Does polyploidy always isolate the polyploids from the diploid source population? I am receiving conflicting information while researching polyploid speciation. On the one hand, some sources state that a polyploid can only reproduce sexually with polyploids having the same number of chromosomes. But I am also finding information claiming tetraploid x diploid reproduction in orchids, or tetraploid x triploid reproduction of orchids (for example,see  American Orchid Society, AOS.org).

Is polyploid sexual isolation always the case, sometimes the case, or never the case? Can someone clarify this?

Ploidy and reproductive isolation in plants

Speaking generally, there is simply no question that for flowering plants there can be a sexual pathway between diploid and polyploidy levels. The question is how wide is the bridge and how much flow is there in either direction. In other words the questions become "How much flow?", "How meaningful the flow?", "How much flow back to the original diploid and polyploid populations?", and "How often over the last 200 million years has such interaction been an important factor in the evolution of flowering plants?".

Examples from Rhododendron

In the following, I will give a number of examples from the plant genus Rhododendron to show how ploidy level can function in relation to sexual isolation. In this taxa, diploid X tetraploid normally produces triploids although occasionally a tetraploid or even a diploid offspring is produced. The triploid offspring of diploid deciduous azalea species X tetraploid deciduous azalea species often look very similar to the tetraploid pollen parent.  'Margaret Abbott', which is a seed fertile tetraploid deciduous azalea, has a fragrant white flower produced by crossing a fragrant pink flowered diploid seed parent with a non-fragrant yellow flowered pollen parent.

Our research on hybrid elepidote Rhododendron indicates that triploids, although reluctant to reproduce sexually, can produce diploid, triploid, tetraploid, and pentaploid offspring when crossed with pollen from diploids, triploids, and tetraploids. 'Phyllis Korn' is an example of a fourth generation triploid. 'Graf Zeppelin', which exhibits polyploid characteristics, is an example of a diploid offspring of a triploid. 'Countess of Derby' is an example of a tetraploid offspring where both parents are triploids. 'White Ginger' is a an example of a pentaploid offspring of a triploid. 'Pink Pearl' is an example of a triploid that has produced diploid, triploid, and tetraploid offspring from interaction with diploids.

In deciduous azaleas triploid X tetraploid crosses often produce aneuploids between triploid and tetraploid. Such crosses can on occasion produce pentaploids.

Our limited experience working with triploids and pentaploids as seed parents indicates that in general pentaploids are better seed producers than triploids.

An interesting finding is neotetraploids can produce diploid offspring in the first generation. In general tetraploids can produce diploids, triploids, tetraploids, and pentaploids when crossed with pollen from diploids, triploids, and tetraploids.

Triploids are common in natural contact zones where diploid deciduous azalea populations overlap with tetraploid deciduous azalea populations. There is strong evidence indicating there is gene flow from the diploid population to the tetraploid population in these contact zones. There is some evidence of gene flow from the tetraploid population to the diploid population. There is some evidence to suggest multi-generational triploids exists in these contact zones.

Worth noting is that the meiosis for triploid deciduous azaleas that do set seed is distributed around 1.5x gametes ranging from 1x to 2x with an occasional 3x gamete. This uneven distributed splitting of triploids is what produces aneuploid offspring between 3x and 4x when semifertile triploids are crossed with pollen from stable tetraploids. Cyril Dean Darlington in the late 1920's and early 1930's documented this uneven distributed splitting of triploids during meiosis. Evidence suggests that neotetraploids can also undergo uneven distributed splitting during meiosis.

Darlington's history of the garden hyacinths showing a triploid pathway from diploid species to tetraploid hybrids parallels the history of the hybridization of the tetraploid elepidote Rhododendron 'Countess of Derby'.

We have some evidence for deciduous azaleas that 3x X 4x can produce aneuploids close to 5x indicating that some of the "3x gametes" are coming from first an uneven splitting of the triploid followed by a failure to reduce in a later phase of meiosis. However this result of aneuploidy near pentaploid has not occurred often enough to be certain that is what is happening.

In general for deciduous azalea species;

diploid X diploid normally produce seedpods and high percentage of
viable seed.
tetraploid X tetraploid normally produce seedpods and high percentage
of viable seed.
diploid X tetraploid normally produce seedpods but a highly variable
percentage of viable seed.
tetraploid X diploid almost never set seedpods.
triploid X tetraploid sometimes produce seedpods and a low percentage
of viable seed.

For hybrid elepidote Rhododendron, 2x X 2x, 2x X 3x, 2x X 4x, 3x X 2x, 3x X 3x, 3x X 4x, 4x X 2x, 4x X 3x, and 4x X 4x are all documented to have occurred.

For deciduous azaleas, we have produced viable seed from 2x X 2x, 2x X 4x, 3x X 4x, 4x X 4x, 4x X 6x, 4x X 8x, 5x X 4x, 6x X 4x, and 6x X 6x.

The flow cytometry for this research on the genus Rhododendon was performed by Dr. João Loureiro, Dr. Silvia Castro, José Cerca, and Mariana Castro
Plant Ecology and Evolution Group,
Centre for Functional Ecology,
Department of Life Sciences,
Faculty of Science and Technology,
University of Coimbra, Portugal.

The ancestry for 'Phyllis Korn' illustrates that triploids can be multi-generational.

The diagram below illustrates how the triploid 'Pink Pearl' has produced diploid, triploid, and tetraploid offspring when interacting with diploids and has produced a tetraploid offspring by interacting with another triploid.

The family tree for the Rhododendron elepidote hybrid 'The Duchess' illustrates that interploidy interaction can be multi-generational.

\

Picture of 'Margaret Abbott' with a quote from Frank Abbott.

Picture showing how much the offspring of a diploid crossed with a tetraploid looks like the tetraploid pollen parent.

Picture showing the successful development of seedpods from crossing a diploid by a tetraploid.

Picture showing the failure in developing seedpods from crossing a diploid by a tetraploid.

Picture showing interploidy hybrid swarm at Audra State Park, WV.

References

Meiosis in Polyploids
by W. C. F. Newton and C. D. Darlington
in Journal of Genetics 1929

The history of the garden hyacinths
by C D Darlington, J B Hair and R Hurcombe
in Heredity 1951

Rules of Engagement: Have Pollen—Will Travel
by John Perkins · Sally Perkins
in Azalean 2010

Frank Abbott's Village of Azaleas
by John Perkins · Sally Perkins
in Journal American Rhododendron Society 2011

Ploidy level estimations in deciduous and elepidote hybrids of Rhododendron
by José Cerca de Oliveira, Mariana Castro, Francisco J. do Nascimento, Sílvia Castro, John Perkins,Sally Perkins, João Loureiro
in Jornadas Portuguesas de Genética, Coimbra, Portugal; 05/2011

Weighing in: Discovering the ploidy of hybrid elepidote rhododendrons
by Sally Perkins, John Perkins, José Monteiro de Oliveira, Mariana Castro, Sílvia Castro,  João Loureiro
in Rhododendrons, Camellias and Magnolias, Royal Horticultural Society, Editors: Simon Maughan, pp.34-48 2012

Untersuchung des Ploidiegrades elepidoter Rhododendron-Hybriden
by Sally Perkins, John Perkins, Mariana Castro, José Cerca De Oliveira, Silvia Castro, João Loureiro
in Rhododendron und Immergrüne , Deutsche Rhododendron-Gesellschaft e.V. , Seite 21: pages 21-42; 11/2013


How to avoid air bubbles while pipetting? I get air bubbles while pipetting small volumes. How can I avoid them ?

You're still pipetting too fast, you should move the piston slowly and evenly to avoid air bubbles. Also make sure that you wait a second or two for the liquid to rise before moving the tip out of the liquid reservoir.

Pipettes can also behave rather weird with any liquid that differs significantly in any physical property from water, e.g. very viscous solutions.

You can find a few more tips in this document from Eppendorf or this one from Thermo Scientific.


What are gram negative and positive bacteria? I've just finished a course of double antibiotics for Helicobacter pylori in my stomach.  I looked up H. pylori and found that it was a gram-negative bacterium.  I looked up gram-negative and didn't understand the definition.  I assume that if there are gram-negative bacteria then there are also gram-positive ones.  Can someone explain the terms gram-negative and gram-positive in basic, layman's terms?

Thanks,

Sachin

The Gram stain is one of a large number of techniques used to characterize bacteria. In particular, a bacterial species is usually either Gram-positive (purple when stained) or Gram-negative (pink when stained). In Gram-postive bacteria, the cell wall is thicker and has much more peptidoglycan compared to Gram-negative bacteria. The chemicals in the stain react with these molecules in the cell wall and result in the purple color. All of this information is well covered in the Wikipedia article on the subject.


How much DNA of Albert Einstein is recoverable? Since there seem to be five biological descendants of Albert Einstein, and the original chromosomes of him distributed among them ...

Is it possible to recover enough DNA of an individual from his progeny and proceed to clone him? Any information would be helpful

During the generation of gametes (sperm, eggs), chromosomes can cross-over - this swaps paternal and maternally-derived genetic material.  So none of the descendant's chromosomes would be a direct copy of Einstein's, and furthermore, each offspring receives half of its genetic complement from each parent.  This means that if you pool the DNA data from small number of offspring you may not obtain all the elements of one parent's DNA or be able to assign that data back to a specific 'original' chromosome. (On top of this you would have to determine which sequences in the offspring came from the other parent).

If I was cloning Einstein, I'd use his DNA.  Is his comb in a museum ? A tooth? A letter he licked?  A large chunk of Einstein still exists (formalin fixed brain) and lab protocols can recover DNA from formalin fixed tissues. It wouldn't be easy, but in theory, you could: i) derive its full sequence and ii) synthesize artificial chromosomes with suitable epigenetic modifications, and iii) inject those into enucleated eggs for human cloning or iv) transfect them into enucleated cells from a cell line, make iPSCs and then fuse those with ~8-cell fertilized embryos.

