Introductory books about evolution - Biology

You won't find a good book that presents the 'weaknesses' of the theory of evolution, and for good reason. There has to date been no convincing challenge to the theory, whilst it has been supported by experimental and circumstantial evidence as well as clear logic over and over and over again, as well as actually being observed taking place numerous times. The closest to what looking for is a book which presents our best understanding of how evolution works, or which discusses competing ideas about how evolution works - there's no question about whether it works.

The Selfish Gene by Richard Dawkins, whilst it contains some errors, has some very clear thinking about evolution in it, and in particular explains why group selection is a misguided idea.

The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene Koonin is a more up-to-date coverage of our current understanding of evolution, in particular with insights from modern genomics.

There are plenty of terrible books about the weaknesses of evolution, but they are deeply flawed. Pick one and I'll be happy to debunk it for you.

galaxy - Trouble understanding speed-dispersion in (elliptical) galaxies

I'm learning about LOSVDs (Line Of Sight Velocity Distributions) and I'm having a bit of trouble understanding the used terms.

As I understand, the LOSVD of a given (elliptical) galaxy is the density distribution of the LOS-velocities. The full LOSVD is difficult to find and it's easier to find 2 parameters of the distribution: $bar v_{_{LOS}}$ and $sigma_{_{LOS}}$ by fitting a (Gaussian) model to the spectrum of the galaxy.

I have a limited understanding of statistics, so I'm having trouble intuitively understanding what these 2 parameters mean later on.

I think that $bar v_{_{LOS}}$ is simply the average value of the LOS-velocity for the whole galaxy while $sigma_{_{LOS}}$ is the equivalent of a standard deviation.

Now later on in my coursebook, there's an explanation of how to get a LOSVDs for every point (/pixel) in the (projection onto the celestial sphere of the) galaxy by using 3D spectrography.
From this we can get a 3D dynamic model from our 2D kinematic model. In this newly found 3D distribution there's also 3 Sigmas, one for every dimension.

But here comes the part I don't understand:
The book is looking at the movement of stars in a spiral galaxy, the Milky way in particular.

We're trying to find a correlation between the age of MS-stars and their dispersion and so there's a dataset of a few stars in the neighbourhood of the sun with their dispersion in every dimension.

What is the meaning of dispersion in this context? How can a single object have a dispersion if it's a parameter of a density distribution?

homework - 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.

neuroscience - Why are melodies/harmonies perceived as pleasurable by humans?

There are strong connections between the auditory cortex and the limbic system, which includes such structures as the hippocampus and the amygdala.

A recent paper [1] builds on earlier notions of emotional "significance" of music without any lyrics. It adds in lyrics, so giving a perspective of which portions of the brain are reacting to which component of the music.

Additionally, contrasts between sad music with versus without lyrics recruited the parahippocampal gyrus, the amygdala, the claustrum, the putamen, the precentral gyrus, the medial and inferior frontal gyri (including Broca’s area), and the auditory cortex, while the reverse contrast produced no activations. Happy music without lyrics activated structures of the limbic system and the right pars opercularis of the inferior frontal gyrus, whereas auditory regions alone responded to happy music with lyrics.

One of the limitations of this particular study is that the subjects self-selected their own pieces, which may limit the reliability of the results. Of course, defining "happy" or "sad" for every individual is slightly subjective and difficult. They cited an earlier "pioneering" study which standardized the musical selection between subjects. Without consideration of the lyrics:

The first pioneer study using functional magnetic resonance imaging (fMRI) by Khalfa et al. (2005) chose a controlled manipulation of two musical features (tempo and mode) to vary the happy or sad emotional connotations of 34 instrumental pieces of classical music, lasting 10s each. Sad pieces in minor-mode contrasted with happy pieces in major mode produced activations in the left medial frontal gyrus (BA 10) and the adjacent superior frontal gyrus (BA 9). These regions have been associated with emotional experiences, introspection, and self-referential evaluation (Jacobsen et al., 2006; Kornysheva et al., 2010).

As an aside to answer your final thought, in cases like this I think trying to jam everything under an umbrella of one "neurotransmitter system" or another can make things overly simplistic to the point where you lose focus of the diversity of receptors expressed. You can say a system is driven by Dopamine, but D1 and D2 receptors have exactly the opposite effects on the neuron.

[1] Brattico, E., Alluri, V., et al (2011) A functional MRI study of happy and sad emotions in music with and without lyrics. Frontiers in Psychology, 2: 308. doi: 10.3389/fpsyg.2011.00308 (free pdf)

(see also, http://www.sciencedirect.com/science/article/pii/S0028393206003083 and related)

fundamental astronomy - What would the night sky look like if the Milky Way were the only galaxy in the universe?

It wouldn't be too apparent, but there are a few objects that you can see in good viewing conditions with the naked eye that would disappear.

Here they are in order of brightness. I marked the objects in a reddish color.

1. The Large Magellanic Cloud, apparent magnitude 0.9, located in the constellation Dorado. Only visible from the southern hemisphere.
   




2. The Small Magellanic Cloud, apparent magnitude 2.7, located in the constellation Tucana. Only visible from the southern hemisphere.
   




3. The Andromeda Galaxy, apparent magnitude 3.4, located in the constellation Andromeda.
   

And that's it. Seriously. Sure, there are a few others, but they're exceedingly difficult to see.

lagrange point - Can we observe what objects exist at the L3 positiion of planets of our solar system?

You asked

L3 is obscured by the Sun, so is that true for our viewpoint of the other planets?

No. Each planet orbits with it's own period because each planet is at a different distance from the sun. So most of the time we can see the L3 point of each planet's orbit from Earth. Occasionally it goes behind the sun from our point of view.

For the Hilda's of Jupiter have we observed them in that position or is it that we have calculated their coordinates to be in the L3 position?

The Hilda family do not occupy the Jupiter L3 point. They generally orbit closer to the sun than Jupiter, and orbit three times for every two orbits of Jupiter. Their orbits are interesting; they have eccentric orbits (up to 0.3) that in some cases cross the orbit of some of the Trojans. You may have noticed that some of the Hildas also approach the Jupiter L3 point. At that point, and when other members of the family approach the Tojans at L4 and l5, the Hildas are moving more slowly. So the Sun's gravity gradually accelerates them, pulling them back to the lower, faster part of their orbits.

I have linked to the Wikipedia Hilda family page. The Lagrangian point page is also helpful.

Can a star orbit around multiple planets or a planet with massive moons?

There's theoretical ways to do it but it's so unlikely as to probably not exist. Assuming you want a system where the planets are in stable orbits around each other. The basic difficulty is the 3 body problem or n body problem. More on it here and here.

For example, a massive planet could (in theory) have a single super-massive moon of similar mass to the planet, though that would probably be considered a 2 planet system. It's not possible for one planet to have two super-massive moons because that wouldn't be stable. In general, planets are many times the mass of all their moons combined, similarly stars are many times the mass of all their planets combined and when that stops being true the system is no longer stable. It's very difficult to generate sufficient mass by adding moons to a system, or by adding enough planets to get more massive than the sun, unless the planets crash into each other but past a certain mass, they'd stop being planets and become a kind of star when enough planets combined.

If we look at gravitational systems, like our solar System, something like 99.7% of the mass is in the sun, so the sun dominates and everything orbits the sun. A few of the larger objects have moons, and curiously, but only cause they're in relatively calm orbits far away from other planets, a few asteroids orbit each other, but the system is very structured around the sun with much smaller stable orbital zones around the planets.

Pluto also has a rather curious orbital system of it's own, likely caused by an impact, where Pluto and Charon are comparatively large and 4 tiny moons orbit around them.

Source:

But these kind of structured systems are only possible if you have a significant mass differential. When you have 3 or more bodies of similar mass and similar distance you get a high degree of mathematical chaos and instability. There are creative mathematical tricks to make it work, but none of them are stable or likely.

This is what 3 similar mass bodies look like, and in such a system, with constant changes, the most likely scenario is that one of the bodies eventually gets ejected. (source, N-body problem above)

There are star systems with several stars, but they are either unstable or contain significant differences in mass. The gravitational structure applies for large planets the same as it does for stars, and there's an article about that here.

You can create stability by having 2 objects orbiting each other and a 3rd massive object quite distant. (Alpha Centauri is that kind of set-up though Proxima Centauri is quite a bit smaller, but it's the same system).

You can even create the heirarchy where you have 2 objects orbiting each other and then 2 more, orbiting each other, but distant so the 2 co-orbitals orbit around each other, and if you do this enough times, you can kind of create enough planetary mass where a more massive star could distantly orbit the entire thing, but it gets very structured and very distant. It's not what I'd consider a normal orbit.

