What does it mean for there to be no correlation between phylogenetic independent contrast? I am testing the correlation between two physiological parameters in plants using the pic function in R. I am a bit stuck on the interpretation of the phylogenetic independent contrast (PIC). Without considering the PIC, I got a significant correlation, but there is no correlation between the PIC. What does the absence of correlation between the PIC mean:

the correlation without PIC is the effect of phylogeny

OR,

There is no phylogenetic effect on the correlation.

Thank you

Your first option is the correct interpretation. The correlation you observe in the raw data is the effect of phylogeny.

Without using PICs, you might expect to see phylogenetic autocorrelation, i.e. your raw data correlate as a function of the amount of shared evolutionary history between different species. Using PICs is one way of testing whether the correlation still exists when the effect of phylogenetic autocorrelation is removed. This is exactly what you observe—you see the correlation in raw data (which are not phylogenetically independent) but it disappears when you use PICs. Without knowing any details of your study beyond what's in the question, it sounds like a textbook case of phylogenetic autocorrelation.

The PIC method originates with Felsenstein (1985). I'd encourage checking that paper out for further details on the method and interpretation of the results.


Why would the stroma have a higher pH during photosynthesis? Here is a question form my test.

  If you could measure the pH of the interior of thylakoids and the
  surrounding stroma during active photosynthesis what would be the
  relative pH of each?

The answer is C.

  the stroma would have a higher pH

I understand that proton gradient is from stroma to thylakoid space, but that does not mean stroma would have less protons than thylakoid space, if stroma would have a higher pH, then the proton will never flow from stroma to thylakoid space, right?

Energy from an electron transport chain is used to actively transport protons from the stroma to the thylakoid lumen. Thus the lumen has a relatively higher proton concentration and therefore a lower pH than the stroma.

Higher [H+] means lower pH.

Lower [H+] means higher pH.

Keep in mind that the flow of actively transported protons from the stroma to the lumen is against their concentration gradient. There wouldn't be a net flow of protons this way without active transport.


Why are clementines easier to peel than oranges? In my experience, clementines have been significantly easier to peel by hand than and orange.  The skin of the orange seems to cling to the rest of the orange much more so than the skin of the clementine does.

What causes this?  Wikipedia (Clementine) merely mentions that they are easy to peel, but leaves it there. What is different between the way the skins are attached?

I think it all comes down to the thickness of the skin and how it's attached to the fruit itself.  For me, it depends on the variety of oranges and/or clementines, mandarins, etc. that I'm peeling.  Usually fruits with thick, hard skin are easier to peel whereas fruits with softer more delicate skin are harder to peel off in one piece.  Factors like growth climate and ripeness effect the skin quality.

If you roll the fruit on a hard surface under your palm before peeling, it makes the skin easier to peel off in one piece.


Why don't plants use radio waves? I heard that the Earth's atmosphere is opaque at most wavelengths and only allows visible light and radio waves through, so why have plants evolved to only absorb visible light?

Even if the atmosphere is mostly transparent in the radio domain, most of sunlight is visible light.

Also, to make photosynthesis work, you need photons of high energy (say: wavelength shorter than 700nm) in order to excite electrons in the reaction centres. Radio waves cannot do that.

The most widespread photosynthetic organisms make use of visible light and water, which are plentiful on Earth.


Where can you find the quantities of each amino acid of a particular protein or food? Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information?

Is there a freely accessible database online with these statistics? Or, one that contains something for each protein from which this could be derived? (and if so how?)

There's a fantastic database available from the United States Department of Agriculture that includes almost 9,000 common foods, including their nutritional information. This database is searchable and available from the USDA Agricultural Research Service. Here is a link for the online searchable database.

Within the database you are able to search for a number of parameters; including, food composition, water content, individual amino acid content, fatty acid and total fat content, vitamins, minerals, phytonutrients, and more! One of the nice things is that you can ask it to rank the foods in order of nutrient composition. For example, ranking all the foods in the database in order of protein content or a specific amino acid (or whatever else you're interested in).

It's a great database, especially for researchers that need a database of trusted nutrient data.

Within the database you can search by nutrient or by food, whichever you are curious about. For example, as you mention in the question, I entered potato and in the second screen shot below you can see the listing of all the nutrients in the potato. These are listed as % weight per 100g of potatoes - with or without the skin.

To get to the amino acid content breakdown, click on Full Report (All Nutrients) at the top.


What created the first ribosome If a ribosome is made of protein, yet is used in protein sysnthesis, what created the first ribosome?

What created the ribosomal RNA?

This is one of the "chichen and the egg" quesitons about early origins of life. The answer is: we don't know. There is a RNA world hypothesis which suggests that RNAs were the primary versatile biomolecules before proteins. This idea stems from the fact that there are self-replicating RNAs and ribozymes (RNA-based enzymes). Also, the fact that the catalytic center  (peptidyl transferase) of the ribosome is RNA, is also used in support of the the RNA world. However, this is still an idea and we cannot conclusively say that an RNA-world existed.


What advantages do birds gain when they mimic other bird species calls in the wild? I've read that birds such as crows and blue jays often mimic other bird species calls.  There seems to be evidence that birds do learn and react to other bird species calls, specifically when they relate to danger.  What I'm curious about is what advantages do birds gain when they imitate other species calls?

There are a number of reasons birds will mimic other birds mostly for deception, but not always.

Impressing a mate: Songs are a large part of bird courtship behavior, and a more varied song that includes different mimicked tones can help attract a better mate. Because mimicked tones are learned, a bird with more vocal variety is demonstrating its intelligence, ability to survive, and other characteristics a mate would find desirable.
Safeguarding Food: Using a hawk or owl call, or the sound of a cat, dog, or other predator, is an effective way for a bird mimic to claim a food source. When it utters such a call, birds monopolizing feeders or nearby bushes, trees, or other feeding spots may scatter, letting the mimic take advantage of a less crowded food source.
Defending Territory: Songs are crucial for many birds to claim territory, and adding mimicked tones into the song can demonstrate the resident bird's strength. Extra sounds may also trick other interested birds into believing that there are far more birds in the region than there actually are. The newcomers may then simply move along rather than challenge the resident mimic bird.
Social Acceptance: Baby birds learn many songs from their families and other birds of their species, and if mimicked sounds are included, young birds will learn them as part of their initial repertoire. This helps birds fit in with their flocks, which will also help them eventually defend their own territories and attract mates. Many pet birds that mimic speech are doing so for social acceptance, as they consider humans to be their flock.Bird to bird mimicry
I have personal experience with one of these where a Blue Jay would come to our feeder imitating the screech of a hawk and all the other birds would scatter so he/her had the feeder to themselves.


Can someone identify the species of this angiosperm? It seems to be from the pea family (Fabaceae) due to the zygomorphic flowers and the pods. It also has stipules at the base of the composite leaves. It's quite high (~ 80 cm). Photographed in spring in Morocco. It was photographed in a dry riverbed.

This is a difficult one to identify down to the species from the photos. It very much looks like a member of the genus Ononis in the pea family. The leaves, flowers, and seed pods are all characteristic of Ononis. It might be Ononis spinosa, but that is a guess.  The bright sunlight make it difficult to discern many morphological details. I can't see any visible spines on the plant to be certain. Links provided:

https://en.wikipedia.org/wiki/Ononis

https://en.wikipedia.org/wiki/Ononis_spinosa


Why do I still see a bright light after looking directly at it? When you look directly at a bright light, maybe accidentally when looking at the sun, the shape of the image may persistently be perceived even after you look away.

Does this image persistence have something to do with the light hitting the back of the eye and leaving an imprint, or is something else going on?

Short answer
The effect you describe is called a negative after image. It can be explained by adaptation effects of the photoreceptors in the eye.

Background

source: Dresden University

Steadily fixate on the black lightbulb for thirty seconds or more and then immediately turn your gaze to the white region on the right. The illusionary glowing white bulb you perceive after fixating on the black picture is called an afterimage.

When the eyes and hence the photosensitive layer therein, the retina, is focused on an image, light-sensitive photoreceptors in the retina respond to the incoming light. In turn, secondary neurons carry the information to the brain via the optic nerve. When photoreceptors are continuously activated, they become desensitized (or fatigued); it is said they adapt to the stimulus (Kalloniatis & Luu, 2012).

Adaptation occurs at multiple stages in the visual system. One of the important processes behind visual adaptation in this example is photopigment "bleaching" due to constant stimulation. The desensitization is strongest  for cells viewing bright stimuli and is caused by the photopigments in the photoreceptors being all used up after continuous activation.

Back to the light bulb illusion above: photobleaching is strongest for cells that were activated by the bright parts of the image, but weaker for cells viewing the darkest part of the figure. Then, when you avert the focus onto the white screen, the least depleted cells (the ones not adapted) will respond strongly, while the adapted cells will be unresponsive. hence, the retina focused on the black light bulb will respond vigurously, while the more peripheral parts of the retina that received the white part of the image surrounding the bulb will be silent. Hence, a glowing light bulb will be perceived in the after image.

This particular phenomenon is called a negative afterimage, in which bright areas of the figure turn dark and vice versa. This will happen when looking for prolonged periods of time to a certain image (this answer), or when looking directly in very bright sources like the sun (as in the question). Positive afterimages also exist, but do not apply to this specific question.

Reference
- Kalloniatis & Luu, Light and Dark Adaptation. In: Webvision (2012). Utah University


What creature is this? Found on a beach in Brisbane, Australia. Only a few cms of it was visible but I dug the rest of it out, it was about 20cm in length.

That is a Priapulid worm, also known as a "penis worm". In its own phylum, Priapulida. https://en.wikipedia.org/wiki/Priapulida


Can animals train to be noticeably stronger, faster, more agile... than other animals of the same species? Humans have a huge variation in physical ability because of exercise differences. Olympic athletes are a number of times stronger than average people on the street. It seems that variation in animals is very small, but I am wondering if one could force an animal to follow a specific program and eat specific food to get a lot stronger, agile, etc. than an average animal of the same species.