(Spoiler - not technically do-able today and almost certainly illegal in most states/countries).
For a related movie treatment, the Boys from Brazil  tells a good story - warning Nazi content.


when does an erythrocyte start carrying oxygen molecules and what is the binding capacity As it is in the title, I am just wondering when does an erythrocyte (especially Reticulocyte) start carrying oxygen molecules and what is the binding capacity for oxygen.
That is, Under normal conditions, reticulocytes are the youngest erythrocytes released from the bone marrow into circulating blood. They mature for 1-3 days within the bone marrow and circulate for 1-2 days before becoming mature erythrocytes. How much oxygen molecule a reticulocytes can carry ?

I mean, I need an approximation of the number of O2 molecules bound to hemoglobin per reticulocyte

Erythrocytes contain many hemoglobin proteins. Each protein has 4 haem groups, and oxygen molecules bind to in porrin ring inside these haem groups. The binding capacity is the affinity each haem group has for oxygen. This changes depending on the external conditions, for example PH.

For example, when the ph is quite low (acidic), this is often due to CO2 build up in the local area, dissolving in the blood to form carbonic acid. This means that there is anaerobic activity happening in the area so it needs more oxygen. The oxygen associated with the hemoglobin will disassociate making it available for the surrounding tissue. It is important to remember that the process is not concrete and is always fluctuating. There are many curves that show the likelihood of association and disassociation. I would recommend looking at these disassociation curves to understand.

Erythrocytes are typically oxygenated in the lungs (supplied by the pulmonary artery from the heart). After oxygenation, the blood goes back to the heart via the pulmonary vein in order to be sent round the body. Reticulocytes are immature erythrocytes and will be carrying increased amounts of haemoglobin as they develop it. The following link leads to a paper which approximates haemoglobin content in reticulocytes.

  https://www.ncbi.nlm.nih.gov/pubmed/18027835


Cerebral activity during exposure to non - visible light Our eyes only have the ability to sense light within a certain spectrum. My understanding is that particular frequencies energize specific cells in our eyes, each responsible for a different "color". When these cells are energized, they each release an appropriate amount of their chemical transmitter to stimulate additional cells and create the perception of the object from which the photos originate.

At what point does this process not occur for non-visible light?

In other words, do we fail to see non visible light because our eyes lack the receptors for other frequencies, or does our brain receive signals that it just dumps because it has not developed to process the information?

Have there been any experiments done involving a brain scan while exposed to non visible light?

Vision is based on a protein interaction with a molecule called retinal from vitamin A.

Wavelengths of light in the visual range cause a photoisomerization of retinal (a cis- to trans- change), which is sensed by the protein that is "holding on" to the retinal.

Wavelengths that do not cause this photoisomerization cannot be sensed by the photoreceptors of the retina, so there isn't any signal produced to transmit to the brain.

However, there is some filtering done by the lens of the eye. Without the lens, humans (and other animals) can see further into the UV range. That UV light is also damaging to the retina, though, so it's best to keep the lens intact.

Note that the image in the answer by @Remi.b is actually from a psychometric experiment, so the lens is intact. The responses there are actually human perceptual sensitivity to light for each cone. The blue curve would go off to the left quite a bit further into the 300nm range if the lens were not present. The research subjects probably prefer the experiment as-is, however.

You wouldn't perceive that UV light much differently than a far violet color, however, because differences between different cones are necessary for color vision, and by that end of the spectrum only the cones responsive to the shortest wavelengths are responsive at all.


Why would mutation rates increase in a tumour? This article describes a tumour:

Swanton found that even the primary tumour was surprisingly varied. He found 128 mutations among the various samples, but only a third of these were common to all of them. A quarter of the mutations were “private” ones – unique to a single sample.
The tumour had also split down two evolutionary lines. One area – part of R4 in the picture – had doubled its usual tally of chromosomes and seeded all the secondary tumours in the patient’s chest. The other branch had spawned the rest of the primary tumour. Even though this tumour looks like a single mass, whose cells all descended from a common ancestor, its different parts arehave all  evolved independently of one another.

My understanding is that if non-cancerous cells normally had such a rate of mutation it would be lethal to the cell if not the organism.

What about tumour cells would lead to a higher incidence of mutation?
How are these cells able to survive when non-cancerous cells would perish?

Cancer cells generally lack the "safety mechanisms" or "check points" that prevent normal cells from replicating, and some of these mechanisms are also involved in ensuring that DNA replication proceeds without serious errors. Inactivating these safety mechanisms lets cancer to cells divide rapidly, but at the same time also causes their genome replication to be "sloppy", introducing various errors.

The P53 protein is probably the most well-known example of such a "safety mechanism". In normal cells, P53 arrests the cell cycle if breakage occurs in the DNA strands; but cancer cells often inactivate P53, and consequently they tend to proceed with DNA replication even if DNA is damaged. A consequence is that DNA is often in a state of disrepair in cancer cells. (A review of P53 here.)

This lack of proper "quality control" can lead to loss of large pieces of the genome, even entire chromosome arms. While it may seem strange that the cells can survive this, keep in mind that the genome encodes information to support the complex working of an entire organism. Loss of a chromosome arm would indeed be lethal to the organism as a whole --- perhaps it would disrupt brain development, or the immune system. But for single cell to survive and develop, most genes are actually not essential, likely because there are so many redundancies. This is frequenly seen in genome-wide RNA interference screens, for example this paper. Remarkably, cells can even lose the entire mitochondrial DNA (which means they cannot even respire anymore!) and still survive.

It is not clear that "non-cancerous cells would perish" if they would similarly lose DNA. They would likely arrest and turn senescent because they detect DNA damage, precisely because of these safety mechanisms --- but that is different. The loss of genes in itself may not be lethal to a normal cell, it's rather that normal cells "choose" not to continue when this happens. But this distinction is probably difficult to test experimentally.


Why are archae and bacteria grouped into separate domains? Archae and bacteria are both Prokaryotes. Why are they group into two separate domain?

Reducing your question to its fundamental misunderstanding

Similarly one could ask "Mammals and birds are vertebrates. Why are they grouped into two separate taxa?" (Bacteria and Archea include all procaryotes unlike my example). Or even better, one could ask "procaryotes and eukaryote are all alive. Why are they grouped into two separate taxa?" At the end of the day, your question boils down to why do we group lineages together?.

Why do we group lineages together?

Population tend to diverge through time. For this reason we end up with a multitude of different lineages. As humans we can enjoy grouping lineages as we like to. One might group all yellow flowers together for example. However, a grouping which is of particular interest is one which represent evolutionary relationship. Insecta for example represents a group that include all currently living insects and all of their ancestors until the most recent common ancestor of all insects (that is the individual toward which all currently existing lineages coalesce). Such groups are called monophyletic.

You should have a look at this post where I made an intro to phylogenetic.

In short, to answer your question,

  [W]hy are [Bacteria and Archea] grouped into two separate domain?

Because they represent two separate lineages.

Phenotypic differences

Of course, different lineages often have distinct phenotypes which makes their grouping intuitive to a naturalist. For Bacteria and Archae, it takes some knowledge in molecular biology to tell how different they are phenotypically. This document from Colorado University does a good job in introducing the similarities and differences between Bacteria and Archae


Ecomorphs as evolutionary definitions There have been demonstrations of ecomorphs in different taxa, where each morphology type is associated to a single environment. I know that it happens because special morphological characters increase the fitness and therefore will be positive selected.

My question is; if we find similar places (talking about natural pressures and climatic conditions) on earth and given enough time, can we expect to see more or less the same ecomorphs living in different places? Also, assuming that, could evolution be a regarded a non-stochastic process?

The phenomenon you describe, where the same result comes about in more than one time/location via evolution, is called "convergent evolution." It is when the same character, or trait, evolve independently of one another. One example is the wing, it has evolved (at least) several times independently, in bats, birds, and insects. Parallels can also be drawn with other traits like dispersion methods of seeds, or the evolution of fins in fish, dolphins, and whales. Here is a classic paper by Ernest Williams from 1972 which describes one of the earliest examples given of ecomorphs, the anolis lizard, also talked about on this site.

This is from a good article on the new scientist website that would be worth reading:

  "Evolutionary convergence occurs at every level, from proteins to
  societies. An unusual antibody once thought to be unique to camels has
  a close equivalent in sharks, for instance, while naked mole rats form
  social colonies like those of ants and bees.

  "What this means is that if we could wind the clock back and let life
  evolve all over again, life might take very different paths but still
  produce organisms that, in some ways, resemble the organisms alive
  today.

  "There would almost certainly be streamlined swimmers in the oceans and
  winged creatures in the skies. In fact, some argue that the evolution
  of intelligence is also virtually inevitable, though intelligent
  organisms could be very different from us."

The answer to your question is yes, with enough time and the same selection effects we would not be surprised if there was a similar pair of independently evolved characters. However, selection acts on random mutations which is not a directed process, therefore for the same characters to evolve you would need mutations to occur that had similar effects. This is why given enough time we can see the same responses. Despite the non-random effect of selection, we could consider evolution to be a stochastic process, it only arrives at the same converged point by chance. This is because selection (the main driver of evolution) acts on randomly generated genetic variation thus the direction of the evolutionary trajectory is random.

  "..often used to represent the evolution of some random value, or
  system, over time. This is the probabilistic counterpart to a
  deterministic process (or deterministic system). Instead of describing
  a process which can only evolve in one way (as in the case, for
  example, of solutions of an ordinary differential equation), in a
  stochastic or random process there is some indeterminacy: even if the
  initial condition (or starting point) is known, there are several
  (often infinitely many) directions in which the process may evolve." -
  wikipedia entry on Stochastic Processes

Following the quote above it may seem that evolution is a directed process, i.e. selection is aiming for a specific target. It is not, selection can only weed out the least fit genotypes and increase the frequency of the better ones, selection has no goal or pre-existing aim. Thus, when discussing stochasticity in evolutionary terms it is perhaps better to use evolutionary trajectories, to describe the randomly created paths they move along, instead of "directions."

As an example of convergent evolution we could use the peppered moth and a little imagination because this is purely a hypothetical illustration I am making up on the spot.

