cosmology - Assumptions necessary for the strong form of Olber's Paradox

From Wikipedia, here's Lord Kelvin's statement of Olbers' Paradox:

Were the succession of stars endless, then the background of the sky would present us a uniform luminosity, like that displayed by the Galaxy – since there could be absolutely no point, in all that background, at which would not exist a star.

This is one form of Olbers' Paradox I've heard, which is that with infinitely many stars scattered in an infinite volume, every ray must eventually intersect a star. I call this the "strong form" because it seems to me stronger than the statement that infinite stars imply an infinite amount of light hitting every point, though not necessarily from every possible direction.

The strong form of the paradox doesn't hold if each star is a point mass and there are countably many stars, since the number of rays from any given point is uncountably infinite. Or imagine instead that stars are balls with small positive radius. If there is such a star at every lattice point in $R^3$ (an assumption that is consistent with my crude understanding of the cosmological principle), I can easily find a ray that intersects no star. I start from (0, 0, 0.5) and choose the ray in the direction of (1, 0, 0.5); the z coordinate will always be 0.5 and therefore my ray will never come close to a lattice point.

Is there another, palatable assumption we can add to make the strong form of Olbers' Paradox true, perhaps an argument that the distribution of stars must be more random than what I've described?

fundamental astronomy - View HD images of space in linux [SOLVED]

I dont know if this is the correct place to ask this. (I apologize if it isnt)

I like browsing through large HD images of space(a weird eccentricity I have), but I always have to go to NASA's image repository and then download them manually.

Is there some place which gets the latest images of space( the kind that make you feel that you'll fall into the ceiling ) and some way that I might get these images as a "live feed" in linux?

You'll be fulfilling something very important to me if you could help me with this.

Thanks

EDIT:

Found a site called Hubble Heritage linked here

Anyone know more?

EDIT: Sorry I wasnt clear before:

1.) Want a site where very awe-inspiring photos of space could be found

2.) From that site, I want to know if there is some way of creating a "live photo stream" to linux. Definition of a live photo stream here being anything ranging from a folder constantly being updated with new images, a photo stream as my desktop wallpaper etc. (I dont know how such a thing is implemented, nor how it would turn out, this is a question to experts in this area to tell me)

EDIT:

Since sometimes I do things that only fall within my wavelength of understanding, I'll post the answer to this thing.

Variety is a linux application which can grab photos off the internet and make it as a "live wallpaper" which updates with the the internet, combine that with NASA's gazillion web galleries out there and you have a winner.

zoology - Fish "coming back to life" after being frozen

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.

Is our supercluster part of a galaxy filament?

The Laniakea Supercluster contains several galaxy filaments, even just reading the wikipedia articles you provided you can see the difference in size of the two:

Galaxy Filament

They are massive, thread-like formations, with a typical length of 50 to 80 megaparsecs, (163 to 261 million light years) that form the boundaries between large voids in the universe.

Laniakea Supercluster

The Laniakea Supercluster encompasses 100,000 galaxies stretched out over 160 megaparsecs (520 million light-years).

The reason why Laniakea isn't the largest "structure" in the universe is because it inst a single object, rather an arbitrarily assigned group of galaxies. From this image below you can see how the supercluster is given an imaginary edge based on the peculiar velocities of the galaxies within it, there is no observable edge to the supercluster, unlike galaxy filaments that have visible edges.

stellar evolution - Metalicity and age of bulge stars vs halo

Your intuition is largely correct: the key is that the proto-bulge region had a deep enough potential well so that the supernovas couldn't expel the remaining gas, and so new stars could form out of the gas (enriched by the supernova ejecta) in a continuing cycle. In the low-mass, isolated protogalactic clouds which probably contributed to the halo, the initial round of supernovas ejected most of the gas (including the original gas that hadn't yet formed stars) -- thus, little opportunity to form more stars (out of higher-metallicity gas) on a continuing basis.

It's really the total mass in a given region that matters. For example, the density of stars in the central regions of a globular cluster is pretty high, but the mass of the cluster as a whole isn't enough to keep most of the gas when its massive stars go supernova.

(Side note: the traditional terms "Population I" and "Population II" aren't used all that much any more, since age and metallicity can vary continuously and aren't always strongly associated.)

cell biology - Macrophage pathogen fixation

The explanation one of my tutors offered was this:

In cell recognition, it is very common for interactions between proteins to be based on weak interactions, but a certain degree of binding can trigger a (conformational) change which will instead establish a very strong interaction between the proteins involved.

In other words, if the contact is specific enough to 'count as a recognised pathogen', the interactions will immediately change to strong forces and the pathogen will not be able to move away.

planet - White dwarf's impact on orbiting bodies

I think Aabaakawad's link gives a complete answer, but to give an astronomy for dummies answer, there's nothing about a white dwarf that causes a planet's orbit to decay at least, not directly. Your article (I've pulled quote below the caption):

Slowly the object will disintegrate, leaving a dusting of metals on
the surface of the star.

That's only talking about this particular situation and there's a difference between disintegrate and decay. This planetoid is enormously close to the white dwarf. So close, that what we think of as normal white dwarf/planet dynamics (very cold) is no longer true. This planetoid is slowly being vaporized.

Looking at the orbital period of 4.5 hours (about 1948 orbital periods in 365.25 days). The orbital distance to orbital ratio relation is exponential to the power of 2/3 (this varies a bit due to eccentricity, but it's generally correct), so an orbital period 1948 times faster means about 156 times closer, and giving the white dwarf equal mass to our sun, that puts the planetoid at a bit under 1 million KM. If this white dwarf is lighter than the sun, the planetoid would need to be even closer. That's close to the Roche limit and would be inside it if the planetoid wasn't dense and rocky/metallic.

