cellular respiration - Why is a lack of oxygen fatal to cells?

Here's an illustrated example in neurons:

ATP, of course, is generated by aerobic respiration. The critical biochemical reaction in the brain that is halted due to lack of ATP (and therefore O2) is the glutmaine synthetase reaction, which is very important for the metabolism and excretion of nitrogenous wastes:

The body uses this reaction to dump excess ammonia (which is a metabolic waste product) on glutamate to make glutamine. The glutamine is then transported via the circulatory system to the kidney, where the terminal amino group is hydrolyzed by glutaminase, and the free ammonium ion is excreted in the urine.

Therefore, as you'd expect, under hypoxic conditions in the brain, excess ammonia builds up which is very toxic to the cells. Neurons are also highly metabolically active, which means they generate more waste products. A buildup of nitrogenous waste products in the cell (and bloodstream) can be potentially fatal due to it's effects on pH (screws up enzymes and a whole slew of biochemical reactions).

In addition, the buildup of ammonia will cause glutamate dehydrogenase to convert ammonia + aKG to glutamate, which depletes the brain of alpha-ketoglutarate (key intermediate in TCA cycle). This basically creates a logjam in the central metabolic cycle which further depletes the cell of energy.

This is just one example of many. Of course, there are many, many other critical metabolic processes that require ATP (i.e. the Na+/K+ ATPase pump that regulates neuronal firing and osmotic pressure), but nitrogen metabolism was the first that came to mind :)

nebula - Why does hydrogen ionization happen in HII regions?

Stars are responsible.

HII regions$^dagger$ can refer to several things, but usually I guess one thinks of the volumes around star-forming regions. The more massive a star is, the faster it burns its fuel, and at a higher temperature, meaning that the peak of their spectra are more toward the high frequencies. The most massive stars of a stellar population — the so-called O and B stars — produce enough photons with wavelengths below the hydrogen ionization threshold of $lambda = 912$ Å that they carve out bubbles in their surrounding HI clouds, giving rise to HII regions.

^{Right: The HII region NGC 604 (from Wikipedia). Left: The spectra of three different stars. Only the B star has a significant portion of its spectrum above the hydrogen ionization threshold. Note the logarithmic scale on the intensity (from here).}

Because of the high densities, the HII quickly recombines to HI. If the recombination goes directly to the ground state, a new ionizing photon is emitted, which again is absorbed by a hydrogen atom, but if it goes to one of the higher states, the emitted radiation is no longer capable of ionizing the gas. In this way the ionizing radiation is converted into photons of specific wavelengths, corresponding the energy differences between the excited level of hydrogen, most notably the Lyman $alpha$ emission line with $lambda = 1216$ Å.

Because hydrogen is the most abundant element in the Universe, and because Lyman $alpha$ is the most common transition, the Lyman $alpha$ line is an excellent probe of the most distant galaxies where other wavelengths are not observable. This is especially so because the most distant galaxies are also the earliest and hence still in the process of forming, meaning a high star formation rate which, in turn, means that the shortlived OB stars are still present.

In addition to this distinct regions of HII, ionized hydrogen also exist in a more diffuse component between the stars of a galaxy, in huge bubbles caused by stellar feedback and supernovae, and in the intergalactic medium.

^{$^dagger$The terms HI and HII refers to neutral and ionized hydrogen, respectively.}

evolution - Is there an "evolutionary species similarity calculator"?

Since the simple value of percentage of nucleic acid identity over whole genomes isn't very useful in taxonomy, you won't find these values published in a database, even if they were computed by someone in the process of other work.

One project that provides ready-for-consumption phylogenetic trees based on similarity metrics, by using orthologous genes between species, is OMA. They compute all orthologous genes between two species, and they are now at 1,235 species:

http://www.biorecipes.com/Orthologues/status.html

You could then read off the "distance" between cat and mouse from the eukaryotes tree. This value would then be more meaningful than the nucleic acid identity percentage.

Apart from the trees, using their OMAbrowser you can get for any species pair the number of common orthology groups, i.e., the number of common genes between those two species.

dust - Why weren't the Hubble light-echo images of V838 Monocerotis supplemented by ground telescopes?

Drawing from this answer

The V838 Monocerotis expansion (not a supernova) and the observation of the subsequent "spectacular" light echo was quite a notable event! From Nature 422, 405-408 (27 March 2003)

The Hubble images are quite spectacular (discussed further in that answer). I've included them again below. The color images are 83x83 arcsecconds.