Can animals train to be noticeably stronger, faster, more agile.. than other animals of the same species?

Yes, of course!

Humans are animals, so yes! But even in non-human animals. You can look for example in a tutorial on how to train a dog (or a horse) for specific skills (speed, high jump, long jump, etc...).

  It seems that variation in animals is very small

Such a general statement can only be wrong. Consider dogs as an example. The fastest dogs go at 72 km/h (~45 mph) while many dog breeds barely reach 5 km/h (~3 mph; and they're all considered as the same species). So, there is a lot of genetic variation among dogs.

Now when it comes to variation caused by training it is a little harder to estimate. Consider having a look at Guy and Snow (1977), McKeever et al. (1987), Evans and Rose (1987) and Rivero and Piercy (2008). For what it is worth, note for example that trained racing horse can go up to 70km/h while most horses can go only up to 40-45 km/h. There are a number of studies showing the effect of training on horses.


How does X chromosome monosomy occur I want to understand how Turner syndrome - monosomy X - occurs at the molecular level. The NIH mentions that there are cases of both complete monosomy and of mosaicism.

I’m particularly interested in the monosomy case, as this really confuses me. How does a fertilized egg end up with only one sex chromosome (an X, in this case)? Is an empty egg fertilized by an X-bearing sperm? Is an X-bearing egg fertilized by an empty sperm?

The case of the mosaicism is easier to imagine - say through X chromosome nondisjunction at a very early point in some cells of the embryo. NB: unsure this is actually how mosaic monosomy X happens.

I haven't found a source that doesn't begin from the point at which monosomy has already occurred.

How do things get to that point? Where and how is a sex chromosome lost, such that a human can develop with only the one?

Thanks so much for any pointers!

Most often, it seems that Turner syndrome is due to fertilization by a sperm cell lacking a sex chromosome. I wouldn't describe such a cell as "empty": it still has the other 22 chromosomes, but in meiosis the sex chromosomes failed to segregate appropriately.

Monroy et al 2002 note that of 10 people with complete monosomy X, 9 had their single chromosome from the mother.

Monroy, N., López, M., Cervantes, A., García‐Cruz, D., Zafra, G., Canún, S., ... & Kofman‐Alfaro, S. (2002). Microsatellite analysis in Turner syndrome: parental origin of X chromosomes and possible mechanism of formation of abnormal chromosomes. American journal of medical genetics, 107(3), 181-189.


Is there a term for a procedure in which the chromatography column is washed with 20% alcohol From a method description in a Russian document:

  After the chromatographic analysis is complete, the column is flushed with at least 2-3 volumes of water at a rate of 0.4 ml/min. The column is then mothballed (?) by washing it with at least 10-15 volumes of 20% alcohol at a rate slowly declining from 0.4 ml/min to 0 ml/min.

The word I translated as "mothballed" is konservirovat (консервировать колонку) in Russian. It has the general meaning of "preparing something for storage" (for instance, "preparing vegetables for storage by pickling").

In an effort to determine the correct terminology, I would like to know the reason why a chromatography column would be washed with 20% ethanol. Any recommendation on the standard biochemical terminology for this procedure, if it exists, would also be welcome.

Prepared or conditioned for storage would probably be perfectly acceptable.

If you're looking for a single-word equivalent, in this case, I would translate as stabilized. From dictionary.com:

  stabilize

  [stey-buh-lahyz]

  verb (used with object), stabilized, stabilizing.

  to make or hold stable, firm, or steadfast.

This seems appropriate, since one wants to ensure maintenance of the proper condition of the column for later usage, when taken out of storage.


How do we memorize something? When we see something, how and where in the brain do we remember it and are able to recognize it later?

What happens in the brain that makes this possible?

The current working theory (note this is still an open question, but there are many leads being followed):

Sensory systems receive a combination of signals from an event, which are initially bound to the hippocampus (this is called episodic memory).  Then, typically during sleep, the memories are consolidated.

A simplified view is that consolidation basically consists of communication between the neocortex and the hippocampus, and the memories are thought to be "saved" in the neocortex.  Thus, amnesia patients with hippocampal damage still have all their long-term memories, they just can't create new memories (because their old memories were already consolidated to neocortex).

Your neocortex has many subregions with many functions.  One is the temporal lobe, where semantic memory seems to be stored.  So your episodic memory may record several interactions apples and, over time, your semantic memory will be updated (as memory consolidation occurs) to "consolidate" your concept of "apple".

The temporal lobe is highly connected with the occipital lobe (where visual information is processed) and the two likely work together to identify objects using the consolidated information.

On the molecular level, how the memories are actually stored.  The most well known concept is connectionism: different connection strengths between neurons carry different information.  But there's also genetic expression going on, and there was recently some research on prion-like proteins contributing to memory as well as astrocytes.

Realize, of course, that a lot of this is cutting edge research... and therefore could be wrong or contain numerous oversights and simplifications.


Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors? When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are known. When there is a mixture of multiple ligands and receptors where each ligand and each receptor can interact with eachother, this is not so simple. For example, lets say you have the following set of information:

$$K_{11} = \frac{[R_1][L_1]}{[R_1L_1]}$$

$$K_{12} = \frac{[R_1][L_2]}{[R_1L_2]}$$

$$K_{21} = \frac{[R_2][L_1]}{[R_2L_1]}$$

$$K_{22} = \frac{[R_2][L_2]}{[R_2L_2]}$$

along with the $K_d$'s ($K_{ij}$) and the total concentrations of $R_1$, $R_2$, $L_1$, and $L_2$. I have not managed to find any publications where this has been demonstrated but I would be surprised if it hasn't been figured out by someone.

The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is that they capture all the intuition without the tedious algebra.

It's interesting that you are asking for the fraction of ligand bound to receptors ($[RL]/[L]_{tot}$). Typically one is interested in the fraction of receptors that have ligand bound ($[RL]/[R]_{tot}$). This is for two reasons:

Typically the fraction of bound receptor is the physiologically relevant variable for a cell, determining the response of the cells to the ligand stimulus. Since the cell can only sense the concentration of ligand when it binds to the receptor, the fraction of bound receptor is the natural variable to study.
In most contexts, the number of receptors is much smaller than the number of ligands. This motivates the approximation found in pretty much all treatments of receptor-ligand equilibrium that the concentration of receptor-ligand complex is negligible compared to the total concentration of ligand. For cells, this is a fairly reasonable assumption. In this limit, the fraction of ligands bound to receptors ($[RL]/[L]_{tot}$) is always negligible. It's the fraction $[RL]/[R]_{tot}$ that is  interesting. Another reason this assumption might be adopted is that in practice, ligands tend to be soluble while receptors are insoluble. In this case, it is easier to control the concentration of ligand, adding it in excess to a pellet of receptors, and then measure the amount of bound receptors (maybe by radioactivity): in this experiment the total concentration of receptors is measured, not controlled, so you want your equation to be a function of your controlled variable, the concentration of ligand. This requires adopting the approximation above.

The situation in which there are two ligands binding to one receptor has been solved (in the limit that $[RL]\ll[L]_{tot}$): this case is known as competitive inhibition. In your notation, the fraction of receptor 1 bound to ligand 1 (ligand 2 is the "competitive inhibitor," i.e. rival ligand):

$$\frac{[RL]}{[R]_{tot}} = \frac{[L_1]}{[L_1]+K_{11}(1+\frac{[L_2]}{K_{12}})}$$

So I'm going to generalize to the case that there are $N$ ligands and I am interested in the fraction of a given receptor $R_i$ bound to ligand $L_j$. The equilibrium constant for this reaction is $K_{ij}\equiv [R_i][L_j]/[R_iL_j]$.

The receptor is also binding to all the other ligands, so that the free concentration of receptor $[R_i]$ is equal to the difference between the total receptor concentration $[R_i]_{tot}$ and the concentration of each bound complex $[R_iL_k]$ for $k$ from 1 to $N$. And the ligand is also binding to all the other receptors. In order to get a reasonable equation, we have to invoke an approximation very similar in spirit to the one mentioned above, namely, that the concentration of all ligand-receptor complexes is small compared to the total concentration of each ligand individually. Thus I can ignore the difference between $[L_j]_{free}$ and $[L_j]_{tot}$.

In this approximation, I expand out the expression for the equilibrium constant (using $[L_j]$ as shorthand to stand for $[L_j]_{tot}$).

$$K_{ij} = \frac{([R_i]_{tot}-[R_iL_j]-\sum_{k\neq j}^{N}[R_iL_k])[L_j]}{[R_iL_j]}=\frac{[R_i]_{tot}[L_j]}{[R_iL_j]}-[L_j]-\sum_{k\neq j}^N\frac{L_kK_{ij}}{K_{ik}}$$

Note that the sum is over $k$ from 1 to $N$ except $k=j$, which I pulled out of the sum early. I also used the definition of each dissociation constant to write the sum in terms of dissociation constants instead of $[R_iL_k]$, which makes the algebra a lot simpler.

This can then be simplified to solve for the fraction of bound receptors:

$$\frac{[R_iL_j]}{[R_i]_{tot}} = \frac{[L_j]}{[L_j]+K_{ij}(1+\sum_{k\neq j}^N\frac{[L_k]}{K_{ik}})}$$

Suppose instead of being interested in the fraction of receptor $i$ bound to a particular ligand $j$, one is interested in the fraction of receptor $i$ bound to any ligand. I'll call this quantity $[R_i\mathbf{L}]/[R_i]_{tot}$. We can figure this out by noting that

$$[R_i\mathbf{L}]\equiv \sum_{k=1}^N[R_iL_k] = [R_i]_{tot} - [R_i]_{free}$$

We obtain $[R_i]_{free}$ from the formula for each $K_d$:

$$[R_i]_{free}\equiv[R_i] = \frac{K_{ij}[R_iL_j]}{[L]_j}$$

And so using our equation for $[R_iL_j]$, we obtain (I'll spare you some of the gory algebra details)

$$\frac{[R_i\mathbf{L}]}{[R_i]_{tot}} = \frac{\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}{1+\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}$$

(these sums are again unrestricted, from $k=1$ to $N$ including $k=j$).