If we estimate the white dwarf to be about the size of the Earth, which is a common size given for white dwarfs, An Earth sized object from 1 million KM would be larger in the sky than the sun appears from Earth, and presumably quite a bit hotter than the surface of our sun too, so this isn't a tiny white dwarf in the sky from the perspective of the planetoid. It's a blazing furnace of a sun, so hot, it vaporizes metallic gas and dust off the surface of the planet.

The article mentions this (end of page 3), that Poynting-Robertson drag see here and here, and that may be a factor in any orbital decay in this scenario. The article is clear that there's a good deal of uncertainty on with that effect, and that only affects tiny particles, but enough tiny particles could create a drag over time. . . . (maybe). The general scenario with this orbit is a planet scorched and as a result, is losing material. It's likely the very high heat that's driving any orbital decay, not gravity.

Gravitational decay / orbital decay does happen, usually much more slowly. That's probably not what's happening here.

There are some interesting orbital effects that can happen when a main sequence star goes red dwarf and later when it creates a planetary nebula, significant increases in tidal forces due to the star's greater size in the first case and increased drag in the 2nd, but at the white dwarf stage, there's no significant orbital decay effects.

Update:

Why not Poynting Robertson drag and Orbital decay effect the planetoid
when white dwarf was a star or even red giant? Is there any
"interesting orbital effects" when a star undergoes red giant?.Can you
update your answer to summarize the forces and their effect on the
planetoid in each phase of the star.
and also what do you mean by orbital decay? Does it have something to deal with the Roche limit.

OK, I think, having read more about it, Poynting-Robertson effect only matters when the orbiting objects are very small. I've linked it twice above, but the simple explanation is that objects in orbit move and so any light or debris from the sun hits the moving object at an angle, not direct on. If the object is small enough, this over time drives the dust and maybe grain of sand sized particles into the sun. This doesn't affect larger objects, so it's not really relevant to any planets or planetoids.

As far as "interesting red dwarf" effects. That really has to do with tides. Using the Moon/Earth example, the Moon creates tides on the Earth, a tidal bulge towards the Moon, but because the Earth Rotates faster than the Moon orbits, this tidal bulge is always ahead of the Moon and this creates a gravitational tug on the moon that pulls it away from the Earth - very slowly.

The same thing happens with planets around stars, but even more slowly, lets pretend it's just the Earth and the Sun - a 2 body system (in reality, with several planets it's much more complicated), but just Earth and sun, teh Earth creates a tidal bulge on the sun, the sun rotates ahead of the earth, this causes the earth to very slowly spiral away from the sun - so slowly that it might take a trillion years for the Earth to spiral away.

Now when the sun goes Red Giant, the sun is essentially the same mass but much more spread out and parts of it, much closer to the Earth and less gravitationally bound to the sun. This creates a far larger tidal tug. Also, as the sun expands it's orbital velocity drops, because orbital momentum is concerved, so when the Sun is Red Giant, the tidal bulge will be behind the Earth which drags it in towards the Sun. Due to the size and proximity of the Red Giant star, this draws the remaining near-by planets towards the sun fairly quickly, at least compared to main sequence stages which, provided the sun rotates faster than the planets orbit, has a much smaller outward tidal pressure on the planets.

And when the sun goes planetary nebula, any debris in the planet's path can also cause the planets to slow down slightly - the precise process there I'm less clear on, but in general, any orbital debris creates drag and can slow down a planet's orbit. This may be a key factor in the formation of hot jupiters, cause they can't form close to their suns but enough orbital debris can drive them in closer to their suns. (or planet to planet gravitational interactions can too).

That's the gist of the Sun-Planet orbital relation. When the sun is young, planets are mostly driven outwards, and young suns can have far greater solar flares and stronger solar wind. How much that effects the planets, I'm not sure.

During the Main sequence stage, stars tend to push planets outwards (unless they rotate very slowly, in which case the tidal effect is reversed), but this tidal effect is very small and very gradual.

During the Red Giant stage, stars tend to drag planets in wards, and I assume, during the planetary nebula stage as well. This effect is larger for closer planets.

You also asked about Orbital Decay - if you click on the link, there are examples of that. That probably gives a better explanation than I could. In general, Orbital decay happens very slowly unless you're talking Neutron Star or Black hole in which case the relativistic effects can cause orbital decay to happen quite fast. There's nothing about a white dwarf star that would cause faster than normal orbital decay but a white dwarf star would lose any tidal bulge tugging that a main sequence star has, so there would be essentially no tidal outwards pressure either which could in theory speed up decay cause you've lost a small outwards pressure but you would still have any debris or space dust clouds causing a small inwards pressure. (if that makes sense?)

That's my layman's explanation anyway.

element - What does oxygen on comet 67P/Churyumov-Gerasimenko mean?

It's not that oxygen should not be in this state, but rather we had not discovered it (e.g. on other comets). One of the reasons for this is that interstellar O2 is very reactive and quickly reacts to form e.g. H20 and O3.

Current models also favoured O2-less comets.

Interestingly, the paper you're referring to also mentions the O2 abundance was rather constant over the half year of observation, which hints to the O2 actually being primordial, i.e. from when the solar system condensed.

To reconcile these observations with models, a couple of possible solutions are offered: a slightly warmer primordial cloud (from which the solar system formed), or reactions with ices.

evolution - Why do men have nipples?

The two key concepts here are

1. sex-specific selection, and the fact that


2. males and females share the majority of genes

1) sex-specific selection

Obviously any population where females lacked nipples would be in trouble. Men, on the other hand, have no evolutionary need for them, but they don't pay much either—there is no strong selection against men with nipples. So at first sight, it seems that nipples are positively selected in females while seem to be quite neutral in males.

