and out of the lungs. The difficulty of breathing this without a ventilator is emphasised by David Blaine at 4:54 in this TED talk who said it was like trying to breathe with an elephant standing on your chest.

Case studies.

As early as the 1920s, poisonous gas research that lead to the infamous mustard gas found that lungs could tolerate large quantities of saline briefly without damage.

Animals.

Kylstra, the first pioneer introducing the idea of land animals breathing liquids (Kylstra et al., 1962), found mice could withstand 4 hours of 160 atmospheres of pressure.

Clark found that mice and rats could breathe oxygen bubbled silicone oils and survive for a few hours after emersion.

In 1965, he discovered that the fluorocarbon known as FC75 not only supported respiration during total immersion but the mice survived indefinitely in apparent good health.

The most recent study I can find is the partial use of fluorocarbon liquid ventilation in adult respiratory distress syndrome (ARDS) of rabbits. The same improvements in breathing were not observed in saline liquid breathing or conventional ventilators.

Humans.

In humans PFCs were first used successfully in 1989 for the ventilation of young infants near death.

  Marked improvement in lung compliance, without a compromise of cardiovascular status was noted in all three patients.

All three infants died of their severe preexisting respiratory complications, but the trial showed liquid breathing can support gas exchange in humans. However developing lungs of infants cannot rely on mechanical ventilators for prolonged periods as nearly a quarter of premature infants of those that do later developed chronic breathing problems.

Biomedical application.

There are a fair few researches and doctors who believe fluorocarbon liquid ventilation has some advantages over gas ventilation. It reduces stress at the area of interfacial surface tension in the distressed, surfactant-deficient lung. This would be ideal and appropriate for ARDS in human adults. A more sophisticated use would be using fluorocarbons as a drug delivery system straight to damaged lung tissue.

(All the above can be found in the 1992 review. There is also data on the different properties of suitable FCs)

Real world potential.

  Is perpetual liquid breathing possible? ...And healthy?

So this is where we stand with the case studies; mice can breath liquids indefinitely and stay in good health, rabbits with ARDS survive where breathable gas would not help, and there is a contingency in the biomedical community that it can be better than gas ventilation for medical treatment. To me it seems that there is nothing to suggest a fully grown adult would suffer from breathing liquids. The inertness of the fluorocarbons implies any toxicity would only reveal itself in a timescale of years, and everything else about the compounds pose no danger and may make gas transfer across the lungs easier.

This relatively modest success is perhaps no surprise. The exchange interface of our lungs relies on a mucous (liquid) so the gases can permeate the lung tissue. Expanding on that idea should certainly not rule out the possibility of liquid breathing.

The biggest drawback, besides the cost of a long term experiment and being dependent on a mechanical ventilator, is that these are very small case studies of success. Given the massive amounts of unknowns (particularly for long term studies), switching to  purely liquid ventilation in an adult human could have unforeseen risks and would be considered dangerous by any ethics board (or insurance company)!

On a lighter note, here is a YouTube video of what Maddie, a biology podcaster from the BBC, had to say on the matter of living in total submersion. Lots of skin problems, risk of infection after a few days etc.

Again, a very interesting, albeit understudied, topic!


Meaning of “gene expression heterogeneity” of embryonic stem cells What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I have found did not really elaborate on what it meant, and I do not know where else to find the definition.
In particular, I want to understand heterogeneity in the context of stem cells. In the paper by Angarica and Sol, 2016, it reads:

“Experimental studies at the single-cell level have revealed that embryonic stem cells (ESCs), and more generally pluripotent stem cells (PSCs), exhibit significant gene expression heterogeneity.”

“Single-cell studies have allowed gene clustering, depending on the levels of heterogeneity in the gene expression landscape in PSCs.”

Does it have more to do with the variation of its expression in the population?