Happily, if there is only one ligand, these formula reduce to the regular result, namely $[L_1]/([L_1]+K_{i1})$. As another check, if all the $K_d$s are equal, then the fraction of receptors bound to any type of ligand is the same as the bound fraction for the same amount of a single type of ligand with the same concentration as the whole pool of different ligands ($\sum_{k=1}^N[L_k]$), and the fraction of receptor bound to a particular ligand $L_j$ is smaller by the fraction of the total ligand pool that is species $j$, $[L_j]/\sum_{k=1}^N[L_k]$.

If you are really interested in the fraction of ligands bound to receptors---that is, you are working in the limit in which there are tons of receptors compared to ligands, so that the number of receptor-ligand complexes is tiny compared to the number of receptors---then you can use the above equations just by switching $L$'s and $R$'s. In this case you would obtain

$$\frac{[R_iL_j]}{[L_j]_{tot}} = \frac{[R_i]}{[R_i]+K_{ij}(1+\sum_{k\neq i}^{N}\frac{[R_k]}{K_{kj}})}\qquad [R_i]\equiv[R_i]_{free}\approx[R_i]_{tot}$$

A caveat

To derive these equations, I made a pretty strong assumption that the total concentration of all receptor-ligand complexes (for different receptors as well as different ligands) is small compared to the total concentration of each ligand individually. In this limit, we can assume that the pools of free ligands of each species are so large that each receptor equilibrates with this pool independently of each other receptor (there's plenty of ligands to go around). You might be interested in the limit in which ligand binding and unbinding to one receptor affects the binding and unbinding to another receptors, so that receptors are not independent. I am not sure how to approach this problem. I'm skeptical that there will be any sort of closed form solution; in my preliminary thinking about this limit, I think I can imagine situations in which stationary equilibria are not possible: depending on rates, receptor A might partially equilibrate, depleting the pool of ligands, affecting the equilibration of receptor B, which would cause receptor B to "pull" more ligands away from A, in some sort of oscillation. However, that is just speculation, and I'd be very curious if someone could provide more insight to this case, in which receptors are able to "interact" through the pool of free ligand.

One of the take-aways of this whole analysis is that it is very helpful to be aware of the assumptions made in standard derivations that lead to the nice results we learn in biochemistry class, and how those assumptions might have to change if we generalize the system somewhat.


What is the Giemsa staining of chromosomes? I got the question in my exam and wrote the following and I do not understand what is wrong in it:

  Giemsa staining is a staining method to stain particularly malaria and other parasital diseases. G-bands occur because Giemsa stain
  consists of A,T rich material i.e. poor gene such that dark and white
  bands occur. Each chromosome has an unique reaction to Giemsa staining
  so G-bands occur.

0 points. I do not understand what's wrong with it, since in their comments about the same question in my first exam they wrote also the extra questions: What are G-bands? How are they formed and why? This time I answered the given things and got zero mark.

Probably, the mistake was that I did not answer to the question in the scope of medical Biology in some way. However, I am not exactly sure what it is exactly.

How would you answer to the question when you know that the course was about medical biology?

Please, add the tag Giemsa.

Giemsa is not a particular methid to stain malaria or any other parasite. It stains DNA. As such, it can be used to stain any DNA-containing organism, or, in other words, any known cell.
Regarding its particular use in chromosomal banding, you can refer to many online resources, such as this one of the University of Washington:

Chromosomes in metaphase can be identified using certain staining techniques, so called banding
(...)
G-bands are most commonly used. They take their name from the Giemsa dye, but can be produced with other dyes. In G-bands, the dark regions tend to be heterochromatic, late-replicating and AT rich. The bright regions tend to be euchromatic, early-replicating and GC rich.


Why does smoking change the human voice? What happens to the biology of the voicebox of smokers?
Women's voices can change to croaky men's voices, and vaper's voices develop "white noise" content, like a TV set to static, compared to their original voice which is closer to an oboe reed. I am curious why the white noise content and What happens to the voicebox and what happens to the sound of humans that smoke?

Smoke is hotter than air and passes through your vocal cords (before getting to your lungs), irritating them.
Irritation produces inflammation and inflammation produces mucus and general edema that could affect the biomechanics of your vocal cords, especially if you're a seasoned smoker.
The edema of the vocal cords is called Reinke's edema, which is classified as a benign polyp and will definetely make your voice more low-pitched.
I just saw that you added vaping in your question.
Since vape contains irritating chemicals too, I think its effects wouldn't be much better than smoke..obviously it depends on how often you smoke/vape.
Also, check this article:

Significant research has been conducted about the effect of cigarette smoking on the larynx and vocal cords. Several studies also suggest that exposure to electronic nicotine delivery systems can cause cellular hyperplasia (growth of cells) and metaplasia (change in cells) in mucosal lining in rats. It is theorized and likely that the same would occur in human tissue. Another experiment assessed the toxicity of vegetable glycerin, which is known to be harmless in liquid form. Its effects change in aerosol form. The experiment concluded that the substance led to squamous metaplasia of the epiglottis epithelium. Other research shows that nicotine in cigarettes is likely to lead to cancer, including in the mouth and larynx.
If the delicate lining of the vocal cords are exposed to hot, vaporized chemicals, the tissues are likely to undergo change and lose their ability to behave normally. This may produce hoarseness, loss of vocal range, voice fatigue, or vocal injury.

and finally:

These diseases and their effects on the voice can deeply affect singers and other people who use their voice for  a living. The only option to avoid these is to abstain from vaping completely.


What is the biological significance of finding palindromes in DNA sequence? I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of finding palindrome in DNA sequences?

My knowledge of biology is extremely limited, but this is what I know of palindromic sequences:

Palindromic sequences are their own reverse complements. I have seen many restriction sites be palindromic. Also, some Transcription Factor Binding sites are palindromic. The canonical E-box site, for example, can be expressed as CANNTG.

Also, these palindromes, when occurring in pairs with a sequence between the occurrences, can double back and bind to each other (when the DNA is transcribed to RNA, say), and this would result in the RNA stem and loop structure.


What data / tools exist for mapping of disease trends? I was just looking at the Google Flu Trends map.  Google Insight could be used to gain similar information for other trends in disease keyword searches.

I started wondering how valid are keyword searches to represent the spread of diseases.  In some ways I think it could be a good representative, but in others I think it would be susceptible to influence by mass media.

Do maps of clinical data exist that could be compared to this Google data?  If so, where could I find some.  =)

You can use official sources such as hospital admissions, prescriptions for drugs fighting the disease you are tracking, sales of over-the-counter medicines.
CDC (cdc.gov/flu/weekly/, cdc.gov/outbreaknet/outbreaks.html, etc), WHO, EuroFlu Weekly Electronic Bulletin map official clinical data, Aurametrix uses these sources.

Several scientific studies have compared GFT, twitter, even facebook with official sources.  Johns Hopkins study (pubmed/22230244) used data from local hospitals in addition to CDC.
My sampling studies too showed that social trends are surprisingly good, despite all the noise, but provide good estimates only for highly populated areas.

You might also want to check Sickweather's algorithm, healthmap, usgs disease maps and industry databases providing coverage of pharmaceutical companies and product sales.


Evidence & discussions of hard polytomy Phylogenetic trees with >2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, called soft polytomy. Alternatively, hard polytomy may exist, this is when there truly is a simultaneous split from one lineage (species) in to more than two. Yang states that "it may be argued that hard polytomies do not exist" but makes no citation or attempts at theoretical discussion. Are there any papers which discuss the theoretical possibility of hard polytomy and any evidence of it occurring?

Image from http://biology.fullerton.edu/biol404/phylo/polytomies.html

I think that changes in features that determine a node may happen in parallel or close together in a sequence. If the fossil record is not complete enough then the cladogram has to contain these stars. From a stochastic statistic point of view, although unlikely, it could actually happen that 2 or more  characteristics develop exactly during a similar time frame, so from a philosophical point of view, I disagree with yang.


Fish "coming back to life" after being frozen I've encountered a clip on Youtube showing a goldfish thrown in liquid nitrogen and immediately after to normal water and swimming normally. In the explanation to the clip it says:

  For everyone that is worried about the goldfish, it survived and was perfectly fine until we fed him and a few of his friends to our turtles. (Which is what they were bought for in the first place!)

I am wondering now as to several issues.

If the goldfish wasn't fed to the turtles and was allowed to live out its life, would it suffer any long term damages from the act?

Is time an issue here, if the fish was kept frozen for a longer time, would it suffer more damage and would it be able to be revived?

Is the size and nature of the fish's body a factor? Would a larger animal or an animal with better resistance to frost that would take more time to completely freeze have damage due to gradual freezing of body and systems?

Does the fact that fish have cold blood affect the result of the experiment?

I have no idea what's the real reason for the survival of the poor fish, but I would guess this is all in the timing. I know for certain ;-) that one can submerge a hand in liquid nitrogen for a short time or in general one can pour liquid nitrogen on the skin with no harm done whatsoever.

The reason is that the difference in temperature that interface (-180 deg C or so for liquid nitrogen and 20-30 for the skin surface) is so large that nitrogen vaporizes instantly and does not penetrate/affect the tissue. The demonstrator could have pulled the fish with bare hands.

I think that for the goldfish the time was too short and while it was cooled/shocked a bit, it might have been too short to do any serious damage. But -

As a scientist, I can't help but notice that we don't really know the condition of the fish before or after the liquid nitrogen 'treatment'. We only see it flapping for a few seconds when back in water. I wonder what happened to the eyes and the mouth, both quite sensitive tissues for such a shock. Also, the water the fish was in was a factor probably, providing additional buffer between the fish and the liquid nitrogen.

Last but not least, the ethical committee quite certainly did not approve that demonstration.