You could also cheat and have several planets in a wildly unstable general proximity orbit and have a star some distance away orbiting the chaotic mess in the middle, but it wouldn't be stable for long.

Does the Moon's magnetic field affect Earth's magnetic field?

So would the Moon's magnetic field affect the Earth's magnetic field, just as its gravitational pull affects Earth's gravitational pull for oceans?

Yes, but only slightly. Firstly, magnetic fields can superimpose, so the field at any point is the sum of the field due to the Earth and the field due to the moon.

However, the moon is rather far away (and has a weak magnetic pole strength), so the magnetic field due to the moon on Earth's surface is nearly negligible (magnetic field also decreases as an inverse-square law)

In addition, the magnetic field of the Moon may bolster or erode the Earth's field as magnets moving relative to each other tend to either lose magnetization or become stronger. But this process has a negligible effect when we take the Moon and Earth.

astrophysics - Relationship between absolute magnitude of a star and its luminosity?

• Why does this relationship involves the absolute magnitude of the sun and its luminosity?


• How to derive an expression relating the absolute magnitude of a star to its luminosity?

So according to the magnitude equation, $$m - M = 2.5logleft(frac{d^2}{d_0^2}right)$$
$$Rightarrow M = m - 2.5logleft(frac{d^2}{d_0^2}right) (eq1)$$

and Luminosity is $$L = 4pi(d^2) times f$$
$$Rightarrow d^2 = frac{L}{4pi times f} (eq2)$$

Plugging eq2 to eq1 would have seem reasonable, but how is absolute magnitude of the sun and its luminosity used?

evolution - Did researchers evolve multicellular yeast or did they just turn on multicellularity?

You're right:

Within the Fungi, simple linear multicellularity of hyphae occurs in all major clades (see below), but only Ascomycota and Basidomycota display more complex two- and three- dimensional multicellularity in the form of sexual spore- producing fruiting bodies. In both of these groups, reversals to unicellular lifeforms have occurred, for example, Saccharomyces and many other related yeasts in the Saccharomycotina (Ascomycota) or Cryptococcus albidus and related species in the hymenomycete clade of Basidiomycota (de Hoog et al. 2000, p. 130).

Medina, M., A. G. Collins, J. W. Taylor, J. W. Valentine, J. H. Lipps, L. A. Amaral Zettler and M. L. Sogin (2003). "Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa." International Journal of Astrobiology 2(3): 203-211. doi:10.1017/S1473550403001551
(PDF)

Update: The authors responded to criticism like this on The Loom, here's an excerpt:

Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it.

Can we (theoretically) spin the black hole so strong that it will be broken apart by centrifugal force?

Can we (theoretically) spin the black hole so strong so it will be broken apart by centrifugal force?

For a Kerr-Newman (rotating, charged, isolated) black hole of mass $M$, angular momentum $J$, and charge $Q$, the surface area of the event horizon is given by
$$A = 8Mleft[M^2 + (M^2-a^2-Q^2)^{1/2} - Q^2/2right]text{,}$$
where $a = J/M$. An extremal black hole occurs when $M^2 = a^2 + Q^2$. Beyond that, if the black hole is even more overspun or overcharged, is an "overextremal" Kerr-Newman spacetime, which wouldn't really be a black hole at all, but rather a naked singularity.

Thus, I interpret your question as asking whether or not a black hole can be be spun up to the extremal limit and beyond, so as to destroy the event horizon. It's very probable that it can't be done.

Wald proved in 1974 that as one flings matter into a black hole to try to increase its angular momentum, the nearer to an extremal black hole it is, the harder it is to continue this process: a fast-spinning black hole will repel matter that would take it beyond the extremal limit. There are other schemes, and though I'm not aware of any completely general proof within classical general relativity, the continual failure of schemes like this is well-motivated by the connection between black hole dynamics and thermodynamics.

For example, the Hawking temperature of the black hole is $T_text{H} = kappa/2pi$, where
$$kappa = frac{sqrt{M^2-a^2-Q^2}}{2Mleft(M+sqrt{M^2-a^2-Q^2}right)-Q^2}$$
is the black hole's surface gravity. Thus, even reaching the extremal limit is thermodynamically equivalent to cooling a system to absolute zero.

space time - What caused gravitational waves detected by LIGO?

It couldn't be Jupiter or the moon because

1. The frequency of the detected waves is too fast. The detector found something that rotated several hundred times a second, and then stopped.




2. The amplitude is too big. Even though Jupiter is close, the gravitational waves it produces in its orbit are extraordinarily weak. Far too weak for us to detect them (good thing too, because if it was producing powerful gravitational radiation, it would start to spiral into the sun)

We know one thing that can produce a chirp of this frequency and amplitude, and that is a black hole merger. In the last few moments before merging, these two black holes converted about three solar masses into gravitational radiation: That is a colossal amount of energy. About $$500,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000$$ Joules. That is why for one moment it was the "brightest" point in the gravitational sky

(Note. standard form is for wimps)

solar system - What good evidence exists for the 9th planet as spoken of by Caltech?

I'm sure Caltech has answered this in some way, but I think it's a good question have on this site.

What good evidence exists for the 9th planet as spoken of by Caltech?

As I see it, Caltech has apparently looked at the orbital parameters of many Trans-Neptunian-Objects (TNOs) and noticed that the lines between their perihilion and aphelion (i don't know what the technical term might be) all run more or less in the same direction. This is evidence that some large body has gravitationally "synced" these planets over millions of years.

Except that alone isn't good evidence. Here are two stats first:

1. Known TNOs: about 1,750 according to the Minor Planet Center's list.




2. Estimated existing Kuiper-Belt Objects: 120,000+ according to Britannica. (That number is only estimating objects of 100-km diameter or more, but that's fine for our purposes.) Note: 120,000 is only for KBOs. There are other TNO sets such as the oort cloud (and the scattered disc if you define it separately), so I expect the number to be much much bigger than 120,000.

Given that we've only measured about 1% or less of TNO orbits, how can we be sure we have a good random sample to say that a massive body must have aligned these orbits? In other words, all the other orbits might be randomly distributed, which would be compelling evidence that some giant body is not "syncing" orbits or else way more than 1% of them would be "synced".

If I recall my statistics class correctly, 1% is not good enough for a random sample. The border-line good enough area starts at 3%, but there's still a catch: It has to be a random sample. There are still observation-bias questions here because obviously we've only mostly discovered the "nearby" TNOs, because they are easier to discover when they're "nearby". That certainly would not be a random sample even if we had 3% of them.

TLDR: There are at least 100,000 distant objects, of which less than 1% of them have some kind of aligned orbit as far as we know today. Is this actually good evidence that something has aligned them?

EDIT: Another analogy that might help. You have a bag of 100 marbles. You reach in and pull out 5 from the top of the bag (notice I didn't say any random 5!). They turn out to be 4 red ones and 1 black one. Is this actually good evidence that about 80% of the whole bag is red?

light - Can't we see all of the Milky Way's supernovae with the naked eye?

So from this I can only come to the conclusion that supernovae did in
fact happen in the Milky Way in the last two centuries, but that we
didn't see any of them.

But now I'm confused. I read about supernovae that have happened in
galaxies billions of light-years from here that lit up as the
brightest source of light in the sky for days. Surely we would be able
to see all of the supernovae that happen in our Milky Way

One problem with estimating how many supernovae have happened in the Milky Way in the last two centuries, is that the remnant from a supernova is far dimmer than the nova itself and far harder to find. Several supernovae could have happened in the Milky Way in the last 2 centuries and remain undiscovered — and just for clarity, we define the date of a supernova by the date the light from the explosion reaches the Earth, so saying saying a nova "happened" in the last 200 years refers to the date the light from the event reached Earth, not the actual date of the event, which you probably already know, but just to clarify.

So for argument's sake, let's say that a supernova's light reached the Earth about 50 years ago, but it took place on the far side of the galaxy. To find that, we'd have to look for a nebula on the far side of the galaxy and that's a hard thing to see. Similar to looking for the theoretical Planet Nine, finding old supernova remnants on the other side of the Milky Way takes a lot of looking. Even with modern telescopes, it's still a needle in a haystack, and especially if the view is blocked by dust like much of the Milky Way is.

A Milky Way supernova remnant was discovered in 1985, supernova remnant G1.9+0.3. It was thought to have "happened" around 1868, though it went unobserved and probably wasn't visible to the naked eye at the time. There's probably been several others more recent than that one. G1.9+0.3 would have been visible if not for interstellar dust. From article above:

It was a type Ia supernova believed to have exploded about 25,000
years ago, and the signal began reaching Earth around 1868. The light
from the supernova would have been visible to 19th century
astronomers, had it not been obscured by the dense gas and dust of the
Galactic Center.