A later conference paper laments the fact that no HST images could be obtained the following year (2003):

"We received HST observing time at five epochs in 2002 through DD allocations: April, May, September, October, and December. All of the observations were made with the Advanced Camera for Surveys (ACS), which had been installed in HST during SM3b in March 2002. I need not emphasize to this audience how extraordinarily unfortunate it is that no HST observations were obtained during 2003—the loss of this opportunity is truly incalculable. However, the echoes were imaged twice in 2004 through the Hubble Heritage program, in February and October. More happily, the HST Cycle 14 allocation committee did award our team observing time for an intensive HST imaging campaign from October 2005 to January 2006, and we also have two more epochs of observations scheduled in Cycle 15 for late 2006 and early 2007".

My question is: Why could't observations from one or more of the ground telescopes that are using Adaptive Optics been used to at least supplement the data in 2003? I understand they may not provide the same quality, but not even close? Not even for the polarization mapping? Is it related to the extended area of the target? Is a field of 80 arcsec too large to correct all at once? Is the pattern too complex, or is it the lack of an isolated bright "guide star" the problem?

note: I need a reasoned and hopefully quantitative answer, not your "best guess" or speculation. Thanks!

Figure 2 of the Nature paper describes the preservation of the actual light curve (history) within the structure of the light-echo shell:

"FIGURE 2. HST images of the light echoes
The apparently superluminal expansion of the echoes as light from the outburst propagates outward into surrounding dust is shown dramatically. Images were taken in 2002 on 30 April (a), 20 May (b), 2 September (c) and 28 October (d). Each frame is 83" times 83"; north is up and east to the left. Imaging on 30 April was obtained only in the B filter, but B, V and I were used on the other three dates, allowing us to make full-colour renditions. The time evolution of the stellar outburst (Fig. 1) is reflected by structures visible in these colour images. In b, for example, note the series of rings and filamentary structures, especially in the upper right quadrant. Close examination shows that each set of rings has a sharp, blue outer edge, a dip in intensity nearer the star, and then a rebrightening to a redder plateau. Similar replicas of the outburst light curve are seen propagating outwards throughout all of the colour images."

From Astronom. J. 135, 2, 2008 or ArXiv

Figure 2. Images representing the degree of linear polarization, p, for each of the four epochs of data shown in Figure 1. Image scales and orientations are the same as in Figure 1. The image stretch is linear, ranging from black representing zero linear polarization to full white representing ~50% linear polarization. These images illustrate the apparent outward motion of a ring of highly polarized light in the light echo.

Triple stars with retrograde orbits

The usual recipe used in the population synthesis literature is that triple stars comprise ~10% of all stellar systems and the mutual inclination is uniform in the cosine. Most of these systems have a large enough semi-major axis ratio that the inner binary is dynamically decoupled from the outer binary, so retrograde orbits will be just as likely as prograde orbits. So, to an order of magnitude, ~5% of stellar systems should be triples with retrograde orbits.

Things get more complicated if you are interested in more details. More massive stars have higher multiplicities, so the fraction is probably somewhat higher for them. For more compact systems, dynamical effects like the Kozai-Lidov mechanism will become important and can lead to prograde orbits becoming retrograde and vice versa. Moreover, in compact systems, retrograde orbits are slightly more stable than prograde orbits, so they are likely to be a little more overrepresented, though I'm not aware of any observational evidence that there is any great difference between the two.

If you want more details on the observations of multiple stellar systems you should read Raghavan et al. (2010). However, I don't think that they measured mutual inclinations. In general those measurements are very difficult to do. Andrei Tokovinin has done a lot of great observational work on triple stars as well, so you might want to look at Tokovinin (2014) and Tokovinin (2008) among other papers. There's also a good review by Duchene & Kraus (2013).

orbit - Is the North star going to stay in the North sky?

The Sun is of course in motion with respect to other stars in our Galaxy, but it does not move quickly compared with the vast distances involved. For instance it takes about 220 million years for our Sun to orbit the Galaxy once, travelling at around 200 km/s. The stars that are closest to the Sun tend to be orbiting in more-or-less the same direction and at a similar speed (that is why they are in the vicinity of the Sun).

Thinking specifically about Polaris. There are three components of its motion with respect to the Sun - two tangential directions on the plane of the sky and a line of sight velocity.

Using the SIMBAD CDS database we see that Polaris has a line of sight velocity of 16 km/s towards the Sun and tangential motions of 28 km/s in the right ascension direction and 7 km/s in the decreasing declination direction.

This sounds a lot, but a velocity of 1 km/s means it takes about 300,000 years for the star to move 1 light year, and Polaris is about 400 light years from Earth.

So, given its net velocity, the position of Polaris with respect to us will show significant changes (of degrees) on timescales of hundreds of thousands to millions of years.

It is heading southward in the sky, but will take around 25 million years to cross the equator at the rate it is travelling now.

You say that the constellations are "constant". Yes, they are on human timescales, but the motions of the stars both radially and tangentially is routinely measured. If you waited some millions of years, the constellations would look very different.