2) Males and females share the majority of genes

If you consider two separate species where the two species undergo different selection pressures, you will just see one species evolve toward one optima while the other one will independently evolve toward the other optima.

However, males and females are not independent entities. The vast majority of our genes can be found in one sex as well as in the other sex. In other words, male phenotypes do not evolve independently of female phenotypes. As a result of this interdependence, you can end up with the trait that is selected in one sex present in the other sex.

Evolutionary equilibrium

This is all much more rigorously defined in terms of selection coefficients and evolutionary pressure. Without going into the math, the questions of who has the highest selection coefficient and How differential is gene expression for this trait are important questions to predict the equilibrium trait value in both sexes.

Lack of a strong selection pressure

Finally, any trait that is seemingly not-useful has to have a significant disadvantage on the fitness of the organism to be selected out (If a trait would be advantageous to an organism, why hasn't it evolved?). Even if a trait is useless for both males and females it may persist. The case of females needing the trait just makes its elimination in males even more difficult, as explained above. However, in some mammalian species the males do lack the nipples (Evolutionarily, why do male rats and horses lack nipples?).

Accelerating universe expansion and standard candle

Most type Ia supernovae are thought to arise from the thermonuclear detonation of white dwarfs that are composed almost entirely out of carbon and oxygen.

These white dwarfs are the cores of relatively low-mass stars that have lived their lives, gone through stages of core hydrogen and helium burning, leaving behind degenerate carbon/oxygen cores that become cooling white dwarfs after the outer envelope has been shed during the asymptotic giant branch and planetary nebula phases. As such, their composition, at least to first order, is almost independent of the initial composition of the star from which they were formed. That is, even if the progenitor star had a very low initial metal content, the white dwarf produced would still be almost exclusively a carbon/oxygen mixture, which had a similar Chandrasekhar mass and a similar explosive potential.

It is well known however that not all type Ia supernovae are the same. It has long been known that their light curves are subtley different and there is a so-called stretch factor that can be applied to get a "corrected" peak magnitude. a.k.a The width-luminosity relation.

More recently there has been a realisation that type Ia supernovae could arise from both accretion or mergers and there is clear evidence that the amount of radioactive Ni varies from explosion to explosion. A very recent paper by Milne et al. (2015) has however challenged the view of metallicity independence. They claim there are two populations of type Ia SNe, connected with progenitor metallicity, and that these populations become more apparent at high redshift when looking at rest-frame ultraviolet emission. The gist of their conclusions is indeed, as your question supposes, that this may go some way to ameliorating (but not eliminating) the need for dark energy.

At what depth on Mars would the atmosphere have equal pressure of that on Earth?

Nasa has a atmospheric model of mars:
$$0.699 *e^{-0.00009 h} $$

A naive application of this model, solving for a pressure of 101 kPa, gives a depth of -55 km.

The Armstrong limit depth (at which water boils at body temperature) is -24km

The model assumes constant temperature, and gravity (it doesn't correct for the fact that at 55 km below the surface you would be well into the martian mantle, and deep enough for a measurable difference in gravity)

These depths are not achievable with current technology. The deepest mines on Earth are about 4km deep, and even the Kola superdeep borehole only managed 12km

space time - How long would it take to reach the edge of the reachable universe?

Jonathan's answer is essentially correct, but as Rob Jeffries comments, he doesn't take into account that the Universe is expanding during the journey.

The edge of the observable Universe is 47 billion lightyears (Gly) away. Even if you are a lightbeam, you cannot reach that point. The farthest you can go if departing today is roughly 5 Gpc, or 17 Gly, but this journey would of course take infinitly long (or else it wouldn't be "the farthest you can go"). This distance is probably what the linked article is referring to (I didn't read the article; it's very, very long).

So, in order for the answer to be any fun, you have to freeze the Universe, using magic, which is what Jonathan's calculator is doing. Here I'll just provide the analytical solution: In that case, the proper time $tau$ (i.e. the time experienced by the traveler) to reach a distance $x$ when traveling at a constant acceleration $a$ is
$$
tau = frac{c}{a} cosh^{-1} left( frac{ax}{c^2} +1 right),
$$
where $c$ is the speed of light. If you wish to decelerate after having reached halfway, you just divide $x$ by $2$ and multiply the result by $2$.

If you plug in the $x=15,mathrm{Gly}$ you request, you get roughly 45 years. To get to the edge of the Universe at 47 Gly actually only takes a few years more. The reason for this is simply that traveling at 1G gets you to (almost) the speed of light in only a couple of years, and hence you experience (almost) no time, no matter how far you go.

The time experienced for the Earthlings for the traveler at constant acceleration is given by
$$
t(tau) = frac{c}{a} sinh left( frac{a tau}{c} right),
$$
which works out to 15 Gyr for the 15 Gly, and 47 Gyr for the observable Universe. The reason is simply that the traveler, from the point of view of the Earthlings, extremely fast reaches a speed which is almost the speed of light.

senescence - What are the effects of combining rapamycin with dietary restriction?

To clarify; administration of rapamycin (a drug) to lab organisms (including mice [1]) extends lifespan. Similarly, restricting the intake of nutrients to the minimum without causing malnutrition also extends lifespan in lab animals (including primates [2]).

Rapamycin inhibits the mTOR pathway (mammalian Target Of Rapamycin) - specifically mTORC1 (Complex 1) - which influences protein synthesis, autophagy and inflammation (among others). Upstream factors of mTOR include nutrient availability and insulin signaling (see "Deconvoluting mTOR biology" for good review [3]).

