Wednesday, 31 December 2014

Which Planet/Star is it? - Astronomy

The site in-the-sky.org has a wide variety of functions and options. In Planetarium mode, I chose a random city at about 24N and in the middle, which helps to get the correct UTC + 05:30 India Time Zone, and then just put in the time and date and turned on alt/az grid.



So it is likely to have been Jupiter, as you suspect. Below are two screen shots - 20:00 and 23:00 local time, with Jupiter climbing from 41 to about 73 degrees above the horizon.



8PM Indian Standard Time



11PM Indian Standard Time

apparent magnitude - What is the share of stars in total radiation input of Earth?

Earth gets its radiation input primarily from Sun, then from reflected sunlight from Moon, and stars. Among these, what is the share of stars (or sources outside solar system) to this total radiation input of Earth. Is it negligible compared to solar radiation? (I am referring to top-of-atmosphere situation.)

Sunday, 28 December 2014

botany - Are there any motile plants?

It depends how you define locomotion.



If you take it to mean moving from one place to another, then yes, almost all plants do this at some stage during their life cycle. Primarily seeds and pollen move around, and generally they do so by harnessing either natural forces like wind and rain, or by manipulating animals to do the leg-work, e.g.:



  • by recruiting pollinating insects

  • by having barbs which snag the fur of passing mammals

  • by producing tasty fruit so monkeys eat them, seeds included, and deposit them with a dollop of fertiliser somewhere else

If you take it to mean moving around under ones own propulsion, then yes, some plants do this. The example that springs to mind is the gametophyte generation of ferns:
enter image description here



The prothallus (i.e. the gametophyte) has rhizoids on the underside and uses them to slide around and find some space in which to start the next generation. I have seen this happen when fern spores are germinated on agar - when they reach the tiny prothallus stage, they start sliding around to avoid overlapping with one another. I can't find any references for this, but I'll keep looking.



Another example of self-directed locomotion in plants is the motile sperm of bryophytes. The male sex cells have flagella, which they use to propel themselves through water to the female sex cells (reviewed by Renzaglia & Garbary 2001).



  • Renzaglia, K.S. & Garbary, D.J. (2001) Motile Gametes of Land Plants: Diversity, Development, and Evolution. Critical Reviews in Plant Sciences. [Online] 20 (2), 107–213.

Friday, 26 December 2014

nebula - Do heavier elements breakdown during supernova?

The answer is that in a pre-supernova star, most of its mass is still in the form of hydrogen and helium. It is only the central core where the primordial H and He has fused to heavier elements.



This picture of onion layers is typically what you see in elementary text books. It is completely misleading in a quantitative sense. It schematically represents what's at the centre of the pre-supernova star, but in terms of the mass that is in each shell (it is obviously a 3d object) you get completely the wrong idea, because this diagram is only about 1 Earth diameter across, compared with the actual stellar radius of something like the distance between the Earth and the Sun!



Onion layers in a pre-supernova star



Here is a more sophisticated plot taken from a paper by Fuller et al. (2015). It shows time until the supernova along the x-axis and the y-axis represents a radial assay of the chemical composition from the centre of the star to the outside. The initial total stellar mass is $12M_{odot}$. As you move leftwards towards the supernova explosion, notice how what is at the core changes - from being H dominated, to He dominated, to C/O dominated then Si and finally Fe (actually iron-peak elements). Note how much mass is contained within these core region for each stage of nuclear burning. The edge of the "helium core" encloses the central $4M_{odot}$ of the star. The subsequent heavier element cores inside the onion ring structure enclose significantly less mass, until the iron core is around $1.3M_{odot}$ just prior to the explosion. Blue shading indicates regions that are thoroughly mixed and homogenised by convection.



After the explosion, the neutron star that is produced will also have a mass of around $1.3-1.4M_{odot}$. In other words most of the rest of the star (about $10M_{odot}$ just prior to the explosion) gets blown out in the supernova. But of the $8.6M_{odot}$ that makes into the interstellar medium, well over half is still in the form of hydrogen and helium; the minority will be carbon, oxygen, neon, silicon, iron etc., and only a very small fraction of that will have been transformed (by the r-process) into elements heavier than iron and nickel.



Thus although the material injected back into the interstellar medium is enriched with heavier elements, there is still plenty of hydrogen to start a new generation of stars. It is also the case that star formation is an inefficient process, so the material from which the supernova progenitor formed will still mostly be around in the interstellar medium. The picture you should have is of a gradual enrichment with heavy elements, especially as the interstellar medium gets churned up and mixed through a variety of processes (including supernova explosions!).



Pre-supernova chemical evolution



EDIT: Here is an even more awesome picture. The lower plot shows the relative mass fraction of each element as a function of enclosed mass as you work your way out from a 15 solar mass star (it has shed 2 solar masses during its evolution). The really awesome thing is that it is animated, so it shows you the first few moments after the core-collapse and how things start to change. Note that the outer $5M_{odot}$ of the envelope is about half H and half He by mass prior to the core collapse. Lots of He and then O in the layers below that. The upper plot show how the density temperature and outward velocity are behaving. The image is from the website of Woosley and Heger (2007), a canonical work on the subject.



Hmm. I can't upload the animated gif. Here it is; well worth a look.

Saturday, 20 December 2014

human biology - Why do we sweat after drinking water and running?

Exercise, such as running, increases muscle activity. This increases the energy demand of these tissues, which increases the rate of cellular respiration. Respiration releases heat as a by-product, therefore the body is hotter during and after exercise.



Sweating is a homoeostatic mechanism to keep core body temperature constant. It is a response to lower the body temperature. When the body becomes too hot, sweat is released onto the surface of the skin. The water from the sweat then takes some of the excess heat energy from the body and uses it to evaporate. Because water has a relatively large specific heat capacity a lot of heat can be carried away by this method.

Wednesday, 17 December 2014

What happens when star spins too fast?

The structure (mass versus radius and density profile) is influenced by its rotation rate, but not by as much as you might think.



Even in Newtonian physics you can think of a mass element $m$ at the surface of a star of mass $M$ and radius $R$, rotating with angular velocity $omega$.



A condition for stability would be that the surface gravity is strong enough to provide the centripetal acceleration of the test mass.
$$ frac{GMm}{R^2} > m R omega^2$$
If this is not satisfied then the object might break up (it is more complicated than this because the object will not stay spherical and the radius at the equator will increase etc., but these are small numerical factors).



Thus
$$ omega < left(frac{GM}{R^3}right)^{1/2}$$
or in terms of rotation period $P = 2pi/omega$ and so
$$ P > 2pi left(frac{GM}{R^3}right)^{-1/2},$$
is the condition for stability.



For a typical $1.4M_{odot}$ neutron star with radius 10 km, then $P>0.46$ milli-seconds.



Happily, this is easily satisfied for all observed neutron stars - they can spin extremely fast because of their enormous surface gravities and all are well below the instability limit. I believe the fastest known rotating pulsar has a period of 1.4 milli-seconds.



You also ask how pusars can attain these speeds. There are two classes of explanation for the two classes of pulsars.



Most pulsars are thought (at least initially) to be the product of a core-collapse supernova. The core collapses from something a little smaller than the radius of the Earth, to about 10km radius in a fraction of a second. Conservation of angular momentum demands that the rotation rate increases as the inverse of the radius squared. i.e. The spin rate increases by factors of a million or so.



Pulsars spin down with age because they turn their rotational kinetic energy into magnetic dipole radiation. However, the fastest rotating pulsars - the "milli-second pulsars" are "born again", by accreting material from a binary companion. The accreted material has angular momentum and the accretion of this angular momentum is able to spin the neutron star up to very high rates because it has a relatively (for a stellar-mass object) small moment of inertia.

Saturday, 13 December 2014

supernova - Why can't neutron stars ignite and explode?

In a white dwarf, the dense matter is not in its lowest energy configuration. Energy can still be extracted from the white dwarf material by fusion, provided it can be ignited.



What exothermic nuclear reactions would there be that could take place in a neutron star? The bulk of the material is in the form of neutrons with a small number of protons and electrons. At these densities, that is the most stable equilibrium composition.



If a neutron star gains mass in a gradual way, then the most likely course of events will be that its radius will decrease (that is what happens in objects supported by degenerate matter) until it reaches a General Relativistic instability where its collapse to a black hole is inevitable (when $R$ is somewhere between 1.25 and 2 times the Schwarzschild radius). It is possible that neutrons may transform before that into additional hadronic degrees of freedom or into quark matter, but these are endothermic processes that suck kinetic energy out of the neutron gas and only hasten the collapse.

history - Acknowledging differentiation of species, in historical times

The branch of science you are looking for is taxonomy, that is the science of identifying and naming species, and arranging them into a classification.