I'm not sure the 4.6 supernovae per century from your article is accurate. It might be, but the number I'm used to hearing is about one per century. But regardless of which number is actually correct, it still doesn't imply high mathematical improbability because many Milky Way novae would have gone unnoticed if they were far enough away. In short, I agree with what you said here:

I can only come to the conclusion that supernovae did in fact happen in the Milky Way in the last two centuries, but that we didn't see any of them.

Here's a related article on Milky Way visibility.

Observation of a distant galaxy nova is possible if we have telescopes looking in that direction. A nova is much more detectable at the time it goes nova. Much less so, years later.

Today, however, with neutrino detection in 7 locations around the globe, I think it's virtually impossible that we'd miss a supernova in the Milky Way, so we have a good chance of seeing one in our lifetime and it's likely that none have occurred since somewhere around 1980. A supernova was detected in the Andromeda galaxy in 1987 by that method, and our neutrino detection has improved since then to give us early warning and pinpoint location.

As far as visibility, size matters, but what matters more is how close and how much dust is in the way. Most of the recorded supernovae were quite bright and fairly noticeable to someone who was familiar with the stars in the sky (list of known supernovae).

Eight Milky Way novae have been recorded by history and observed by the naked eye in the last 2,000 years, well below the number that should have happened in that time. Five of those eight had brightness greater than $-3$, which is brighter than Jupiter and would have been immediately noticed by anyone familiar with star charting. Two others had magnitudes around zero, which is still brighter than most stars. SN386 was less bright, but is still easily visible and recorded by Chinese astronomers. And finally, Cassiopeia A was quite dim, but it was still observable. Only about 10% (ballpark estimate) of the Milky Way is close enough and unobstructed enough to provide supernovae that would visibly get noticed. Most would have gone unnoticed until recently.

Hope that's not too wordy, I can try to clean up if needed.

the sun - Term for altitude of the sun?

The term for when the sun is at its highest is "solar noon".

https://en.wikipedia.org/wiki/Noon#Solar_noon It is the moment the sun crosses the meridian. The meridian is an imaginary half-circle that goes from the northernmost point on the horizon to the highest point directly above you and then to the southernmost point on the horizon. The sun is always at its highest point in its daily path when it crosses the merdian.

You're right that in earlier centuries, each town would set its clocks at noon for when the sun was at its highest point. Those of us who are familiar with astronomy and history would call that type of timekeeping "apparent solar time". You can't guarantee an exact 24 hour day with "apparent solar time", so some people used "mean solar time" instead. (Historical note: Having each town choose its local noon became a nightmare for railway companies that wanted to set train schedules. So the railway companies urged the creation of 4 time zones in America and encouraged each small town to use "standard time" instead of "apparent solar time".

And as rgettman already mentioned, the term for the sun's height above the horizon is "altitude". Astronomers use the term "elevation" for a person's distance above sea level.

general relativity - What's the relation between Einstein's Gravitational Theory and Dark Matter?

Dark matter was originally hypothesised because there is a greater degree of rotational energy in galaxies than visible matter would allow for - crudely they rotate so fast that they ought to spin apart and therefore it was hypothesised that there is an additional source of gravitational force in some form of invisible matter.

This is not as a result of a discrepancy in Einstein's General Relativity. Newtonian gravitation is a very good approximation of Einstein's GR at most ordinary scales and energies and this is true in this case also.

I am not sure, exactly, what your "what about dark energy" question means, but assuming you mean, does this imply an incompleteness in GR, then again the answer is no, or at least not necessarily, but it's a more subtle point.

Dark energy is the hypothesised source of the energy that causes the universe to expand at an accelerating rate. It can be inserted as a term into the field equations of GR (other explanations of DE exist though) - but that is just a mathematical term, rather than an explanation of the physicality of it.

Einstein originally inserted such a term into his solutions - to predict an essentially static universe. When it was shown that the universe was expanding he described this as his "greatest mistake".

The evidence for the accelerating rate of expansion is relatively recent and came long after Einstein's death so he never lived to see the essential idea - of a "cosmological constant" in his equations - revived.

This explains more - https://en.wikipedia.org/wiki/Cosmological_constant

exoplanet - Are there any common characteristics of habitable planets?

I think I will answer your question from two vantage points. Firstly, what do we have to measure about a new exoplanet to consider it potentially habitable? Keep in mind that in detecting these 1000 or so new exoplanets, we've only gone so far as to show that they (statistically) exist and to measure some very very basic properties of them. It is on these very basic properties that we make our judgement of habitability and further research and observation is necessary to confirm these suppositions. When a new exoplanet is announced, we generally know the following information, which we use to determine habitability:

1. Distance from the star. This is a crucial piece of the puzzle because it tells us generally how hot or cold the planet is. We presume that life cannot exist on planets which are boiling hot or freezing cold. This information can be ascertained from either the radial velocity method or the transit method.


2. Size of the planet. Note here, size generally refers to diameter or radius. This is important because we want to generally know what type of planet we've detected. Gas giants are, well ... giant and inhospitable to life as we know it. We want to make sure the planet we've found is small enough that it is likely terrestrial. Although size is not a guarantee that it is terrestrial, its a piece of the puzzle. We can measure size by the transit method, however there is some degree of uncertainty to this process because we need to know the size of the host star to a good degree of accuracy, which is not always possible.


3. Mass of the planet. This is a crucial component in determining habitability. Size alone may tell us that a planet is what we call a "Super Earth" or "Sub Neptune" in that it is slightly larger than our own planet. The problem with that is, if the planet sits on the size border between Earth and Neptune, how are we to know whether it is rocky or gaseous? This can be resolved by looking at the mass, which is ascertained by the radial velocity method. The mass combined with size, gives us density and density is a surefire way to know if the planet is made of dense material or light gases.

That's really about it for basic information gleaned from simple planet detection methods. If you have distance from star, size, and mass (all of which you can get from the RV and transit methods) then you can presume that the planet is Earth-like and at a good temperature. That's enough to claim potential habitability, but not enough to actually show it can support human life. For that, you need to investigate the planet further and show it meets a variety of other conditions. As of know, some of those conditions are measurable with enough work, some aren't. These conditions may include, but are not limited to:

1. An atmosphere with water in it. We have the technology to measure this fact, but I'll say that it is very very difficult to do so and I don't know if anyone has really successfully shown water exists in an exoplanetary atmosphere (some have convincing evidence though). Generally, the process to do this is to measure the radius of the planet as a function of wavelength. Different wavelengths of light will refract through the atmosphere differently (just like in a prism) and so you measure a different radius of the planet (radius being the physical size of the planet plus the extent of the atmosphere) at different wavelengths. From this information, you can model what the atmosphere must be made of to cause the radius to change depending on wavelength. The issue with this process is that is requires removing all possible false detections and having a great signal to noise which is very hard.


2. A magnetosphere. We believe this is a necessity for life. Every second of every day our planet is being bombarded with high energy particles from our Sun. Most of these particles are harmlessly deflected by our magnetosphere and so we're protected. Planets without this protection would have a hard time hosting life as that life would be destroyed by radiation (or at least life like us). There is currently no way to detect whether a planet has a magnetosphere, although I believe there are potential ideas on the chalkboard.


3. The presence of a moon. This one is a bit iffy. Some people will argue our Moon has been instrumental to our development and for life in generally. The argument generally goes that the Moon has helped stabilize our tilt and thus kept our seasons and global weather well regulated. While we might be able to exist on a planet without such conditions, some believe life cannot begin on such a harsh planet without that regulating moon. There is also the benefit that the Moon has shielded us from a large number of impacts by taking the blow itself. Again, we could live on the planet, but the lack of a moon might not foster growth of life naturally. Moons, at this time, are out of our reach to detect.

There are numerous other factors for what helps define whether a planet is habitable, be it by us or in hosting new life. The list could go on and on, but these are the major points I think.

homework - Does chicken embryo form the disc called "discoblast" in the cleavage and blastulation of chicken?

This thread is related to my previous thread which is still unsolved mainly. I need to be able to compare chick and human cleavage and blastulation of zygote.
My friend says that

Chicken have discoblast, human not. That is the main thing to get the idea of the difference.

I know that chicken have yolk sac with yolk, while human have yolk sac without yolk.

My notes say that

Cleavage in birds is partial discoidal (embryo forms disc and cells called blastodisc are on top of the yolk).

So embryo forms some disc, lets call it #1. Some cells called blastodisc are on top of the yolk. So are the cells called blastodisc on top of the yolk and the disc #1?

What is the name of the given disc that chick embryo forms?
It seems that human is not forming the given disc. Apparently, the name of the given disc is discoblast, the thing he says is very important.

human biology - What actually happens when my leg 'falls asleep'?

The explanation in the link Polynomial posted is essentially correct.

