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.