Modern taxonomy was born from the studies of the Swedish zoologist Carl Linnæus (1707-1778), who first introduced, in his books Systema Naturae (Systems of Nature) and Species Plantarum (Plants Species) the now common binomial nomenclature where each different species is given a Latin name composed by two parts: one identifying the genus and one identifying the species.



For instance, various species of mice are in the genus Mus: the common house mouse is Mus musculus, but in the West Mediterranean you have another type of mouse, called Mus spretus.



Although this rigorous type of classification is quite recent, taxonomy existed much earlier.



Shennong, Emperor of China somewhere around 4000BC apparently tasted hundred of plants to test their curative properties. He wrote his observations in a book called the Shennong Ben Cao Jing.



On a similar note the Ebers Papyrus, dating ~1550 BC contains description of the properties of many plants.



To more "recent" times, around 300BC Aristotle was the first who actually classified animals (e.g. vertebrates and invertebrates) and his student Theophrastus wrote a classification of plants in his Historia Plantarum (Hystory of the Plants).



Some 400 years later Plinius in the Naturalis Historia (Natural History) enumerated many plants and animals and gave some of the first binomial names to certain species.



As to the point of how did they distinguish species: well, with their eyes and ears, of course!
You can distinguish a mouse from a vole because it is skinnier and has a longer tail.
Even more similar species can be easily distinguished without needing special equipment.
A good birdwatcher can distinguish a chiffchaff from a willow warbler by listening to their songs, looking at how they behave how they fly, the subtly different tones of their feathers etc.
We can do that now, without any special equipment, so they could before the Renaissance!

Thursday, 11 December 2014

dna - Does an annealing temp higher than primer's Tm contribute to primer dimer?

I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.



Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using?



Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).



If you start seeing non-specific products at that Tm, I'd do what we call a "Touchdown" PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it "touches down" to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the "restrictiveness" of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.



Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.

Weighing 2 vertical halves of the human body

Humans, like all vertebrates, belong in subregnum bilateria, a broad class of animals whose characteristic trait is having a bilaterally symmetric body plan at least in some of their life stages.



The common ancestor of all bilaterians was presumably something like a small marine worm. For a primitive animal living in water, an obvious advantage of bilateral symmetry is that it makes directed swimming easier. If the animal were completely asymmetric, it would have to continually exert active control over its heading to be able to swim straight. On the other hand, an even more symmetrical animal (such as one with 90° rotational symmetry) might have trouble controlling its vertical and lateral heading separately, which could be a problem in aquatic habitats where staying at a certain depth is often useful.



(Indeed, in many ways these reasons are the same as why pretty much all aircraft are bilaterally symmetric: in the absence of active steering, we want them to fly straight and level. That requires at least rough left–right symmetry and generally also some degree of top–down symmetry, although some breaking of the latter is usually needed both for landing and to account for the effects of gravity on flight dynamics. We could build completely asymmetric aircraft if we wanted, they just would be harder to fly.)



As for why this ancestral bilateral symmetry has survived so well throughout the course of evolution, that's presumably both because it's so deeply embedded in the genes that control our ontogeny, but also because the basic reasons why such symmetry is useful still remain, even though our size, shape, habitat and locomotion are very different from those of the first "urbilaterian". Even though we mostly move by walking instead of swimming, it's still useful for us to be able to walk straight without having to pay constant attention to it. Furthermore, once we've first learned to walk (or crawl) straight, it's useful that we can also learn to run, swim and jump (and ride a bike or drive a car) straight without having to always re-learn the exact amount of control needed to maintain a given heading with each of these modes of locomotion.




Ps. To answer your actual question, I'd guess, like Rory M, that the two halves of a human body probably won't weigh exactly the same, both due to the asymmetrical distribution of the internal organs and also due to uneven muscle development.



However, the difference is quite small compared to the total mass of the human body, so that the center of mass is presumably still quite close to the body's centerline. As I noted above, any significant deviation from that would cause issues with gait and balance. Although such issues can certainly be adapted to and overcome with active control — after all, even people who've lost a whole leg manage to get around one way or another — they're presumably still significant enough to be selected against over evolutionary timescales, which is why our body shape remains so nearly symmetrical.

human biology - Do eye muscles relax when you close your eyes?

I would guess that the eye muscle relaxes when the eye is closed. After having the eyes closed, just in the moment after opening them, it seems that the focus is in the distance. It takes a fraction of a second before you can read some text on your computer screen for example . This focusing-duration seems to be shorter when looking into the distance after opening the eyes.



Another effect is when you look at an object in short range for quite a moment and then close your eyes. You can feel the relaxation.

Tuesday, 9 December 2014

cosmology - How to find the distance between two quasars

I want to calculate the distance between two quasars of which I know the angular position and the red shift. Let $Q_1=(alpha_1,delta_1, z_1)$ and $Q_2=(alpha 2,delta 2, z_2)$ and suppose $z_2 > z_1$.



I know how to find the angular separation $theta$ between them by means of the angular coordinates. But how to find the comoving distance (at epoch $z=0$) from them ? I know how to find the comoving distance from the Earth of the two quasars, can we find the distance between them using these two distances?



A related question is to find the redshift of $Q_2$ as seen by $Q_1$ at the epoch when $Q_1$ received the light emitted from $Q_2$ .



There is some standard method to solve this problem ?

Monday, 8 December 2014

What conditions would lead to this event around the black hole in the Pictor A galaxy?

This is a clear example of an astrophysical jet, in this case, most likely a relativistic jet. In short, an accretion disk forms around a black hole (supermassive or otherwise). Matter is pulled towards the black hole and further energized, before being accelerated into a jet emanating from the black hole's poles. Two different mechanisms have been proposed for the formation of jets:



  • The Blandford-Znajek process requires that a magnetic field forms (from the accretion disk) that is centered around the black hole. Charged particles then move along the field lines, into jets. I recently wrote an answer about the details (see How does an accreting black hole acquire magnetic fields?). For this process to work, you need an accretion disk. It is generally considered the most likely explanation for black hole jets.

  • The Penrose process takes rotational kinetic energy from the ergosphere outside the event horizon and gives it to particles moving in jets. Note that this does not rely as heavily on the accretion disk as the Blandford-Znajek process does. For this process to work, you need a rotating black hole surrounded by some matter, likely in a disk.

The hotspot is, to me, much more interesting. It reminds me of structures seen around young stars: bipolar outflows (streams of gas that can form shock waves) and Herbig-Haro objects (the results of shock waves from relativistic jets. Obviously, the mechanisms are different, so no clear analogy can be drawn. But what is interesting about bipolar outflows and Herbig-Haro objects is that the shock waves produced therein result from collisions with the interstellar medium.



If a similar mechanism were to cause the shock waves by the hotspot, then we could conclude that the jets have hit the intergalactic medium. But I don't think this is necessarily the case, in part because of just how long these jets are prior to the formation of the hotspot. One would think that if the hotspot and shock waves are because of collisions with the intergalactic medium, the jets would be much shorter, because they would likely have reached higher density regions of it sooner. So that's why I find it interesting, and why I can't give you a good reason as to why the hotspot formed where it did, or the precise reason for it being there at all.

Sunday, 7 December 2014

dna - Are human chromosomes connected or separate molecules?

Do the 46 human chromosomes form a single unbroken DNA helix? Or is it rather that a human's genome consists of 46 disconnected helices?



If it is the former, does the common numbering scheme for the chromosomes have any correlation to their actual ordering in the one large strand?



If is the latter, is there a convention on how the chromosomes are ordered in genomic datasets? Also, is there a clear understanding of how sister chromosomes "find" each other in Meiosis I?



Generally, during periods when Mitosis/Meiosis are not occurring, what's a good physical picture for how the chromosomes are physically arranged (e.g. a bowl of 46 spaghetti noodles, or maybe the sister chromosomes always stay close together, etc)



thanks!

solar system - What measures are currently in place to detect asteroids on possible collision courses with earth?

NASA doesn't have its own asteroid tracking program. They are rather coordinating activities and provide funding for asteroid research and discovery programs.



The most successful dedicated asteroid discovery programs at the moment are Pan-STARRS (http://pan-starrs.ifa.hawaii.edu/public/) and the Catalina Sky Survey (http://www.lpl.arizona.edu/css/); see http://neo.jpl.nasa.gov/stats/ for some discovery statistics. Both these programs, as well as many others, run telescope that survey the night sky for yet unknown asteroids. On average, both programs together find 4 new near-Earth asteroids (and many others) per night.