Whenever there is a reduced or blocked blood supply (ischaemia) to your extremities, the 'five P's' can occur: pulselessness, pain, pallor (colour), paresthesia (numbness) and paralysis (or weakness).(1).

The numbness and weakness happen after the blood flow have been reduced for a particularly prolonged period.

Cells in our body require a blood supply to stay alive (think about a stroke or heart attack for example). So a reduced supply can cause them to function abnormally or after a time (depending on the cell or tissue type) die.

So with a 'sleeping leg', staying in an awkward or particular position where arterial blood supply is blocked or reduced to the leg, the muscle, nerve tissue etc all lack supply hence causing sensory disturbance and weakness.

The possible buildup of metabolites could also contribute to the symptoms (pain).

Hope that helps!

1. Miller's Anaesthesia - Miller.

human biology - Why does scar tissue change color?

The main mechanism behind the scar changing its color is the dilation of blood vessels within the scar tissue. The dilated vessels lead to the congestion of blood flow. The red blood cells moving more slowly leave more oxygen due to its diffusion to the tissue and the hemoglobin -- the oxygen holding protein -- changes its color from scarlet (bound to oxygen) to cyan (released/bound to CO₂). Since scars are not covered by skin, the blood vessels are clearly visible here and you see this characteristic color.

The triggering mechanism here is cold that increases the energy barrier for many biochemical reactions, first of all those required for smooth muscle contraction.

Cold-induced vessel dilation (that can be seen, for example, on cheeks and extremities) with mild circulatory disturbances ultimately undergoes into so-called cold vessel paralysis when smooth muscles of blood vessel walls completely loose their ability to contract and are maximally dilated. The cyan color of the scar is usually seen at the very last stage, that can occur unexpectedly quickly because scars do not have any warmth insulation layer compared to the regions covered by skin.

fundamental astronomy - How to plot orbit of binary star and calculate its orbital elements?

If it's a binary, it's fairly simple (in comparison with a ternary system), because the stars of the binary orbit about their common barycenter in Kepler ellipses.

An orbit simulator, see here; replace the central star by the barycenter of the binaries.

Calculation of an Orbit from Three Observations. Kepler problem on Wikipedia.

If you don't find a ready-to-use software, try to solve it numerically by simulating the orbit of the binaries according to Kepler's law, and vary mass, distance, excentricity assumptions until they match to the observations. Use optimization methods, e.g. hill climbing algorithms, or gradient methods.

expansion - How can an infinite universe expand?

I understand the expansion of the universe as actually an increase in the ratio of space to matter. Is this a correct understanding?

It isn't wrong. The ratio is increasing. But it isn't a "correct understanding". It's merely an observation of one of the results of the expansion of space.

If the universe is infinite how can it expand?

I don't know. Nor do I know how big bang cosmology can be reconciled to an infinite universe. If you look around on the internet, you can find articles like this which say this:

"The linear dimensions of the early universe increases during this period of a tiny fraction of a second by a factor of at least 10$^{26}$ to around 10 centimetres (about the size of a grapefruit)".

However in 2013 results from the WMAP mission appeared to confirm that space is flat. Then a non-sequitur crept in. See this article and pay careful attention to this:

"We now know (as of 2013) that the universe is flat with only a 0.4% margin of error. This suggests that the Universe is infinite in extent; however, since the Universe has a finite age, we can only observe a finite volume of the Universe. All we can truly conclude is that the Universe is much larger than the volume we can directly observe."

That's a massive error. It absolutely doesn't suggest that the universe is infinite in extent. Or that the Universe is much larger than the volume we can directly observe. But this myth has legs, and people repeat it ad-infinitum, even though they can't explain how it fits in with Big Bang cosmology. What you tend to hear is that the observable universe was the size of a grapefruit, but it absolutely doesn't satisfy. Moreover there's a dreadful flaw lurking in the shadows. Take a look at the stress-energy-momentum tensor, and note the energy-pressure diagonal. A gravitational field is something like a spatial pressure gradient, and you can think of space as having an innate "pressure". So you can reason that the universe must expand. As to why Einstein didn't, I just don't know. But anyway, for an analogy, squeeze a stress-ball down in your fist, and let go. It expands because of the pressure. However if that material was infinite in extent, the pressure is counter-balanced at all locations. So it can't expand. In similar vein, in my opinion, an infinite universe can't expand.

People claim the universe must be infinite because of the cosmological principle. But this is merely an assumption. There's an assumption that the universe is homogeneous and isotropic, but this isn't fact. You cannot use it to make sweeping claims about an infinite universe that was always infinite. For all we know some observer 50 billion light years away might be looking up at the night sky wondering why half of it is black. Or a mirror-image of the other. Or some kind of edge.

It is said that in days gone by, people could not conceive of a world that was curved. They could only conceive of a world with an edge. Nowadays I rather fancy that there are some people who cannot conceive of a world that is not curved. They cannot conceive of a world with an edge.

Edit:

See The Foundation of the General Theory of Relativity: "the energy of the gravitational field shall act gravitatively in the same way as any other kind of energy". Energy is the source of the stress-energy tensor. Matter is only a source because of the energy-content. Also see Inhomogeneous and interacting vacuum energy which refers to spatial energy. An interesting read is the article Universe 156 billion light-years wide
featuring Neil Cornish. This isn't entirely accurate, but the compound interest and the hall of mirrors concepts are of interest. As for the non-sequitur, see this interview with Joseph Silk:

"We do not know whether the Universe is finite or not."

I hope nobody will argue with that. Reading on:

"To give you an example, imagine the geometry of the Universe in two dimensions as a plane. It is flat, and a plane is normally infinite. But you can take a sheet of paper [an 'infinite' sheet of paper] and you can roll it up and make a cylinder, and you can roll the cylinder again and make a torus [like the shape of a doughnut]. The surface of the torus is also spatially flat, but it is finite".

This is akin to the old Asteroids game. But the Planck mission found no evidence of any torus. Reading on further:

"So you have two possibilities for a flat Universe: one infinite, like a plane, and one finite, like a torus, which is also flat."

I dispute that. There is a third possibility. A flat finite universe with no intrinsic curvature. If anybody can cite some reliable sources that support the assertion that a flat universe must be infinite, I'd like to see them.

Would humans hear gravity waves from a binary BH fusion nearby?

Gravity would warp your entire body, or at least tug on it, because bodies that aren't bound together by gravity largely resist it's deformation, at least that's the major point I'm working on here.

That being said, it should pull on some structure in your ear, be it the bones or the tiny Philae (I believe that's the right word, edit if not), either way it results in a deviation from their original position.

Depending on proximity you might also be able to feel it, in likeness to standing in front of a large speaker. However the ears would be far more sensitive.

I hope I've answered your question :)

biochemistry - What effect has changing pH and salt concentration on protein complexes?

The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into chaotropes ('disorder-making'), which destabilise protein structures and kosmotropes ('order-making'), which stabilize them. [1, 2]

Chaotropic salts interfere with intramolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which, at high cosolvent concentrations, results in protein denaturation.

Kosmotropic salts, on the other hand, cause water molecules to favorably interact, which also stabilizes intermolecular interactions in proteins. The salt molecules readily interact with water from the protein's hydratation shell and remove it from the protein surface, which produces thermodynamically unfavourable interactions that are reduced when proteins associate to form complexes. With increase in salt concentration the protein precipitation (salting out) increases.

Both cations and anions have been ranked separately by their capacity to precipitate proteins, to form a Hofmeister series [3, 4] (first set in 1888 but still hotly debated), e.g.:

SO₄²⁻ > H₂PO₄⁻ > CH₃COO⁻ > Cl⁻ > Br⁻

At large salt concentrations protein solubility is given by the empirical Cohn equation [6]:

lnS = α − βc

where S is the protein solubility, c is the salt's ionic strength, α and β are empirical constants characteristic of particular salt.

Salting-out agents are very widely used in protein purification (to concentrate proteins eg. with ammonium sulfate), chromatography or crystalization.

The influence of pH on protein-protein interactions in solution works through altering of the electrostatic properties of protein surfaces. At pH equal to the protein's isoelectric point (pI), where its net charge is neutral, charge repulsions of similar molecules are relatively low and many proteins will aggregate. Very low and very high pH will case proteins to denature; during digestion, for instance, proteins are in extremely low and then extremly high pH that exposes their backbones for enzymatic degradation.

For more information, please refer to:

1. Martin Chaplin, Kosmotropes and Chaotropes, http://www.lsbu.ac.uk/water/kosmos.html




2. Zangi R. Can salting-in/salting-out ions be classified as chaotropes/kosmotropes? J Phys Chem B. 2010 Jan 14;114(1):643-50.