It has been hypothesized that the lifespan-extending effects of caloric restriction (CR) are mediated by mTOR (one can see why - mTOR is affected by nutrient availability). In fact it may depend on the method of CR;

Greer et al [4] report that different methods of CR in C.elegans, for instance feeding them a diluted food source, or conversely feeding them on alternate days, do not necessarily require the same genetic pathways. Not only this but CR combined with a genetic mutant (eat-2) have additive lifespan-enhancing effects.

So whilst the evidence is not concrete, and I look forward to other studies in mammals similar to the one by Greer et al, it looks as though rapamycin and CR have similar but not exactly the same effects on lifespan; rapamycin specifically inhibits an individual pathway which is involved in many processes, and some of its effects are not necessarily desirable (e.g. rapamycin inhibits the immune system [5]). On the other hand, CR (most of the different types) seems to be mediated by mTOR - this difference is critical: mTOR is not necessarily inhibited by CR, it is just required for its effect.

Therefore combining rapamycin and CR is unlikely to have an additive effect as rapamycin may override any influence CR has on mTOR signaling, but I have not seen a study in which this has been tried. Combing different methods of CR (or developing drugs to do just that) may well have additive lifespan-enhancing effects.

1. Harrison DE, Strong R, Sharp ZD, et al. Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature. 2009;460(7253):392-5.


2. Colman RJ, Anderson RM, Johnson SC, et al. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science (New York, N.Y.). 2009;325(5937):201-4.


3. Weber JD, Gutmann DH. Deconvoluting mTOR biology. Cell cycle (Georgetown, Tex.). 2012;11(2):236-48.


4. Greer EL, Brunet A. Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans. Aging cell. 2009;8(2):113-27.


5. Thomson AW, Turnquist HR, Raimondi G. Immunoregulatory functions of mTOR inhibition. Nature reviews. Immunology. 2009;9(5):324-37.

planet - Internal heat and differentiation

Your argument (large temperature leads to greater mixing) is correct so long as there are no other large scale forces acting on the system. This isn't true in planet formation, because gravity plays a very important role.

I'm not an expert on planet formation, but I think the argument goes something like this: As a planet forms from material from the protoplanetary disc it will begin very homogenous, something like an asteroid, just rock and metal all the way through. If the planet is heated enough in the core, some material will melt. Buoyancy (due to gravity) will drive lighter material "higher" in the planet, away from the core. The more heat you generate the more melting can happen and the more material will start to separate by density.

Of course, there's a lot more to the story. Fluid material obeys the laws of hydrodynamics, so large scale convective flows can form in some regions, mixing those areas quite well. Planetary rotation adds centrifugal and Coriolis forces to the mix, which pull more material to the equator. The surface of a planet is exposed to space and can radiate excess heat, cooling to a solid (like the Earth's crust). If the core is magnetic and rotating, metals in the planet may be pushed by the magnetic field.

All this is just to say that planetary formation is a balancing act of a lot of competing forces. These forces can differentiate (or not!) different types of material, but first (for rocky planets at least) they need to be freed by internal heating.

deep sky observing - Has the most luminous object in the universe been found?

As it stands I think the answer is no. The most luminous object in the (observable) universe is probably hidden behind many magnitudes of dust extinction. There are lots of faint, infrared-detected objects that may be extremely luminous galaxies in the early universe (and indeed some have turned out to be) but it is difficult to get their redshifts, so it is difficult to be sure we have a complete luminosity function. We now know that objects with central black holes $>10^{9} M_{odot}$ already exist in the universe after a billion years or so. To get to that size there must have been an awful lot of accretion and an awful lot of accretion luminosity.

In addition, the most luminous galaxy/quasar is going to be a rare object and only ridiculously small areas of the sky are covered by things like the HST ultra-deep field. i.e. There is almost bound to be a more luminous one in some other patch of sky that has not (yet) been surveyed. The logistical problems of getting a UDF over the whole sky (or even a significant fraction of the sky) means that isn't going to happen any time soon.

Finally, the brightest quasar is certainly not the most luminous. 3C273 is quite a modest object, in terms of luminosity, but it is very close to us as quasars go. But perhaps you didn't mean bright in that sense? Brightness is normally reserved to refer to the apparent brightness. Luminosity is the extinction-free, distance-corrected power.

botany - Do trees really get a large share of their mass from the carbon in the air?

Yes. In fact the organic compounds' mass comes mostly from the air, since Photosynthesis essentially builds up glucose by only adding hydrogen to CO₂. The 2 H₂O → 2H₂ + O₂ reaction can be treated seperately, as was determined by Sam Ruben and Michael Kamen with ¹⁸O isotope tracing, i.e. in fact only the hydrogen in the carbohydrates comes from the soil, and this has of course a much smaller mass.

As said by Nick T, the more complex compounds also incorporate other elements that the plants get from the soil, but most of them still consist mainly of C and O. The total mass of a tree of course also has a lot of water and some minerals in it, but it's still safe to say that a tree "consists mainly of air".

To your question about surface area and air CO₂ content, neither is usually the limiting factor: in nature, light exposure, water and mineral supply are (although in enclosed spaces like greenhouses CO2 fertilization is sometimes necessary).

orbit - Ambiguity in Earth's "Tilt"

It’s well-known that the axial tilt of the Earth (with respect to the ecliptic) is about 23.4 degrees. However, two angles is needed to specify the orientation of any rigid body, so it’s unclear to me exactly how Earth is oriented with respect to its orbital plane.

To be more precise, consider the plane that satisfies these two conditions:
1. Perpendicular to the ecliptic plane
2. Contains the line connecting the Sun and the Earth when Earth is at perihelion (Jan. 2).