Saturday, 6 December 2014

expansion - Looking for an equation that describes how star (x,y,z) positions are affected by expanding universe

The position of stars change very slowly for a couple of reasons, but not due to an expanding universe.



Galaxies distant from our own, are all moving away from our galaxy at a rate proportional to their distance. The equation is simple:
$$mathrm{speed}=H_0 times mathrm{distance}$$



and $H_0$ is a constant of proportionality, with a value of about 70 km/s per kiloparsec. Since the galaxies are moving away, they don't change their position in the sky at all.



(The nearest galaxies are exceptions to this rule, they may be moving towards us)



Stars in our galaxy are also moving. They have their own proper motion, but the motions of the stars relative to our own are essentially random. You can look up the proper motion of stars on the SIMBAD database.



Stars also appear to wobble due to the annual rotation of the Earth about the Sun and our consequentially changing perspective. The amount of wobble is in inverse proportion to their distance (the nearest stars appear to wobble most)

Wednesday, 3 December 2014

Why does gravity increase in star formation?

Some good answers, I'm going to give kind of summary, cause you touched on a few points.




Why does gravity increase in star formation




Gravitation is a product of a few forces. Mass, density and, not to be ignored, rotation speed.



It's not actually the fusion process that keeps the sun from contracting, at least, not directly. It's heat that keeps the star expanded. That's the balancing act. High temperature wants to expand, gravity wants to contract.



The fusion process is actually pretty slow, which is why stars like our sun have a main sequence of about 10 billion years, and a lot of the heat that a star starts out with is from the heat of formation. Potential energy gets converted to heat due to the coalescing and condensing of all that matter so stars start out hot, even before fusion begins.



In fact, a star in formation can be many times brighter than the star is during it's main sequence due to the high heat of formation. Here's an article that says the forming sun was 200 times brighter than it is now.



Young proto-stars, as a result of conservation of angular momentum, tend to rotate very fast and that fast rotation can create a bulge and increases ejection of matter. The formation process is pretty chaotic compared to the main sequence stage. Lots of ejected matter, much bigger solar storms, lots of lheat from formation, etc.



Once the main sequence stage is underway and rotation is slowed down, then there's more of a balance between heat and gravity mentioned above. The fusion process continues to add heat to the core of star which the star, convects or conduct heat away from the core into the outer layers and then, radiates from it's surface, but during the main sequence, in general, the core of the star gradually heats up and in most cases, the energy added from fusion isn't nearly strong enough to blow apart the star, unless the star is enormously large like over 150 or 200 solar masses, then the star doesn't really work without blowing off a bunch of matter. See: here.




I get that the fusion of hydrogen atoms releases energy... fine...



How does gravity keep it together if the mass is lessening as a result
of fusion( mass being converted into energy from fusion) while gravity
is weakening( as mass lessens )?




As others have said, mass loss by solar wind is a bigger factor especially for young and smaller stars, but there's a few factors at play. The short answer to this question is that the mass loss, at least by fusion, is quite very compared to the total mass of the star. Another factor, as hydrogen becomes helium, the core of the star becomes denser and greater density tends to be smaller and that increases gravity, but there are competing factors. The inner core grows denser as it becomes more hydrogen rich and the fusion tends to expand outwards on the outside of the helium core, so a star like our sun gets a denser inner core over time, but the layers around the core can grow hotter and larger, even as they lose mass.




Wouldn't the radiation overpower the force of gravity and tear the
star apart?




As mentioned above, this happens if you have 150 or 200 solar masses. lower mass stars, the fusion isn't nearly powerful enough to blow the star apart. Stars and white dwarfs blow apart when they go supernova, but that's different than the main sequence fusion process.



Our sun will blow off some of it's matter when it has it's helium flash, so there are examples of what you're describing happening, but not during the main sequence for stars like our sun when material is expelled primarily by magnetic storms causing coronal mass ejections. Fusion is, generally speaking, more like a slow burn, than a big explosion when it's up against the enormous gravitational binding energy of a star.

Monday, 1 December 2014

Does the mass of the Earth change?

Every day, babies are born and people grow, which makes their respective masses greater. However, this change in mass (should) come out of the food that they consume - it is used as energy and thus converted into this growth. Likewise, building new structures is just a redistribution of mass already on Earth.



Thus, the only way I can see the actual mass of the Earth changing is by meteors that have landed here (increase in mass) and things that leave Earth such as space shuttles and rockets which would be a decrease in mass.



But have I missed anything out? If no meteors crashed into Earth, and we had not yet figured out how to make machines that could fly, would the mass of the Earth remain constant? Or is it somehow loosing or gaining mass? Am I wrong in assuming that the growth of animals doesn't affect the mass?



Thanks, Toastrackenigma.



EDIT: Mass includes atmosphere :)

Saturday, 29 November 2014

cosmology - Looking for help in understanding how black holes can move


  1. I saw Dr. Kip Thorne in a documentary on black holes state that there is no longer any matter in a black hole once it forms. He said something like, the matter was there, but it has been crushed out of existence and basically has been transformed into the energy that produces such a great curvature of spacetime.



Isolated black holes are indeed vacuum solutions to general relativity. Thus in particular, the mass and energy density is identically zero everywhere in spacetime. Because of some technical issues, this does not imply that black holes have no energy or mass; rather, it means that we can't directly think of them as an integral of mass or energy density. See also this question.




  1. I also saw Dr. Andrew Hamilton in another documentary state that within the event horizon of a black hole (again paraphrasing), space is falling toward the singularity so fast that it effectively drags everything with it (including light).



For an isolated black hole in a particular frame field, this is a valid picture. For example, the Schwarzschild spacetime in Gullstrand–Painlevé coordinates can be interpreted as Euclidean space falling into the black hole. However, the spacetime is itself is stationary (even static) in the geometrical sense—there is a timelike field representing a direction in which spacetime geometry is left unchanged (this corresponds to Schwarzschild time, in fact). Similarly, rotating black hole spacetimes are stationary.



But generally speaking, you really can't think of black holes as some sort of suck-holes for space. It's just an analogy that applies to simple situations (isolated black holes, with nothing else in spacetime) and then only in a particular frame or coordinates. That's not to say it's useless--e.g., acoustic horizons in fluids are interesting analogies to event horizon--but don't take it too literally. See also this question.




  1. Based on 1 (no matter remains in the black hole) and 2 (space is being pulled towards the gravitational singularity from all directions), I try to picture the black hole moving, and it seems to me that if, say, the black hole moves in one direction, I can see how its event horizon is also moving, bringing that bit of space into it.



So what's the problem?




But how can the other end of the black hole let space "escape" in order to complete the motion?




For realistic black holes, there is no "other end". If you really want to tie everything together, then interpret Dr. Thorne's comment about stuff falling into the singularity as crushed out of existence as also applying to space. It doesn't come out of any "other end". It stops existing.



But really, that's past the point where the fluid analogy make sense anyway. I think Dr. Hamilton might note that the full maximally-extended Schwarzschild spacetime is a black hole, so one may be able to think as it "coming out" of the corresponding white hole, but he would also tell you that this white hole is a mathematical artifact that doesn't have anything to do with actual astrophysical black holes.




But I want to understand why it is that space itself can cross the event horizon when other things can't.




Of course they can. In the infalling-fluid analogy, they're carried along by the space that's being sucked in. Perhaps you're thinking of the fact that it takes an infinite Schwarzschild time for an object to reach the event horizon. But that doesn't imply that things can't cross the horizon; rather, it's just a symptom of Schwarzschild coordinate chart not covering the horizon.



Intuitively, think of a coordinate chart as a "grid" drawn on a patch of spacetime. That patch may be the entire spacetime, or it might be just a piece of it. In the case of the usual Schwarzschild coordinates, it's just a piece... one that simply doesn't cover the horizon.





Regarding the last part, I meant space crossing the event horizon the other way - out of the sphere demarcating the event horizon - whereas material objects go one way - in but not out, spacetime itself does not seem so restricted, at least not in the sense of "pinning" a black hole to one part of itself.




OK, your edited question provides some more context. But the answer is completely the same: what Dr. Hamilton is talking about in the video is the maximal analytic extensions of the rotating black hole solution, which does contain a passage into a completely different region (sometimes called different 'universe'). This is very much analogous to the maximally extended Schwarzschild spacetime, which contains a wormhole that comes back out of a white hole in another spacetime region, except that the extension of the rotating Kerr black hole spacetime contains an infinite chain of such connected regions.