Why do animal teeth get darker if exposed? I was wondering why the teeth of cats (And dogs, as far as I know, plus possibly some other animals or even humans) get darker if they are exposed to air / light?

Example:

(See the lower end of the tooth, which sticks out if the mouth is closed. No, the cat was not resisting, just slightly annoyed.)

So, my question is:

Why does this happen?
Would it happen to human teeth, if they would stick out of the mouth like the ones of cats do?

My guess is that it has something to do with the teeth reacting to air and corroding, but all my knowledge about biology comes from two years of biology in school, so I'm asking here.

The incisal and occlusal edges of teeth are more translucent since there is only enamel in this area and the dentin core is deeper inside. The dentin is more opaque and reflect the light back and it looks lighter whereas the enamel is translucent and allow more light to pass through and less light is reflected back so it looks darker. Many human teeth the incisal edge is translucent or darker for the same reason.


DNA extraction for LAMP assay I am trying to set up a LAMP assay (Loop-mediated isothermal amplification) for the detection of E.coli.

I was told that EDTA can chelate the Mg in my reaction and thus prevent the assay from working (similarly to PCR). Therefore, I hesitate to use TE buffer. Can I prepare my primer mix and extract DNA (using the boiling method) in DNAase free water?

will that affect the quality of my DNA and primers during storage?

Thanks a lot!

Alex

Although this is theoretical a problem, in fact it isn't one. Lets do the calculation around it. EDTA complexes equimolar amounts of bivalent cations (e.g. Magnesium), so 1mM EDTA will complex 1mM Magnesium ions. Lets assume that the PCR reaction contains 2mM Magnesium.

A typical PCR reaction I do has a total volume of 25ul and contains 1ul DNA template in TE buffer (10mM Tris, 1mM EDTA). The final reaction contains 1/25th mM (or 0,04mM or 40nM) EDTA which can complex 0,04mM Magnesium. So instead of running the reaction with 2mM Magnesium, you do it with 1,96mM, which will not be noticable.

Additionally other errors in setting up (pipettes not accurately calibrated, not setting small amounts into the liquid etc.) easily add up to 5-10% error in total, which has a much higher impact in the Magnesium concentration of the reaction than the EDTA. If you use much higher template concentrations (which is usually not necessary), then you can correct for this, but normally this is not necessary.


How do the pharmacodynamics of the NSAIDs differ and are there "resistant" COX phenotypes? I know that the non-steroidal anti-inflammatory drugs (e.g., aspirin, ibuprofen, naproxen) affect the enzymes cyclooxygenase (types I and II).

Is there any difference in the degree to which these drugs manipulate/inhibit the enzymes (I assume their affinities for COX-1 and COX-2 are at least somewhat different)?  Is there any evidence as to whether the the NSAIDs collect in certain areas of the body in a compartmental fashion?
Are there differences in fat solubility, etc., between the different drugs?

Finally, are there any known phenotypes of COX-1 and COX-2 enzymes that are present in the general population that affect the ability of these drugs to act?

This is a draft.

How do the pharmacodynamics of the NSAIDs differ - -?

Merck's manual ch. 36 to start little bit at an introductory level:

  The anti-inflammatory activity of the NSAIDs is mediated chiefly
  through inhibition of biosynthesis of prostaglandins (Figure 36–2).
  Various NSAIDs have additional possible mechanisms of action,
  including inhibition of chemotaxis, down-regulation of interleukin-1
  production, decreased production of free radicals and superoxide,
  and interference with calcium-mediated intracellular events.  Aspirin
  irreversibly acetylates and blocks platelet cyclooxygenase, while most
  non-COX-selective NSAIDs are reversible inhibitors.

and see the coming answer below.
These questions should be answered together.
To split them can be confusing.

Is there any difference in the degree to which these drugs manipulate/inhibit the enzymes (I assume their affinities for COX-1 and COX-2 are at least somewhat different)?

Please, see ch 1.03.3 in Comprehensive Natural Products II: Chemistry and Biology: 10 Volume Set:

and their conclusions about the structure

and please, see the whole chapter of the book, since its about the topic - and I think good one.

From Katzung et al.

  Selectivity for COX-1 versus COX-2 is variable and incomplete for
  the older NSAIDs, but many selective COX-2 inhibitors have been
  synthesized. The selective COX-2 inhibitors do not affect platelet
  function at their usual doses.

  On the other hand, selective COX-2 inhibitors may increase the
  incidence of edema and hypertension.

  To varying degrees, all newer NSAIDs are analgesic, anti-inflammatory, and antipyretic, and all (except the COX-2- selective
  agents and the nonacetylated salicylates) inhibit platelet
  aggregation. NSAIDs are all gastric irritants and can be associated
  with gastrointestinal ulcers and bleeds as well, although as a group
  the newer agents tend to cause less gas- trointestinal irritation than
  aspirin.

In short, there must be differences to which these drugs manipulate/inhibit the enzymes.
Please, see

Selinsky BS, Gupta K, Sharkey CT, Loll PJ. Structural analysis of
NSAID binding by prostaglandin H2 synthase: time-dependent and time
independent inhibitors elicit identical enzyme conformations. Biochemistry 40, 5172–5180 (2001).

Defining the COX Inhibitor Selectivity of NSAIDs: Implications for Understanding Toxicity. Expert Rev Clin Pharmacol. 2010;3(6):769-776. And see the chapter Expert Commentary which locates at the end of the publication there:

  Not withstanding the caveats on the merit of IC50 values, in vitro
  analyses of COX-1 and COX-2 selectivity of NSAIDs has driven the
  concept that inhibition of COX-1 explains the predominant reduction in
  synthesis of mucosal protective PGs and hence gastrointestinal
  toxicity of NSAIDs relative to COX-2 inhibition, which plays a role in
  ulcer healin

Merck's manual chapter 36

  The discovery of two cyclooxygenase isoforms (COX-1 and COX-2) led to
  the concept that the constitutive COX-1 isoform tends to be
  homeostatic in function, while COX-2 is induced during inflammation
  and tends to facilitate the inflammatory response. On this basis,
  highly selective COX-2 inhibitors have been developed and marketed on
  the assumption that such selective inhibitors would be safer than
  nonselective COX-1 inhibitors but without loss of efficacy.

Inflammatory processes are expressed by both COX-1 and COX-2 differently.
This means that a change in the cell membrane expresses lysosomal enzymes differently:

  The cell damage associated with inflammation acts on cell membranes to
  cause leukocytes to release lysosomal enzymes; arachidonic acid is
  then liberated from precursor compounds, and various eicosanoids are
  synthesized.

Also, the cyclooxygenase (COX) pathway of arachidonate metabolism produces prostaglandins, which have a variety of effects on blood vessels, on nerve endings, and on cells involved in inflammation. (See Merck, ch. 18)

I like the Figure 36.2 in Merck's manual.
To better answer your question, one could label the arrows there with relevant enzymes in each processes and compare those between COX-1 and COX-2 and relate to corresponding publications (only few existing!).

Adrenaline and other compounds activate the cyclooxygenase pathway, COX-1 pathway for instance, and the conversion of arachidonate to PGs and TXs. [2, p. 67]
The classic law of mass action allows to describe the reversible binding:

\begin{equation}
    [Protein] + [L] \rightleftharpoons^{k_{1}}_{k_{-1}} [Protein-L]
\end{equation}

where $L$ is ligand, Protein-L the protein-ligand complex, $k_1$ the rate constant of the forward reaction, while $K_{-1}$ the rate constant of the reverse reaction.
This fine regulation differs between COX-1 and COX-2 at enzymatic level regulated by cytokines.

COX-1 becomes only little activated in inflammation, in comparison to COX-2.
COX-2 is present in macrophages (chronic inflammation! - cytokines), fibroblasts, endothelial cells, synovial fluids, and chondriocytes.

[A]re there “resistant” COX phenotypes?

I have not heard about this that there would not be.
There are so many components in PGHSs which can develop resistances.

[A]re there any known phenotypes of COX-1 and COX-2 enzymes that are present in the general population that affect the ability of these drugs to act?

Please, see for the phenotypes of COX-1 here, while about COX-2 much less has been research, see here - no known phenotypes, see this.
Please, note also that COX has at least two isoforms: COX-1 (PGHS-1) and COX-2 (PGHS-2).

COX-1 phenotypes

176805, here

Is there any evidence as to whether the the NSAIDs collect in certain areas of the body in a compartmental fashion?

No.

Each disease has its own characteristics.
Gout, for instance, has swelling of syvovial joints and usage of NSAIDs with COX-2.
My professor of abdominal surgery answered to this question directly - impossible to answer generally which I agree with her. (17.10.2014)

I think the OP has in mind some antibiotics which concentrate in some parts of the body (such as 1st generation quinolones concentrating in the renal tubules and bladder, thus exerting local antibacterial effect).
There is no similar effect with NSAIDs.

Instead, NSAIDs have local and systemic effects, not because they are concentrating in some parts of the body, but because they have several mechanisms itself.
Please, see this thread about Effect of NSAIDS on stomach.

Are there differences in fat solubility, etc., between the different drugs?

Fat burner - of course, there are differences in fat solubility between different NSAIDs.
Please, see this publication Solubility of Nonsteroidal Anti-inflammatory Drugs (NSAIDs) in Aqueous Solutions of Non-ionic Surfactants.
I will update this part next week more.

Other sources

Basic and Clinical Pharmacology, 11th edition, 2009, Bertram Katzung.
My notes during Biochemistry classes in Tartu 2011-2013


When does histone synthesis occur in relation to DNA replication? Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?

Yes, they have to. But that is just half of the story.

The (canonical) histones which are used in DNA replication are synthesized at the beginning of the S phase, and subsequently transported into the nucleus. Studies have shown that newly synthesized DNA is immediately packed into nucleosomes. Thus, it is necessary that these structures are available prior to (or at least just in time with) the replication.