The peppered moth is famous for once being a white moth that turned dark during the industrial revolution, when towns and cities grew and pollution killed the light coloured lichens that helped the light morph hide. This meant, rather suddenly by evolutionary time-scales, the white morph of the moth was not very well camouflaged against the dark bark of the trees. This created a positive selection for darker morphs, as such, alleles which made for dark moths would have spread rapidly in the population.

Using a little imagination we can think about two different parts of the world where this same event occurred independently - e.g. Glasgow and Plymouth in Britain which are quite far apart but both grew expansively during the industrial revolution. In both of these locations we would have seen a simultaneous rapid loss of lichens and increase in the dark moth ecomorph. This would have been convergent evolution because it is likely that they were independent of each other, i.e. the dark moth probably did not evolve in Glasgow and then fly itself down to Plymouth.


Can the human body store protein? I am interested to know if a human body can store protein.

Absolutely for the bodybuilders, does it really matter if they divide their protein consumption during the day or eat all of it in one meal at anytime they want?

Is there any constrain on protein absorption per hour?
What will happen for the extra protein we eat?

The human body can not store Proteins (technically).
BACKGROUND :
PROTEIN is a very broad term and there are hundreds and thousands of proteins.[1]
Proteins are heteropolymers consisting of amino acids held by peptide bonds.
Amino acids :
There are 9 amino acids which we need to intake.

Phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine.

Amino acids our bodies can produce:

These five are alanine, aspartic acid, asparagine, glutamic acid and serine.

These amino acids combine in different arrangements to give those thousands of Proteins. This process is carried out by Ribosomes (cook) and mRNA (recipe) inside every* cell.
Protein metabolism in humans :
During human digestion, proteins are broken down in the stomach to smaller polypeptide chains via hydrochloric acid and proteaseactions. This is crucial for the absorption of the essential amino acids that cannot be biosynthesized by the body.
Trypsin and Chymotrypsin as Trypsin and Chymotrypsinogen are the enzymes  necessary.
.
MAIN ANSWER  :
The excess Amino Acids are broken down into Glucose ( carbohydrate like stuff ) and the Nitrogen moiety is converted into Urea / Uric acids. This is then excreted by kidneys.

Amino acids can be broken down into precursors for glycolysis or the Krebs cycle.
Amino acids can also be used as a source of energy, especially in times of starvation. Because the processing of amino acids results in the creation of metabolic intermediates, including pyruvate, acetyl CoA, acetoacyl CoA and so on; amino acids can serve as a source of energy production through the Krebs cycle.

Therefore excess protein is simply used to make energy like carbs and the Nitrogen part is excreted. Now the excretion process can strain the kidneys due to increased work load, and prolonged stress can lead to malfunctions.
Also,
Our body is very concerned with conserving nitrogen levels, since our body can't fix nitrogen gas (N2) into ammonia (NH3). but, we can't just store huge amounts of ammonia because it's toxic. sugars and fats aren't toxic, so we can store them. because of this, our body either quickly utilizes excess ammonia to make nitrogenous compounds like amino acids and nucleotides, or it excretes it via Urea in our urine.
Problem with Protein storage :
If our bodies had to store proteins, it would need several sophisticated mechanisms and specialised storage cells.( Like we have adipose tissues short fats and lipids storage ).
if you examine the structure of amino acids, they are very similar to many of the carbon-hydrogen-oxygen metabolic intermediates. for example, alanine is an amidated pyruvate, glutamine is an amidated alpha-ketoglutarate, etc. many are easy to make, and most don't cost much to do so, so the body would rather use these intermediates to either:

Create acetyl-CoA, NADH, FADH2, and ATP for energy. this would happen during exercise or starvation.

Create glycogen, fatty acids, nucleotides, NADPH, and other metabolic compounds. this would occur after a big meal, during sleep, and when energy is not needed in high amounts. these compounds are very expensive ATP-wise.

So there's no need to store whole Amino Acids because they can be immediately used for whatever the body needs and then remade when necessary.
We do not store amino acids because we don't need to.
Right dose of Proteins :
Research shows:

A total of 80 g of whey protein was ingested in one of the following three conditions: 8 servings of 10 g every 1.5 h; 4 servings of 20 g every 3 h; or 2 servings of 40 g every 6 h. Results showed that MPS was greatest in those who consumed 4 servings of 20 g of protein, suggesting no additional benefit, and actually a lower rise in MPS when consuming the higher dosage (40 g) under the conditions imposed in the study.

Check here for the interesting results ( this is very relevant to your second question )
Therefore distributed intake of right amount of protein is important!
Scientific literatures :
Proteins:
https://en.wikipedia.org/wiki/Protein_(nutrient)
https://en.wikipedia.org/wiki/Amino_acid
Protein Metabolism:
https://opentextbc.ca/anatomyandphysiology/chapter/24-4-protein-metabolism/
Protein intake and storage:
https://newsnetwork.mayoclinic.org/discussion/are-you-getting-too-much-protein/
https://www.self.com/story/what-protein-does-in-your-body


Infer distance since duplication from tree? Question
I have a really simple question, but I'm not able to figure it out.
I made a tree (using BLOSUM62). Here is a part of the tree:

How can I calculate the distance till the duplication event occured between HBD en HBB?

just for HBB 36.21 and for HBD 38.79
or 38.79 + 36.21 = 75

More info
I determined if this set of sequences follows a molecular clock, and indeed this was the case. So I determined the rate at which these sequences envolve. If I can determine the distance between HBD and HBB I can devide this by the rate to obtain the time since the duplication event happened.

How could you calculate this one?

Assuming a molecular clock, the distance between the sequences and the duplication event is 75/2 = 37.5. Ideally, these sequences should have the same distance from the internal node (under a clock), and you could use a model that explicitly assumes a clock -- which will lead to ultrametric trees.  One example is the program promlk (or dnamlk) from the phylip package. A faster alternative would be the  UPGMA method, which also gives you an ultrametric tree.


Does one memory cell take part in different memories? Does one memory cell take part in different memories? For example, both in the visual memory of a bird and a monkey?

According to engram theory: Yes.

However, you need more than one cell to encode a memory engram.
The idea is that the combination of cells encodes the memory, not the cells themselves.

I am most familiar with the hippocampus, in which cells participating in the encoding of "concepts" like Jennifer Aniston, Bill Clinton or the Sydney Opera House have been found in humans Quiroga et al. (2008)


Standard curve for real time When performing a standard curve for some new primers to test for fold change, is it necessary to run the standard curve? I mean, in case your experiment has several genotypes for the same ecotype background, with correspondent control and treatments, must I run the standard curves for all this scenarios, or rather may I pick, just to say a random genotype of treated ones, see that it R=0.99 is or higher and efficiency 2?
It is in order to not to waste material.

Do the standard curve once for each primer pair to determine efficiencies. You can use the efficiency values for any number of replicates with any template.

I think we have somewhat discussed this issue in your previous post.


Is "cell proper" considered a biology term / well defined concept? I am asking this question after writing an answer on English Language & Usage sent me on an expedition through the internet. The originating question asked about the meaning of the word proper after the word cell.

At first I was certain that it was a biology term, describing some sort of cell. I am not a biologist. After some pushback, I researched a bit and found what seems to be the original definition in a book from 1853.

  It is a mistake to apply the word cell sometimes to the cell with a membrane, sometimes to the cell without a membrane, and sometimes to the membrane without the cell. Since the contents of the cell constitute the essential part of it (see p. 155), since it forms, before the secretion of the (cellulose-) membrane (pp. 156-167), a separate entity, possessing its own, essentially proper, membranous boundary (the primordial utricle, pp. 169-173), we must call this internal body the cell proper, unless we restrict the term cell to the enclosing wall or chamber, and give the internal body another name. If the name is restricted to the internal body, we cannot, in the great majority of cases, say that new cells are formed in the old, but merely that they are formed out of the old, for even the primordial utricle shares in the division, in the propagation of cells by division. Therefore when daughter-cells are said to be formed in the mother-cells, or to slip out from the mother-cells, or mother-cells are said to be dissolved and absorbed, these phrases must be admitted only as conveniently abbreviated expressions, "mother-cell" being here used instead of maternal cell-membrane.
  (bold emphasis added)

My question is: Is cell proper considered a biology term or concept that would be understood by an expert of cellular structures?

This isn't a special biology term, it's just an English usage thing. "The X proper" just means "the X, strictly speaking". As well as the question you quote, see also this question on ELU.SE. I would expect this use to be understood by many biologists who speak English as a first language, but there are certainly clearer ways of saying it.

Regarding this particular example, the author appears to be proposing a way of defining a vacuolated plant cell. It sounds like he is proposing a definition that excludes the cell wall, but he confusingly calls the cell wall the "(cellulose-)membrane" (the 'primordial utricle' is the cytoplasm, I think). However, I am afraid I am not an expert in the history of plant cell biology and can't really comment on whether it is a useful contribution to, or synthesis of, the state of knowledge at the time.


Are there enzymes found in nature or the man made world that can help break down metals? The title says it all.

Do natural or human engineered enzymes exist that can speed up the break down kitchen utensils, aluminum cans, wires, etc. into small particles or powders?

To be clear I am not talking about chemical transformation (e.g. iron turning to rust).

There are bacteria, which can assist the proces of rust.

"Some sulfate-reducing bacteria produce hydrogen sulfide, which can cause sulfide stress cracking. Acidithiobacillus bacteria produce sulfuric acid; Acidothiobacillus thiooxidans frequently damages sewer pipes. Ferrobacillus ferrooxidans directly oxidizes iron to iron oxides and iron hydroxides; the rusticles forming on RMS Titanic wreck are caused by bacterial activity. Other bacteria produce various acids, both organic and mineral, or ammonia." (http://en.wikipedia.org/wiki/Microbial_corrosion)

As you see, many of these active ingredients, like hydrogen sulfide, sulfuric acid, other acids or ammonia are not enzymes per se, although they are produced by enzymatic processes in bacteria.