I haven't watched the entire video, but it's clear that's what they're talking about when they say "in a ship propelled by pure mathematics", because the causal structure of such spacetimes is well-known. Once again, I direct your attention to Dr. Hamilton's own page, linked above, that explains that this dual waterfall picture is an artifact of mathematical idealization and not something that actually happens in reality.



However, even if you take the maximal analytic extension of such black hole spacetimes overly seriously, it's important to emphasize that you don't come back out into the same region, but rather a different one connected by a wormhole inside the horizon. If you're up to it, I also recommend Dr. Hamilton's conformal diagrams of said black hole spacetimes, which make it quite clear that's what going on is a whole "chain" of black holes and white holes.

Friday, 28 November 2014

age - Dating very old objects/events


I have wondered how they managed to make these assumptions about various events like when the first black holes form.




When the first black holes formed ( and many other things ) are things we predict from theoretical models of the development of the universe. They are no proven facts, but better classed as speculative predictions based on theories. Different theories give different predictions.



The way it works ( broadly ) is this : We try and develop theoretical models of the universe's creation and early development that will develop into a universe that matches what ours looks like. Doing this has led to such controversial concepts as string theory, which are not proven facts in a scientific sense, but theories subject to ongoing investigation.



We try and verify ( or disprove ) theories by comparing what they predicts with what we see.



So these "histories" should be considered as "best guesses" to some extent.



The approximate date of the Sun's formation, for example, is based on our current best models for the evolution of stellar bodies like the sun, which of course are based on our current best measurements of whatever we can measure in relation to it.



For history related to objects we can examine in more detail, like stuff on Earth, some of which came from space, we can perform detailed analysis and look for patterns in related objects and areas. This makes estimates dating from the start of life on Earth on reasonably good.



So the far distant history beyond that is concerned we're relying primarily on models driven by astronomical observations and the law of physics we regard as "safe".

Thursday, 27 November 2014

telescope - What makes small interferometers useful? Like NIRISS on JWST

NIRISS is an instrument on the James Webb Space Telescope. It has a "non-redundant aperture mask" which obviously covers most of the area of the sensor. It seems to be advantageous for high contrast imaging (like finding an exoplanet next to a star) and an alternative to coronagraphs. But however does that work? Why is it good to cover most of a sensor?



I have associated interferometers with creating as large as possible baselines for higher resolution, like the Very Large Baseline Array and the Spectr-R radio space telescope which gives up to a 390,000 km long baseline. So what is the magic with sacrificing sensor area to turn a single small telescope into an interferometer? Aren't all photons welcome? Would such an instrument do as well with a correspondingly smaller main mirror (maybe in separate fragments)?



enter image description here

Wednesday, 26 November 2014

galaxy - Is there a strong galactic magnetic field?

My main question is: Is there a strong galactic magnetic field, perhaps driven by the supermassive black hole at the center of our galaxy? I am also wondering if this field would be strong enough to make it so that the galaxy rotates in the way it does (with the outer stars moving faster than would be expected), and if this would be an alternate explanation for dark matter.



The thing that led me to ask this question is reading about Jupiter's magnetic field interactions with the plasma emitted by IO. Jupiter's magnetic field forces the plasma to orbit Jupiter about as fast as Jupiter spins, and I am wondering if likewise, the supermassive black hole at the center of our galaxy "herds" the rest of the galaxy in a similar manner as per the article and image below.



http://en.wikipedia.org/wiki/Magnetosphere_of_Jupiter#Role_of_Io



IO's plasma and Jupiter's magnetic field

Tuesday, 25 November 2014

How Much Overlap Will the Andromeda Galaxy and the Milky Way Have When They Collide?

Measurements of Andromeda's blue shift let us conclude that the distance between the Andromeda galaxy and the Milky Way is decreasing and in a few billion years they will "collide".



The blue shift only yields the radial component of Andromeda's velocity vector. It is my understanding that measuring the tangential component is crucial in determining whether a "collision" will actually happen (in a gravitationally bound two body system, for point-like bodies to collide, the relative velocity component must point exactly towards the other body, i.e. the tangential component must vanish).



Now, galaxies are not point-like, so some small nonzero tangential component might lead to a collision where at least some galaxy arms intersect.



Has the tangential velocity been measured? If so, how? How central is the collision (bulge into bulge, bulge into arms, arms into arms)?

molecular genetics - How does the stem-loop cause intrinsic transcription termination?

In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the transcription process.



My question is, why does it halt the transcription process, considering that the RNA polymerase moves in the opposite direction of where the stem loop is created? Does it somehow change the RNA conformation such that no further bases can be added? Interpreting it as a physical obstacle doesn't seem to make any sense here.

Monday, 24 November 2014

redshift - How do we know that light is redshifted/blueshifted and not the original light of a star/galaxy?

If you had a simple slit spectroscope, and looked at an incandescent light, you'd see a smear of light with red on one end and blue on the other. This is because the filament is producing light by glowing from being heated.

If you looked at one of those orange colored sodium vapor street lamps, instead of a smear of color, you'd see a group of lines. This light is produced by ionizing the gas.

The lines represent specific frequencies of light coming from the lamp. You could add a horizontal scale and find that the lines represent a specific frequency in the light spectrum.

If the street lamp was coming at you at a significantly high speed, the individual lines would be shifted in frequency towards blue, but would still have the same pattern. Conversely, if the light was moving away from you, you'd again see the same pattern of light lines, but their frequencies would be shifted toward red.

This is what's being measured when the spectra of stars and galaxies are measured: not just what the color looks like, but whether the spectra of things like hydrogen, helium and iron are shifted in frequency towards red or blue.

So, it's the specific line patterns produced by these elements when they are ionized in stars that helps us identify them. Comparing the light frequencies of locally ionized elements to the frequencies coming from distant stars that tell us if the stars themselves are approaching or receding.

Sunday, 23 November 2014

black hole - Is antimatter also attracted by gravitational field?

The consensus opinion of physicists is that antimatter has mass, and it is attracted to other massive objects by gravity in exactly the same way as matter: Antimatter isn't anti-gravity.



Proving this is difficult. It is hard to obtain enough antimatter in one place to observe any gravitational interactions. The best observations aren't even able to conclusively show that antimatter "falls" in a gravitational field. However for theoretical reasons it is considered extremely likely. If antimatter were repulsed by matter, it would allow for violations of the conservation of energy.



A black hole is a region of extreme gravity, and a black-hole would attract matter in just the same way as it attracts antimatter. It would even be possible for antimatter to form a black hole. In fact there are only 11 numbers that define a black hole: mass (made of either matter, antimatter, or energy), position, velocity, spin rate and direction, and electrical charge.

orbit - Best planets profile for a tattoo of the solar system

[Not sure if I should answer this, but I will try to answer something while trying hard to not go off-topic.]





Mercury surface is essentially a collection of small random craters with no discernible pattern at all, so you might not consider which side is presented. The only distinguished feature is a set of dark craters in its north pole.



Venus features few discernible aspects in visible light to the human eyes. There are only a few and faint distinguishable cloud bands, so you might also not consider which side is presented.



Earth is the most important, because it have continents and oceans with distinct designs. It also features a lot of clouds.



Mars has polar caps and a system of canyons. It's northern hemisphere is also much less cratered and has a lower altitude than its southern hemisphere, except that the greatest crater is in the southern hemisphere.



Jupiter has a banded structure of clouds covering the entire planet. It features a large red spot with some nearby fainter and smaller whiter spots.



Saturn also has a banded structure, which is faintier to Jupiter's structure but still clearly visible. It also features a curious hexagon on its north pole. But it is barely noticeable.



Uranus have very homogenous atmosphere (as seen in visible colors by human eyes), so it have almost no visible features to be drawn in your tatoo. Their presented side do not matters, because it is essentially a bland featureless ball.



Neptune has also few visible features. There are no more than a few cloud bands with low variation on color or hue. However there is a dark spot.





Saturn has an extensive system of rings, which also contains some defined gaps.



Jupiter, Uranus and Neptune also feature faint sets of rings (1, 2, 3). Uranus has a weird orientation, so its rings are not aligned with the orbital plane, but roughly perpendicular to it.





All the planets rotates at different velocities, so any side of them would do. No planet is showing always the same face to any other planet or to the Sun.



All of the planets, except Uranus, are rotating roughly in the same plane. So, their north is all pointing to a side and their south to another side (lets call those north/south axis Y). Their north-south axis is perpedicular to their planet-Sun axis (which we will call X). Uranus is special because at their summer/winter, its north/south axis points roughly to the Sun (i.e., in the X axis) and in its autumn/spring it is in a direction that is perpendicular to both X and Y (so it's the Z).



Also, don't forget the Sun. It may also feature flares and sunspots sometimes. The Sun rotates in the same way as most of the planets, with its north/south axis along the Y direction.