“In mouse ESCs genes exist that are uniformly expressed in most cells and exhibiting a unimodal distribution (Oct4, Rest, Tcf3, Sal4); other genes exhibit bimodal expression and are expressed in some populations but not in others (Nanog, Rex1, Tet1, Esrrb), and yet another group of genes display sporadic expression (Neurod1, Klf4, Otx2, Pax6) and are undetected in most cells but highly expressed in some speciﬁc subpopulations.”

Reference:

Angarica and Sol, 2016, Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation.

Heterogeneity is a noun meaning:

the fact of consisting of parts or things that are very different from each other

In scientific use the context determines what is differing.
The context here is gene expression in individual embryonic stem cells (presumably single-cell RNASeq). Here the heterogeneity in expression would be for the genes

…(Neurod1, Klf4, Otx2, Pax6)

for which the expression is

…undetected in most cells but highly expressed in some specific subpopulations.

The conclusion is that although the embryonic stem cells may appear to be a homogeneous population (all alike) and do show similarities in many genes that they express, they must, in fact be a mixture of two (or more) types. (This makes the generally accepted assumption that the basis for distinguishing cells is the genes they express and the proteins they make.)
Thus the idea, expressed in the question, that the cells are identical is incorrect. I know little about stem cell differentiation, but I would assume the implication is that the subpopulation will differentiate on a different path to the rest of the population, or that it has already started to differentiate, or something of the sort (which I imagine is discussed in the paper).


What is effectiveness of methyl-alcohol as sporicide? Methyl-alcohol is the weakest alcohol in terms of bactericidal properties. However, I have read that it also works as sporicide.

What is the effectiveness of methyl-alcohol in killing the spores of fungi and bacteria compared to other substances and what is the best dilution?

Methanol (methyl alcohol) tends to lack sporicidal activity on its own. However, fresh mixtures of methanol and hypochlorite, with at least 15% methanol, are known to have low sporicidal activity.

With an increasing methanol concentration, right up to about 50% methanol, the sporicidal activity can be increased. The preparation, however, isn't overly stable and the sporicidal activity will start to decrease after 8 hours. It is thus recommended, should a methanol + hypchlorite mix be used to counteract spores, to only use a freshly prepared solution of 50% methanol and a sufficient amount of (sodium) hypochlorite that provides 2000 parts per million available chlorine in distilled water and allow for a contact time of at least 15 minutes.

Sources:

Russell 1990 - Bacterial Spores and Chemical Sporicidal Agents
Kelsey JC, Mackinnon IH, Maurer IM Sporicidal activity of hospital
    disinfectants Journal of Clinical Pathology 1974;27:632-638.


Is AT or GC content important in electrophoresis? Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?

It does make a difference on polyacrylamide. A and C are faster while G and T are slower.

Image from publication:

The "standards" are AAA/TTT/GGG/CCC molecules.


I2D vs STRING for protein-protein interactions Can someone clearly explain me the differences between STRING and I2D(Interlogous interaction database) ? What does each database do best ? Which database is better for what kinds of studies etc ?

I just looked and it seems I2D use the PPI from 5 organisms to predict interactions in those organisms, which have not yet been experimentally demonstrated, so its interolog PPI prediction tool by design (http://genomebiology.com/content/pdf/gb-2007-8-5-r95.pdf), where as STRING can be used to see what proteins are known to interact with a given protein, and what evidence is present for a particular interaction, which you then get a (confidence like) score.


Will this strategy work for verifying successful cloning of a DNA fragment into a plasmid vector? So I am in a bit of a time constraint. Essentially, I inserted a DNA fragment via molecular cloning which contains a unique RE site. I need to confirm whether my colony has or does not have the fragment.
I need to do this in one day so would this work as a confirmation strategy:

Pick colony and perform colony PCR with primers around RE site.
Cleanup the PCR product and digest using the enzyme which was inserted.
Run on a gel. If a cut is noticed, this confirms that the colony had the inserted fragment (containing the RE site).