Closer to your specification is Ferrobacillus ferrooxidans (synonyms: Acidithiobacillus ferrooxidans, Thiobacillus ferrooxidans, Ferrobacillus sulfooxidans), which directly acts on iron by enzymes associated with the cell membrane:

Valid XHTML http://c431376.r76.cf2.rackcdn.com/18185/fmicb-03-00096-HTML/image_m/fmicb-03-00096-g001.jpg.

Figure 1. Schematic representation of ferrous iron oxidation by the Gram-negative autotrophic acidophile, At. ferrooxidans. Controlled influx of protons is used to generate ATP via the membrane-bound ATP synthetase complex (ATPase). Iron oxidation is mediated by a cytochrome located on the outer membrane and electrons transferred via periplasmic cytochromes and rusticyanin either to a terminal oxidase (“downhill pathway,” indicated in brown text and by **) where they are used to reduce oxygen, or used to reduce NAD+ (“uphill pathway,” indicated red text and by *) in a reaction also driven by the proton motive force across the inner membrane (Bonnefoy and Holmes, 2011). Source: Johnson et al. 2012.


Why do eggs lack an endoplasmic reticulum? Trueman's Elementary Biology book I found says that the endoplasmic reticulum is absent in eggs, but no reason is given. Why is it absent?

I could find no indication that eggs are lacking an endoplasmic reticulum. On the contrary, I could find papers written on the ER in eggs of several species.

Mouse: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis

Sea urchin: Structural changes of the endoplasmic reticulum of sea urchin eggs during fertilization

Human: The relationship between pregnancy outcome and smooth endoplasmic reticulum clusters in MII human oocytes

Frogs: The onset of activation responsiveness during maturation coincides with the formation of the cortical endoplasmic reticulum in oocytes of Xenopus laevis

However, as can be read in the sea urchin paper, the ER changes after fertilization:

  We interpret these observations to indicate that in the first few minutes after fertilization, the egg's ER is fragmented

For other species, I could only find evidence that the ER reorganizes after fertilization because of changed calcium signaling needs


Why can't we defibrillate the heart within 1 minute after ventricular fibrillation by electroshock? We mostly can defibrillate the heart before 1 min of ventricular fibrillation by electroshock.Then we often can't do defibrillate it with electroshock.

What's the reason and What's the best way to defibrillate heart within 1 min after ventricular fibrillation?

To say that there is a cutoff of one minute at which time shocking becomes ineffective is incorrect. The best way to defibrillate a heart within one minute of VFib onset is with electric shock. In fact, short of certain drugs in certain instances, it's the only way to defibrillate Vfib, regardless of the amount of time that has passed.

If the one minute cut-off were true, survival rates of out-of-hospital arrests would be more dismal than they are. Even with the availability of automated external defibrillators (AEDs) to treat out-of-hospital arrest, the collapse to response time is well over a minute. Someone has to notice a collapse, feel for a pulse, and call for a defibrillator (or get it themselves), expose the chest, apply the paddles, wait for the monitor to display the rhythm, clear the area and shock. If you were told that this usually occurs in under a minute, you were misinformed.

Seattle is the best city in the US (probably the world) in which to have a heart attack.[1] The population has a high rate of training in CPR, a highly trained corps of paramedics and EMTs, and a quick response time. So it's logical to do studies about factors affecting survival of out-of-hospital arrests in Seattle.
A study published in 1999 found that CPR did not have any effect on outcomes of out-of-hospital arrests unless the interval time (from arrest to defibrillation) was greater than 4 minutes.[2] (In other words, shocking without CPR was no different in outcome than shocking preceded by CPR; both resulted in cardioversion to a stable rhythm and a return of of spontaneous circulation in the same percentage of patients.)

However, that is not to say that CPR (chest compressions +/- respirations) are unimportant. A 2003 study found an unacceptable level of CPR was performed when AED paddles were connected (i.e. there was an over-reliance on shocking).[3]

The new Advanced Cardiac Life Support guidelines call for CPR to be initiated immediately, regardless of witnessed or unwitnessed arrest (i.e. down time).[4] It needs to be noted, though, that this recommendation does not rest on defibrillation with the aim of return of spontaneous circulation(ROSC), but on improved neurological outcomes.[5] This, not ROSC, is what the new ACLS recommendations are based on, because ACLS is not considered highly successful if the patient leaves the hospital only to be hospitalized elsewhere in a persistent vegetative state.

[1] King County may be the best place to have a heart attack
[2] Influence of Cardiopulmonary Resuscitation Prior to Defibrillation in Patients With Out-of-Hospital Ventricular Fibrillation
[3] Interruption of cardiopulmonary resuscitation with the use of the automated external defibrillator in out-of-hospital cardiac arrest
[4] VF/Pulseless VT
[5] Delaying Defibrillation to Give Basic Cardiopulmonary Resuscitation to Patients With Out-of-Hospital Ventricular Fibrillation A Randomized Trial


How many proteins could participate in a complex Disclaimer: I’m a computer science student with minimum knowledge of biology.

I’m working on an algorithm to cluster proteins in Protein-Protein-Interaction Networks to find protein-complexes. While working on that I stumbled upon the question how many different proteins can be part of a protein complex. (I'll call this the size of the complex from this point.)

I started by counting the the participants from all Corum complexes.
I got sizes ranging from 1 to 143:

[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37, 38, 40, 44, 45, 47, 48, 62, 68, 78, 80, 104, 143]

The distribution is skewed to smaller sizes with 3 participants counted 1465 times and most of the bigger sizes from around 30 counted 1 or 2 times.

{44: 1, 36: 1, 32: 1, 47: 1, 78: 1, 48: 1, 31: 1, 143: 1, 40: 1, 26: 1, 38: 1, 62: 1, 104: 1, 23: 1, 20: 2, 22: 2, 33: 2, 80: 2, 37: 2, 45: 2, 28: 2, 68: 2, 27: 2, 30: 3, 19: 3, 24: 4, 25: 4, 18: 6, 17: 11, 15: 19, 1 6: 21, 14: 23, 11: 25, 12: 28, 13: 30, 10: 55, 9: 57, 8: 72, 7: 83, 6: 100, 1: 127, 5: 237, 4: 499, 2: 1370, 3: 1465}[Sorry for not sorting...]

My main question from this first dip into data is, are there any assumptions to make about the size of complexes? Are these big complexes for example special cases and normally complexes are limited to a size of around n?
Is there maybe even an upper limit of participants in a complex?

Anything would be helpful for me to minimize runtime.

The problem with coming into bioinformatics from a non-biological background is all too apparent in your question, and very real. You are dealing with a category of object called a protein complex, you suspect that it will be reasonable to exclude a proportion of them, but as you don’t really know what they are (other than at a basic level) you don’t understand the implications of doing so. As generally in such cases, you need to find an appropriate biologist to help you.

All I can do is try to make an analogy. Consider an entity that the biologist who knows nothing about computing calls a ‘program’. As a surrogate for the number of components, let us consider that it is written in Java and so that one can judge its complexity by counting the number of classes. (I know that the examples I am giving are not all normally written in Java, but in theory they could be.) I could write a simple program that just parses a file and outputs a second file in a different format. That would use very few classes (especially without a GUI interface). Then I might write a modest web application to query a database and return biological information to the user. That could have perhaps two dozen classes. A more sophisticated commercial web application would have more. And then we get into commercial desktop applications from the relatively modest utilities to the monsters like Microsoft Word.

But just classifying computer programs on the number of Java classes would have severe limitations, just as would an alternative approach such as programming language (python for scripts, C++ for large applications). What I would really need to decide is what kind of program to include or exclude.

Likewise with protein complexes. I am not familiar with Corum (I just checked the website on my phone) but one might assume that the protein complexes it contains range from basic enzymes and proteins with two different subunits (perhaps in two or more copies, generally in a regular structure) like haemoglobin or immunoglobulin G, through proteins that interact with several species and posses half a dozen different subunits, to what are in effect machines of greater or lesser complexity, like the ribosome, the two subunits of which may together have 70 to 80 proteins.

So, yes, it would be reasonable to exclude the relatively small number of very large complexes which constitute a class of “machines” (and your size distribution suggests where the cut-off might be). But for your work to be valid you need to know specifically what class of complex you are excluding so as to be able to state that you had deliberately decided to ignore large complexes like ribosomes, splicesomes etc. And name them.

It’s tough at the moment, I know, but in my opinion you do need to sit down with a biologist and have this explained in more detail, reviewing the names of the complexes in the Corum list that you are considering excluding.


Spider identification: male black widow? Unfortunately I didn't snag a picture but I found a small spider with reddish legs and enlarged fangs in Victoria, BC, Canada. The spider was very quick and looked similar to pictures of male western black widows I found online. The difference was that the spider I found had a light brown body but pictures I found online typically had white stripes.

Is it likely the spider I saw was a Western black widow or are there other species that look similar in this region?

I think it's unlikely.  Without a photo, it's hard to be sure of anything, but Black Widows don't have reddish legs or enlarged fangs, and it's hard to think of any circumstances in which they could be called "very quick".
Your description might fit a spider called Dysdera crocata (here's a link: https://bugguide.net/node/view/3388 ), but that's purely a guess on my part.
The problem with trying to ID something from photos when you're not very familiar with it, is that you may not be sure what to look at to distinguish it.  If you can't get a photo, make sure you include the most detailed possible description, including anything about it, no matter how seemingly insignificant.  What it was doing, where it was, etc., etc.


How does our body produce new antibodies? My professor said that in human body nearly 10$^9$-10$^1$$^2$  antibodies are produced by VDJ recombination and all the antigens that a person encounters in his lifetime are dealt by antibodies already present in his body. But he didn't explain what if the body in infected by a new mutated microbe(antigen) whose corresponding antibody is not present in the body.

My question is does our body have the mechanism to judge the epitope of the new antigen and synthesise an antibody with completely new paratope? If so what is it?

After reading the following I was forced to wonder whether the specificity of the antibodies improve(improve by synthesising new paratopes) after encountering antigens in the course of response.