3. Pace CN, Treviño S, Prabhakaran E, Scholtz JM. Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc Lond B Biol Sci. 2004 Aug 29;359(1448):1225-34; discussion 1234-5.




4. Shimizu S, McLaren WM, Matubayasi N. The Hofmeister series and protein-salt interactions. J Chem Phys. 2006 Jun 21;124(23):234905.




5. Zhang Y, Cremer PS. Interactions between macromolecules and ions: The Hofmeister series. Curr Opin Chem Biol. 2006 Dec;10(6):658-63. Epub 2006 Oct 10.




6. Ruckenstein E, Shulgin IL. Effect of salts and organic additives on the solubility of proteins in aqueous solutions. Adv Colloid Interface Sci. 2006 Nov 16;123-126:97-103. Epub 2006 Jun 30.

positional astronomy - Why do stars seem not to move relative to each other?

They do move - just far too slowly for you to detect by eye even over several human lifetimes.

Space is big. Really big. You just won't believe how vastly, hugely, mind-bogglingly big it is. I mean, you may think it's a long way down the road to the chemist, but that's just peanuts to space

Douglas Adams, "The Hitch-hikers Guide to the Galaxy"

Even the closest stars are a very, very, very long way away so their apparent movement relative to each other is going to be very small.

You can see the same effect when looking out of a moving vehicle through the side windows. You see the objects closest to you rushing past, but objects on the horizon appear to move much more slowly. Now, scale that up by many orders of magnitude to interstellar distances and you'll see why the stars don't appear to move relative to each other.

There's software that simulates the night sky and you can run time backwards and forwards - if you wind it far enough you'll see the constellations change.

telescope - Equation to find distance between objective and eyepiece

1 A.U. is same as infinity. The difference in terms of eyepiece position is infinitesimal, you can't measure it. Anything beyond a few kilometers away is pretty much "at infinity".

Regardless of that - from the practice of designing and building telescopes, calculations only offer you a starting point. You do the math, and the distance is 105 cm. But in practice lenses will deviate from the ideal focal length. Even if they didn't deviate at some temperature, put them in a cold environment, and the focal length will change a fraction of mm.

So take the calculations as a starting point, and build the instrument in such a way as to allow fine adjustments of the position of the eyepiece. There's a device called focuser that allows such fine adjustments. Or simply rely on friction to move the eyepiece back and forth until the image looks best, and hold it there.

When using the instrument in practice, you'll forget the ideal distance. What you will do is adjust the position of the eyepiece until the image looks best. You will do that every time you observe, and often multiple times during the same observation.

---

If you want some math, take a look at the thin lens equation, and apply it to the objective lens.

f = focal length of the lens

o = distance from lens to object

i = distance from lens to image

Then the thin lens equation is:

1/f = 1/i + 1/o

i = 1/(1/f - 1/o)

If o = infinity, then i = f.

But what happens if o = 1 A.U.?

i = 1/(1/1 - 1/(1.5 * 10^11)) = 1.0000000000067 meters

The difference is something like 6.7 * 10^-12 meters. It's smaller than an atom.

black hole - Why is metallicity important in the death of stars?

I can't give a detailed answer; the details are buried in the depths of numerical stellar evolution models.

The thing that changes most with the metallicity of a newborn star is the radiative opacity of the gas. Higher metallicity leads to more opacity.

This has two immediate effects - it makes energy harder to get out of the stellar interior and makes it more likely that convection will take over.

Convection has the property of mixing up all the material within the convective zone. This can have knock on effects as to how long each nuclear burning phase lasts and how much material is consumed. It also mixes synthesised material from the interior outwards.

A further important effect is that mass loss from massive stars is very extensive and is due to radiatively accelerated winds. For a given luminosity, high metallicity gas is more opaque and easier to accelerate. Hence mass loss is very sensitive to metallicity and determines how massive the star is as it reaches the end of its life. This in turn has a large bearing on what the remnant will be.

There is a further feedback in that the wind metallicity is the metallicity at the surface, but this in turn can be affected by interior mixing that is in turn metallicity-dependent.

If that sounds complicated, that's because it is, and detailed numerical models are required to see how these things play out.

entomology - Do insects' muscles become stronger with exercise?

There are instances of insect muscle growth in response to increased use. The flight muscles of the tsetse fly (Glossina morsitans) have been observed to grow at a faster rate when subjected to enforced exercise (Anderson and Finlayson, 1976). Also larger mandibular adductor muscles (which power the feeding apparatus), and associated head capsule have been noted for caterpillars and grasshoppers feeding on particularly hard grasses (Bernays, 1986). However these examples occur immediately post-eclosion (i.e. after emergence as adults), and during immature stages respectively. Insect muscle typically grows during larval/nymphal (immature) stages, and often for a brief period at the start of adulthood - known as the teneral period. During immature stages, insects typically have a flexible membrane to allow for tissue growth and expansion, this can also be the case during the teneral period, before the inflexible exoskeleton has fully hardened. However at full maturity, insect growth is limited by the rigidity of their exoskeleton.

As far as excessive exercise is concerned, that some insects may be weakened permanently may be more to do with the fact that their life strategy is different to ours. Due to the vast number of offspring per adult, and subsequent low survival chance of any given individual, there could be an evolutionary advantage for individuals pushing themselves to possibly deadly extremes. This could lead to many deaths, whilst retaining a viable population and thus accelerate the emergence of a population of fitter individuals.

References

• Anderson, M. & Finlayson, L.H., 1976. The effect of exercise on the growth of mitochondria and myofibrils in the flight muscles of the tsetse fly, Glossina morsitans. Journal of Morphology, 150(2), pp.321-326.


• Bernays, E.A., 1986. Diet-Induced Head Allometry among Foliage-Chewing Insects and its Importance for Graminivores. Science, 231(4737), pp.495-497.

How does a plant cutting develop roots?

Plants grow only from regions at the tips of the roots and shoots called meristems.

Within the meristem areas there are stem cells ("blank" unspecialised cells). Unlike animal stem cells, plant stem cells are totipotent - meaning that they can differentiate into any type of cell. Therefore when the cutting is taken from the end of the shoot, the stem cells can differentiate into root cells or shoot cells depending on their conditions.

Because the meristems (therefore the unspecialised stem cells) are only located at the tips of shoots, you cant grow a cutting from the middle of a branch.

extra terrestrial - How should one rationally deal with the issue of space travelling alien civilizations?

What kind of reasoning is appropriate to understand the as of today unanswered question of whether there are (other) interstellar space travelling civilizations in the Milky Way?

We have already sent probes towards the border of the Solar system. And even landed human beings on another celestial body and brought them home alive and well. If we extrapolate the 50 years of space travel, the 100 years of electronics (radio), the 400 years of physical science, to just a fraction of the biological age of humankind into the future (like a few thousands of years), interstellar travel is not out of the question for us or at least our artefacts. So I imagine two possible alternatives:

1) The Milky Way is cluttered by lots of space travelling civilizations like us and our future. Once one of them/us gets going, they'll soon be everywhere. The Sun orbits the Milky Way every 250 million years, about 2% of the age of the galaxy. Going to the nearest stars is enough to soon be everywhere. But if they are everywhere since almost always, they should be here, we should be their seed.

2) We are the only space travelling civilization in the entire galaxy, ever. But then what makes us unique? We consist of the most common elements and volatiles of the universe and our planet and star and galactic location all seem to be very typical. There's no known trace of any uniqueness here. Whatever could it be?

Are there more alternatives?

While we cannot say today which alternative is true, we should be able to at least specify the possible alternatives. But to me they all seem to be absurd! What would be a rational logical scientific approach to this apparent paradox?

light - What does the filter name I+z' mean

They must be referring to two different filters:

• the (Bessel) I filter which has a central wavelength of $lambda simeq 800,mathrm{nm}$ and a width of $Deltalambdasimeq 150,mathrm{nm}$, and


• the (Sloan) z' filter, which has $lambda,Deltalambda simeq 970,255,mathrm{nm}$.

Hence their transmission is in the near infrared ("NIR"), and they're both above 700 Å.

The exact transmission curves vary a little depending on the producer, so if you want to calculate exact magnitudes, for instance, you need to find the transmission curves for the telescope in question. From the TRAPPIST equipment website, it seems they use filters from Astrodon. Astrodon don't seem to provide filter curves for these exact filter, but if you're okay with a good approximation, you can find the curves here:
Bessel I and
Sloan z'.

genetics - What do the variants on the PolyT sequence mean?

My son has been diagnosed with Cystic Fibrosis. I am not looking for medical advice regarding his condition, but I am very interested in understanding the genetic causes of his condition.

In addition to the common CF mutation Delta F508, my son's genetic testing revealed both 6T and 9T variants of the PolyT sequence.