NB: I am ignoring the precession of the Earth's rotation axis, since this is just a rotation of the coordinate system and not a change of position of the stars with respect to the Earth.

telescope - Communicating with distant planet with life possibility

So, telescopes are like time machines. If we get an image and data for analysis from a planet say 1000 light years away, we are essentially looking 1000 years back in time. Now, if we notice presence of liquid water on it and somehow notice there is life on it, how do we know it still exists. There are so many possibilities.

It existed 1000 years back, then asteroid came and destroyed it. Or, the evolution on that planet was 10K times faster than what we have and life on that planet already existed to a better planet somewhere else.

Even if we send signals, we will have to wait for 2000 years to communicate assuming they send response instantaneously.

So, have the smarter beings on our planet already figured out a solution to this? I am sure they have thought of this problem already.

gravity - Why doesn't the sun pull the moon away from earth?

Why doesn't the sun pull the moon away from earth?

Short answer: Because the Moon is much closer to the Earth than it is to the Sun.

Longer answer:

The gravitational force exerted by the Sun on the Moon is more twice that exerted by the Earth on the Moon. So why do we say the Moon orbits the Earth? This has two answers. One is that "orbit" is not a mutually exclusive term. Just because Moon orbits the Earth (and it does) does not mean that it doesn't also orbit the Sun (or the Milky Way, for that matter). It does.

The other answer is that gravitational force as-is is not a good metric. The gravitational force from the Sun and Earth are equal at a distance of about 260000 km from the Earth. The short-term and long-term behaviors of an object orbiting the Earth at 270000 km are essentially the same as those of an object orbiting the Earth at 250000 km. That 260000 km where the gravitational forces from the Sun and Earth are equal in magnitude is effectively meaningless.

A better metric is the distance at which an orbit remain stable for a long, long, long time. In the two body problem, orbits at any distance are stable so long as the total mechanical energy is negative. This is no longer the case in the multi-body problem. The Hill sphere is a somewhat reasonable metric in the three body problem.

The Hill sphere is an approximation of a much more complex shape, and this complex shape doesn't capture long-term dynamics. An object that is orbiting circularly at (for example) 2/3 of the Hill sphere radius won't remain in a circular orbit for long. Its orbit will instead become rather convoluted, sometimes dipping as close to 1/3 of the Hill sphere radius from the planet, other times moving slightly outside the Hill sphere. The object escapes the gravitational clutches of the planet if one of those excursions beyond the Hill sphere occurs near the L1 or L2 Lagrange point.

In the N-body problem (for example, the Sun plus the Earth plus Venus, Jupiter, and all of the other planets), the Hill sphere remains a reasonably good metric, but it needs to be scaled down a bit. For an object in a prograde orbit such as the Moon, the object's orbit remains stable for a very long period of time so long as the orbital radius is less than 1/2 (and maybe 1/3) of the Hill sphere radius.

The Moon's orbit about the Earth is currently about 1/4 of the Earth's Hill sphere radius. That's well within even the most conservative bound. The Moon has been orbiting the Earth for 4.5 billion years, and will continue to do so for a few more billions of years into the future.

How would a plant sprout and grow in a zero gravity environment?

I find over 100 articles returned by a PubMed query for "Arabidopsis microgravity." Arabidopsis was taken aboard at least one if not more Space Shuttle missions to answer this and other similar questions. A couple recent papers from this search are:

Spaceflight transcriptomes: unique responses to a novel environment.
Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ.
Astrobiology. 2012 Jan;12(1):40-56.
PMID: 22221117

An endogenous growth pattern of roots is revealed in seedlings grown in microgravity.
Millar KD, Johnson CM, Edelmann RE, Kiss JZ.
Astrobiology. 2011 Oct;11(8):787-97. doi: 10.1089/ast.2011.0699.
PMID: 21970704

Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana.
Paul AL, Manak MS, Mayfield JD, Reyes MF, Gurley WB, Ferl RJ.
Astrobiology. 2011 Oct;11(8):743-58. doi: 10.1089/ast.2011.0659.
PMID: 21970703

Gene expression changes in Arabidopsis seedlings during short- to long-term exposure to 3-D clinorotation.
Soh H, Auh C, Soh WY, Han K, Kim D, Lee S, Rhee Y.
Planta. 2011 Aug;234(2):255-70.
PMID: 21416242

A novel phototropic response to red light is revealed in microgravity.
Millar KD, Kumar P, Correll MJ, Mullen JL, Hangarter RP, Edelmann RE, Kiss JZ.
New Phytol. 2010 May;186(3):648-56.
PMID: 20298479

solar system - As viewed from Mars, what are Jupiter's and Saturn's maximum brightness in apparent magnitude?