In case of T-cells and Abs our organism first generates a great diversity of T- and B-cell receptor variants so that any new foreign antigen is likely to be recognized by some of them. When a B-cell encounters its antigen it begins proliferating and changes it phenotype. Additionally, B-cell (but not T-cell) receptor starts to mutate (so-called somatic hypermutation) generating new B-cell receptor variants that differ a bit from the original one. This process acts like evolution, with B-cell carrying a receptor with higher affinity being more likely to proliferate. So the specificity of antibodies improves indeed, this is called affinity maturation.


Can anyone identify this dragonfly spotted outside of Boston, MA? Can somebody identify this dragonfly please? It was seen about 15 miles west of Boston.

It is a male Green Darner.

Pretty common in general, especially in the US.


Is there a maximum amount of antibodies your body can keep? I am wondering if you were theoretically able to get vaccinations or antibodies for any and every diseases and/or illness, would there be a limit to how many you can get and keep in your body at one time? If so, what is the limiting factor?

What would be the possible effects of this on the body and immune system? Thanks.

Antibodies are simply proteins and like any other protein have a relatively short "life", so after clearing out an infection, they are not retained for long (most of them anyway). What the body keeps is memory cells which can produce a much more rapid response if they come in contact with the same pathogen again.

You could see it as a selective process: the body produces immune cells, one or more specific cells for nearly every potential antigen that might exist in the world (there are more steps involved of course but they are of little relevance here). Only those which are used at some point mature into memory cells.

Unfortunately, I just realised that I can't explain why the immune system goes through this selective process; producing cells equivalent to memory cells in the first place would make the immune response much stronger. One explanation I can think of for why the body produces naive cells first is that either a) their production or b) their maintenance is less costly.

The other explanation I could think of is that even immune cells in the periphery which have undergone the proofing mechanisms of immune cell development already, may not be perfect and target body cells every now and then - in that case it would be devastating if they would go all-out like a memory cell.

From my three explanations, only alternative b) would mean there could be a limitation to how many vaccinations our immune system can bear (if memory cells take more effort to maintain than naive cells, having too many of them may overstrain whatever systems maintain them). Otherwise I don't see any limiting factor for how many memory cells you can retain; except if their numbers become so large that your lymph nodes swell and that causes problems.

Edit note: I'm not aware of any research about that question and couldn't find anything either.


Why summation takes place at Initial segment? I know that many EPSPs summate at initial segment to produce action potential.

But I don't understand why if EPSP can travel from dendrite to initial segment, then why it doesn't travel further?

What halts it there and make it to wait for other EPSPs to come and add to make Action Potential?

Why does it can't propagate as such and cause release of small amounts of neurotransmitters?

Why don't EPSPs travel passively through axons?

EPSPs decay over distance. The decay is described by the length constant, which can be calculated based on the electrical properties of some compartment (i.e., a length of dendrite or axon). By definition, the length constant is the distance at which the amplitude of the signal will decay by about 37%. If you are familiar with the concept of a "time constant," the math is exactly the same.

There are two main factors that influence the length constant: the number of open channels (i.e., how "leaky" the membrane is) and the diameter of the neurite. The "leakiness" of different parts of the cell is often modulated by inhibition. Preventing EPSPs from reaching the soma or decreasing their amplitude by increasing leak is called shunting inhibition. However, for your question, it is the diameter and overall length that is important.

Dendrites tend to be a bit bigger than axons, so they have a longer length constant: that is, EPSPs travel further. Dendrites are also not entirely passive: dendrites can actively propagate signals (see review by Yuste and Tank) using voltage-gated channels to boost EPSPs, especially in cells that have a long distal dendrite, such as the deep-layer pyramidal cells in neocortex. These voltage-gated channels give the dendrite a longer effective length constant

The most important thing is that even relatively short axons are just way too long for passive conduction: that's the reason for action potentials. Length constants depend greatly on the size of the neurite, but you can expect the distances to be on the order of millimeters to 10s of microns.

That said, it isn't ever true that a subthreshold EPSP won't flow into an axon: it just will get weaker and weaker with distance. Neurotransmitter release depends on a substantial depolarization which opens voltage-gated calcium channels; a small little EPSP that has decayed several-fold from the soma has no chance to cause calcium influx and subsequent vesicle release.

Spatial and temporal summation

EPSPs don't 'wait' anywhere, the EPSP is constantly decaying because all membranes are somewhat leaky, and current isn't restricted to any compartment. Current is constantly flowing out of the membrane and out into all the other processes of the neuron (and then out through those parts of membrane too!). In fact, if you are talking about passive conduction of EPSPs, you are really talking about a form of "leak", not through the membrane but through the cytosol! The EPSP isn't traveling to the soma in any directed way, there is current "leaking" in all directions, and some of it happens to go towards the soma. To get summation at the soma or anywhere else, EPSPs have to arrive both close enough in time and close enough in space.

EPSPs can sum with each other in the dendrites if they occur close enough in space, but of course that also only works if they occur around the same time. Similarly, at the soma, an EPSP slightly depolarizes the soma but only for a brief time. If one EPSP has an amplitude of, for example, 5 mV, and another EPSP has an amplitude of 3 mV, they will only sum to close to 8 mV if they occur simultaneously. If the 3 mV EPSP comes a few milliseconds later, the peak voltage might only be 6 mV, or if they are separated even more in time, there may be no summation at all.

Why do spikes start at the axon hillock?

The axon hillock is a special part of axon, right at the beginning of the axon. This area is more than just the first section of axon, it also typically has the lowest threshold for initiating an action potential due to a greater density of voltage-gated sodium channels. Sort of by definition, a cell's threshold is going to be the threshold for whatever part of that cell has the lowest threshold (at least near the soma, which is so big compared to axons/dendrites that it is nearly isopotential).

For example, take an example cell whose overall threshold is at -45 mV. If you were to somehow remove the axon hillock, leaving just the rest of the soma and the dendrites, the threshold wouldn't be -45 mV anymore, it would be much higher, maybe -10 mV. Even if you had some really huge EPSP (or manually injected some current) to bring the cell towards -10 mV, the axon hillock would still hit its threshold first and start the action potential well before the EPSP reaches a peak sufficient to start a spike in the soma proper.

If it helps you could think of a balloon analogy. The EPSP is air flowing into the balloon, and the action potential is the balloon popping. If one part of the balloon is thinned/weakened, that part will always be the site where the popping starts. It doesn't matter if you put in enough pressure to cause the thick part of the balloon to pop, because before you can possibly get it to that pressure the weak part has already burst.

Also note that for this analogy to fit with all the rest of this answer, it has to be a leaky balloon, so it only pops if you put enough air in fast enough before it has a chance to leak out.

References

Yuste, R., & Tank, D. W. (1996). Dendritic integration in mammalian neurons, a century after Cajal. Neuron, 16(4), 701-716.


Can too low oncotic pressure lead to Third spacing and Edema? I know that low oncotic pressure is associated with many pathologies.
I am interested how it is associated with Third spacing.
My professor says that it can permit edema formation.

The opposing pressure of oncotic pressure is hydrostatic pressure.
So that would suggests mean that the blood pressure is too high if low oncotic pressure and thus fluid would like to go to the third spacing (not sure) and edema.

Can too low colloid oncotic pressure lead to Third spacing?

Yes it can! Its a very important cause of third spacing a.k.a. peripheral oedema, mainly due to decreased protein.

Below is a list of causes of peripheral oedema due to fluid moving from the vascular bed to the peripheral spaces gathered from the following source: http://www.patient.co.uk/doctor/Peripheral-Oedema.htm

Immobility: Increased fluid pressure from venous stasis. Varicose veins.

Obesity: Increased fluid pressure from sodium and water retention; should not to be confused with non-pitting lymphoedema.

Cardiac: Increased fluid pressure: right heart failure, constrictive pericarditis.

Drugs: Increased fluid pressure from sodium and water retention: calcium antagonists, non-steroidal anti-inflammatory drugs (NSAIDs), prolonged steroid therapy, insulin.[1]

Hepatic: Decreased oncotic pressure: cirrhosis causing hypoalbuminaemia.

Renal: Decreased oncotic pressure from protein loss, and increased fluid pressure from sodium and water retention: acute nephritic syndrome, nephrotic syndrome.

Gastrointestinal: Decreased oncotic pressure: starvation, malabsorption, protein-losing enteropathy (eg Crohn's disease, ulcerative colitis, tumours of stomach and colon, coeliac disease and other intestinal allergies).

Pregnancy: Increased fluid pressure both from sodium and water retention and venous stasis from pelvic obstruction.

High-altitude illness: Oedema of face, hands and ankles may occur.

Idiopathic oedema: Associated with cyclical high lymph volume overload, or dynamic insufficiency: usually in a woman aged 20-40 years. Variable and not related to menstrual periods. Diagnosis is based on the exclusion of other causes of oedema.

Post-thrombotic syndrome: Late complication of deep vein thrombosis (DVT) which occurs in up to two-thirds of patients. May present with pain, oedema, hyperpigmentation, and even skin ulceration. May result from remaining venous obstructions, from reflux, or both. Rate of reflux is highest during the 6-12 months after an acute DVT. It may be temporary and self-limiting or not resolve and persist at variable severity.

Pitting localised limb oedema:

DVT: Compression of large veins by tumour or lymph nodes.

Following hip replacement or knee replacement.

Local infection, trauma (including burns, which may also cause generalised oedema because of protein loss), animal bites or stings.


What is the thickness of endothelial lining in blood vessels? In capillaries, endothelial lining is one cell thick. Is same the case with bigger blood vessels?

I believe apart from natural fluctuations of cellular size, the size of squamous epithelial cells (the cells making up the endothelium of blood vessels) remains the same. Therefore, the thickness of the endothelium does not significantly change for any blood vessel.


Is it true that there is a spider that eats parasites from caterpillars I think I once saw a video of a caterpillar that could get infected by a parasite, and could die of that, unless a specific kind of spider would eat the parasite, and so once the caterpillar is infected it goes looking for that spider. I can't find that video anymore though, nor any reference on this, so I'm beginning to doubt myself. Does this behaviour really exist?