If I understand it correctly, it seems that the variants (I have found repeated reference to 5T, 7T, and 9T variants, but almost nothing on 6T) are tied to errors in the RNA transcription of the CFTR protein, but I don't understand how, or what the difference between these variants are.

What does "variant of the PolyT sequence" mean in this context, what are the difference between 5T, 6T, 7T, and 9T, and how do they impact the production of the CFTR protein?

physiology - What happens to a human body once a sugary snack is consumed?

The human/animal digestive tract breaks down food chemically (with low pH/acid), enzymatically (like proteases and glycolytic enaymes which break down protein and sugars respectively), as well as symbiotically (bacteria participates in the breakdown of some compounds in the gut). The results are released into the blood stream for the most of the body to assimilate.

With foods with complex carbohydrates (scenario 1), the results can be only a modest change in the glucose level in the serum. This depends upon the specific food which you can understand better by researching the 'glycemic index'. Highly glycemic foods result in rather short term release of simple carbohydrates glucose/sucrose into the blood. Lower glycimic food contain complex carbohydrates (which are elaborate chains of sugars) which need to be broken up into simple carbohydrates before they are metabolized the the cells.

Foods which contain a lot of simple carbohydrates change the sugar levels in the blood nearly immediately and it can go quite high. simple carbohydrates are monomers or dimers of sugars. BTW complex carbohydrates have few pictures on the web, but you can imagine them as chains and networks of many many simple carbohydrates linked together.

Not all simple carbohydrates are used by human beings for energy. For instance the glycosamine in 'joint juice' is the sort that makes cartilidge, which just to show you how different some complex carbohydrates can be. BTW i don't recommend joint juice, just trying to give a familiar example. Its unlikely that the glucosamine you drink will be directly used for your joints!

So glucose is the energy currency in the blood. when the glucose level goes up insulin is secreted by the pancreas which tells the cells to take up the glucose for glycogen (internal cell energy storage in a complex carbohydrate) or to be metabolized directly. Diabetes results when insulin is not produced (type I) or when the cells stop responding to insulin (type II).

Human tolerance to glucose in the blood is estimated to be up to about 100 mg/dl long term. higher than this on the average is not healthy and can go up to several hundreds and cause lots of degeneration in the kidney, liver, and eyes, and more. Exercise and fasting increase insulin sensitivity and athletes have blood glucose that is quite low even if they have a sugary beverage.

hope this helps - many keywords embedded within...

One last note. Fructose, which is about 45-60% of high fructose corn syrup (the rest is sucrose) is almost entirely metabolized in the liver. This is why fructose can be harmful to people who drink too much sweetened beverages. With the liver taking in the vast majority of fructose, it tends to make fat out of it, sort of overdosing it to make it fatter than the rest of you relatively quickly. Fatty liver is a marginally disfunctional liver and can cause health problems down the way. Abdominal body fat (not on your love handles, but amongst your chest cavity and internal organs) is particularly harmful as it interferes with all sorts of organ function. Probably something everyone should be aware of.

endocrinology - What is the mIU unit as used in hCG hormone levels?

IU stands for "International Units" and it is an arbitrarily chosen unit of measure used mostly to quantify hormones, vitamins or various substances found in the blood.

The idea is well explained by the Wikipedia article on international units)

Many biological agents exist in different forms or preparations (e.g. vitamin A in the form of retinol or beta-carotene). The goal of the IU is to be able to compare these, so that different forms or preparations with the same biological effect will contain the same number of IUs. To do so, the WHO Expert Committee on Biological Standardization provides a reference preparation of the agent, arbitrarily sets the number of IUs contained in that preparation, and specifies a biological procedure to compare other preparations of the same agent to the reference preparation. Since the number of IUs contained in a new substance is arbitrarily set, there is no equivalence between IU measurements of different biological agents. For instance, one IU of vitamin E cannot be equated with one IU of vitamin A in any way, including mass or efficacy.

For hCG, in the 55th report for of the WHO Expert Commitee on Biological Standardization, you could find:

The Expert Committee on Biological Standardization, after consideration of this issue (11), concluded that the choice of unit should be made on a case-by-case basis and reflect, and be based on, the biological and medical as well as the physicochemical information available.
Many biologicals exist in both active and inactive states, and the clinically relevant form of the analyte may depend on the diagnostic aim. For example, the active state of the placental hormone chorionic gonadotrophin (hCG) is the relevant molecule to measure in the diagnosis of pregnancy, whereas the biologically inactive free beta subunit (hCG-beta) is measured to diagnose choriocarcinoma. Generally, a measurement of biological activity is expressed in IU, whereas measurement of the amount of a protein or of a specific protein structure is expressed in SI. In this case there would be a compelling reason to relate the measurement of hCG to a unit of biological activity, and the measurement of hCG-beta to an SI unit of quantity. Accordingly WHO has established a reference preparation for hCG (currently the fourth International Standard, with an assigned content of 650 IU/ampoule) (7) and a reference preparation for hCG-beta (currently the first WHO Reference Reagent for immunoassay of hCG beta subunit, with an assigned content of 0.88nmol/ampoule) (18). The former preparation was assigned a value based on bioassay, whereas the latter preparation had been extensively characterized by physicochemical and
immunological methods and calibrated in nanomol by amino acid analysis. Applying these considerations of the properties of biological analytes, and their measurement in the clinical situation allowed the WHO biological reference standard for hepatitis B surface antigen, assigned a value in arbitrary IU rather than in SI units, to be adopted by the medical devices sector of the European Commission as the standard required for the fulfilment of the so-called Common Technical Specifications (CTS) for in vitro diagnostic devices. The Common Technical Specification document supporting the European (IVD) Medical Devices Directive 98/79 EC is a legally binding document within the 25 countries of the European Union.
Where it is appropriate for a WHO biological reference standard to be calibrated in SI units, the principles outlined in ISO 17511 (8) should be followed. This will necessitate the existence and use of an appropriate single reference method and an assignment of uncertainty, derived from calibration data. Such a reference method should not be a biological assay because the factors that affect the results of such assays are not fully understood. Where they are used, SI units assigned to biological reference standards should be derived from, and traceable to, physicochemical procedures.

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Note that IU are not the same as enzyme units (U) which is a measure of enzymatic activity

galaxy - Galactic extinction as a function of distance

You might want to have a look to the GALExtin models. The official site is still not finished (not even sure if it's still being developed), but you can access the original article here, and download the models here.

Here's a poster that provides a quick introduction.

Basically this is composed of two models of the Galaxy (one with spiral arms and one without) to which you give a (l, b) direction and a distance, and it gives you back the extinction.

It's a little bit old but perhaps it can be useful to you.

Also, the advice given by Rob is a good one: for such small distances perhaps the best thing to do is to assume zero extinction.

Magnetic fields of peculiar HgMn A type stars

One thing that seems to be clear is that HgMn stars have only an extremely weak net longitudinal magnetic field component, if any. Shorlin et al. (2002) did an early survey of HgMn, Am, and Ap stars, and detected no longitudinal magnetic fields in the former, with a median 1$sigma$ uncertainty of 39 Gauss. Makaganiuk et al. (2010) also found $B_z$ values of 0 in the stars they surveyed, with a higher precision - a 1$sigma$ uncertainty of 0.81-10 Gauss, varying between stars. Other studies also yielded precisions of less than a few Gauss for some stars (see mentions by Makaguniak (2011)).

Some reports have found longitudinal values in the 10s to 100s of Gauss, but as Kochukhov notes, subsequent inveistigations have failed to confirm these findings, which have had extremely high uncertainties. One example is Hubrig et al. (2012), the paper you cite, which claimed to have found weak longitudinal and quadratic fields in several stars, including HD 65949. Kochukhov et al. (2013) then found no longitudinal fields on the star, to within a few Gauss, and Bagnulo et al. (2013) attributed to 2012 findings to instrument error, leading to flawed data.

Non-longitudinal magnetic fields have not been observed in much detail (small-scale longitudinal fields have not yet been ruled out, either, by large-scale global ones appear to be nonexistent), and complicated ones could still exist. Kochukhov et al. (2013) do say that they have ruled out large so-called tangled magnetic fields, but small-scaled ones are still possible, according to Hubrig.

One thing worth noting is that the vast majority of these studies, including the one you referenced, which has been disputed, are focused on B-type HgMn stars, in part because fewer A-type HgMn stars have been discovered.

Since the Universe is expanding, is it accurate to say that a galaxy is 5 billion light years away?

I'm not 100% sure if I'm understanding what your asking, but if your question could be rephrased as "how do we measure distances in an expanding universe?", then I can try to answer that.