Would this strategy work? Are there any notable issues people can for see in this strategy?

Yes, your strategy would work, with the caveats already mentioned by @Cell.
Depending on which restriction enzyme and PCR buffer you use, you might even be able to skip step 2. NEB has a good list over their restriction enzymes and their activities in some common PCR buffers. With some reasoning that information is often applicable also to restriction enzymes of other brands.
Depending on your primer availability, another quick strategy is to simply use a primer pair such that one primer binds inside your fragment, and the other binds to the backbone. This should result in a PCR product only if your cloning was successful, and also verifies correct direction (in case you used blunt-end or single-site cloning). Two possible problems with this approach is:

If you get no bands at all you may not know if what failed was your cloning or the PCR reaction. The latter can be easily controlled for with a well-thought positive PCR control.
You may detect cases in which more than one copy of your fragment have been inserted. Although such cases are rare, it sometimes happens that inverted repeats of 3, 5, 7, ... etc copies get inserted in tandem.


Where do the H+ ions come from in light reactions? In the light-dependent reactions of photosynthesis, H+ ions pass to the thylakoid space. Where do these protons come from?

The photolysis of water is coupled to the reduction of plastaquinone (Q) in photosystem II (PSII) as summarized in this diagram, adapted from Berg et al.:

The overall reaction (which balances) is:

2 H2O + 2 Q + 4 H+ = O2 + 2 QH2 + 4 H+

But the 4 H+ on both sides of the equation are not the same. The generation of the hydrogen ions in the thylakoid lumen is coupled to the uptake of hydrogen ions from the stroma as the plastoquinone is reduced. This is made possible because of the membrane disposition of the components of photosystem II. Hence an electochemical gradient is established that can be used for generating the ATP needed for photosynthesis.


Why is the upper respiratory tract so vulnerable to infections? Wikipedia has the following statement on its Upper respiratory tract infection page:

  In United States URIs are the most common infectious illness in the
  general population.

What is it about the upper respiratory tract that makes it so vulnerable to infections?

Mostly because it is in almost constant contact with aerosols from the outside world (with regard, of course, to a thin layer of mucus), therefore any pathogens they might contain.

You also have to remember what separates an airborne pathogen from any other pathogens- infection location. A pathogen is airborne when it infects and irritates the throat or nasal passage enough to make the organism's normal deterrence functions kick in. In most cases this would be coughing or sneezing, which produce contaminated aerosols for other organisms to inhale through their own upper respiratory tract.

I hope this answers your question!


Woodpecker pecking, an effective evolution? I was sitting out on my balcony earlier and saw a woodpecker land on a tree nearby. It began pecking at the tree, and did so about five times, in intervals of about four pecks each time, before finally giving up and flying away. My question is quite simple, were woodpeckers gifted(did probability glean favorably upon) with a positive form of evolution? Does the reward justify the amount of energy they have to exert for food? Were they given an improper and doomed form of evolution?

My question is quite simple, were woodpeckers gifted with a positive form of evolution?

Though this has been addressed in comments, it's an opportunity to address a popular mind frame about evolution, that is anthropormorphizing it.

Evolution does not think or bestow in the sense that a philanthropist might. Evolution does not doom or treat unfairly as a dictator might. Evolution is merely the process of predominantly random changes in genetic material that result in a change in the expression of that genetic material. If it is a change that radically affects expression of a critical gene (say, that encodes the structure of hemoglobin), the organism experiences a lethal point mutation and ceases to exist. Evolution for that organism stops there; if death occurs before reproduction, the mutation is lost.

Evolution seems beneficial because the environment exerts selective pressures on life: if two animals (say, birds) in the same habitat (say, woodlands) eat the same food (say, larval insects), competition for resources exists, decreasing the numbers of both animals. However, if a mutation (say, a marginally different beak shape) allows even a slight chance that the animal will have a competitive advantage, it is kept in the population. A staggering number of mutations similarly either harmless or advantageous may eventually allow two animals to inhabit the same habitat without competition - a net gain for both animals.