Oddly enough it is a bit difficult to find good field studies where the diet of spiders was studied.  I have a feeling it's a hard thing to get funding for.  Luckily some do exist.

Peucetia viridans has been shown to eat from the Chrysididae family and Lepidoptera order, but I didn't find an explicit statement that it ate the larvae out of the caterpillar.  Likewise Oxyopes globifer was found to have eaten from the Braconidae family and Lepidotera.

At this point you might be wondering why I'm looking for spiders that have been shown to eat both parasitoids (Chrysididae and Braconidae) and caterpillars (Lepidotera).  It my assumption that in the scenario you describe a spider that would normal eat ether the caterpillar or the larvae would be just as happy to eat them both if it was lucky enough to find them.

I could find one example where it seems wolf spiders under the right conditions might seek out larvae, and I found a fun photo of a wolf spider eating larvae (though not the kind in the study).

I never saw the video you were talking about, and I too could not find it.  It is not unreasonable to assume that an opportunistic spider wouldn't just take the opportunity to feed on both, or that it might find the larvae more tasty and just eat them.  I've not found a spider seeking caterpillar as of yet.


How do baby birds get fed when they are only a day or two old? The eggs belonging to the robin on my porch hatched. The baby birds are very tiny, just lumps. They are not opening their mouth and cannot even seem to lift their heads. How do they get fed when they are so helpless?

The hatchling's neck muscles are stronger than you think, because hatching from the egg requires strong neck muscles. Newly hatched songbirds and others do indeed open their mouths after they have had sufficient rest following hatching, though you don't seem to have witnessed this. They have little neck control and their heads wobble initially, but feeding is so important that they are born with this ability.

  Songbirds and most seabirds have altricial young, meaning that the newly hatched birds are blind, featherless, and helpless. Immediately after hatching, altricial birds can do little more than open their mouths to beg for food. They remain in the nest where the parents can feed and protect them while they continue to develop. For the first week of life, most altricial birds cannot control their own body temperature and must be constantly brooded (kept warm) by their parents.

This makes sense, as most altrical birds only spend about two to three weeks before flying off to start their own separate lives.

Newly hatched poultry chicks (precocial birds, which also include ducks and sea birds) can live for 48 hours on the last of the egg yolk that they take in just before the strenuous work of hatching out of the egg.

  Incubation periods are longer for precocial birds than altricial birds, allowing for increased embryonic development in the egg, and therefore they have relatively advanced motor and sensory functions at hatching.

Feeding poultry is actually not necessary during that time. The chicks are strong enough to stand, drink, and peck for food soon after birth, but it's not necessary for life. What they cannot do is regulate their body temperatures well.

Nesting Cycle


How do drugs tests check so many substances? There are about 170 drugs banned for sports and many other drugs that can be used in crimes.

How can blood tests practically detect so many different substances? Do they divide the sample into 170 different micro samples? How are sports and criminal blood tests arranged to be comprehensive?

There are a lot of different methods to test samples for drugs. The most common for a "screening" test, like one might encounter before being hired for a job, are based on immunoassays. These use antibodies to detect certain substances in the sample. These are good for testing for a few drugs or categories of drugs (like THC, benzodiazepines, opiates, amphetamines, etc.), however they can't test for a large number of drugs at once, and often won't tell you the specific drug (e.g. it'll say "positive for benzodiazepines", not "positive for alprazolam"). If someone tests positive on one of these screening tests, then the samples can be re-submitted for further testing to clarify what is causing the positive result.

Drug testing for elite athletes is a whole different story. The World Anti-Doping Agency has established protocols for the Athlete Biological Passport, which uses standard methods to test samples and record various biological parameters over time, to ensure that athletes aren't manipulating their bodies artificially.

The exact details of how this is done is pretty complex, but they don't need to divide samples into a bunch of separate samples and test each one for a single drug. These standardized kits are able to be run on one urine sample (divided in two) and a couple of tubes of blood, the same size you'd get drawn at a doctor (just 3-5 mL each).

One way they test for many different substances using a single tube is through gas-chromatography mass-spectoscopy (GC-MS), which is a combined method to separate apart substances in the blood and identify them by their molecular weight. By comparing athlete's blood and urine samples to known patterns produced by banned substances, they're able to test for many different compounds using a single sample.


Do organisms have a mechanism to control how fast mutations occur? Sometimes the environment and other species can change rapidly (climate changes, changes in terrains from erosion, new river paths, etc), and it seems like a regular slow mutation rate would be bad, and faster-mutating species would thrive. On the other hand, this fast mutation rate seems wasteful and inefficient when the environment is changing slowly, thus slower mutating species thrive with less waste in this situation.

Organisms capable of responding to the pace of environmental change would seemingly do well in both situations. Does such ability to modulate the rate of mutation/evolution exist in nature?

The ability of a population to respond to environmental change through evolution occurs over generations, and so the generation time of an organism has to be less than the time scale of the environmental change for such an increase in mutation rate to be beneficial.

For bacteria at least, the answer to your question is yes. Bacterial stress responses involve upregulation of error prone polymerases and thus lead to an increased mutation rate. Check out this paper (links and emphasis added):

Foster PL. 2005. Stress responses and genetic variation in bacteria. Mutat Res 569(1-2):3-11.

  Under stressful conditions mechanisms that increase genetic variation can bestow a selective advantage. Bacteria have several stress responses that provide ways in which mutation rates can be increased. These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases. Adaptive mutation appears to be [a] process by which cells can respond to selective pressure specifically by producing mutations. In Escherichia coli strain FC40 adaptive mutation involves the following inducible components: (i) a recombination pathway that generates mutations; (ii) a DNA polymerase that synthesizes error-containing DNA; and (iii) stress responses that regulate cellular processes. In addition, a subpopulation of cells enters into a state of hypermutation, giving rise to about 10% of the single mutants and virtually all of the mutants with multiple mutations. These bacterial responses have implications for the development of cancer and other genetic disorders in higher organisms.

This mechanism may be involved in the evolution of antibiotic resistance, for example (emphasis added):

Cirz RT, Chin JK, Andes DR, de Crecy-Lagard V, Craig WA, Romesberg FE. 2005. Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance. PLoS Biol 3(6):e176.

  The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.


Where are action potentials initially created? Is the axon hillock still the place where one thinks and talks of that action potentials are initially created? (I've heard this place moved into the direction of the axon initial segment.)

If one doesn't want to commit oneself whether it's the axon hillock or the initial segment where action potentials are initially created – because it's somewhere inbetween or at both of them, or it depends on the type of neuron, or we don't know, or we don't care:

  How does one talk about that place unequivocally?

Is there an abstract (non-anatomical) terminus technicus for "the place where action potentials are initially created"?

Action potentials are initiated where there is a high density of voltage-gated $Na^+$ channels and that may vary from cell to cell, as you guessed. For an illustrative example see the figure below, reproduced with permission from Kole et al. (2008).

Density of voltage-gated $Na^+$ channels and $Na^+$ influx along the axon of a cortical pyramidal neuron.
Reproduced with permission © Nature Publishing Group

As you can see, in this cell type voltage-gated $Na^+$ channels, labelled in green in the left-most image, are predominantly expressed away from the axon hillock. We can also observe that the expression of voltage-gated $Na^+$ channels correlates with the degree of $Na^+$ influx in a monotonic relationship (right-most panel).

In smaller cells action potential initiation can happen closer to the axon hillock and in cells of some invertebrates even in multiple locations (Kole and Stuart 2012). What may be the advantage of using the axon initial segment (AIS) as the sole site of initiation of action potentials (APs)? Here is a direct quote from Kole and Stuart (2012):

  [The AIS] has a small local
  capacitance ($C$) and therefore requires less inward current ($I$),
  that is, a smaller number of $Na^+$ channels per unit area, to
  generate APs compared to larger structures, such as the soma
  or proximal dendrites. Hence, the AIS is also an energetically
  favorable site for AP initiation. Furthermore, the small capacitance
  of the AIS favors rapid changes in membrane potential,
  as occurs during the upstroke of the AP ($dV/dt = I/C$). Finally, it
  is worth noting that having a single site of AP generation provides
  neurons a single locus where inhibition can gate AP initiation. [...] Initiation of APs
  further from the soma, taking advantage of the electrical isolation
  of this region, is a strategy used in some neurons to increase their
  capacity to discriminate the arrival time of different synaptic
  inputs.

References
M. H. P. Kole et al., Action potential generation requires a high sodium channel density in the axon initial segment. Nat. Neurosci. 11, 178–186 (2008). doi: 10.1038/nn2040
M. H. P. Kole, G. J. Stuart, Signal Processing in the Axon Initial Segment. Neuron. 73, 235–247 (2012). doi: 10.1016/j.neuron.2012.01.007


Is this a soldier beetle? Bug identification I'm curious to find out what kind of bug this is. Reverse Google image search suggested a type of soldier beetle, but I am not convinced.

The photo is taken in summer, in England

Thanks!

It looks very much like Arhopalus rusticus, a species of long-horned beetle (Cerambycidae) that is found in England. https://en.wikipedia.org/wiki/Arhopalus_rusticus


What percentage of fish are herbivorous vs. carnivorous? It appears that the majority of fish we eat are carnivorous, such as salmon and tuna. This got me wondering how common herbivores and carnivores are among fish species. I couldn't find an answer to this question through a cursory search of the internet.

I don't have an answer to this but there are a number of elements I think can be helpful for you in finding an answer.

First, a helpful word for searching here if you didn't know or hadn't thought of it is "trophic", as in "trophic level", as in "how high this organism is in the food chain".