The inverse-fourth-power law you're referring to is valid for light emitted from a source, reflected non-specularly — i.e. in all directions — from a reflector, and detected by the original emitter. If the reflector is a mirror, the observed flux just follows the normal inverse-square law with the nominator equal to $(2d)^2$ instead of $d^2$, since the light has to go back and forth. But if the reflector scatters light in all directions — i.e. into a $2pi$ hemisphere — then the detected flux is $sim r^2/d^4$, where $r$ is the radius of the reflector (see this answer for a more throrough explanation).

An example of this is a radar. But in our case, it isn't us that emit the light, it's the Sun. The amount of light reflected from Jupiter and Saturn depends on their distance to the Sun, and that distance doesn't change if you move to Mars. The relevant distances (that I got from NASA's Planetary Fact Sheet) are:

• Earth semi-major axis $d_mathrm{E} = 1.00,mathrm{AU}$


• Mars aphelion$^dagger$ $d_mathrm{M} = 1.64,mathrm{AU}$


• Jupiter semi-major axis $d_mathrm{J} = 5.20,mathrm{AU}$


• Saturn semi-major axis $d_mathrm{S} = 9.58,mathrm{AU}$

Now the differences between them:

• Earth to Mars $d_mathrm{M-E} = 0.64,mathrm{AU}$


• Earth to Jupiter $d_mathrm{J-E} = 4.20 ,mathrm{AU}$


• Earth to Saturn $d_mathrm{S-E} = 8.58,mathrm{AU}$


• Mars to Jupiter $d_mathrm{J-M} = 3.56 ,mathrm{AU}$


• Mars to Saturn $d_mathrm{S-M} = 7.94 ,mathrm{AU}$

Hence, from Mars the distance to Jupiter is $d_mathrm{M-J} = 0.85 d_mathrm{J-E}$, and the received flux is thus $1/0.85^2 = 1.4$ times that on Earth. The change in apparent magnitude is then
$$
Delta m = -2.5 logleft( frac{0.85^2}{1}right) = -0.36,
$$
i.e. Jupiter would be $m = -2.94 - 0.36 = -3.30$ as viewed from Mars (assuming the values you provide are correct; I didn't check this).

Following the same approach for Saturn, I get $m = -0.41$.

$^dagger$_{The reason I used Mars' aphelion instead of Mars' semi-major axis is because Mars has a rather eccentric orbit ($esim0.09$). Jupiter and Saturn are somewhat closer to circular orbits, though ($esim0.05$). This of course is still an approximation. If you wish to take into account the eccentricities of all orbits, you also need to know the angle between their semi-major axes. This also doesn't take into account the inclination of the orbit; however, these are only 1º-2º.
And of course this minimum distance will not occur every Martian year.}

astrophysics - Why dust is optically thin in Far Infrared wavelengths?

The term "optically thin" means that the optical depth is small. The optical depth is a measure of the opacity of a medium, in this case dust, experienced by light traveling through that medium, and is defined as
$$
tau equiv n , r , sigma,
$$
where $n$ is the density of the particles in question, $r$ is the distance traveled through the medium, and $sigma = sigma(lambda)$ is the cross section of the particles, which is dependent on the wavelength $lambda$ of the photons. If $taull1$, the medium is said to be optically thin, while if $taugg1$, it is said to be optically thick. The fraction of the light that is extinguished by the journey through the medium is $e^{-tau}$, so the two cases indicate when the light is mostly transferred and mostly extinguished, respectively.

Cosmic dust is composed of particles spanning a large range of sizes. Photons interacting with the dust are either scattered in another direction, or absorbed, depending on the albedo of the dust. But in both cases, a photon has a larger probability of interacting with a dust grain which is comparable to its wavelength. Because of the size distribution, an ensemble of dust grains hence has a characteristic extinction curve. In the figure below (modified from Laursen et al. 2009), I plotted the (functional fits to the observed) extinction curves of dust in the Small (dashed line) and Large (solid line) Magellanic Clouds$^dagger$:

The extinction is here given in terms of "cross section per hydrogen atom", but you can just think of it as an average dust grain cross section. The colors show the ultraviolet (purple) and infrared (red) regions of the spectrum.
You can see that the extinction, or the cross section, is largest for UV photons, and as you go to longer wavelengths, the cross section decreases sharply and is very small in the far infrared ($lambda gtrsim 30 , mumathrm{m}$; the exact definitions depend on your field of interest).

This is what your statement refers to. But in fact it's badly phrased, because the optical depth is also a function of density and distance, so for instance for a distance $r = 1 , mathrm{cm}$ through a dust cloud, the optical depth is $ll1$ for all photons.