(Basically, this plane cuts through the orbit of the Earth such that for half the year Earth is one side and for the other half Earth is on the other side.)

Questions:
1. When the Earth is at perihelion, what is the angle between its rotational axis and the plane described above? I would guess this angle is very small from the images of Earth’s orbit. Is there a technical term for this angle?
2. Does the direction of the axis remain approximately the same throughout its entire orbit?

Please ignore precession for this question.

atmosphere - Public Data Set on Atmospheric Absorbtion / Extinction

Is there a publicly available data set for mean atmospheric absorption / extinction? I would like to be able to process and plot a graph similar to this image from NASA on wiki commons.

The HITRAN database appears to offer individual lines and might possibly be used to compute mean absorption at standard atmosphere. However, the process is unclear and the data search appears to be broken.

Spectral Calculator by GATS also appears to have done the calculations for various configurations pulling from the HITRAN database and using standard atmosphere, but access to transmittance and absorption plots is limited to subscribers paying $50 per month.

A lot of individuals seem to be generating or copying these plots, but very few citations are given. Furthermore, indications are that there may be a fair amount of variability depending on conditions so a plot based on standard or mean conditions looking upward or downward through the atmosphere would be helpful.

physiology - Why do some mammals not have testes in a scrotum?

Having descended testes is a derived characteristic within mammals; monotremes and the Afrotheria (including elephants) all retain the ancestral character state (Kleisner, et al., 2010)². Among those mammals with descended testes, these can be ascrotal or scrotal. Testicular descent is hypothesized to have only occurred once within Mammalia, with the ascrotal Laurasiatheria. Descended ascrotal testes are found in cetaceans, phocid seals, hippos, tapirs, rhinos, and some bats. Descended scrotal testes are found in horses, pigs, camels, and Carnivora.

Since basal mammals would presumably have to regulate testicular temperature just as much as derived mammals, the temperature regulation hypothesis seems to not hold up. So the real question is: why have a scrotum? One hypothesis has to do with evolution of fast locomotion (e.g., galloping).

According to Frey (1991, 40)⁴:

The strong flexions and extensions of the vertebral column during
gallop should cause intense fluctuations of intra-abdominal pressure.
Fluctuations of intra-abdominal pressure severely impede continuous
flow of blood in the abdominal veins. Periodically reduced venous
drainage resulting in fluctuations of intra-testicular pressure would
impair the process of spermiohistogenesis, which is dependent on an
absolutely constant pressure within the testis.

Chance (1996)⁵ suggests that the temperature hypothesis might represent a secondary adaptation:

Because in the human male, scrotal testes function optimally at
temperatures below that of the body, much speculation, and a
considerable amount of research, has gone into attempting to see what
(metabolic) advantage might accrue from this lower temperature,
without considering the possibility that this is a secondary
adaptation to an enforced external position.

Kleisner, K., Ivell, R., and Flegr, J. 2010. The evolutionary history of testicular externalization and the origin of the scrotum. J Biosci 35:27-37

Frey, R. 1991. Zur Ursache des Hodenabstiegs (Descensus testiculorum) bei Säugetieren. Z Zool Sys Evolut-Forsch 29:40–65

Chance, M.R.A. 1996. Reason for externalization of the testis of mammals. J Zool 239:691–695

How do we know the current state of the universe by observing it from Earth?

Since light travels at a constant and finite speed, looking into the Universe means looking back in time.

No matter in which direction we look, on average we see the same: Locally, we see evolved galaxies, far away we see young galaxies, and even farther we see the so-called cosmic microwave background, which is light from so far back in time that galaxies hadn't yet formed.

That is, the Universe seems to be isotropic. Unless we occupy a special place in the Universe, this implies that the Universe is also homogeneous, i.e. it would look more or less the same if you were located in another part of it.

This is turn means that the current state of the Universe can be inferred by observering the local region. The most distant observed galaxies can then be concluded be in the same state (statistically speaking; of course they don't look exactly the same, but any given property, e.g. the distribution of their sizes, will be the same as in our neighborhood).

What would harnessing of gravitational waves look like?

To put this in perspective, consider a fifty-plus year old human whose main source of exercise for the last twenty-plus years has been walking back and forth between work and the parking spot where the person parks his or her car. Let's strap that person to a bicycle connected to a generator. The energy output of that feeble source of energy easily exceeds the feeble 200 watt gravitational waves produced by the Earth's orbit about the Sun.

Gravitation is extremely feeble compared to electromagnetism. The electrostatic repulsion between a pair of electrons is 10⁴⁵ times stronger than is the gravitation attraction between a pair of electrons. Gravitational waves are in turn extremely feeble compared to gravitation itself. I mentioned the Earth's orbit about the Sun. The total mechanical energy of that orbit is about 10³⁴ times greater than the paltry amount of energy lost due to gravitational waves.

Imagine a Kardashev level III civilization, a civilization that has learned to harness the equivalent of the energy output of an entire galaxy. Aside: Humanity isn't even at Kardashev level I. That's another few hundred years in the future. Also note that the Kardashev scale is logarithmic. Karadshev level I is near future science fiction. Kardashev level II is also in the realm of science fiction. Kardashev level III? That's beyond science fiction.

Even that Kardashev level III civilization would not harness gravitational waves. It would instead go out of their way to avoid them. A Kardashev level III civilization might, for example, intentionally feed matter to a supermassive black hole at the heart of a galaxy to make that black hole become an active galactic nucleus. The energy output of an AGN is immense, exceeding that of a normal galaxy. The gravitational waves produced by an AGN are minuscule compared to the electromagnetic output, by a factor of about 10^-80 or so.

gravity - Is it certain that dark matter consists of particles? (And not just curved space)

In terms of dark matter, there are two notions which are incorrect. One is that dark matter is a clump of stuff traveling with the matter. The other is that dark matter does not interact with matter.