Making searches related to fish and trophic levels I didn't find a single result for all fish; there are plenty of papers and graphs about the trophic distribution of fish but it's usually within a specific context or ecosystem. For example this graph gotten from Google Images, from a paper that looks at reef fish in Hawaii:

You can see in that graph, and plenty of other papers confirmed, that "herbivore/carnivore" may not always the most relevant distinction in terms of what a fish eats; unlike on land, where the base of the food chain is plants which are pretty big and visible and so are most of the organisms that eat them, in the ocean the base of the food chain is phytoplankton, which is eaten by zooplankton, both of which are what most of the fish we consider "at the bottom" of the fish food chain eat, so by that standard almost all fish are carnivores. But it doesn't seem to be how the word is used by everyone in the field; the graph in question being an example, distinguishing "Benthic carnivores" from "Planktivores" (Plankton-eaters) and "Piscivores" (fish eaters; presumably the "carnivores" eat non-fish animals).

See also this graph looking at reef fishes at various sites in the Caribbean:

Or this graph looking at the trophic structure in a stream

both of which similarly distinguish things more finely than "herbivore/carnivore".

And this, that I got from a search for "fish trophic histogram", ties the concepts to trophic levels (but on a local scale only again, this time the Mediterranean):

Otherwise the FishBase database seems to contain trophic pyramids but they need to be seen per ecosystem and there are a lot of available ecosystems, and given the shape of most pyramids they might include more than just fish.

As an aside, this paper might give a good explanation for why most of the fish we eat are carnivorous:
Trophic level scales positively with body size in fishes


Requirements for soil sample transportation over long distance I need to collected soil sample from agricultural area far away from my lab. It would required about a week for the sample to arrive to lab. I need the soil sample for genomic DNA isolation (metagenomics) as well for isolation of certain species and culture them.

Therefore, the cells in the soil sample needs to be viable. What are the possible ways to long distance transportation of soils sample with intact viable cells?

We did a soil sampling expedition around farms in the UK a few years ago.  We took with us some insulated plastic picnic drinks cool boxes, and a lot of pre-frozen camping freezer blocks.  We bagged up the soil samples, and put the bags in the drinks coolers with the frozen blocks.  This worked fine for our 48 hour trips.  If you were going for longer, you could try to arrange access to a rotation of frozen freezer blocks, or buy bags of supermarket ice along the way to top up the drinks coolers.  The idea for us was not to freeze the samples, but just to keep them cold enough that the organismal diversity was not changed too much during the transportation.


Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli I would like you to point me out some literature about putative epigenetic state changes in mouse/mammal sequences after cloning steps in Escherichia coli.

This are the last search details I used in NCBI PubMed:

  "epigenomics"[MeSH Terms] AND "cloning, molecular"[MeSH Terms] OR
  "molecular cloning"[All Fields] AND "sequence"[All Fields] AND
  ("escherichia coli"[All Fields] OR "e. coli"[All Fields])

E.coli strains that have dam or dcm methylases can methylate plasmid at adenines or cytosines respectively. See here — It is a NEB web page but has links to the cited references.

DH5α has both the methylases- dam+ dcm+ , BL21 is dam+ dcm− and ET12567 is dam− dcm−


What is the need for lobules in (human) testicles? While I was studying the reproductive system, the question popped up in my mind. Each testicle has lobules formed out of the tunica albuginea, in which there exist seminiferous tubules. Why is the testicle divided in these lobules? What's the point? Why isn't it one single big cavity?

The structure of the testes as with many other organs in living things has all to do with form, function, and efficiency. The testes are extremely efficient sperm producers, with on average 1,500 sperm cells being produced per minute in the average human male. If the testes were just an open space of fluid with free-floating sperm producing germ cells, it would not be as nearly an efficient design, not to mention the waste caused by an inability to sort through sperm producing cells and the cells they produced.

According to this site, each lobule in the testes contains about 1-4 seminiferous tubules, each an average of 50 cm in length. Like many structures in the human body, intestinal walls, nephrons in kidneys, etc, the complex structures and organization of the cells that have a specialized function involves increasing access to the inputs and outputs of their function and increased surface area to increase that function.

This site has a helpful graphic showing the structure of the seminiferous tubules that are wrapped up in each lobule. The germ cells which split and create sperm cells are lined along the wall and when the new sperm cell they produce have developed enough, the sperm cell is released to be moved through the tubule where it can be prepared and developed further. This complex structure allows for uniform, controlled, and efficient production of sperm, essentially, a sperm factory running with an assembly line, and is a design that nature has kept and improved upon for millions of years.


What does the root "phyllum" mean used botanical binomial nomenclature I often encounter the root "phyllum" in binomial names in botany, but I've had trouble finding an actual definition for this root in any Latin dictionary outside of its taxonomic meaning. From context it seems to mean "leaf":

Acer macrophyllum - Bigleaf Maple
Tsuga heterophylla - A Hemlock with distinct two-ranked needles

But the Latin for leaf should be folium. Is there any real rhyme or reason to this? I don't know if this is a question better directed towards the Latin stackexchange, but I thought a botanist might have some insight on the subject.

Binomial names often use of greek words. Phyllum means -- as you correctly stated -- "leaf", but is not derived from latin but from the greek φύλλον, 'phyllon'.

By the way, there are also lots of examples where the latin word 'folium' is used. To stick with the genus Acer from your example, there is another species named Acer gracilifolium. So don't be confused by the linguistic chaos in binomial nomenclature.


Why we have to damage our muscles to build them? I know that new muscle cells are made when actin fibers are disrupted. My hypothesis is that muscle mass is limited, from birth, and that nutrients (protein) are only directed to grow muscle when those muscles are actually used. Is this hypothesis true?

Muscles are developed as required by the surrounding environment. This means your body is constantly physically stimulated to grow muscles according to the external forces it experiences (e.g. gravity).

When you train your body, e.g. with weights, you are applying an unusual amount of pressure to your muscle cells, damaging them in the process. In the process of healing your muscle cells, your body will strengthen them in order to adapt to the new physical stimuli, but only when a vast amount of required elements through nutrition is available (proteins).

Quite an impressive feature, right. :-)

I know this from researching personal training/weight training.


Where do the phosphate units come from when EGF units dimerize? Upon EGF binding, EGFR units dimerize and cross-phosphorylate. The phosphate groups are transfered to intracellular c-terminal tyrosine rich regions. Where do the phosphate units come from in this cross-reaction? Is it from bound GTP units?

In protein phosphorylation, the phosphate group transferred from the kinase to the substrate comes almost universally from ATP. However, there is evidence of some protein kinases using GTP as their phosphate source, although they are few and far between.


Experimental evidence for the selfish gene vs. the selfish individual In the Selfish Gene, Dawkins makes the argument that a better  view of evolution (i.e. more in accordance with experiment) is obtained if you view the basic unit of evolution to be the gene rather than the group. Having read the book, I am convinced (inasmuch as a layperson can be convinced) that group selection comes up with incorrect predictions about evolution, so is a fallacious interpretation of evolution (is this a correct interpretation of the book and is this conclusion common opinion among biologists?).

I have heard that historically, his book was part of a backlash against the then prevalent viw of group selection.

TL;DR

However, is there an experimental way to prove whether the gene-selection or individual-selection interpretation of evolution is more correct?

I hope my question is not ill-defined whilst leaving 'unit of evolution' vaguely defined.

My understanding of this is that the complete reference for molecular centralized evolution is The Selfish Gene itself.  I'm going to cite Alan Grafen's essay here,
Richard Dawkins, proposes that the logical, fundamental unit of evolution is the replicator.

The replicator is the fundamental unit of reproduction - whether these replicators survive or do not defines the properties of the biological system they reside in.  These words were chosen carefully because DNA sequences themselves are not replicators exactly - many individual copies make up the animals in a gene pool and the replication of one copy or another doesn't matter.  The distinction between a physical strand of DNA and the replicator is the bulk of more than one of Dawkins book.  It shows why the life of an individual means nothing to biology or evolution, how the boundaries of genes as transcriptional elements do not define the replicon (commonly misunderstood by molecular biologists).  The replicon (a genetic unit of replication) manifests a behavior or phenotype in the organism that helps it reproduce and is reproduced.  This can be cooperation with other members of your species or egg rolling or killing other sperm and is usually the result of many individual mRNA transcripts working in concert.  A given gene as defined by mRNA transcription commonly participates in multiple replicon type behaviors.

But DNA is in the mind of the molecular biology camp highly intertwined as a replicator because it is the physical medium through which the replicator is passed from one generation to another.  Without DNA, meiosis and the rest there are no replicons.  The earliest replicators were possibly simple transcripts which self replicated and not much more, but over time they have become a network of intertwined molecules working in a system.

To my understanding this is axiom more than proof.  It does not need to be proven because the physical transmission of DNA replication over time is the minimal necessary scenario to picture biology and evolution as we understand it.  The selection amongst groups of genes or groups of cells or groups of individual multicellular animals seem unnecessary given the physical framework of DNA replication.

Certainly that these connections have been shown.  The inspiration for The Selfish Gene is the confirmation of Robert Triver's Selfish Gene hypothesis with the discovery of t a terribly selfish gene which takes up the better part of chromosome in drosophila and increases its chances of showing up in the next generation by showing up in sperm more than half the time.  There are lots of other examples in the Selfish Gene and the Extended Phenotype, which answers many of the common questions about this thesis.  The literature since has been pretty productive. That being understood, its one thing to prove that something is true in biology, and another thing to prove that all other similar mechanisms are simply not true.

Yet even in Dawkins essays we see that the replicator is a bit of an abstraction some practically indefinable group of genes. Even as they each compete against each other, they create phenotypes collectively and the replicon becomes abstracted from the fundamental mechanism of replication.  The most popular example of replication Dawkins creates - the meme - has no relationship to DNA at all - a sticky idea that spreads socially and replicates in the minds of individuals.

When we look at terribly complicated but obviously advantageous behaviors, the connection between the replicator and the competition of individual genes gets muddy.  EO Wilson, having discovered pheromones and started ecology and sociobiology as disciplines still publishes group selection arguments.  Having studied social behavior in insects over his career and co-authored one of the most complete compendiums on the subject, he has put forth consistant arguments since the 70s that group selection still has a place in evolution. Unlike others, Wilson has I think always kept the conversation scientific and isn't jumping off any ideological cliffs (though responses say differently, the whole conversation is still published).