---

$^dagger$_{Extinction curves in other galaxies look similar. In particular, the extinction along most sightlines in the Milky Way features the same bump around $lambda simeq 2175$ Å. The origin of this bump still isn't well understood, but may be partly due to graphites and/or PAHs.}

gravity - Why does Earth have more gravitational force than the Moon if I stand on it?

The Earth doesn't cover the hole, the Earth is the hole. Gravity is an attractive force, so were you not standing on the Earth, the Earth's gravity would cause you to accelerate towards it. As you are standing on the Earth, you feel this acceleration as your weight, just as you would feel pressure if you were to push against a wall.

To take a more complex view, we would say that you are being attracted to the local center of gravity, which is located within the Earth. Take your bridges example, it doesn't matter that something obstructs you from reaching the center of gravity. You will feel the attraction of gravity regardless. If you jump while standing on a bridge, you would land just the same as if you jumped while standing on the ground (though please try not to miss the bridge). The graphic is meant to illustrate the strength of the force based on the mass of the attractive object and distance.

If we were to put you on a more massive object, which would have a steeper curvature, you would experience this as increased weight, which is why our lunar explorers bounced around on the moon instead of walking.

terminology - Direction Names Within a Galaxy

Are there commonly used names for objective directions within a spiral galaxy?

Central and peripheral describe objective directions, because the observer's frame of reference doesn't affect whether something is closer or farther from the middle. "Clockwise" or "counterclockwise" don't work, because they depend on which side you're viewing from.

Are there names that can describe one object's location relative to another object, either in the galaxy's direction of spin or against it? Or words to describe whether something is farther or closer out along a particular arm of a spiral galaxy?

evolution - Are there any structures in mammals that are used only by males?

Females of Rangifer tarandus have horns which only used by males in competitions. Other species of deer only have males with horns.

Apart from this, possibly, clitoris and vulvar lips have no purpose in women: the vulvar lips are underdeveloped halves of scrotum, and clitoris has no need to be so sensitive as it is because it plays no role in sexual reproduction in females.

star - In 31.5kyr, Epsilon Eridani and Luyten 726-8 will be

Greetings! Based on Wikipedia and more precisely this paper, it is said that, in about 31,500 years, the stars Epsilon Eridani and Luyten 726-8AB will "meet" at a very close distance (less than 1 light year); I found that anecdote very interesting in the context of some SF writings I'm trying to do (not in English, quite obviously!) to bring some "subtle consistency" in it, but I was unable to either answer nor calculate with my very little knowledge of astronomy this simple question: to what distance will those stars be from the Solar System in 31,500 years?

Thank you very much for your help!

P.S.: oh, a friend of mine told me that my question could lack of useful information, such as the current distance of each of those stars from the Solar System, so here there are:

• Current distance from Epsilon Eridani to Solar System: 10.5ly



• Current distance from Luyten 726-8 to Solar System: 8.7ly




• Other info about Epsilon Eridani: declination 9.46° south of the celestial equator (no idea if this can help) | Right Ascension 03h 32m 55.84496s | Radial velocity +15.5 ± 0.9 km/s



• Other info about Luyten 726-8: declination –17° 57′ 01.8″ | Right Ascension 01h 39m 01.54s | Radial velocity +29.0 km/s

[EDIT]
As suggested in the comments, I added the Right Ascension and Radial Velocity for those two stars and I'm looking for the "Velocity vectors" (even if I have no idea what this means)

[EDIT 2]
Added links to the Extended Hipparcos Compilation (XHIP) Epsilon Eridani and Luyten 726-8AB pages with all sort of info I don't understand, but there are things such as "Heliocentric Velocity" on 3 axis, maybe it can help. (Got the XHIP thing thanks to the following thread: Position and velocity vectors of nearby stars?)

human biology - How was the guided daily amount (GDA) calculated?

The total calories are not in fact a recommended value - they are an example amount that is derived from some calorie intake that seemed reasonable to someone (I don't know the details). It does not mean that the government is recommending that you eat exactly 2000 calories per day.

The relative content is, however, a recommended value, based on presumably research. So, if you do take 2000 calories a day, then you know how much of it should be fat/carbs/proteins.

I think that there is some controversy about whether the recommended values were influenced by industry lobbying. Moreover, science is definitely not clear on what the optimal food content for a human is, which is why we keep having the different diet fads, oscillating from no-fat to no-carbs.

date time - When will a day on Earth & Mars be the same length?

I read on Wikipedia that:

As on Earth, the period of rotation of Mars (the length of its day) is slowing down. However, this effect is three orders of magnitude smaller than on Earth because the gravitational effect of Phobos is negligible and the effect is mainly due to the Sun.[19] On Earth, the gravitational influence of the Moon has a much greater effect. Eventually, in the far future, the length of a day on Earth will equal and then exceed the length of a day on Mars.