But there's no gift involved. Just a mind-numbing number of non-lethal mutations over a mind-numbing number of years, under the influence of the selective pressures of the environment. You don't see all the mutations that were deleterious, resulting in countless deaths and dead ends because you are standing in one point in time, seeing what exists around you now. The woodpecker seems almost fantastical.

  Were [woodpeckers] given an improper and doomed form of evolution?

Evolution follows the same principles for all species: predominantly random mutations without rhyme or reason or form. If you want to speak of doomed animals, look to mankind's effects on the environment in the last 2000 years, or the last 20. When ecological niches are wiped out, that, not evolution, dooms an animal. The Monarch Butterfly is a poignant example of dooming a species by destroying it's habitat.

A great way the understand selective pressures of habitat is to read about marsupial evolution in Australia. The effect of ecological niches on evolution is very clear.


Clarification on BMI formula In the BMI formula= (Weight)  X  703) / (Height^2) , what does 703 represent? What is a reliable source that I can cite for this answer?

weight= lbs    height= inches


How does the frequency of a visual stimulus affect the steady-state visually evoked potential? I want to design a project for EEG signal processing. In my research I found the concept of SSVEP. SSVEPs represent the electrical activity of the brain as measured via EEG, and are evoked by visual stimuli with low frequency applied to the eye.

My question is whether it is known how the electric activity of brain will change? And a second thing, does it mean that each frequency applied to the eye has a fixed reaction for the brain?

Short answer
SSVEP frequency corresponds to stimulus frequency and SSVEP amplitude decreases with stimulus frequency.

Background
The simplest form of steady state visual-evoked potentials (SSVEPs) are those to flash stimuli. Herrmann (2001) studied the SSVEP by recording the EEG from the visual cortex at various flash frequencies. He found that SSVEPs occurred at a frequency corresponding to the flicker stimulus. Amplitudes decreased steadily with frequency and SSVEPs could be recorded up to ~90 Hz flicker frequencies. The shape and frequency following of SSVEPs are shown in Fig. 1.

Fig. 1. SSVEPs and FFT spectra at various frequencies. Source: Herrmann (2001)

Interestingly, SSVEPs in response to some frequencies showed resonance phenomena, indicating a selective frequency preference of the neural oscillators. Specifically, SSVEPs at around 10, 20, 40 and 80 Hz resulted in higher amplitudes than stimuli flickering at adjacent frequencies (Fig. 2).

Fig. 2. SSVEPs showing resonance at 80 Hz. Source: Herrmann (2001)

Reference
Herrmann, Exp Brain Res (2001); 137: 346–353


What is it called when one human eye is seeing brighter color than the other? What is the name of a phenomenon where one of the human eyes is seeing brighter/more saturated color than the other? I can observe the same object from the same position while alternating which eye is closed, and there's a visible difference in the saturation of color. Like one color is more pale than the other.

Here's an example of what the difference looks like between image perceived by two eyes:

here is forum discussing similar effect ,

where as similar problem which leads to double vision is single eye is called monocular Diplopia.

There are two possible causes discussed in that forum. One is a cataract or an early indication of a cataract, for which a vision specialist visit is recommended.

Another solution is much simpler one of the pupils is more dilated than the other:

  The way your eyes see colors changes throughout the day, not dependent
  only on external conditions. Try this: gently press the palm of your
  hand against one eye (closed), for about a minute; leave the other eye
  open during this time (feel free to blink, of course...). Now, look at
  the world with one eye covered (for a couple of seconds), then the
  other — the eye you help closed will see things as quite more
  saturated, partly because you've fostered its pupil to dilate in the
  time during which it was shut. I recall being confused by this when I
  first started noticing that, upon awaking, either eye would see colors
  differently from the other; simply, the eye rested on the mattress
  would be seeing colors with greater saturation.