I don't see how an unbiased forum can ignore the fact that the editors of Nature still call this an open discussion.  Some may object, but calling the subject closed is overreaching I feel. There are others besides Wilson; I'm not familiar enough with the whole discussion to go into David Sloane Wilson and the rest, though they publish in reputable places.

I've started in this post since the question has been sitting around for a while. I expect others will post their corrections/objections/views - please do!  Whenever group selection is mentioned it often happens that someone will pop up and say 'this is not appropriate for a scientific discussion of biology here' but never any justification of disqualifying questions - I think that's not really scientific.  The fundamental attraction to academic thought to me is that minority voices that have legitimate observations are tolerated and often result in scientific revolutions, after which they are venerated for their persistence.

Here's a good place to tell us why some questions are beneath discussion in biology.  I personally do not agree; even if a position is intertwined by politics and religion, its the scientific value that should be judged, not by the company it keeps - lest science become just another intolerant clot, not driven by logic, observation and facts.  I ask you, why bother then?


Why does my eyes see a red spot when over exposed to light? When I looked into my projector when it was on the blue screen it left a red spot in my vision. I should not have tried it but all the colors left a red spot. Why not a blue or yellow spot was left?

You are describing the phenomenon of negative afterimages, a type of physiological afterimage, which is a result of how the cells in the retina work. Specifically, it is a result of the adaptation of photoreceptors.

  According to the opponent process theory of color vision, our
  perception of color is controlled by two opposing systems: a
  magenta-green system and a blue-yellow system. For example, the color
  red serves as an antagonistic to the color green so that when you
  stare too long at a magenta image you will then see a green
  afterimage. The magenta color fatigues the magenta photoreceptors so
  that they produce a weaker signal. Since magenta's opposing color is
  green, we then interpret the afterimage as green.

There is a well-known illusion, called the negative photo illusion, which exploits exactly that. It is required not to move the eyes, because you need to bleach the photoreceptors in an exact place on your retina. This is why you have to fixate on a dot in the middle of a picture, otherwise the bleaching will not occur.

EDIT: I mention a two-axis (magenta-green system, blue-yellow) system, but the exact color system - which would predict which afterimage you would see - is most likely a trichromatic system, which includes red, green and blue channels, based on the principle of the three types of retinal cone cells. It is important to remember that this is a phenomenon in perception, and thus may, in some cases, not be reducible to the fact that there are three types of cone cells, or that bleaching of a photoreceptor has occurred. Please see the comment thread below for some clarification.


At what temperature do human bones disintegrate? I know, the human skin can get damaged as quickly as 2 seconds, when exposed to temperature above 80 Celsius.

However, what about human bones, say the skull?

For example, when you cook a meal, at great temperature, the chicken bones, still stay hard and intact, that's why I am asking.

Boiling point of hydroxyapatite is around 1500°C so you will need this temperature to make bone literally evaporate.
Prolonged exposure to lower temperature (like reference in other answer 220°C) will break collagen and make bones weak and extremely fragile.


What is the importance of hydrogen bonds in water? and other questions: These are extremely simple questions — basic biology — but I would like to make sure that the way I have answered is at the very least correct.

Hydrogen bonds are very weak, so how is it possible that they are so important in the properties of water? Hydrogen bonds in water provide many characteristic benefits to water: cohesion (holding water molecules together), high specific heat (absorbing heat when breaking, releasing heat when forming; minimizing temperature change), high heat of vaporization (several hydrogen bonds must be broken in order to evaporate water), lower density of ice (molecules in ice are spaced farther apart), and solubility (polar molecules are attracted to ions and polar compounds, making them soluble in water).
Why do we feel cooler immediately after we go swimming than we do after we have fully dried off? We feel cooler immediately after we go swimming than we do after we have dried off because it takes a lot of heat to evaporate water; however, once we dry off we remove much of the water from our skin, and the water is evaporated much more quickly.
If water were non-polar, would our temperature heat up less quickly or more quickly if we went outside on a hot day? Why? More quickly. Because hydrogen bonds within water slow down the movement of molecules and allow for water to have a very high specific heat.

You are saying what hydrogen bonds are doing, not why are they able of such achievements, despite being so weak. Their strength is in numbers. At room temperature, fully one fifth of the water molecules are engaged in four bonds with other water molecules, while the remainder forms two such bonds. (More detail at http://www1.lsbu.ac.uk/water/hbond.html ). In contrast, hydrogen sulfide forms essentially no hydrogen bonds with other hydrogen sulfide molecules, despite significant similarity between oxygen and sulfide. The difference in size between oxygen and sulfur makes the former much more electronegative. I could go on with other hydrogen compounds, but the fact that answers your first question is: each water molecule is involved in a series of bonds with other water molecules, on an unequaled scale.

Also, hydrogen bonds are stronger, pickier about distance and angle than the alternatives available to other molecules (dipole-dipole, van der Waals etc.) So even if they seem feeble, and even if the alternatives were as plentiful as hydrogen bonds, the latter would still be more capable of tying up molecules.

The effect of water drying (which comes after swimming, but also after sweating, bathing, or cleaning oneself with a hot oshibori) is caused by water evaporation. Each state transition, including that from liquid water to air-borne vapors, is a heat-consuming phenomenon. When skin dries, the heat to turn water into vapors has to come from somewhere. In perspiration's case, it is one's body.

Note that cooling down while water evaporates is not only something we feel, but a physical reality, occurring even in innate systems. For example, Amazon forests and Sahara are similarly close to the Equator, but the former is cooler than the latter, in part because heat it receives is in part used up to evaporate water.

Your answer was good.

Again, you are right. Were water non-polar, it would have lower latent heat, or, in lay terms, it would evaporate without much heat consumption. Were sweat made of a non-polar liquid, it will fail to consume heat when evaporating, leaving one to warm up sooner / faster.


Why aren't the antibodies in the mother's milk digested by the infant's digestive system? Why aren't the antibodies in the mother's milk digested by the infant's digestive system?
Enzymes like pepsin have been found to be present in infant's digestive system(1). Though the pH in the stomach of infants is high(The gastric pH of neonates between 2 and 13 days increases from 3.5 to 5-7 for 2 h after ingestion of human milk)(2) activity of pepsin like enzymes from mother's milk itself or infant's stomach is appreciable(1). Moreover tryspin function in infant's intestine is equal to the level in adults by the age of one month(3). Many more proteases are also seen in both mother's milk and in infant's digestive system(1). If this is the case why are antibodies present in mothers milk not digested by the infant?
I have two hypotheses regarding this

Glycoproteins by their nature cannot be digested by the enzymes in infant.
Antibodies are present in such large amounts that many of them are undigested by chance.

I have no idea whether either of these are true. Any ideas will be appreciated.
References:
(1)Thérèse A. Holton et al. Following the Digestion of Milk Proteins from Mother to Baby.Journal of Proteome Research 2014, 13 (12), 5777-5783
(2)Mason, S. Some aspects of gastric function in the newborn Arch. Dis. Child. 1962, 37 (194), 387-390
(3)Lebenthal E, Lee PC. Development of functional responses in human exocrine pancreas. Pediatrics. 1980, 66(4), 556-560

Demers-Mathieu et al. 1 used ELISA to quantify immunoglobulin concentrations from milk after 2 hours of digestion in the stomachs of preterm-delivered and term-delivered infants.  From the abstract:

Total IgA concentration decreased by 60% from human milk to the preterm infant stomach and decreased by 48% in the term infant stomach. Total IgM and IgG concentrations decreased by 33% and 77%, respectively, from human milk to the term infant stomach but were stable in the preterm infant stomach.

The authors note that the infants enrolled in this study had a variety of medical conditions, but "no overt gastrointestinal tract issues or other medical conditions that have been associated with an effect on gastric emptying or digestion capacity." Two hours of digestion was chosen to ensure recovery of sample from the stomach while maximizing digestion time, per the gastric emptying times observed in Siegel et al. 2
So, it appears that term infants are digesting antibodies from their mothers, but a substantial portion of immunoglobulins remain intact.  Weaver et al. 3 report IgA concentrations between 0.311 and 1.247 g/L across 1600 breast milk samples, with negative correlations to maternal age and parity.
Taking the median IgA concentration of 0.708 g/L, a 48% reduction gives 0.368 g/L post-digestion.  Dewey et al. 4 report that 3 month-old infants consume 818 mL of breast milk (assuming 1 g/mL) per day, on average, which suggests that ~300 mg IgA are available to the infant intestine from daily breast milk consumption.  If the adult human gut produces 40 to 60 mg IgA per kg body weight per day 5, then ~300 mg IgA is in the ballpark of what a 6 kg infant would need to phenocopy IgA concentration in the adult gut, assuming limited immunoglobulin production by infants themselves.
So, it seems like hypothesis #2 is close to the truth, at least for highly abundant antibodies like immunoglobulins:

Antibodies are present in such large amounts that many of them are undigested by chance.

Demers-Mathieu V, Underwood MA, Beverly RL, Nielsen SD, Dallas DC. Comparison of Human Milk Immunoglobulin Survival during Gastric Digestion between Preterm and Term Infants. Nutrients. 2018 May 17;10(5):631.
Siegel M, Lebenthal E, Topper W, Krantz B, Li PK. Gastric emptying in prematures of isocaloric feedings with differing osmolalities. Pediatr Res. 1982;16(2):141-147.
Weaver LT, Arthur HM, Bunn JE, Thomas JE. Human milk IgA concentrations during the first year of lactation. Arch Dis Child. 1998 Mar;78(3):235-9.
Dewey KG, Heinig MJ, Nommsen LA, Lonnerdal B. Maternal versus infant factors related to breast milk intake and residual milk volume: the DARLING study. Pediatrics. 1991;87(6):829-837.
Jacob Campbell, James Berry, Yu Liang. Chapter 71 - Anatomy and Physiology of the Small Intestine, Editor: Charles J. Yeo, Shackelford's Surgery of the Alimentary Tract (Eighth Edition). [via ScienceDirect]