So, how far into the future exactly will it be when the length of a day on Earth and Mars will be equal? Also, for how long will their day lengths be within say, one second of each other?

By "day", I mean the Mean Solar Day.

orbit - Are there any hot jupiters orbiting red dwarfs?

I found one "hot Jupiter" in the Kepler data (Kepler 45b). The star is a M dwarf with an effective temperature of 3820K. The planet has an estimated mass of 160.5 M(Earth) and radius of 10.76 R(Earth). This gives a density of about 0.8 g/cm2 which is consistent. The planet is located at approximately 0.03 AU from the star with an orbital eccentricity of 0.11. Also, it may be interesting that the star has a very high metallicity of Fe/H = 0.28. (This data is from http://kepler.nasa.gov/Mission/discoveries/ ).

It must be said, however, that M dwarfs only made up about 4.3% of the initial Kepler study which found 82 "Jupiter size" planets (as of my tally in April of 2015). Thus, there is an indication that there are less "hot Jupiters" around M dwarfs, but sample size is way too small. There does seem to be a correlation between stars hosting "hot Jupiters" and their metallicity (more common around higher Fe/H stars).

My gut feeling is that "hot Jupiters" in general are uncommon. They are just the easiest thing to find.

bioinformatics - TFBS predictions for yeast and pombe?

This question is quite old, but I think it might be useful to mention this:

You can also look at RSAT (Regulatory Sequence Analysis Tools):

go in the Fungi portail, in "motif discovery" choose "oligo-analysis"; there you can predict putative TFBS from upstream sequences for example. It detects repeated motifs. To be more specific of Saccharomyces cerevisiae or S. pombe, select these species in the "Background model" section.

the sun - How are the element abundances calculated for a meteorite in the Hydrogen log10 scale?

In astronomy, solar abundances are often calculated or tabulated per $10^{12}$ H atoms. I understand that in case of the Sun this can be done because H atoms are in majority or are present for a scale comparision.

How can the same element abundance be calculated for an example meteorite which does not have any volatile gas such as H? In particular, I am referring to the table 1 of http://astro.uni-tuebingen.de/~rauch/TMAP/grevessesauval2001.pdf. It lists Solar abundance and lists meteorites abundance as a comparision. How have they calculated the element abundance for a meteorite in the $log_{10} epsilon_{H} = 12$ scale?

Finally, I have a sample rock which has its's composition given in Weight $%$ of various oxides such as $SiO_{2}, MgO, FeO$ etc. I have to convert these into elemental abundances in $log_{10} epsilon_{H} = 12$ scale. How should I do this?

Thanks in advance!

At what stage of meiosis does "first meiotic arrest of oogenesis" occur?

Meiosis consists of two divisions. Both are somehow similar to "ordinary" type of cell division - mitosis, but there is no DNA replication between them. As mitosis, each of two meiosis divisions might be divided into 5 stages:

1. Profaze (condensation of chromosomes, formation of microtubular spindle apparatus between two centrosomes)


2. Prometaphase (the nuclear membrane desintegrate and chromosomes and microtubules attach to kinetochores of chromosomes)


3. Metaphase (The chromosomes align at the metaphase plate)


4. Anaphase (segregation of chromosomes)


5. Telophase (restoration of nuclear membrane, cytokinesis)

The first division is crucial for reducing number of chromosomes. The prophase is subdivided to following stages:

1. Leptotene (condensation of chromosomes)


2. Zygotene (homologous chromosomes form tetrads )


3. Pachytene (crossing over)


4. Diplotene (chromosomes separate a little, sister chromosomes remain bounded in chiasmata)


5. Diakinesis (futher condensation of chromosomes, the nuclear membrane desintegrates)

In animals the function of meiosis is producing gametes. In case of oogenesis (in human) this process starts during prenatal development. Between 12-th and 25-th week of female fetus development cells called oogonia become primary oocytes and enter meiosis, but become arrested in stage of dictyotene, which is prolonged diplotene of prophase of first division. Then they wait 12 up to 50 years (too long waiting increase risk of chromosomal disjunction disorders such as Down syndrome in children of old mothers), covered by a layer of cells - primordial follicle. At the beginning of each menstruation cycle one or a few of the follicles become growing (the follicle cells divide, but oocyte is still waiting). At the stage of Graafian follicle the follicle is about 75 times bigger and there is a cavity full of liquid between oocyte and surrounding cells. The hormone signal - LH from pituitary gland - brakes the meiosis block, the primary oocyte divide into secondary oocyte and small first polar body (which quickly degenerates). At this time the follicle breaks - its ovulation. The oocyte starts second division, but stops at the metaphase. This second arrest ends when sperm cell penetrates into oocyte. The second, small polar cell is released and haploid nuclei of ovum and spermatozoon fuse together.

more:
http://www.ncbi.nlm.nih.gov/books/NBK10008/

newtonian gravity - Attraction to barycenter

The Newtonian gravitational acceleration of a test object (a small object with negligible mass) toward a point mass is given by

$$vec g =frac {GM}{||vec r||^3} vec r tag{1}$$

where $vec g$ is the acceleration vector, $G$ is the Newtonian gravitational constant, $M$ is the mass of the point mass, and $vec r$ is the displacement vector directed from the test object toward the point mass.