However, there are different models on how the histones are inserted into new DNA. One model assumes that old and new nucleosomes are both incorporated into newly synthesized DNA after the replication fork. Others assume a semi-conservative approach where the old histones are disassembled into their subunits and then mixed together with the newly synthesized ones. For example, there is a model that proposes that the parental H2A/H2B and the H3/H4 dimers disassociate, while another assumes a disassociation of the H3/H4 dimers as well.

Figure: Nucleosome synthesis models for DNA replication

References

a Angélique Galvani and Christophe Thiriet (2013). Replicating – DNA in the Refractory Chromatin Environment, The Mechanisms of DNA Replication, Dr. David Stuart (Ed.), InTech, DOI: 10.5772/52656. Available from: https://www.intechopen.com/books/the-mechanisms-of-dna-replication/replicating-dna-in-the-refractory-chromatin-environment


How are there multiple varieties of the potato? The potato appears to propagate by growing an 'eye'/'bud' which eventually grows into a new plant. So there would probably be single representative of the potato species in the world with all others being genetically identical.

Yet wikipedia indicates there are several closely related species of the potato; apparently as a result of selective breeding. To my understanding (which is probably wrong) there is only a single potato that grows the eyes without the need for a second parent - so there should probably only be the same genes repeated in each potato/plant.

What am I missing here? Why are there multiple varieties of the potato?

You're missing that potatoes also reproduce sexually.

They're flowering plants, and they produce seeds that are not genetically identical to their parent plants.


Can ants learn things? I have an ant nest in a jar. Whenever I want to observe them, I have to remove the cover and therefore put them in light - that scares them. They also can see shadow cast by myself.

I often throw in some food when I'm uncovering the jar.

I was curious if ants will ever remember that I'm not dangerous and that light means food.

If not, are there other things they can learn? Do they teach each other to hunt? Can queen learn things ants can not (queen has shown a lot of individuality compared to ants)?

Ants can usually learn patterns, colors and sequences. Species that do not use pheromone trails rely heavily on landmarks for navigation, that is they perform learning walks during which they look backward and circle around the nest to learn what the landscape looks like so they can easily return to the nest after foraging.

  Harris, R. A., de Ibarra, N. H., Graham, P., & Collett, T. S. (2005).
  Ant navigation: Priming of visual route memories. Nature, 438(7066),
  302.

  Chameron, S., Schatz, B., Pastergue-Ruiz, I., Beugnon, G., & Collett,
  T. S. (1998). The learning of a sequence of visual patterns by the ant
  Cataglyphis cursor. Proceedings of the Royal Society of London. Series
  B: Biological Sciences, 265(1412), 2309-2313.

This is usually the case in large ants that tend to rely less on pheromones and more on visual cues to navigate. Studies commonly focus on species such as Gigantiops destructor or Myrmecia spp.

  Macquart, D., Latil, G., & Beugnon, G. (2008). Sensorimotor sequence
  learning in the ant Gigantiops destructor. Animal Behaviour, 75(5),
  1693-1701.

  Jayatilaka, P., Murray, T., Narendra, A., & Zeil, J. (2018). The
  choreography of learning walks in the Australian jack jumper ant
  Myrmecia croslandi. Journal of Experimental Biology, 221(20),
  jeb185306.

The type of learning you are referring to may be termed habituation, and habituation has been shown in ants, for example some ants tend to be less aggressive to other colonies that they encounter frequently.

  Langen, T. A., Tripet, F., & Nonacs, P. (2000). The red and the black:
  habituation and the dear-enemy phenomenon in two desert Pheidole ants.
  Behavioral Ecology and Sociobiology, 48(4), 285-292.


How are bones growing, if bones are not connected to the brain? If the bones are not connected to the brain, how is their growth controlled?

This question is not a duplicate of the question Mechanisms of bone growth, as this question deals with how bone growth is controlled, and not which bone structures or bone tissues are involved.

The developmental growth of bone tissue is hormonally controlled. It is, as far as I know, not under direct neuronal control. Before reaching adolescence, the long bones (mainly in the arms and legs) grow in the epiphyseal plate, the area of the bone where cartilage is formed and ossified on the diaphyseal side, thereby lengthening the bone. The longitudinal growth of long bones continues until early adulthood at which time the chondrocytes in the epiphyseal plate stop proliferating and the epiphyseal plate transforms into the epiphyseal line as bone replaces the cartilage (boundless website). The growth and stop of growth in adulthood is hormonally controlled. Bone tissue growth is controlled by various hormones including parathyroid hormone and growth hormone.

Growth hormone (GH) is secreted by the pituitary, in turn controlled by the hypothalamus in the brain. So although the brain is involved, it is not directly involved, in that it regulates growth, and cessation of it through hormone release. Growth hormone is probably the most important hormone and is released by the pituitary, but parathyroid hormone released by the thyroid, among other hormones, may play a role as well.

Edit: Your question implies bone growth, which at first seemed to point toward developmental growth to me. However, there is also the more dynamic control of bone mass due to the forces that act on them in everyday life, referred to as bone mass accrual. This process is controlled by the sympathetic and parasympathetic system (Bajayo et al., 2012):

This system acts through direct neural innervation of bone tissue and stimulates bone formation when needed (after imposed strain on the skeletal system), but by default stimulates the breakdown (resorption) of bones to salvage its components for other uses (use it or loose it principle). So yes, the skeletal system is directly connected to the brain (with credits to @anongoodnurse).


How to evaluate the efficacy of an antibody for fluorescence microscopy? I'm trying to evaluate data taken from fluorescence microscopy with antibody staining, and am wondering whether there is any standard way to evaluate the specificity of the antibody for such measurements? In particular, I am interested in evaluating whether there is specific binding of the antibody to the cells in the experiment, or only unspecific binding.

By leaving out the primary antibody or taking a control antibody without specific binding, I can compare fluorescence intensity, and an increase in intensity in the actual experiment towards this control will indicate qualitatively that the antibody binds specifically. But I wonder whether there is a standard statistical test or something to get such a result in a more quantitative way?

When testing an antibody for an imaging application, it is almost always a good idea to test it in another application like ELISA or Western blotting to see if it binds the target of interest. For example, try to find high- and low-expressing cell lines, load equal amounts, and see if there is a difference in signal at the expected molecular weight. Check the company's literature or contact their technical support to see if they have tested the antibody by immunofluorescence (IF), and if so what their results were and how they validated them. Check the literature to see if other people have published with this product. http://highwire.stanford.edu is a pretty good full-text search engine, but they don't have all journals in their database. Google Scholar can help, too.

You can also use your high- and low-expressing cell lines to see if there is a stronger IF signal in the high-expressing line. Look at your images to see if the signal is localizing where you expect it to, and do co-staining with antibodies to other proteins that should co-localize with your target of interest. For example, if your target is expected to localize to mitochondria, co-stain with COX-IV. A quick Google search found this Cellular Localization IF Antibody Sampler Kit that has controls for several different organelles and other specific locations.

Make sure you are following the manufacturer's recommended protocol. Don't crank the gain up too high on the scope, because non-specific background goes up, too. Look at the induction of signal between high- and low-expressing cell lines. Generally you would want at least a 2-3 fold shift, especially if you see a strong change in signal intensity by Western. Try using siRNA or similar silencing technology to knock down the signal in your cells, and validate using Western and IF.

Ultimately, you can never be absolutely 100% certain that an antibody is binding a certain target, and only that target, but you can accumulate a lot of evidence to show that it is likely. Try to put yourself in the mindset of a reviewer, and objectively convince yourself that the signal is real. If you can't, then shop around and try something else. Good luck!


Various Genetic Loads and their Definitions In population genetics, we talk about several types of genetic loads (also called just loads). I am asking for a exhaustive list and a short definition.

Here are for example some genetic loads that come to my mind..

Mutation load
Segregation load
Drift load
Lag load

The genetic load is a population construct, a way of quantifying the fitness reduction in a population due deviations from the optimal genotype.

One type of load comprises all the others, namely genetic load.

  Genetic load is just the loss of mean fitness relative to the ideal fitness.

You forgot to include substitution load in your list, but otherwise I think you included all the main ones.

  Substitution load is the total loss of mean fitness caused because favorable alleles substitute gradually by selection rather than
  instantaneously.

As for the ones you mentioned:

  Mutational load is just the accumulation of deleterious alleles in a population.
  Segregating load is the decrease in fitness in a population due to homozygotes being less fit.
  Drift load is the fixation of deleterious alleles due to small population size. The smaller the population, the greater the risk of
  this happening.
  Lag load is the loss of fitness due to a change in environment.

Another type, mentioned by rg255:

  Gender load, which is the deviation from the optimum due to an allele drifting back and forth because the version that is optimal in one sex is not the one that is optimal in another.


Is fructose really a poison like alcohol? I came across this video claiming that fructose is like a poison with detailed explanation on how it is metabolized. With a search on internet I found an article which challenges the claim and sounds convincing. In the article I also learned that the original claim was made by Dr. Robert Lustig.

Dr Lustig is a scientist and the article is not a peer reviewed scientific article. I am not an expert in the field and I am not sure which side is right.

Could you tell me which side is right?

Everything is a poison with the right dosage  Here is a fun chart you can use to see what I mean. Even water is poisonous if you drink enough of it.

fructose in no more poisonous than glucose. No study has shown fructose to be dangerous when eaten in normal healthy diet. It is poisonous but only in the sense that water is poisonous if you drink to much of it.

And you should reread your own source the article concludes it is NOT more poisonous than glucose. It also concluded that the paper that claimed so was erroneous because it used animals with different metabolic pathways and the differences were not significant in any case. Nor is it possible to eat a diet high in fructose without it also being high in glucose (see above study) so it would not be an issue even IF Dr. Lustig was right about the lipid metabolism.

News media loves to focus on single isolated studies with odd conclusions which is basically the worst way to represent science, wrong or erroneous things get published all the time and get quickly found out but the media tend to latch on to the former and never report the latter.