Dark matter fills 'empty' space. Dark matter is displaced by matter.

The Milky Way moves through and displaces the dark matter.

The Milky Way's halo is the state of displacement of the dark matter.

The state of displacement of the dark matter is also known as the deformation of spacetime.

The Milky Way's halo is the deformation of spacetime.

Dark matter is the physical manifestation of spacetime.

'Ether and the Theory of Relativity by Albert Einstein'
http://www-groups.dcs.st-and.ac.uk/~history/Extras/Einstein_ether.html

"Think of waves on the surface of water. Here we can describe two entirely different things. Either we may observe how the undulatory surface forming the boundary between water and air alters in the course of time; or else-with the help of small floats, for instance - we can observe how the position of the separate particles of water alters in the course of time. If the existence of such floats for tracking the motion of the particles of a fluid were a fundamental impossibility in physics - if, in fact nothing else whatever were observable than the shape of the space occupied by the water as it varies in time, we should have no ground for the assumption that water consists of movable particles. But all the same we could characterise it as a medium."

if, in fact nothing else whatever were observable than the shape of the space occupied by the dark matter as it varies in time, we should have no ground for the assumption that dark matter consists of movable particles. But all the same we could characterise it as a medium having mass which is displaced by the particles of matter which exist in it and move through it.

positional astronomy - Angular distance/apparent separation between AE Aurigae and Orion's belt

Given the cords of AE aurigae:

RA 05h 16m 18.1s DEC +34° 18' 49"

And Alnitak in Orion's belt:

RA 05h 40m 45.52666s DEC −01° 56′ 34.2649″

I get an angular separation of 34.83°

By this formula:

$cos(A) = sin(mathrm{DEC}_1)cdot sin(mathrm{DEC}_2) + cos(mathrm{DEC}_1)cdot cos(mathrm{DEC}_2)cdot cos(mathrm{RA}_1 - mathrm{RA}_2)$

communication - Is there a biological basis for different accents?

No. Accent is purely environmental. The ability to pick up the unique sounds of a language or variation of a language ceases around puberty: http://en.wikipedia.org/wiki/Language_acquisition

This is why adults learning a second language have trouble distinguishing the unique sounds of the second language. For learners of English, the "th" sounds and the difference between "l" and "r" can be difficult. For languages based on Sanskrit, there are a variety of aspirated/unaspirated consonants somewhere between "b" and "v" that English-speakers have a hard time distinguishing, much less imitating.

proteins - When does oxidation destroy prions?

If you google "prion oxidation" you'll see that there has been some research into this over the last 10 years, though it seems to be a minor focus of the overall field. There seems to be some interest currently in using ozone to inactivate prions. One company that offers a ozone-based sterilizer claims to be testing for effectiveness against prions, but that is an extremely long-term process (you have to isolate prions, subject them to your sterilization process, then inject them into the brains of mice or hamsters and wait to see if disease develops).

If you're curious as to how researchers sterilize material in the lab, I may be able to shed some light on that (I worked in a prion lab in 2006-07). Generally, disposable instruments and materials are used whenever possible and incinerated after use. Glassware is submerged in acidic detergent and autoclaved for 4 hours at (I believe) 132C. As far as I know, there is still no known way to completely sterilize stainless steel instruments - this was being studied at the time in the lab where I worked. Any piece of equipment that came in contact with human or bovine prions was kept in Biosafety Level 3 facilities permanently. I'm not sure what the decontamination process was for retired equipment. Separate equipment was maintained for "non-human pathogen" prions - hamster, mouse, etc.

genetics - What is the smallest number of amino acids required for life?

You can divide the 22 (including selenocysteine and pyrrolysine) proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique features like cysteine which can form disulfide bonds.

Some amino acids are very similar, for example isoleucine and leucine, it is plausible that one of those would suffice to create most protein folds.

There are several examples of proteins designed with a smaller alphabet of amino acids, one example is the E. coli orotate phosphoribosyltransferase (Akanuma et al., 2002). The simplified enzyme consists of only 13 different amino acids and 88% of it are composed of only nine different amino acids. Even after those drastic changes the enzyme still folds correctly and has enzymatic activity.

There is one study (Fan and Wang, 2003) that tried to answer exactly the question you asked. They came to the conclusion that around 10 amino acids are necessary to create properly folding proteins:

First, we study the minimum sequence complexity that can reserve the
necessary structural information for detection of distantly related
homologues. Second, we compare the ability of designing foldable model
sequences over a wide range of reduced amino acid alphabets, which find
the minimum number of letters that have the similar design ability as
20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different
approaches give a remarkably consistent view, that the minimum number
of letters required to fold a protein is around ten.

---

Akanuma, S., Kigawa, T. & Yokoyama, S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proceedings of the National Academy of Sciences 99, 13549 -13553 (2002).

Fan, K. & Wang, W. What is the minimum number of letters required to fold a protein? J. Mol. Biol. 328, 921-926 (2003).

evolution - Why does so much variation exist within species?

I think there are two elements to this answer. To cut to the short answer skip to the bold summary at the bottom...

Firstly, genetic variation exists because of mutation. Genes get mutated every generation, the . Larger populations will have more mutants within them because: more individuals = more nucleotide base pairs (C's G's A's and T's) = more potential sites of mutation. However mutation is not likely to explain the persistence of variation because mutation rates are very low (1 in 100,000 to 1,000,000 gametes have a newly mutated loci at any individual locus) and singleton alleles have only a 50% chance of reproduction (assuming no selection) so are likely to be lost by drift (Falconer & Mackay, Intro to Quantitative Genetics 1996).