Equation (1) cannot be used to compute the net gravitation acceleration of a test object toward a pair of point masses by pretending that the pair of point masses is equivalent to a single point mass located at the barycenter of the two point masses. Instead, what needs to be done is to apply equation (1) to the point masses individually and then form the vector sum of these individual accelerations. This in general will not point toward the barycenter.

There are two classes of points where the net gravitational acceleration vector to a pair of point masses is directed toward the barycenter of the point masses:

• Points along the line connecting the point masses, less for two regions where the net gravitational acceleration vector points away from the point mass, and


• Points away from this line and whose projection onto this line is exactly midway between the point masses.

For a test object located anywhere else, the net gravitational acceleration vector does not point toward the barycenter.

biochemistry - What is the origin of "melting" in molecular genetics?

The melting temperature (Tm) of a double stranded DNA tract is defined as the temperature at which 50% of the DNA molecules are dissociated into single strands (and 50% form duplexes). Sure, it has a different meaning than in physics... but it is a really common term in molecular biology and I doubt people will stop to use it anytime soon!

There is a vast amount of literature about the calculation of Tm, which is very important also for practical applications, such as designing PCR primers. This page has some explanations and references about the maths behind it.

I am not sure when the term first appeared, but it has clearly be used since the dawn of molecular biology.

DNA denaturation/renaturation dynamics were first studied in the '60s.

See for instance:

STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: BIOLOGICAL STUDIES - J. Marmur and D. Lane - PNAS, 1960

Although Marmur and Lane do not talk about melting temperature, we can find the term already two years later in this 1962 paper:

Effect of Concentration on the Formation of Molecular Hybrids from T4 DNA - Andrzej W. Kozinski and Michael Beer - Biophys J., 1962

Evidently the term was already common there, as they don't care to define it (it's even in the abstract).

Who first used it? I'm not sure, if anyone knows feel free to add a comment or edit the answer.

star - Create a signal to noise map from heatmap

Recently, I obtained my heatmap from a sky survey. But now, I'm trying to get a signal to noise map from my heatmap.

My heatmap looks like :

My colour bar indicates the number of stars per pixel (I assume, but I'm not totally sure).

There are several steps in order to get my "S/N" map, but firstly, I need to get mean value from pixels around pixel i. To do that, I must draw a circle around the pixel i (circle with a radius about 10 arcmin, for exemple).

To know where I am, that's to say on which pixel I'm working. I scripted a red cross which indicates the pixel. I want to determine the mean value around this cross for each pixel in the heatmap.

I searched on this website and I found this post: Get pixel value after a colormap. I think that it will be interesting in my case also.

But I really haven't an idea to script this. After that, I need to calculate lots of things like gaussian RMS etc .. but for that, it will be easier.

This is my script :

    # -*- coding: utf-8 -*-
    #!/usr/bin/env python

    from astropy.io import fits
    from astropy.table import Table
    from astropy.table import Column
    from astropy.convolution import convolve, Gaussian2DKernel
    import numpy as np
    import scipy.ndimage as sp
    import matplotlib.pyplot as plt



            ###################################
            # Importation du fichier de champ #
            ###################################

    filename = '/home/valentin/Desktop/Field169_combined_final_roughcal.fits_traite_traiteXY_traiteXY_final'

    print 'Fichier en cours de traitement' + str(filename) + 'n'

    # Ouverture du fichier à l'aide d'astropy
    field = fits.open(filename)         

    # Lecture des données fits  
    tbdata = field[1].data             


            #######################################
            # Parametres pour la carte de densité #
            #######################################

    # Boite des étoiles bleues :
    condition_1 = np.bitwise_and(tbdata['g0-r0'] > -0.5, tbdata['g0-r0'] < 0.8 )    # Ne garder que les -0.4 < (g-r)0 < 0.8
    condition_final = np.bitwise_and(tbdata['g0'] < 23.5, condition_1)      # Récupere les valeurs de 'g0' < 23.5 dans les valeurs de blue_stars_X

    Blue_stars = tbdata[condition_final]

    RA_Blue_stars = Blue_stars['RA']                        # Récupere les valeurs de 'RA' associées aux étoiles bleues
    DEC_Blue_stars = Blue_stars['DEC']                      # Récupere les valeurs de 'DEC' associées aux étoiles bleues