Processed sugar is bad for you for completely different reasons, basically the same reasons donuts and bacon are bad for you, they are empty calories, it is just that Americans (and a few others) eat way way more refined sugar than the other two, absurd levels of it, for comparison it is as if you were eating large amounts of bacon for every meal levels of absurd. There is also the aspect of diabetes which has to do with how much and how often we eat sugar not an issue with the sugar itself. (if we instead ate half a pound of bacon grease every day that would be the thing causing problems.)


Are humans more aggressive during a full moon? Is it true that we are more agressive during the night when there is a full moon?
If true, could this be a remnant from times where we needed to hunt for our food and so could see more at night when there was a full moon?

Source of question: article

This seems to be a piece of pseudoscience commonly seen these days. The truth is that this effect has never been statistically observed.

From the Skeptics Stack Exchange site:

  Ivan Kelly, James Rotton and Roger Culver (1996) examined over 100 studies on lunar effects and concluded that the studies have failed to show a reliable and significant correlation (i.e., one not likely due to chance) between the full moon, or any other phase of the moon, and each of the following: The homicide rate, traffic accidents, crisis calls to police or fire stations, domestic violence, assassinations, kidnappings, aggression by professional hockey players, violence in prisons, assaults, gunshot wounds, stabbings

... and many more seen here.


What is the Cordil that Edward Topsell describes? In his "History of four-footed beasts and serpents", Edward Topsell describes a "serpent" called Cordil. Since he lists everything that crawls on the ground as a serpent, regardless of being a reptile, amphibian or even insect, there seems to be a wide array of possibilities.

So far, I couldn't find anything about what the cordil described here seems to be. Does anybody know more?

Your link says:

  [...] whereof the Latines derive or rather borrow their Cordulus, and
  Cordyla [...].

Wikipedia says about this:

  The genus Cordylus (Sauria: Cordylidae) includes a wide variety of small- to medium-sized spiny lizards from Africa, collectively called girdle-tailed or girdled lizards.

Tropical girdled lizard (Cordylus tropidosternum)
Source: Wikipedia


Are these springtails and isopods? G'day!
I'm based in Victoria, Australia.
I'm hoping to culture springtails for my terrariums, so I went out and tried to collect some. I found them underneath a rock, which was sitting on damp ground. They certainly look like springtails, and gee they're tiny! 1-2mm. But they don't jump at all.
My first question is -- is this little fella a springtail?

Fast forward a few weeks, and these little critters still seem to be alive in a jar. However, what I believe are isopods appear to have joined them. They're super tiny though, < 2mm. And they're always hovering around what appears to be eggs.
Here's two pictures:

I read online about the lifecycle of isopods. They don't lay eggs; rather, the mother keeps them in a pouch on her underside. I also read that, absent better food sources, they can feed on the eggs of other insects.
So what I suspect is, that these are springtail eggs, and the isopods are eating them. Is that a correct assessment? And are these indeed isopods?
Thank you in advance for your help!
TLDR

Is the first picture of a springtail?
Are the second/third pictures of isopods eating springtail eggs?

It seems like they're both springtail species, as suggested by Arthur's comment.
The white one appears to be a type of folsomia, which is easy enough to guess from the appearance (mine don't jump though, I guess ruling out folsomia candida?).
You can compare it to this image of one, from Wikipedia:

I purchased a cheap USB microscope to inspect the second one further. Indeed, as Arthur suggested, it only has three sets of legs:

Additionally, I turned it around and got a look at the underside. I can only guess this is the furcula (though, interestingly, this one doesn't jump either!)?

I'm not sure what the genus is. Could be folsomia, or perhaps hypogastruridae? Either way, they're both springtails! Great news!


Why does the ring finger not move independently? Why is it that we need to move little finger in order to move ring finger with it? For example, put your palm on a table and fold your middle finger inside. You won't be able to move your ring finger unless you move your little finger along with it. Why? Paul Gilbert and Buckethead and various other guitarists are the only people that I'm aware of that use the ring finger and looks independent. Is it possible to have surgery to make the fingers independent or is it not functional to do that?

The reason for this phenomenon is in both the muscular structure and neural connections of the little and the ring finger. Lets start with the following diagram:

As you see (click on the image to see full version), the fingers contain extensor muscles for movement. However, the index finger and the little finger have separate extensors, because of which they can move more independently as compared to the middle finger and ring finger, which contain a common extensor muscle called extensor digitorum. Some people lack the interconnections between these extensors, and can thus move their ring finger quite easily. One can also achieve this through practice.

Now, as to why the ring finger moves easily when moved along with another finger, have a look at another image:

The fingers are connected to brain via two nerves:

radial nerve, which connects with thumb, index finger and one side of middle finger
ulnar nerve, which connects with little, ring and the other side of middle finger

As you see, the branching between these nerves is what causes dependence of the fingers on each other for movement. Since the nerves for ring finger and little finger are intertwined, it becomes difficult to move each of these fingers separately. Similarly, you may find it easier to move your ring finger along with your middle finger. But you can easily move your middle finger independently because it gets signals from radial as well as ulnar nerves.

Thus, it is the combined effect of muscular and neural anatomy of ring finger which causes this effect.

PS: Since the effect is due to the neural and muscular anatomy of the ring finger, I don't think surgery would help in this case.

References:

Wikipedia contributors. "Extrinsic extensor muscles of the hand." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 29 Jan. 2017. Web. 27 May. 2017.
Ross and Lamperti, 2006, p. 300
Flexor Tendon Anatomy - Medscape
Wikipedia contributors. "Median nerve." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 1 May. 2017. Web. 27 May. 2017


Understanding the Amino Acids I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and absolutely, defeated me...

How do I think about the amino acids, without any memorization, and be able to 'derive' all the names, all the categories they fit into, and their important properties? Memorizing some crazy mnemonic is of no help when it says nothing about the amino acids, I can't memorize it without meaning that explains a lot of things. I ultimately just want to be able to read Albert's Molecular Cell Biology and appreciate it, but I can't without conquering this little issue!

On a side note regarding memorization tricks: is there a mnemonic scheme for the amino acids analogous to the thermodynamical Zhao square, (which gives all the info you need about basic thermo by drawing lines and squares)?

Any help is greatly appreciated, thank you.

I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less).  I really wanted to figure out how the amino acids resulted in the resulting protein structure.  So I started to break them down into categories.  The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique way, but it starts to give you a sense of what the sidechains do.

  Aliphatic : G A L I V M P
  Aromatic : F Y W H
  Polarizable : F Y W H M C R
  Polar: S T Q N D E K C
  Small: A S T G C
  Large : F Y W H R K
  Strong Structural variation: P G

you still have to memorize them eventually, but you can make it easier to put them in categories and in these groups its easier to bring them to mind.


Help ID this plant with balloon-like feature containing seeds I noticed this plant creeping over another Ipomoea quamoclit near my house in Kerala, South India. It has these balloon-like projections over them that break when popped. These projections do bear seeds. No visible flowers.

Leaves:

The balloons:

The seeds:

EDIT: This plant is a creeper, obviously.

I searched Google for Lantern plant and came across this http://tabibito.hopto.org/display_one_file.php?article=494

Which is the same plant, but not the best of references, it doesn't give a scientific name and I am not sure Paper lantern plant is their right identification.

It is definitely of the genus Physalis

https://en.wikipedia.org/wiki/Physalis

but as yet haven't been able to find the species that matches your leaf exactly. But I'd thought I'd post for now as it may help you, or others.


Is process, opposite for growth, known for mammals? Every animal born small, then grow larger and larger.

The same is true for parts of the animal bodies.

Is there any cases, when body or part of the body diminishes in size and mass, while staying healthy?

In humans at least (I'm not sure about other mammals), the thymus grown until puberty and then shrinks gradually, a process called involution. I'm not sure if this meets your criteria. The thymus remains "healthy," but it's function greatly diminishes over time.


Why can newborns swim? I am wondering for someone to discuss the phenomena that newborn babies (humans) are able to submerge underwater up until a few months where that ability is lost again? What is the explanation for this?

It's called the Diving reflex, also known as the bradycardic response. It goes away around six months.

From https://www.breatheology.com/articles/mammalian-dive-response/

  Another action of the diving response can be observed in infants when they are under water. The windpipe by the vocal chords spontaneously closes to prevent water from entering the lungs. This reflex is initiated as soon as there is contact with water. However, it disappears when the child reaches the age of roughly six months.


What can cause incompatible sticky ends to be ligated? Actual question

I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated together, a process during which at least the EcoRI site was lost: the plasmid had a BamHI site very near the XmaI site, and a BamHI/EcoRI digest produced only one band compared to three bands in the undigested control (three conformations of circular plasmid).

How could ends as incompatible as EcoRI and XmaI be ligated?

Detailed Background or: Why I believe incompatible sites were ligated

This is chronologically further to: What are common causes of unexpected ligation products?. Briefly: I digested two plasmids, one with EcoRI and XmaI (p1), the other with EcoRI and AgeI (p2) [XmaI and AgeI produce compatible sticky ends], then carried out a ligation between a 1.4kb insert isolated from p2 (structure EcoRI-1.4kb-AgeI) into the 3.4kb backbone isolated from p1 (structure XmaI-20bp-BamHI-3.4kb-EcoRI). After transformation, I tested the ligation product by digest with EcoRI and BamHI, which should produce again 3.4kb + 1.4kb. The gel was poor quality but allowed the conclusion that there were different ligation products.

Repeating the EcoRI/BamHI digest and gel more carefully showed there were only two variants: Variant A (8 colonies) produced the two expected bands 3.4kb and 1.4kb. Variant B (4 colonies) only produced a clear 3.4kb band, nothing else visible in the lane: in other words, it only carried either an EcoRI or a BamHI site and was in total smaller than variant A (confirmed by undigested controls). Thus, I conclude that B was simply the same 3.4kb backbone, re-ligated without the 1.4kb insert. Since the BamHI site was untouched in the backbone during the preparatory EcoRI/XmaI digestion, I assume that the EcoRI site was not recovered during the ligation of variant B.