You also talk about acne, which is likely to have a large component of environmental variance. Therefore you should remember that not all phenotypic variance is genetic its source and it is highly likely that an individual trait has some degree of environmental variance component. Simplistically:

Phenotypic variance = genotypic variance + environmental variance

So the bigger question is why does variation persist? There are many potential causes of this which continue to be widely debated. Essentially it seems paradoxical because selection should reduce variation as it drives the fixation of all loci to the fittest allele. However, selection is transient, both spatially and temporally, and is not efficient against rare alleles (especially recessive alleles because they are hidden by dominant traits - e.g. disease "carriers"). Another important point is that some mutations will be neutral, therefore remain unaffected by selection.

In the spatial context, this means that selection is not always favouring the same allele in all places a species inhabits. Selection might be different based on the where it is occurring (within a species, traits like fur would be beneficial to populations in cold climates but not to those in warmer climates - here I am assuming that the sole effect of fur is to improve the ability of retaining heat).

Temporally there are also key elements. Principally, over time selection changes. Again sticking with my fur example, climates change. Ice ages come and go bringing with them different selection coefficients for fur growth.

Another variance in selection can be sexually antagonistic selection, where different alleles are favoured in either sex. In this case selection does not deplete variation but instead maintains it. It has recently been shown that sexual antagonism is prevalent throughout the genome.

the divergent reproductive strategies of the sexes could promote the
maintenance of sexually-antagonistic variation (Sharp & Agrawal 2012... yesterday!)

Other hypotheses suggest mechanisms by with selection can maintain variation such as assortative mating.

Long story short, you stated that you expect variation to reduce as a consequence of selection. However genetic variation persists for many reasons, and can even be maintained by selection in several ways. Furthermore, phenotypic variation which is what you actually describe with your acne example (and I with my fur example) can be caused by non-genetic components of variation.

.

Suggested reading:

Cox & Calsbeek 2009, Sexually Antagonistic Selection, Sexual Dimorphism, and the
Resolution of Intralocus Sexual Conflict.

Falconer & Mackay 1996, Introduction to Quantitative Genetics.

Singh & Krimbas 2000, Evolutionary Genetics: from molecules to morphology.

Sharp & Agrawal 2012 (in press, accepted on-line version released yesterday, print may be 2013) Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster, Evolution.

Innocenti & Morrow 2011, The Sexually Antagonistic Genes of Drosophila melanogaster, PLoS Biology.

Arnqvist 2011 Assortative mating by fitness and sexually antagonistic genetic variation, Evolution. (also see his book sexual conflict).

genetics - Co-transformation of plasmids from the same incompatibility group

It turns out that there doesn't seem to be a specific mechanism to prevent multiple incompatible plasmids from coexisting. Velappan et al put in more than one incompatible plasmid with different selection genes in them and put the bacteria on a single antibiotic and periodically checked for the second vector (by testing for second antibiotic resistance). It apparently took weeks for the second vector to disappear - many generations.

Higher copy number plasmids did better, with longer times to lose the second plasmid. They seem to conclude that its just the natural rate of loss of plasmids that will cause the bacteria to lose the second plasmid without selection. I imagine with two antibiotics in the culture it would take some months and you could potentially store the bacteria at -80C indefinitely. Still in most experiments its going to be an additional headache where compatible origins of replication seem to have a more typical half life for retaining the plasmids.

They also state that the frequency of double transformations is more frequent than is usually appreciated, which seems to imply that you will get some colonies from a typical high efficiency transformation from plasmid preps. However, they introduced the multiple plasmids by phagemid infection rather than transformation in this study.

atmosphere - Is it accurate to compare comets to clouds and rain?

I'm trying to avoid an opinion-based question, so before I outline the comparison I'm proposing, I will qualify the specific facts that yield this comparison. By focusing answers on the relative accuracy of those facts, hopefully we can avoid primarily opinion-based answers.

Facts

1. Over the course of millions of years, planetary bodies, especially those closer to the sun, tend to lose their water and atmosphere as it is blown away by solar wind, and radiated or boiled off by other forces, unless they have a strong magnetosphere to repel the bulk of that solar wind, or enough gravity to hang on to their matter. On a much faster time scale, this also happens to comets as they approach the sun; thus, the tail.


2. Over the course of millions of years, bombardment of planets by comets can increase the water and gas on a planet, or at least counter-balance the gradual loss of the same (depending on other factors like proximity to the sun, size, and magnetic protection).


3. The Oort cloud is composed mostly of icy bodies (including solids that would be a gas at Earth temperatures). And it is from this region that comets "fall" toward the inner solar system.

Also Fact?
So I started wondering what ultimately happens to the water and gas that gets blown off of planetary bodies. I would guess that given the outward pressure of solar wind and solar radiation, the direction of such material is generally outward, away from the sun. Well, where to? Media coverage of the departure of Voyager 1 from our solar system into the realm of interstellar space alerted me to the idea that there is an outer edge to solar influence, and I would guess that this is where the lighter molecules, like water and gases would tend to land. And indeed there is a collection of similar material out there at that solar radius.

Given these facts, is it accurate to view the Oort cloud as behaving similarly to a terrestrial cloudscape? Our clouds form at the altitude where water tends to deposit after it evaporates from the heated surface of the Earth. It gathers there and coalesces to a form which is then overcome by the opposing force of gravity. Then it returns from whence it came. Similarly, I imagine water and gases ultimately being driven from the heat of the sun to an “altitude above its surface”, where ultimately, over a much longer time scale, that material coalesces until other forces eventually drive them back toward the hot sun. Is this an accurate understanding? Is this comparison justified?

genetics - Does the word "polymorphism" refer to the gene, the phenotype, or both?