    # Boite des étoiles tres bleues :
    condition_2 = np.bitwise_and(tbdata['g0-r0'] > -0.5, tbdata['g0-r0'] < 0.2 )
    condition_final2 = np.bitwise_and(tbdata['g0'] < 23.5, condition_2)

    Very_Blue_stars = tbdata[condition_final2]

    RA_Very_Blue_stars = Very_Blue_stars['RA']                      # Récupere les valeurs de 'RA' associées aux étoiles bleues
    DEC_Very_Blue_stars = Very_Blue_stars['DEC']

    # ==> La table finale avec le masque s'appelle Blue_stars & Very_Blue_stars

            ##################################################################
            # Traçage des différents graphiques de la distribution d'étoiles #
            ##################################################################


    fig1 = plt.subplot(2,2,1)
    plt.plot(tbdata['g0-r0'], tbdata['g0'], 'r.', label=u'Etoiles du champ')
    plt.plot(Blue_stars['g0-r0'], Blue_stars['g0'], 'b.', label =u'Etoiles bleues')
    plt.plot(Very_Blue_stars['g0-r0'], Very_Blue_stars['g0'], 'k.', label =u'Etoiles tres bleues')
    plt.title('Diagramme Couleur-Magnitude')
    plt.xlabel('(g0-r0)')
    plt.ylabel('g0')
    plt.xlim(-1.5,2.5)
    plt.ylim(14,28)
    plt.legend(loc='upper left')
    plt.gca().invert_yaxis()

    fig1 = plt.subplot(2,2,2)
    plt.plot(RA_Blue_stars, DEC_Blue_stars, 'b.', label =u'Etoiles bleues', alpha=0.15)
    plt.title('Carte de distribution des etoiles bleues')
    plt.xlabel('RA')
    plt.ylabel('DEC')
    plt.legend(loc='upper left')

    fig1 = plt.subplot(2,2,3)
    plt.plot(RA_Very_Blue_stars, DEC_Very_Blue_stars, 'r.', label =u'Etoiles tres bleues',alpha=0.4)
    plt.title('Carte de distribution des etoiles tres bleues')
    plt.xlabel('RA')
    plt.ylabel('DEC')
    plt.legend(loc='upper left')

    fig1 = plt.subplot(2,2,4)
    plt.plot(RA_Blue_stars, DEC_Blue_stars, 'b.', label =u'Etoiles bleues', alpha=0.15)
    plt.plot(RA_Very_Blue_stars, DEC_Very_Blue_stars, 'r.', label =u'Etoiles tres bleues',alpha=0.4)
    plt.title('Carte de distribution des etoiles bleues et tres bleues')
    plt.xlabel('RA')
    plt.ylabel('DEC')
    plt.legend(loc='upper left')

            ######################################################################
            # Traçage des différents graphiques de la carte de densité d'étoiles #
            ######################################################################


    # Carte de densité des étoiles bleues pour 1 pixel de 1 arcmin^2 (bins = 180)

    X_Blue_stars = Blue_stars['X']
    Y_Blue_stars = Blue_stars['Y']

    heatmap, xedges, yedges = np.histogram2d(X_Blue_stars, Y_Blue_stars, bins=180) # bins de 180 car 3° de champ en RA = 180 arcmin de champ en RA
    extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]

    RotatePlot = sp.rotate(heatmap,90)

    plt.clf()
    #fig = plt.subplot(2,2,1)
    plt.imshow(RotatePlot, extent=extent, interpolation='none')
    plt.colorbar()
    plt.title('Carte de densite des etoiles bleues (non lisse)')
    plt.xlabel("X")
    plt.ylabel("Y")


    # Carte de densité lissée (par convolution avec une gaussienne 2 sigma) des étoiles bleues pour 1 pixel de 1 arcmin^2 (bins = 180)
    # ==> Avec Astropy

    plt.clf()
    fig = plt.figure(1)
    smoothed_heatmap = plt.imshow(convolve(RotatePlot, Gaussian2DKernel(stddev=2)), interpolation='nearest')
    plt.colorbar()
    plt.plot(100,120,'rx', markeredgewidth=3, markersize=10)
    plt.title('Carte de densite des etoiles bleues lisse (astropy)')
    plt.xlabel("X (arcmin)")
    plt.ylabel("Y (arcmin)")
    plt.xlim(0,180)
    plt.ylim(0,180)
    print smoothed_heatmap.cmap(smoothed_heatmap.norm(X_Blue_stars[100],Y_Blue_stars[120]))

    #plt.savefig('/home/valentin/Desktop/Final.png')
    plt.show()

    print "Création du Diagramme"