You might also be tempted to include the planets moons. Those are:



You can get more data (and also some images) about them here and also here.





Also, you might want to include the dwarf planets. The confirmed dwarf planets are Ceres, Pluto, Charon, Eris and Makemake. Ceres is located in the main asteroid belt. Although technically being a dwarf planet, for practical purposes Charon is Pluto's main satellite and they always shows the same face one to the other. Makemake and Eris are beyond Pluto.



To complete the Solar Sytem, you could also add other transneptunian objects (likely to also be dwarf planets) like Quaoar, Sedna, Haumea, Orcus, Salacia, 2002 MS4, 2007 OR10, 2012 VP113, 2010 GB174, 2004 XR190, 2000 CR105 and 2004 VN112. Those 12 transneptunian suspected dwarf planets, along with Eris and Makemake, are no more than singular dots of light on the telescopes, their appearance is unknown and even their size is known only crudely, with very large error margins in their size estimatives (see more about that below).



If you want also specific asteroids, you might see this page.





  • The Sun's diameter is roughly 10 times Jupiter's diameter.

  • Jupiter's diameter is almost 11 times Earth's diameter.

  • Saturn has almost the size of Jupiter, having 9.5 Earth's diameters. Also, it is visibly oblate (oval).

  • Uranus and Neptune are about the same size, with 4 times the Earth's diameter.

  • Venus is almost the same size of Earth's (95% of Earth's diameter).

  • Mars is a bit larger than a half of Earth's diameter (53%).

  • Mercury's diameter is 38% of Earth's diameter.

  • Moon has 27% of Earth's diameter.

  • Pluto and Eris were determined to be essentially of the same size, which is 18.6% of Earth's diameter.

  • Ceres has 14.8% of Earth's diameter.

  • Charon has 9.5% Earth's diameter.

  • All the others known transneptunian objects, although surely smaller than Pluto, have uncertain sizes.

  • All the dwarf planets and asteroids are significantly smaller than the Moon. Check the links for more details.

  • Some satellites of Jupiter, Saturn, Uranus and Neptune are pretty large. Titan and Ganymede are even larger than Mercury.

For more details about sizes, check this page.



About the transeptunian objects, only Pluto and Charon have a known appearance (due to being photographed by New Horizons). This way, all that you would need to draw in your tatoo beyond Pluto and Charon is a group of little spheres smaller than Pluto (I named 14 of them above), with only the one representing Eris with the same size as Pluto.





You will find images and further detailed information in the previous links, all of them points to wikipedia. I hope that you can get a perfect tatoo with that information!

Saturday, 22 November 2014

cosmology - Why is dark energy preferred to the cosmological constant?

A cosmological constant should be considered a special case of dark energy. The effective stress-energy tensor for a cosmological constant is proportional to the metric $g_{munu}$, so in a local inertial frame will be proportional $mathrm{diag}(-1,+1,+1,+1)$. This is equivalent to perfect fluid with energy density and pressure directly opposite one another, but more importantly, it is the only possible form for the stress-energy that would give the exact same energy density and pressure in all local inertial frames.



If by 'dark energy', we understand it to mean all the contributions to stress-energy in the above form, then there is no reason for this to be constant, and plenty of reasons why it might not be, as this situation is not exceptional in fundamental physics. For example, there could be false vacua with various different energy densities, and they must be invariant across inertial frames.



In particular, the basic idea of inflation considers a flat FRW universe with expansion driven by a scalar field $phi$ at a local extremum of its potential, $V'(phi_0) = 0$, which yields an exponential expansion with constant energy density $T^0{}_0 = V(phi_0)$. More refined models, such as slow-roll inflation, could therefore be directly interpreted as a time-varying dark energy density, while eternal inflation would also include spatial variability. There's plenty of other inflationary models besides.



One the interpretational flip-side, one could always have a $Lambda$ that corresponds to the energy density of the true vacuum, and the rest as separate contributions on top of that. It's just not as useful in a cosmological context compared to grouping all 'dark energies' together, as all stress-energy gravitates equally.

Thursday, 20 November 2014

Does Mars contain more iron than the Earth?

Unless 100+ years of studying solar system formation didn't get us anywhere then you'd actually predict that mars would have less iron than earth (in relative terms). This is because the further out in the solar system you go, the lighter the materials that make up the celestial bodies become. You start off with the inner planets for example, which are made of rock and metal. At its most extreme is mercury, which has a metallic core that makes up the vast majority of its volume. As you start to move to the outer parts, there's much less metal. Even further out rocky material starts to peter until you're just left with frozen ices and covalent compounds. This pattern exists because when the solar system formed the heavier materials condensed near the centre while the lighter gases were blown away to the edges. Mars, being the last terrestrial planet, should have formed in an orbit that had less iron and heavy materials than earth and all the other rocky bodies.



However, its good to bet that on average there is more relative iron on mars surface than there is on earth. This would be because despite it's lower abundance of iron overall, it's much more spread out among the lithosphere rather than being entirely concentrated deep in its core like on earth. Mars being smaller planet might not have ever built up enough heat during its formation to completely liquefy its surface, which a planet needs in order for the heavier materials to sink to the centre, making differentiated layers such as the ones we see on earth like the crust, core and mantle etc. Don't get me wrong, mars does have these differentiated layers, but they probably aren't as pronounced as they are here on earth. This is what I think we can safely say is thus the reason for mar's red surface, despite it's location in the solar system.

Saturday, 15 November 2014

solar system - Angular momentum in planetary disk formation

Reading about the formation of planetary disks, one of the major problems, it seems like, is the evacuation of angular momentum. Aparently planets can't form with the amount o angular momentum the system has in its early stages. I think I understand where that excess comes from, the collapse of the nebula onto itself and provoking a spin. Then there are many hypothesis on how it's evacuated, which are mostly pretty logical.



Now my question, as a beginner in the study of physics, is this: Why does the angular momentum even need to be evacuated? If the angular momentum is too big, why can't planets still form? Does this have something to do with too much kinetic energy in the system?
Thank you!

Friday, 14 November 2014

galaxy - Is there a strict chronological order that determines the shape of galaxies?

Galaxies evolve from spiral to elliptical. The spirals are formed by patterns of new star formation in the disk surrounding the bulge, which contains mostly old stars.



As galaxies run out of hydrogen gas clouds, which is the raw material from which stars are formed, then no new stars form, and with no new star formation, the complex structures of the arms are lost. Elliptical galaxies are made of old stars and have little new star formations. They were formed when spiral galaxies merged, causing a burst of star formation, and leaving a bulge of old stars and little gas to make new ones. The ultimate fate of the milky way and the andromeda galaxy is to merge and form a giant elliptical galaxy.

What is the direction of a comet's dust tail before and after perihelion?

Comet tail always aims away from the sun, as it's torn from the comet's gas cloud by solar wind. It trails slightly behind, as the comet moves along its orbit while the gas travels directly away, but that's relatively minor - the speed at which the gas and particles are pulled away forming the tail is much higher than the comet's orbital velocity.



Your visualisation shows it trailing behind the comet as if it was moving in some gaseous/liquid medium that stops the lighter particles while letting the heavy comet head travel ahead. This is not the case - as the comet is far away from the sun, the gas cloud just forms its atmosphere and travels with the comet. As it approaches though, the intensity of solar wind increases and it pulls away the atmosphere which can't be protected against it by magnetic field or strong gravity, as the comet has neither.

Tuesday, 11 November 2014

the sun - Could our Sun be a companion star of a massive black hole?

There is no indication nor any astrophysical reason for such a scenario. The most relevant constraints are



  1. The Solar velocity is typical for stars in our immediate Galactic neighbourhood.

  2. Soft binaries (those with orbital velocity smaller than the local velocity dispersion $sigma$) dissolve (Heggie's law: soft binaries become softer and hard binaries harder).

These are in contradiction with a Solar binary nature: a viable binary has a large orbital velocity that would put the Sun outside of the typical velocity for local stars. This contradiction can only be temporarily avoided if the current (but not in $sim1000$ years) orbital velocity and the velocity of the massive binary companion add up to a typical stellar velocity. This is an unlikely chance.



Binaries with a stellar-mass black hole always form from an ordinary stellar binary, with one of the stars going supernova. Often, such binaries are quite compact. All this is ruled out for the Sun.



Finally, black holes of intermediate masses (100 to $10^5$ M$_odot$) haven't (yet?) been detected unambigously (though there are several objects that have been claimed to be such intermediate-mass black holes also IMBHs).

cosmology - How could we tell if the Universe is infinite?