Depending on what astronomers measure they use different distance measurements. For example the comoving distance between two objects takes into account the expansion, and so does not change with time. If you know the redshift of the galaxy, for example by measuring the spectrum, and have a cosmological model, then you can calculate the comoving distance. Here cosmological model means constraints on the amount of dark energy, matter (both dark and regular) and radiation. The current accepted model is that the universe is around 70% dark energy and 30% matter, most of which is dark (with negligible radiation). The percent here refers to the fraction of energy density. Note that these values change over time, mostly since dark energy is like a property of space and so increases as the universe expands.

For some more info see:
https://en.m.wikipedia.org/wiki/Distance_measures_(cosmology)

Note that light years is a definite measurement, and so we can use it a valid unit for all distance measures.

black hole - How can a naked singularity be possible?

Nobody likes the idea of naked singularities, as they would have a toxic effect on causality. If a singularity existed that was not separated from us by an event horizon, then not only would the future not be predictable, but the past would not be fixed. Like the grandfather paradox, it wouldn't make sense, so it cant exist. The trouble is that GR doesn't implicitly rule them out.

If a black hole is spinning fast enough, or has enough charge then it seems a naked singularity could form. Naively you may think that the centrifugal force in the first case, and the electromagnetic force in the second are sufficient to overcome gravity.

I particular if $G^2M^4/c^2 < J^2$, where J is angular momentum, M is the mass, G is the gravitation constant, and c is the speed of light. The there will be a naked singularity. For a small, stellar mass black hole would need an angular momentum of $10^{42} mathrm{kg m^2 s^{-1}}$ to lose its event horizon

human biology - Fetal development, gastrulation and embryonic disc

I am completely confused by the images circulating on the internet of human gastrulation.

First, lets see how it happens in deuterostomes. This image depicts the process:

(image is from Wikipedia)

From here we can conclude that blastula becomes gastrula when some of the ectoderm beecomes endoderm, the place where it goes inside becomes anus and then mesoderm is formed.

Ectoderm here is the outermost level and gastrula already has anus.

However, in this image of human gastrulatuion we see completely different things:

(image source)

The mesoderm here is the outermost layer, ectoderm is inside and the gut cavity is formed by the separation of a part of the yolk sac. There is no anus and the posterior end of the gut is blind. Also other similar images suggest that a twins may be separated already after the mesoderm was formed (thus uniplacental twins).

The lack of agreement between the images disturbs me.

Just to point out some of the differences in the depicted processes:

• In first image mesoderm forms after gastrulation, on the second it forms far before gastrulation


• In the first image anus forms in the process of gastrulation, in the second image anus remains blind


• In the first image ectoderm is the outermost layer, while in the second picture mesodem is the outermost level that encloses all, including ectoderm.

evolution - Can two humans with 44 chromosomes produce viable offspring?

Interesting question. You refer to aneuploidy.

I don't have idea, but I loved to make some calculations. Feel free to edit because there are some very approximative assumptions.

Aneuploidy, the loss or gain of a chromosome, is estimated to occur in 13-25% of oocytes, 1-4% of sperm, 20% conceptuses and 0.3% of newborns. (reference)

The 46 chromosomes are made of 23 pairs, if the chromosome loss is evenly distributed, we have 0.3% / 23 newborns with the same chromosome loss (0.013 %).

Now, consider that the lost chromosome is likely not really lost, but just translocated on another of the 22 chromosomes. For instance, the individual you refer was having two chromosomes (the 14 and the 15) fused together.

So individuals with the same chromosome loss (0.013%) should have also the same translocation on one of the remaining 22 chromosomes (0.013% / 22 = 0.00059%).**

Chances are now that two of the 0.00059% newborns with exactly the same chromosome loss, will mate together.

Assuming random mating between humans, we have 0.00059% x 0.00059% = 0.0000003 % of possibilities, which is 1 possibility every 333,333,333 human beings.

We are now 7 billions on the Earth, so assume 3.5 billion couples all fertile despite of the age. If we assume also no spatial constraints, so that everyone could mate with every else one on the Earth, there could be no more than 10 couples with the same aneuploid mutation.

Provided the mutation does not affect genes important for reproduction, for instance genes between the two chromosome junctions that get interrupted, this couple could reproduce I guess.

To find that child, chances are now that he/she will have a kariotype done. Quite difficult to find isn'it?

protostar - Is the conversion from proto-star to main sequence an event or a process?

Astronomers distinguish a prototstar from a star based on whether the object is visible. A protostar is hidden by the gas cloud that surrounds it. Protostars aren't visible. At some point in their evolution (and where this occurs depends on mass and metallicity), a protostar will start clearing the surrounding cloud of gas. This process happens very quickly from an astronomical point of view. (Aside: From a human point of view, this is anything but quickly.)

In the case of very massive stars, the newly emerged star is already on the main sequence. Very massive stars are "stars" (objects with a stable mass, stable size, and fusing hydrogen into helium) well before astronomers can see them. In contrast, very small stars spend hundreds of millions of years of evolution between being a "star" (visible to astronomers) and being on the main sequence. The star is a pre-main sequence star during this long span of time.

Intermediate mass stars also spend some time as a pre-main sequence star. How much time depends on mass and metallicity. In the case of a star with a mass of ~1 solar mass and metallicity comparable to that of the Sun, the time spent as a pre-main sequence star is on the order of tens of millions of years. In contrast, the time spent as a protostar is very short, tens of thousands of years. The time taken to clear the star system of gas (the transition from protostar to PMS star) is shorter yet, hundreds to a few thousand of years.

There is no point at which one can say fusion starts. It's a probabilistic thing, with probability increasing sharply with density and temperature. What about objects at the low end of density and temperature? This is the boundary that separates red dwarfs from brown dwarfs.

There is very little difference between the smallest red dwarfs and the largest brown dwarfs. The smallest red dwarfs are quite cool. They fuse hydrogen into helium via the p-p chain, but rather infrequently. The largest brown dwarfs also fuse hydrogen into helium via the p-p chain, but here the fusion reactions are so very infrequent that the brown dwarf gets cooler and cooler. In a trillion years, we might be able to point to a marked boundary between old red dwarfs and old brown dwarfs. Right now, that boundary is rather arbitrary.

evolution - How many times did endosymbiosis occur?

Well, it seems quite obvious that it was not a single I-eat-you-but-you-survived act but rather a convergence of endosymbiotic and host species into a greater and greater cooperation.
Of course this leaves a question if there was one or more species of endosymbionts involved.

Mitochondria are a very primeval story forced by the oxygen catastrophe, so it is hard to say, although great majority of mitochondria seems to have a single origin.

Plastids are much more divergent, however it seems that they did originated from a single source, diverged into chloroplasts, cyanelles and rhodoplasts and were later mixed up by numerous acts of secondary and even tertiary endosymbiosis (plus a further evolution); this variety can be especially seen within Euglenas, and they are the main group investigated in this manner.

Under what circumstances and why is terrific broth preferred to LB broth for E.coli growth?

I have used terrific broth to grow up transformed E. coli so they grow faster. Often people will conduct a transformation, screen the cells, and grow them up in broth for plasmid extraction. This growth would be for 12-16 hours. Instead a person could use terrific broth to grow up the cells and it would take may 6-8 hours for adequate cell density for plasmid extraction. If you are trying to express a protein then I would go with LB.

Also, I learned recently that terrific broth is also preferred over LB when needing to express proteins after transformation.

special relativity - What is the bulk Lorentz factor?

I think it is referring to the speed and Lorentz factor $(beta = v/c$ and $gamma = [1-beta^2]^{-1/2})$ of the gas as a whole. Within the gas, there could be particles moving with a variety of velocities.

So if you pick up a ball of gas at 10,000 K (ouch) and throw it at 100 m/s then the bulk speed is 100 m/s, but obviously the particles in the gas have their own individual velocities.

mycology - How do fungi react to being grown in a tissue culture?

Generally, fungi are cultured on agar with a food source such as malt extract. One way to do this is to clone a mushroom from the fruitbody of a mushroom or from colonized substrate (e.g. rotting wood). Another approach is to germinate spores.

The fungus will grow as vegetative mycelia until it runs out of food. At that time, some species will grow tiny fruitbodies or sporulate before entering a more dormant phase, dying out. Unless refrigerated, standard agar plates dehydrate. Also, fungi may take on different textures: wispy, bumpy, root-like (rhizomorphic), leathery, powdery, and may darken or change color as they age.

Some cultures start to adapt their metabolism to the media after a large number of transfers (based on observation and discussed in Stamets' "The Mushroom Cultivator".) at this point, cultures may also start to grow more slowly.

The mycelia can be transferred from one plate to another or to another media (substrate) such as a log, 'fortified sawdust' (sawdust with ~30% w/w wheat bran), or pasteurized compost. With the appropriate nutrition and environmental stimuli (CO2 levels, temperature, moisture, light, etc), the mycelia will fruit, creating mushrooms - generally after fully colonizing the substrate.