(The ligation was carried out overnight at 16 deg C, using Promega T4 DNA ligase and buffer and a molar ratio of 3:1 insert:vector at a total volume of 20uL. The E.coli for transformation were Invitrogen OneShot Stbl3 and have been routinely and successfully used in the lab for a long time. The analytical digestion used Promega EcoRI and BamHI in Buffer Multi-Core, which Promega claims offers 75-100% efficiency for both enzymes. Incubation was 1.5h at 37°C.)

The answer from @Armatus got me looking at star activities again. EcoRI is prone to exhibit star activity in non-optimal buffers. In the case of this enzyme this tends to be a relaxation of site specificity, so HAATTC and GAATTD would be possible cut sites. The cleavage at such sites produces the standard sticky end.

So, what if there is a star site near to the XmaI site such that a digest at the true EcoRI site and also at the star site removes the XmaI site and so allows recircularisation. If the configuration was, for example:

....GAATTC.................[XmnI].GAATTD...GGATCC....

the ligated product would have neither EcoRI nor XmnI sites.


What is a good multiple alignment of large genome sequences when working with limited hardware? I need to align bacterial genomes (namely mycobacteria, over 4 Mb in length), and my choice would have been either 'muscle' or 'clustalW'; however these algorithms are too memory demanding for such long sequences thus I can't run the multiple alignment on my machine.

Is there any other program that I could use to align multiple bacterial sequences?

First of all, do not, I repeat not, use ClustalW. That is horribly out of date and was never very good to begin with1. It was just the first to become common. At least use ClustalΩ. Anyway, while I haven't done much aligning in the past few years, back when I did, I got the best speed/quality ratio from MAFFT.

MAFFT has been used in various sequencing projects and can deal with whole genomes easily. Whether or not it will run correctly on your machine depends on the specs of your machine, of course. However, it should be considerably more efficient than clustalW, although not necessarily more than muscle.

Before doing any of this though, are you sure you need to align whole genomes? Could this be an XY problem? You might want to consider posting a new question here and explaining what your final objective is. Also, if these are published genomes, you might be able to find an existing alignment.

If you really do need to run a whole genome alignment and your machine can't use MAFFT or muscle or any of the other modern aligners, you need a new machine. No matter how efficient your aligning algorithm, a genome is a lot of data and you need a strong machine with serious RAM for it. If you are on a *nix machine, you could ask about how to create a swapfile to increase your memory on Unix & Linux.

1Don't get me wrong, it was state of the art and everything back in the day, but the state of the art wasn't very good, that's all.


How does this illusion work? I found this image on Google+

If you shake your head you can see a portrait of a person. Can anyone explain how the image is constructed in the brain?

If you zoom in on the image, you can see that it is not just composed of black vertical lines, but also has pixels with different gray tones in the white areas. When you move your head sideways, you perceive the gray tones more.

If you were to remove the black lines, you could see the face clearly. Initially I thought that by blurring the gray shapes when your head moved, they became more visible as they seemed larger. On reflection though I think that actually what's happening is that the high contrast between the black lines and the mostly white background causes your perception to adjust so it doesn't easily see the mid tones. This is because we have a low dynamic range in our vision (relative to absolute brightness, but compared to camera CCDs we have a high dynamic range) - we have to adjust the light sensitivity to compensate for the overall brightness of the image. This is called brightness adaptation. There's a good free textbook for further reading about this at Utah U's Webvision.

When you move your head, the black and white lines blur together which makes the overall brightness appear to be the average brightness of the black and white. So against that background your light sensitivity increases and the areas where the pixel tone is different from the average - the gray pixels of the face - start to stand out.

By reducing the brightness you can see the faint image in the background much more clearly...


Is a wild-type strain more "fit" than its mutant strains? Question's context

In the context of a presentation on mathematical models for antibiotic-resistance bacteria research, someone mentioned that wild type strain (WT) are expected to be more fit than mutant strains.

Assume that there is one WT introduced to an environment E (no drugs present), and consider the WT mutates, yielding a certain number of fit-enough mutant strains.

Question

Is WT expected to be the ONLY strain to persist in the long run?

How common is this scenario?

What about co-existence?

Examples and references for beginners will be very appreciated.

My context:
Please note that this may be a very naive question, and I may even be using the wrong terminology, given my background on mathematical modeling and a very, very basic knowledge on evolution.

Thinking about dynamical systems, I would have guessed that coexistence would be possible, so I didn't understand how strong was such an assumption.

I will assume the mutation is not under some kind of balancing selection such as negative frequency dependent selection. As fitness is conditional upon the environment, I will assume a constant environment (heterogeneous environment can also lead to balancing selection).

  Is WT expected to be the ONLY strain to persist in the long run?

Yes. In fact, even if the mutation was beneficial, as it starts out at low frequency it still has a low probability to actually fix (fixation = reaching a frequency of one).

  How common is this scenario?

Mutations happen constantly. For example, every new human baby carry something like 10-100 new mutations that were not present in any parent. Most mutations are neutral or deleterious, only very few are beneficial. New mutations have a low probability to reach fixation even if the mutation is beneficial. The exact probability depends upon the selection coefficient $s$, the dominance coefficient $h$ and the effective population size $N_e$.

  What about co-existence?

In absence of balancing selection (or frequent recurrent mutations) and assuming that ressources are limited, then one strain will necessarily end up fixing. Note that this is also true under genetic drift only and does not even require any selection.

  Examples and references for beginners will be very appreciated.

Evo101 is a very short, very easy introduction to evolutionary biology. You should probably have a look at it.

Then, for something a bit more advanced, and because your background in mathematical modelling, I recommend having a look at the book Population Genetics: A Concise Guide by Gillespie

For more book recommendations, please have a look at the posts

Books on population or evolutionary genetics?
Text Book Recommendation: Organic Evolution


Do we know a complete list of nutrients that humans must ingest to live? When the people who are making "nutritionally complete" foods like Soylent are developing their product, how do they know that they've covered all their bases? You need to have protein, carbohydrates, fats etc., but what about vitamins or minerals?

Has science produced a commonly accepted list of all the nutrients that humans need to live?

For babies there is certainly a formula available for a complete menu for survival: formula*

Here are the nutrition facts from Nestlé's "Good Start":

Formula nutrition facts. source: Nestlé

Comparable lists are available for people that cannot eat normally (e.g. people in a comatose state) and are fed enteral or parenteral nutrition.

*. Remember though, breast is best :)


How fast can a human run? I'm a runner (cross country) and I'm always amazed at how fast Olympic sprinters are. There's a lot of hype about those in the 100-meter dash being the fastest in the world, and we're constantly seeing the 100-meter time dropping. But is there a limit? How fast can human being, propelled only by its own energy (i.e. without any external assistance) run?

An older answer that referred to the physiological feats of ancient humans, and why modern humans are wimps made me look up a couple of papers on running speeds a while ago. One of the examples used to support the statement that modern humans are "wimps" is a study of ancient fossilized footprints from Australia, which claim that the individuals making the footprints were running close to Olympic record times. The footprint studies (Webb, 2007) basically attempts to describe the humans that have created the footprint paths, and also tries to calculate the speeds they were running at. For one of the individuals (T8), the estimated running speed is 37 km/h (i.e. 10.3 m/s). The interpretation by Peter McAllister in his book Manthropology seems to be (I haven't read the book) that these barefoot individuals running on mud could easily have outrun current day sprinters, especially with training and on a rubber track (also see this huffintonpost article on the book). If the estimates in Webb (2007) are close to accurate, it would seem that modern top-trained athletes might not have reached the edge of what is humanly possible when it comes to top speeds.

There is also a biomechanical study on potential human running speeds (Weyand et al., 2010) that you will probably find interesting. This paper looks at factors such as gait, stance, force application etc, and includes empirically estimated values from 10 subjects to discuss the limits to human speed. They conclude that (natural) human speeds are likely to be limited to ~50 km/h (as reference: Bolt's top speed during his 9.58 WR was ~44 km/h).

  Consequently, human running speeds in excess of 50 km/h are likely to be limited to the
  realms of science fiction and, not inconceivably, gene doping.

They also look at different scenarios and e.g. point out how important limb length is for top speed:

  Second, limbs lengthened through evolution or perhaps prosthetically could
  substantially increase the top running speed attained at the minimum period of foot-ground force application. For example, a relatively small increase in leg length of 10 cm would
  increase contact lengths by 9 cm and the top speeds of the subjects tested here from 9.1 to 9.8 m/s.

In general, important factors for maximum speed in animals are ground  reaction force and ground contact time. An earlier study by Weyand et al. (2002) also show how faster human runners in general have shorter ground contact times compared to slower runners. As a sidenote, this seems to be in contrast to cheetahs, which have longer ground contact times than greyhounds, while still being much faster (Hudson et al. 2012 and popular summary).

View these as a couple of interesting examples and a starting point. This is not my area, and I do not know the literature well.


Primer design for introduction of restriction sites flanking a gene of interest I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods.

1) Primer first partially hybridises to the gene, has a mis-match where the restriction site and extra bases are on the primer, then has a hybridised site following the restriction site, to DNA upstream of the gene.

or

2) Primer first partially hybridises to the gene, then completely dangling and non-hybridising has the restriction site and extra bases.

I think the best way is option #2:

Suppose that your gene of interest is AAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGG

and you want to insert EcoRI restriction site GAATCC

Then your Fwd primer will be  GAATCC AAAAAAAAAAAAAAAA

and your Rev primer will be GGATTC CCCCCCCCCCCCCCCC

But in general, it shouldn't matter which option you choose, as long as you calculate the Tm of only the part of the primer that hybridizes to your template.


Difference between dysentery and bloody diarrhea The difference between diarrhoea and dysentery is quite clear; but the appearance of blood in stool or bloody diarrhoea is a very confusing term when compared with dysentery. Are they different in the amount of blood or their etiology or pathogenesis or something else. I searched a lot in the internet and medicine and pathology books but nowhere I could find a straight answer. If anyone knows about it please reply with proper reference and values (if its about the amount).