We don't know for sure, but it certainly fits into our theories. There is, of course, no way to actually test if the Universe is infinite, but right now we think it is likely.



Also, if you read my updated answer on your other post, the Universe has always been infinite in size. I explain over there how it actually works: space is created in between everything, and thus one could say the Universe is expanding.



These objects can actually drift away from each other faster than the speed of light. That is, light from them eventually won't make it to us, since they'll be drifting away too quickly.



Now, this doesn't actually go against Einstein's theory that the speed of light is the fastest thing in the Universe. Einstein said that nothing can travel through space faster than light — but here, space itself is actually being created between the objects. Distances are increasing because space itself is dilating, and thus we can drift apart from other objects faster than light.



Really, there is no limit (as far as I know) to how fast we can drift away. Farther objects will keep drifting faster and faster away, since our gravity has a much weaker effect on them.

Monday, 10 November 2014

bioinformatics - Difference between strand-specific and not strand-specific RNA-seq data

I would like to ask the difference between strand-specific and not strand-specific dataset.



As far as I know, strand-specific data means that we know which strand the transcript is from.



I do not have biological background. Please confirm whether it is correct. If we have a transcript, which is from sense strand, when RNA-seq is producing reads, is that first the cDNA is synthesised. Then this cDNA is used for PCR to amplify the sample? Then the reads generated could be from both strands of the original DNA?



For strand-specific protocols, what is different?



========================================================



Follow up.



Please correct me if I am wrong. There are multiple protocols to produce strand-specific RNA-seq libraries. The basic process is like:



  1. Get the RNA;

  2. Get its cDNA;

  3. Somehow mark the cDNA as sense or antisense when amplifying (PCR?) (here comes the differences between different protocols);

  4. Then REMOVE all antisense (or sense) cDNAs;

  5. Read the reads from clean cDNA library.

The result is that, the reads from this RNA can be used to assemble the sense cDNA. And for not strand-specific libraries, using the reads would be able to assemble both the anti-sense and sense cDNA.



Am i right about this problem? Thanks.

Sunday, 9 November 2014

Star like light moving in the sky, what could it be?

Most likely a satellite. They look exactly like stars, but they glide across the sky smoothly. Airplanes may have multiple light sources, some blinking lights, and you can definitely perceive how low it seems to be: An airplane somewhat seems to come from the horizon and disappear the same way, while a satellite "seems to always be at the same distance from you", like gliding on an imaginary half-sphere or dome of a night sky covering you. Last summer I went for a night bike ride, just riding a bike, sometimes sitting down to have a snack and look around. The trip lasted for 6 hours and during this time, I spotted 12 satellites just by observing. They're a very common thing. This time I got very lucky though, because one of the 12 satellites unexpectedly was something called an Iridium flare and I had never seen one of those in real life before. There's a lot of man-made space junk orbiting the Earth, some satellites still operated, some not. There's a bunch of satellites known as Iridium, which happen to have a design that includes large, reflective solar panels. I live in the North so in the summer, the sun only barely goes below the horizon and the summer nights are short. When I'm just in the dark side but an Iridium satellite happens to fly approximately above me, if everything is in a specific angle, the sun from behind the horizon hits the satellite's solar panels, and like a mirror, reflects those rays to the dark side, into a viewer's eyes. It was my first time seeing that and I must say, it's extremely impressive when you're merely looking at a "moving star", then unexpectedly it grows very bright, brighter than any star in the night sky, and finally reverts back to the normal looking gliding satellite. Because people are very much aware of all of the space junk that's up there, there are plenty of websites and mobile apps that you can use to see where the most common satellites are at the moment, and, because we know the route of each satellite, as well as the year and location specific data regarding the Earth and the Sun, Iridium flares can also be predicted, like you would predict things like Solar eclipses.

supermassive black hole - Mass distribution in the early universe

It is unfortunate that the usual poor journalism labels the growth of the black hole as "inexplicable" and then further down in the article refers to some possible explanations.



The basic problem is a growth timescale one. Radiation pressure introduces a negative feedback, such that there is a "theoretical" maximum for spherical accretion called the Eddington limit, which occurs when the quasar is radiating at its Eddington luminosity. The shortest growth timescale is achieved if the efficiency with which mass is converted to luminosity is low; but if it's too low we wouldn't see the quasar at all. This is the crux of the problem. You can look at this Physics SE answer for some more of the details.



The thing is there are ways and means by which this limit can be exceeded - non spherical accretion for one - so there are lots of ideas about how this can be achieved. Another possibility is that you start off with a seed black hole that is pretty big to begin with, perhaps as a result of a merger. Or the quasar could have been less efficient in the past and is more efficient now, which is why we can see it.



Is there enough matter? Well, yes, galaxies have masses that can be much bigger than the mass of this black hole. They are rare, but of course so are > 1 billion solar-mass black holes, and these tend to be the only ones that we can see at distances of >10 billion light years.



One way of assessing the feasibility would be just to ask what a freefall timescale would be. If you have say $10^{11} M_{odot}$ in a sphere of radius 10 kpc (I am just using typical sorts of numbers for a big galaxy), then the average density is $5times 10^{-22} kg/m^{3}$ and has a freefall time $sim (Grho)^{-1/2}$ of 200 million years. Of course there are other problems, like shedding angular momentum, but it looks like this timescale is short enough for gravity to do its thing (in the absence of radiation pressure).



Of course the short answer to your question is that yes, there must be enough time, because this is just the latest in a population of such objects. We know that quasars with supermassive black holes have formed within a billion years after the big bang.

Saturday, 8 November 2014

python - Plot an AltAz grid over a square grid of RADec points

first post here. As I'm new, StackExchange won't let create or use the wcsaxes tag. wcsaxes looks like the most appropriate tool for the job, but astropy is closely related.



I think the title says it all, but I'll give a little more detail. I have a bunch of sources in (RA, Dec) and want to plot them in the simplest possible projection (i.e. square, but if this is not possible we can make allowances). I want to see the geometry of the Earth over my region of interest, mostly to identify the Earth's magnetic field lines.



The following code gets me close, but I get this error:



AttributeError: 'NoneType' object has no attribute 'to_geodetic'


If I change "altaz" to "galactic", I get a Galactic coordinates grid over the points, which is what I want, but obviously in the wrong coordinate frame.



#!/usr/bin/env python2

import numpy as np
from astropy.wcs import WCS
from astropy.time import Time
import matplotlib.pyplot as plt


# time = Time(2606629, format="jd", location=("116.670810d", "-26.756528d")).iso
w = WCS(naxis=2)
w.wcs.ctype = ["RA---MER", "DEC--MER"]
# w.wcs.dateavg = time

ra_min = 0
ra_max = 15
dec_min = -45
dec_max = -15
N = 1000

sim_ra = np.random.uniform(ra_min, ra_max, size=N)
sim_dec = np.random.uniform(dec_min, dec_max, size=N)

fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.9, 0.9], projection=w)
overlay = ax.get_coords_overlay('altaz')

overlay[0].set_ticks(color='white')
overlay[1].set_ticks(color='white')
overlay[0].set_axislabel('Longitude')
overlay[1].set_axislabel('Latitude')
overlay.grid(color='black', linestyle='solid', alpha=0.5)

plt.scatter(sim_ra, sim_dec)
plt.xlabel('RA')
plt.ylabel('Dec')
plt.show()


I played a little with trying to get the observation time into the WCS header (note that the actual time is artificial, but should work regardless), without success. Any ideas?

Friday, 7 November 2014

human anatomy - Does red light preserve your night vision?

This is a very good question. Red light is routinely used by scientific laboratories to do low light dissections of retinas, and of course it is used in other low light contexts such as printing plate development.



In both of the above contexts, you have a clear subject: the retina being dissected or the printing plate being developed. In the case of the printing plate the film has been designed to be specifically non-reactive to red light, so red light is used because your eyes can see it, but the film doesn't react to it. Similarly in some scientific settings it makes sense to use red light during dissections. Mice lack a long wavelength opsin, and therefore using a dim red light allows the experimenter to have a relative sight advantage compared to the mouse when keeping the mouse dark adapted.