The term "polymorphism" itself is more generally defined as "the quality or state of existing in or assuming different forms" (Merriam-Webster dictionary). So I guess semantically, it would be correct to say that there is polymorphism in a gene that can occur in different allelic variants, or polymorphism in phenotype because of variant traits (such as sexual dimorphism).

However, when biologists today speak of polymorphisms, often they refer to variations at the level of individual nucleotides (single nucleotide polymorphisms or SNPs; some people use the terms polymorphism and SNP interchangeably). These SNPs have become popular for genotyping and for correlation with a variety of diseases or other observable phenotypes.

And regarding the bonus question, I think "polymorphism in" is the most correct usage--it's definitely the most widely used. For example, you could say "there is a polymorphism in nucleotide 257 of..." or simply "there is polymorphism in nucleotide 257 of..." or even "nucleotide 257 of ... exhibits polymorphism".

abiogenesis - Why is there so much methane in space?

Often for molecules to form in interstellar space, dust is used as a catalyst. The reason is that in typical interstellar environments, densities are so immensely low that even for just two atoms to meet, the probability is so small that formation time scales are very long. For 3+ atoms, the chance decreases rapidly. Instead, an atom can stick to a dust grain and wait for ages until other atoms stick. The atoms slowly "crawl" around on the surface of the dust grain, eventually meet and make bonds. If the formation of a bond releases energy (is exothermic), the molecule can be ejected from the grain surface. This process is call adsorption.

The dust also helps shielding the molecules from stellar radiation which would otherwise easily destroy them. This is why molecular clouds are also very dusty. But actually UV irradiation helps with the formation of very complex molecules by ionizing less complex molecules that subsequently can make bonds with other atoms and molecules.

If the environments are extremely dense, as when a star dies and ejects its gas either as a supernova or a planetary nebula, molecules can also form. This is probably also how the dust itself is formed, although it might also be formed later on (this is currently debated; the problem is that supernovae are so powerful that their shock waves tend to destroy dust shortly after it forms, and planetary nebulae are created from stars that live so long that they can't explain the abundance of dust in the very early Universe where they wouldn't have had the time to live their lives).

As Stan Liou and LocalFluff says, methane is actually an "easy" molecule to form, both because it's rather simple, and because its constituents, hydrogen and carbon, are the most and the fourth most abundant elements in the interstellar medium, respectively.

In fact, far more complex molecules are regularly found in interstellar space, as can be seen on this list.

structural biology - How can I pare down a PDB file in Python to only include specific residues?

ProDy works quite well, especially from within an existing Python script.

The following code takes an existing PDB file, performs some selection query on it, then saves it to another file.

import prody

def pdbsubset(inpdb, outpdb, selection):
    with open(inpdb) as protf:
        prot = prody.parsePDBStream(protf)
    atoms = prot.select(selection)
    prody.writePDB(outpdb, atoms)

An example selection query builder

• residues is a list e.g. ['A12', 'A39'] with each element in the form <chain><residue number>. They were captured from the command line using argparse with

  
  
  

      parser.add_argument('-i', '--residues', nargs='+')
  

  
  
  
  • so you would specify -i A12 A39 or whatever.
  
  


• pdb and outpdb are file paths


• radius is the distance in angstroms to expand the selection by.

reslist = ["(chid {0} and resid {1})".format(res[0], res[1:]) for res in residues]
selector = 'within {0} of ({1})'.format(radius, ' or '.join(reslist))

# and running it:
pdbsubset(pdb, outpdb, selector)

The documentation on ProDy selection queries is not the most straightforward, but fairly analogous to PyMol, so doable.

homework - How do fibers control muscles?

Read "supply" as "carry action potentials to." When the action potential reaches the junction with the muscle (i.e., the neuromuscular junction), neurotransmitters are released into synapse. A similar membrane depolarization occurs on the muscle cell, ultimately leading to contraction.

Nerves visible to the naked eye are actually bundles of individual axons (hundreds, thousands, or tens of thousands of axons). Nerves have the appearance of branching because the individual axons that travel to muscle fibers don't all go to one muscle.

For example the oculomotor nerve branches:

So what you see as the oculomotor nerve is really a collection of neurons. Some of these carry action potentials to the ciliary muscle and some to the sphincter pupillae. These are the parasympathetic components. There is a completely separate set of neurons (but still contained in the same nerve) that carry signals to the extraocular muscles.

This is really basic material that your professor should have explained to you.

Space Travel and length of time

You're actually describing the twin paradox.
That's a little beyond Special Relativity, since the astronaut accelerates, and deaccelerates. Since Special Relativity treats only inertial frames of reference, accurate treatment would require some extension towards General Relativity.
But you may consider two astronauts, one travelling with constant velocity towards Earth, the other one with the same (by amount) velocity away from the Earth, and then apply the formula for time dilation of Special Relativity to both astronauts, as an approximation, and to avoid the twin paradox.
Then you get the almost ubiquitous factor $sqrt{1-beta^2}$ of Special Relativity, with $b=v/c$ the ratio of the relative velocity to the speed of light. For $beta=0.1$, hence 10% the speed of light, we get a factor of

$sqrt{1-beta^2}=sqrt{1-0.1^2}=sqrt{1-0.01}=sqrt{0.99}approx 0.9949874371$.

Divide 10 years by 0.9949874371, and you get 10 years plus 18.4 days on Earth.

For $beta=1$ this division would fail, implying a break-down of the formulas of Special Relativity. That's why travelling with the speed of light doesn't work for astronauts respecting Special Relativity.