Diarrhoea
Diarrhea is loosely defined as passage of abnormally liquid or unformed stools at an increased frequency. For adults on a typical Western diet, stool weight >200 g/d can generally be considered diarrheal. Diarrhea may be further defined as  acute  if <2 weeks,  persistent  if 2–4 weeks, and  chronic  if >4 weeks in duration.
~Harrison's principles of internal medicine, 20$^{th}$ edition, page 261.

Dysentry
Dysentery is bloody diarrhoea, i.e. any diarrhoeal episode in which the loose or watery stools contain visible red blood. Dysentery is most often caused by Shigella species (bacillary dysentery) or Entamoeba histolytica (amoebic dysentery).
~WHO definition

One can also follow WHO definition of diarrhea for practical purposes but still I mentioned it from Harrison as it is more specific and quantified.
'Blood in stools' generally describe visible blood in stool, and the quantity of stool passed here can be normal like in upper GI bleeding if compared to diarrhoea or dysentry.
Diarrhoea can be classified into four major categories: Secretory, Osmotic, Malabsorbtive, and Exudative, in which exudative diarrhoea show such features of bloody stool.(~ Robbins basic pathology 9$^{th}$ edition page 577).
In fact, it is also clearly mentioned in Harrison in the topic of diarrhoea that:-

Invasive bacteria and  Entamoeba histolytica  often cause bloody diarrhea (referred to as  dysentery).

Conclusively, bloody diarrhoea and dysentry are the same.


How well do we notice asynchronicity? I'm stopped at a stoplight and, with nothing to do, my thoughts wander to the timed don't-walk sign that governs any pedestrians who might wish to cross the street I'm driving along.

I can see two such signs, one on my side of the cross street, and one across the way. They are synchronized: each counts down the seconds at exactly the same time as the other, as far as I can tell, lighting up as "5", then a second later as "4", etc. Nothing's wrong with my ocular nerve or brain, as far as I know. Can you fill in the blanks please?

I can be …% sure that the lights are synchronized within … seconds of one another. (Not something trivial like "100" and "1", of course.)

Short answer
I can be 75% sure that the lights are synchronized within 0.02 - 0.2 seconds of one another.

Background
Interesting question, but hard to answer! Because it has been unanswered for quite a while I will try to formulate an answer that may provide an approximate value for the minimal asynchrony perceivable.

The temporal resolution of the visual system can be quantified in a number of ways. As you are referring to relatively simple stimuli, the critical flicker fusion frequency is probably the most relevant. At a certain critical frequency, a flickering stimulus will appear as a continuous stimulus (Holcomb, 2009). For example, the good old CRT screens can sometimes seem to be flickering. The mains is 50 Hz (US) or 60 Hz (Europe, Australia), and indeed the critical flicker fusion frequency is 5 - 50 Hz, dependent on the lighting conditions (Kalloniatis & Luu). Hence, stimuli separated by 200 ms (low lighting) to 20 ms (high lighting conditions) can be temporally resolved.

I am aware that your question is different, as you ask whether two stimuli on the retina can be perceived as being asycnchronous. Flicker fusion testing is mainly done with flash stimuli, i.e., a single stimulus per image, not two. However, from the various measures of temporal resolution of the visual system that have been used to date, the critical flicker fusion has the most conservative value, in that it provides the top-value of temporal resolution. Higher-level processing is much slower and values of around 4 Hz are obtained. For example, when subjects are tested on a stimulus of dots that are white when moving right and black when moving left, and they change directions/colors at a certain frequency, it becomes hard to tell whether the color change and direction change are synchronized at alteration rates of ~5 Hz and higher (Kalloniatis & Luu).

As to your question what the percentage chance is that stimuli separate by 20 -200 ms are separable, I can say that in general, psychophysical procedures determine the threshold defined as halfway between chance and 100% correct. Assuming a typical yes/no tasK (are the traffic lights synchronous yes/no?), chance would be 50% (guessing), and threshold would thus be defined as halfway between 50% and 100%, i.e., 75% correct.

References
- Holcomb, Trends Cog Sci 2009; 13(5): 216-21
- Kalloniatis & Luu, WebVision, chapter "Temporal Resolution" 2007


What has caused life to choose this unfathomably tiny subset of all possible proteins? I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever come into existence anywhere in the visible universe, let alone on Earth. And evolutionary selection only works on stuff that exists.

Is there some chemical or other explanation, or is this an unresolved paradox in biology?

The median number of amino acids in a human protein is 375. Most are longer than 200 and maybe all are longer than 100. The 20 different kinds of amino acids can be combined to 20^375 = 10^487 different proteins which have the length 375.

If the entire crust of the Earth consisted of proteins which all were 375 long and each protein mutated once every nanosecond during 5 billion years and each mutation resulted in a protein which is unique in time and space, and there exists 100 such "protein Earths" around every star and 1000 billion stars in each of 1000 billion galaxies in the visible universe, it still only adds up to something like 10^100 proteins. Adding 10^37 years until the last star remnant has cooled down to less than 1 Kelvin, doesn't change this picture, almost all of the possible proteins will literally never exist anywhere. Even if I'm off by a factor a million on each of those numbers, only one in 10^300 of all possible median length proteins could ever exist.

Since our mind-bendingly small subset of possible proteins supports life, shouldn't we expect that many many (as in 10^300) other potential subsets of different proteins would do so too? And can we conclude that if DNA/protein based life has originated somewhere else, it will not have even one single protein in common with us or with any other independent origin of life? Or is this focus on proteins somehow invalid?

The answer is chance or, even better, contingency.

About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the scaffolds and functionalities have been. It is true that protein-based life could be evolved somewhere else, and it is true that the overall sequence space evolved somewhere else would be different from the one evolved on this planet. However, I would expect to find almost the same palette of biochemical reactions that we have discovered on our proteins.

I would suggest reading the work of P.L. Luisi here. He makes really good points on this issue.

A new paper just came out, I think it is a nice addendum to this answer.


Why do human females have periods? Why do human women have periods when most animals don't? It is known that the unfertilized egg needs to be shed from the uterus. But why shed the whole endometrium? Why didn't evolution put macrophages to work to simply digest the ovum and only the ovum, instead of the physiologically, energy-draining process of menstruation and accompanying blood loss? Also, are there any other purposes for menstruation, besides wiping out dead ova?

Sites I used for references:
 1. Jensen et al., Am J Reprod Immunol (2012); 68(5): 374–386 -                       Menstruation seems energy draining, in my perspective, given that 30-40 ml of blood is lost × 3-4 days × 12 months × 15 years on average - that is a lot of blood loss.
 2. Also see this Quora post.

Related question: Why is menstruation in wild animals not a disadvantage to organismal survival?.

My question is different from this related question because there the OP is concerned about the survival advantage of the menstruation with respect to the predators. Here I've asked why menstruation and why not phagocytosis as the former to me seems to be highly energy consuming process. Also as the fellow post writer had earlier suggested though the two questions  seem to be one and the same, they are subtly different and aimed for two different audiences as I emphasise more on the physiological aspects of menstruation and the related question's OP needs clarification about survival advantage and other ecological aspects of menstruation.

Short answer
Shedding or reabsorbing the endometrial lining is energetically advantageous to the female.The advantage of shedding over re-absorption may be that sperm-born pathogens are removed from the uterus. A more parsimonious explanation, however, is that the endometrium in primates has developed into too large of a structure to be completely reabsorbed by the uterus wall.

Background
Basically you ask why are estrous cycles in mammals accompanied by regression and build up of the endometrial lining? The main reason for either reabsorbing or shedding the endometrial lining is thought to be to save energy. It has been calculated that, when implantation fails, a cyclical regression and renewal of the endometrium is energetically less costly than maintaining it in a metabolically active state required for implantation. In the regressed state, oxygen consumption in human endometria declines nearly sevenfold. Metabolic rate is at least 7% lower, on average, during the follicular phase than during the luteal phase in women, which signifies an estimated energy savings of 53 MJ over four cycles, or nearly six days worth of food (Strassmann, 1996; Crawford, 1998).

In fact, impaired shedding of the endometrial lining may lead to pathologies. If no egg is released and the estrogen/progesterone system becomes imbalanced, the endometrium may continue to thicken, instead of breaking down and being shed normally as a menstrual period. This abnormal thickening is called endometrial hyperplasia. Periodically, the thickened lining is shed incompletely and irregularly, causing irregular and more heavy bleeding. If this cycle of abnormal thickening and irregular shedding continues, precancerous cells may develop, increasing the risk of cancer of the uterine lining (endometrial cancer), even in young women (source: MSD manual).

Now the question of why human females shed the endometrial lining instead of resorbing it? Indeed, shedding the endometrium is mainly limited to primates, as opposed to reabsorbing it (like in most other mammals). Here, I do not have a definitive answer, but I like to share two opposing hypothesis on the matter.

Hypothesis 1:  Profet (1993) hypothesized that shedding the endometrium may be an effective way to get rid of sperm-based pathogens. The accompanying bleeding, Profet hypothesizes, delivers immune cells into the uterine cavity that can combat pathogens.
Hypothesis 2: Strassmann (1996) surmises that the endometrial microvasculature is designed to provide the blood supply to the endometrium and the placenta, and that external bleeding appears to be a side effect of endometrial regression that arises when there is too much blood and other tissue for complete reabsorption. The relatively large blood loss as seen in humans and chimpanzees can be attributed to the large size of the uterus relative to adult female size and to the design of the microvasculature in the uterus wall.

References
- Crawford (ed), Handbook of Evolutionary Psychology: Ideas, Issues, and Applications, Psychology Press (1998)
- Profet,  Quarterly Rev Biol (1993); 68(3): 355-86
- Strassmann, Quarterly Rev Biol (1996);71(2): 181-220