But in the case you're asking about, there is no film or animal to serve as a second party. So is there any intrinsic advantage to using red light? As it turns out, there is. The fovea, which is in the center of our eye and used for high acuity vision, has no rods and primarily L- or red sensitive cones. Note the high density center area which lacks blue sensitive cones and has 2:1 red to green cones.



retinal mosaic



So by having red light present, you stimulate this area. But red light is present in white light, too, why not just use that? Leonardo's answer comes the closest, but it's a little off. Red light is used because it preferentially stimulates L cones more than rods, but you are definitely not able to preserve night vision by using red light. Why not? Well it may look like it is possible to exclusively stimulate cones from the chromatic sensitivity figure



chromatic sensitivity



But that figure is 1) normalized and 2) not indicative of synaptic signal processing. 1000's of rods can converge onto a single ganglion cell, where cone convergence in the fovea can be on the order of a single cone per ganglion cell. When it comes to perception, in order to compare the black rod line above with the red L-cone line you'd have to magnify it dramatically in size. Practically speaking, it is nearly impossible to stimulate cone pathways without stimulating rod pathways when using a relatively broad spectrum LED that you're powering with a battery. Maybe with a high power infrared laser.



So the purpose of using red light is to attempt to balance the activation of high sensitivity (red insensitive) rods with that of the low sensitivity (but red sensitive) cones in the fovea. While using a similar level of rod activation with blue light, you would perceive a "blind spot" where your fovea is.



Finally, instrinsically photosensitive cells (the melanopsin cells brought up) do not factor into this processing. These cells are activated only with extraordinarily bright levels of light, and the therefore do not enter into conversations dealing with night vision.

Wednesday, 5 November 2014

human biology - Mechanism of syndesmophyte growth in AS

Ankylosing Spondylitis (AS) causes inflammation around joints and the growth of syndesmophytes that may eventually fuse vertebrae. I'm familiar with the genetics (HLA-B27, IL1A) related to the condition, but I can't find any information about the mechanism that causes the actual growths to occur.



My current assumption is that AS causes the over-production or under-production of a particular compound or enzyme at the growth site, but I can't find any studies or papers that explain this. Is the mechanism known? Is it directly related to abnormal levels of a particular substance?

Tuesday, 4 November 2014

What are the differences between matter, dark matter and antimatter?

Matter is the stuff you are made of.



Antimatter is the same as matter in every way, looks the same, behaves the same, except its particles have electrical charges opposite to matter. E.g., our electrons are negatively charged, whereas a positron (an antimatter "electron") is positively charged. The positron is the "anti-particle" of the electron.



When a particle meets its anti-particle, they "annihilate": the two particles disappear, and gamma photons are released carrying off their energy. For this reason, should a lump of matter touch a lump of antimatter, they would annihilate, and a giant explosion would result because of the huge energy released (E=mc^2).



Matter and antimatter are definitely related: same thing, but with opposite signs. Twins, but opposites.



It is not clear why, but it seems like there isn't that much antimatter out there, more like trace amounts. Definitely not as much as regular matter as far as we can tell. This is puzzling to physicists and cosmologists, because you'd expect the Big Bang to make roughly equal amounts of matter and antimatter. Scientists agree that the paradox of "excess matter" will advance physics even further once it's solved.




Dark matter - we don't really know what it is. It's not even sure it's "matter" in a conventional sense, or related to it in any way. We just know that galaxies are rotating in such a way that indicates there's a lot more mass out there, but it is mass that we cannot see and cannot be accounted for in the usual ways. Hence the name "dark" (as in invisible) matter.



Dark matter doesn't seem to interact much with regular matter, except gravitationally. Right now dark matter could be passing through you and you wouldn't notice. Dark matter also does not interact with light, so you can't see it. It doesn't seem to interact much with itself either, so for this reason dark matter cannot form "clumps" such as planets or stars. Instead, it probably exists in a diffuse form. Bottom line, dark matter interacts pretty much only via gravity.



The shape of galaxies is a proof of the existence of dark matter, and is a result of the interaction between matter and dark matter. Without dark matter, galaxies would be much less massive, and the outer parts would rotate much more slowly compared to the center. Due to dark matter, galaxies are quite massive, and they rotate almost as solid objects - the outer parts rotate approximately as fast as the central parts.



Estimates vary, but it seems like there's something like 5x to 6x more dark matter out there compared to regular matter.

Sunday, 2 November 2014

proteins - What are the most important differences between HSP70 and HSP90?

Often cells have multiple types of the same protein — this redundancy can have different effects for different requirements such as having proteins function under different physiological conditions, or providing specificity to a certain class of ligand proteins or so on.



But here, it seems like the two have some synergistic interaction, a tag team if you will.



Wegele H, Müller L, Buchner J. 2004. Hsp70 and Hsp90 — a relay team for protein folding. Reviews of physiology, biochemistry and pharmacology 151: 1–44.



Unfortunately this article's full version can only be accessed if you're at a university or somewhere that has a subscription to some of the large research databases, but the abstract is free and it may provide more clarification.

Friday, 31 October 2014

botany - Why do cucurbits produce so much fluid when their stems are cut?

Members of the Cucurbitaceae family (squash, pumpkin, cucumber, melon etc.) are unique* in that they possess two distinct phloems, see figure below. The fascicular phloem (FP) is the main transport conduit, and more closely resembles the phloems of other plant families. Its role is to transport photosynthates and other nutrients (Turgeon & Oparka, 2010).The extra fascicular phloem (EFP), is more minor and has an atypical composition for a phloem. Although we have been aware of this dual phloem system for centuries (Crafts, 1932; Fischer, 1883, 1884, 1886), it is often ignored!!



The minor strands of EFP have been found to be the source of the extreme bleeding observed in cucurbits (Zhang et al., 2010). However this excessive bleeding has meant that cucurbits are a very popular model plant for phloem composition studies, since copious amounts of phloem contents are easily accessible. This is problematic since we now know that the exudate originates from the atypical EFP strands, making it a poor model (maybe is isn't even a phloem at all)!



The reason that the EFP does not block upon wounding is that it lacks blocking and sealing mechanisms (such as P proteins and pectins), which usually exist in order to protect the phloem from damage or disease, and to prevent the loss of vital metabolites. The fact that these are not present in EFP, along with the fact that EFP is rich in defensive proteins (Walz et al., 2004), may suggest a defensive role for this secondary phloem. Its anatomical placement around the vital vascular transport conduits supports this idea.



The dual phloem system found in cucurbits



*No others are known, but could definitely exist.



Bibliography



  • Crafts, A. S. “Phloem Anatomy, Exudation, and Transport of Organic Nutrients in Cucurbits.” Plant Physiology 7, no. 2 (1932): 183–225.


  • Fischer, A. “Das Siebröhrensystem von Cucurbita.” Berichte Deutsche Botanische Gesell 1 (1883): 276–279.


  • Fischer, A. “Neue Beiträge Zur Kenntniss Der Siebröhren.” Berichte Über Die Verhandlungen Der Königlich-Sächsischen Gesellschaft Der Wissenschaften Zu Leipzig, Mathematisch-Physische Klasse 38 (1886): 291–336.


  • Fischer, A. Untersuchungen Über Das Siebröhren System Der Cucurbitaceen. Berlin, 1884.


  • Turgeon, R. and Oparka, K. “The Secret Phloem of Pumpkins.” Proceedings of the National Academy of Sciences 107, no. 30 (2010): 13201 –13202.


  • Walz, C. and Giavalisco, P. and Schad, M. and Juenger, M. and Klose, J. and Kehr, J. “Proteomics of Curcurbit Phloem Exudate Reveals a Network of Defence Proteins.” Phytochemistry 65, no. 12 (2004): 1795–1804.


  • Zhang, B. and Tolstikov, V. and Turnbull, C. and Hicks, L. M. and Fiehn, O. “Divergent Metabolome and Proteome Suggest Functional Independence of Dual Phloem Transport Systems in Cucurbits.” Proceedings of the National Academy of Sciences 107, no. 30 (2010): 13532.


Thursday, 30 October 2014

launch - Why are spacecraft not air-launched from airplanes

Lots of good stuff on this topic in Wikipedia.:
Air Launch to Orbit



Air Launch



A typical rocket spends the first few seconds going straight up (almost) to get out of the atmosphere. After that it spends almost all of its time accelerating to orbital velocity. Thus getting out of the atmosphere, while hard (rocket is heaviest at this point) is really only a very small portion of the process.



The mass you would need to carry to a higher altitude is so large as to exceed the capacity of the largest aircraft ever built, let alone a balloon.



Consider the case of StratoLaunch. They intend to build a carrier aircraft composed of parts from 2 Boeing 747 (in the top 3 of the biggest aircraft commercially available. A380, B747, and C5 Galaxy are probably the biggest). It will be the largest airplane (in mass, wing length, etc) flying if it succeeds.



Even then, it can only carry a scaled down version of a Falcon (The original payload was to be a SpaceX Falcon 9 but with 5 engines instead of 9 and a concomitant reduction fuel/oxidizer load and thus mass). So the biggest aircraft yet to be built could only carry a smaller version of a medium size booster.