Here is a figure of 35 agar plates with 16 different fungal cultures that I isolated from the wild (soil, wood, mushrooms, as described in Allison et. al, 2009; LeBauer, 2010), and have transferred from a mature culture (about a 2 months old) to a new plate, which are about two weeks old in this picture. Parent cultures are in the first and third row, with children below (they are genetic clones; instead of counting generations, I count number of transfers.

You can also find cultures of fungi (Yeast) in unfiltered beer.

I have used many techniques to isolate and culture fungi (Isikhuemhen and LeBauer, 2004; LeBauer, 2010) but I would recommend the books "The Mushroom Cultivator" and "Growing Gourmet and Medicinal Mushrooms" by Paul Stamets for more information on sterile culture techniques used in mushroom cultivation.

positional astronomy - How/where to check where the Sun is (constellation)?

In this case, Wolfram|Alpha has you covered. For example, look at the result for "which constellation was the Sun in Jan 1 1400". That said, I'm not sure this calculate includes the precession of the Earth's rotation axis, since I would've expected it to get my astrological birth sign right in 500 BC.

Would it be possible to equip an asteroid to collect space junk in Earth's orbit?

This is plausible, and might even be a good idea if used right.

First off, NASA has been working on plans for an asteroid redirect mission, called ARM. While it remains to be seen whether this will be approved, and they plan to put it into lunar orbit, this is a hypothetical scenario anyways so I'll ignore that.

Now, putting an asteroid into earth orbit is a little bit of a difficult subject. Sure, you could do it, but messing up would net you a whole lot of problems. I presume it would have to go into high earth orbit if it goes into orbit at all.

This rules out using the asteroid directly like a satellite, but that would have been impractical even if it was sanctioned by everyone with enough influence to have an opinion on earth. From there the satellite would be best used as a base of operations, from which you could send drones to collect junk and keep refueling stations. I'd also include a telescope or two, but that's personal preference.

If you want a list of targets though, here would be a good place to look.

general relativity - Does mass create space?

This is a tough question to answer because the dimensions of your proverbial cube would be affected by the mass inside (as dimensions can only exist in space, so anything that affects space will also bend your cube), and mass does not bend space, it bends spacetime. You have to keep in mind that when talking about special and general relativity, you are talking about four-dimensional spacetime. This is what is curved by mass. For example, due to the curvature of spacetime due to Earth's gravity, you feel the same effects on its surface that you would if you were accelerating upwards at 9.8 m/s^2 through deep space (where we assume there is no gravity). This doesn't mean the physical space is curved - if you draw a straight line on a piece of paper in space and then travel down to Earth's surface, it will remain straight. Instead, spacetime is curved, which can affect objects' paths of motion, but not the objects themselves. Now to your questions:

• The volume inside of the cubes would be exactly the same, but two identical objects flying through each cube would follow two different paths, and if either looked at the other, it would see that the other's clock is moving at a different speed than its own due to time dilation (due to the curvature of spacetime towards mass, time moves more slowly closer to massive objects). We can see evidence of the effect of gravity on paths with gravitational lensing. Light travels in a straight line through spacetime, but when looking at the space around a star, you will actually see objects that should be directly behind the star and blocked from sight. This is because light rays that, in the absence of gravity, would pass next to the star and continue off at an angle are pulled towards the star by it's gravitational field (in reality they're just following the curvature of spacetime around the massive star), so they curve around the star, becoming visible to us, even though, in space alone, they should be blocked by the star.


• The distribution of the mass has no effect on the gravitational field around it (same with electromagnetic fields). If you look at any equation that has to do with gravity (gravitational potential energy, gravitational force, etc.), you will find a term for the total mass of the object, but unless you are within the bounds of the control volume containing the mass, the distribution does not matter. This is one of the reasons why black holes are so hard to study - we can tell how much mass is inside of them, but without the ability to see inside, we have no other way of detecting their properties.


• Like I said above, the volume is not affected because space is not warped by gravity, only spacetime. If you made a physical box (or we'll say a cube frame) around empty space and then moved it to a space that contained a star, it would remain the same size and shape (assuming that it was strong enough to withstand the force of gravity pulling it towards the massive star).


• Neither, it simply curves spacetime.

cosmology - Three-torus model of the universe

A three-torus is the boundary of the solid three torus, just like the two-torus is the surface of a solid donut. You can imagine it as a cubical room where each wall/ceiling/floor is a portal to the opposite-facing wall (i.e. the wall to your right is a portal that sends you to your left), but preserves orientation (when you walk out of the portal, your heart is still on your left).

You can also think of it as a world where your position is described by three coordinates (like x, y, and z in Euclidean space), but each coordinate corresponds to an angle on the unit circle. If you go far enough in one coordinate, you loop back to where you started (360 degrees is the same as 0 on a circle).

history - Which stars have been named after astronomers?

You probably need someone better versed in the history of astronomy than me, but I'll give it a stab.

As you've already noticed, the Wikipedia article on stars named after people has some entries, and that's probably about it. In terms of modern naming procedures, we tend to use catalogue names. Unlike, say, asteroids, there's no systematic way of naming stars after people or anything else, so stars usually continue to be referred to only by catalogue number. Those rare stars that are named after people (or something else) are usually because they are now somehow historically associated with that system. Unless, of course, the catalogue is named after someone! Another exception are those very bright stars with pre-telescope names, but those aren't named after people (e.g. many scientific papers refer to Betelgeuse as such).

I guess in short, there's just no standard modern naming procedure by which a star can end up with a person's name, so few exist, and probably most are listed in the Wikipedia article.

asteroids - Dynamic Method-Please explain

I have, for years, been an Astronomy and physics nerd. For the first while, I was a total astronomy nerd. Then I slowly transitioned into physics and have been, for less than a year, a physics nerd. In this shirt while, I have taught my self calculus up to Calculus II (over summer and early this school year; I was 14 then). I know how to do geodesics, Schrodinger's equation, classical physics, etc and I'm teaching myself QFT and even planning to make one on quintessence. When I was an astronomy nerd, I didn't know how to do a lot of this math, and so I quit. Now, I am in an "astronomy comeback" phase. There's still one particular thing involving classical physics and astronomy that I still can't quite get-

The question-
How exactly, with steps and math shown, do you derive the masses of asteroids via perturbations? please, no links, because I have searched and searched for years and can't find anything. Thank you!

P.s. An extra thank you if you read the whole thing(including the story)! 😄

star cluster - What exactly is a stellar association?

A stellar association is a loose cluster of stars, that formed at the same time from the same molecular cloud, and so have the same proper motion. Unlike open clusters, they are not gravitationally bound together, so the stars in a stellar association will gradually separate, forming a moving group of stars.

An example is the Scorpius–Centaurus Association

human biology - What is the relationship between migraines and histamine?

Yes, this is true.

Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase. NO is then available to act locally on the vasculature as a vasodilator.

NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to the production of cyclic GMP, which in turn forms phosphorylated protein kinase G. PKG phosphorylates Ca²⁺ channels, slowing the influx of calcium into the cell, which leads to smooth muscle relaxation, and vasodilation, which leads to migraine.

The only silver lining is that there is a check in place: with the binding of histamine to H3 receptors on c-fibers in the central nervous system, feedback inhibition prevents the further release of histamine from these sites.

References:

Akerman S, Williamson DJ, Kaube H, Goadsby PJ. (2002). The role of histamine in dural vessel dilation. Brain Res. 956(1):96-102.

Gupta, S., Nahas, S.J.,Peterlin, B.L. (2011) Chemical Mediators of Migraine:
Preclinical and Clinical Observations. Headache: The Journal of Head and Face Pain, 51(6): 1029–1045.

apparent magnitude - Why do dark objects look white from a distance? (Moon, Ceres, but not Earth!)

The photo in your question is -- well, not exactly fake, but a composite. The biggest clue is that Earth is too close to the horizon; it would have had to be taken from within a few degrees of the boundary between the near and far sides of the Moon, and none of the Apollo missions landed there.

Furthermore, take a close look at the cloud patterns. The view of Earth appears to be identical to that in famous Earthrise photo taken from lunar orbit by Apollo 8 (click to see a larger version):

As you can see in that photo, the surface of the Moon is considerably darker than the Earth.

In the photo in the question, ignoring the inserted image of the Earth, the sunlit surface of the Moon is the brightest thing in the photo. The light balance must have been adjusted to make everything in the image easy to see.

As for why the Moon looks white in the night sky, it has an albedo of about 0.37, whereas the night sky has an albedo of about 0.00. Human eyes are very good at adapting to varying lighting conditions. When you look at a dark object against an even darker background, it's going to look white or light gray, even if it's intrinsically dark gray.