The primary benefit of air launch is not extra mass, but rather launch constraints. If you launch from a fixed site, you have limited launch options to differing orbits, and inclinations. An aircraft can in theory fly to wherever is convenient to hit the right orbital parameters. (Assuming there is a big enough runway for something the size of Stratolaunch vehicle within flight range fully loaded).



Currently, there is the example of Virgin Galactic's SpaceShip Two that uses the White Knight carrier vehicle, whose payload to actual orbit (LauncherOne if they actually build it) would be in the 100 kilogram range.



Pegasus, launched beneath a Lockheed L-1011 (3 engine airplane), maxs out around 500-1000 kilos to orbit.



There was a European proposal to launch an orbital payload (in the 200Kilo range) from the top of an Airbus A300.



The scaling up, that would be required just does not work.

Wednesday, 29 October 2014

molecular biology - Absorption ratios 260/280 and 260/230 for RNA

DNA and RNA absorb at 260nm. Proteins absorb at 280nm. The 260/280 ratio is a good estimate of how pure your sample is. For RNA, the 260/280 should be around 2. If it is lower, this might be an indication from contamination or proteins, phenol, or other contaminants in your sample. The 260/230 ratio is a second measure for purity of the sample, as the contaminants absorb at 230nm (like EDTA). The 260/230 ratio should be higher than the 260/280 ratio, as it is usually between 2 and 2.2. Lower ratio might be an indication of contamination.



In your case, I would be worried about the purity of the sample which gave you 260/230 ratio of 0.98. If you are using nanodrop, looking at the plot can also be a good indication of the quality of your sample. For a pure sample, a well defined peak (no shoulders or wiggles) at 260nm is expected.



Take a look at the NanoDrop manual for more information.

amateur observing - How were the orbits of planets first mapped out?

I think your question covers a lot of ground cause you're asking it from 2 different perspectives.




How were the orbits of planets first mapped out?




and




How do we know what position in space a planet will be at certain time
so that spacecraft trips to planets could be planned etc.




These should probably be separate questions, as they're quite different.



First one first, here's a bit of history: Using parallax Hipparchus was able to get a pretty good estimate of the distance to the Moon about 200 BC. The distance to the sun was much more difficult but Aristarchus was the first to come up with a method and others were able to improve upon it to get more accurate measurements.



The relative orbits of the planets wasn't hard to calculate once you had one of them, more on that here.



We can measure the length of a year on Mercury or Venus quite easily, as well as their relative angle to the sun (though Mercury's orbit is quite eccentric, you'd want to take several measurements). Even the wacky Copernican model with just circles on top of other circles made pretty good distance calculations with the sun in the center and the planets orbiting the sun.



Kepler was the first to recognize that the planets orbited at slightly different orbital planes, and from what I've read, Kepler was prouder of that discovery than the discovery of the elliptical orbits that he's most often remembered for. The combination of slightly different orbital planes and elliptical orbits and Brache's improved accuracy to his measurements was a huge step forward in planet mapping. Kepler still didn't have the distance to the sun well plotted out, but he figured out the model for planetary orbits. After that, it was just a matter of improving the distance measurements.



As to how NASA does it now. I'm not an expert, so somebody else might be able to answer that one better. It gets pretty mathematical, 3 position vectors, 3 direction vectors and velocity changes based on position, but we have nearly pinpoint laser measurements now.




I'd also like to know the most primitive way that this could be done
and if there is anyway this could be done using only maths and simple
measuring tools assuming no previous knowledge about the planets
positions.




It depends what you mean by primitive. Galileo's telescope enabled him to see phases of Venus, and that isn't possible without a telescope. The telescope also made it possible for Galileo to see 4 of Jupiter's moons, which orbited Jupiter and not Earth.



Aristarchus tried to eyeball the difference in shadow from the sun between the earth and the moon and he estimated the Sun was some 18-20 times more distant than the moon. Details here. To his credit, he successfully deduced that the Sun is much further than the moon, and he estimated the angle ratio to be 87 degrees when it was 89.83 degrees. Despite his efforts, his estimate was off by a factor of about 20, in distance though he was only off by 2.83 degrees.



Brahe used the best equipment available to him at the time, much of it made specifically for his observations. More on that here. Brahe also had the advantage of having accurate time pieces.



Brahe believed in the Ptolemaic model but he was unable to get it to match his data and he urged Kepler to figure it out when he was old and knew he wasn't going to figure it out himself. (There are rumors that Kepler poisoned Brahe to get more credit for himself, but I don't think that actually happened, Brahe's body was even exhumed to test that theory some time later but no traces of poison were found).



Kepler, unlike Brahe, liked the Copernican model but he couldn't get that to work because he believed in Copernican circles. He tried ellipses, more out of desperation because he couldn't get circles to work and the ellipse model matched the data. Kepler had not only Brahe's but years of Copernicus' records to work with as well as observations preceding them, some going all the way back to ancient Greece.



I'm not sure it would be possible to figure out that planets have elliptical orbits and how far they were from Earth without good equipment. Kepler had a lot to work with and a determination to find a simple explanation.



Hope that's not too wordy. I can try to clean it up a bit later if you like.

Sunday, 26 October 2014

botany - How do plant galls form?

I'd like to add to Amy's excellent answer.



Generally, galls are induced by the forced accumulation of plant hormones at different levels to those naturally maintained by the plant, in a localised area. Usually the hormones targeted are auxins and cytokinins which are both involved in the regulation of normal growth patterns; disrupting these patterns leads to disorganised growth, or in some cases a differently organised growth. There are several methods that I know of:



  • The gall inducer directly synthesising the hormone.

  • The inducer chemically inducing the host to synthesise more hormone.

  • The inducer chemically inducing the host to transport more hormone to the site.

  • The inducer genetically modifying the host to cause synthesis of the hormone in the host cell.

Some examples of the different methods:



Direct production: The bacterium Pseudomonas savastanoi directly produces indole-3-acetic acid (IAA, a type of auxin). This direct accumulation has been shown to be responsible for gall formation in oleander knot disease. Some key papers: Palm et al. 1989, link 1; Glickman et al. 1998, link 2.



Chemical induction of transport: Root-knot nematode worms induce root gall formation in clover. They probably do so by producing flavonoids which up-regulate transportation of auxin into cells (see link 3).



Genetic induction: As already mentioned by Amy, Agrobacterium tumefaciens is a very well characterised example of induction by genetic modification, however, A. tumefaciens is also known to directly produce auxins in large quantities. Another interesting example of genetic modification is in viral gall-inducers. They are not so well studied as their bacterial counterparts, but in some cases (e.g. white clover mosaic potexvirus) it has been shown that virus infection initially leads to a complex change in the types of cytokinins produced by the plant (e.g. Clarke, 1999; see link 4). It has also been shown that if cytokinins are applied exogenously (i.e. injected into the plant) after viral infection, that the virus cannot replicate well. This suggests that the virus is manipulating the host's hormone production in a complex way.



There is also the interesting case of Rhodococcus fascians, which seems to produce a chemical which is not structurally similar to any known cytokinin, and yet has similar effects (Goethals et al., 2001; link 5).



You specifically asked about gall wasps, but unfortunately this mechanism is, as far as I can tell, not completely known. It is speculated (e.g. in Shorthouse & Rohrfritsch, 1992; link 6) that this involves direct injection of phytohormones. The evidence to support this is simply that other insects, particularly aphids, excrete phytohormones in their salivary sheaths when they inject them into a plant.



Finally, I'll just say that the fact that gall induction is carried out by bacteria, viruses, nematodes, fungi and wasps, and that some mechanisms are shared across all those associations, demonstrates the ability of evolution to converge on the most elegant solution to a problem. It also shows that plants are so great, everyone wants a piece (but I would say that, because I'm a plant biologist).



References:



  1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209694/

  2. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.1998.11.2.156

  3. http://www.publish.csiro.au/?paper=PP98157

  4. http://www.plantphysiol.org/content/120/2/547.full

  5. http://www.annualreviews.org/doi/full/10.1146/annurev.phyto.39.1.27

  6. http://www.nhbs.com/biology_of_insect_induced_galls_tefno_3838.html

homework - When does Coelom form exactly?

Related to my other question.
I know that the coelom is derived from mesoderm.



Coelom seems to form during organogenesis within 3rd and 8th week of embryogenesis.
However, that answer is not either enough exact or it is wrong.



I am reading the thing in Kimball 5e and Gilbert 9e, but cannot find an exact mention about the thing. I know for sure that the coelom develops within gastrulation and organogenesis, since it is forming from mesoderm.



When does coelom form exactly?