Sunday, 30 August 2009

Mars night sky - how many stars visible?

I'll add to Wayfaring Stranger's comments. In fact most of the time you would be able to see fewer stars in the night sky of Mars, than in a good dark night sky on Earth, because of dust obscuration.



Even in favourable conditions, the optical depth of the Martian atmosphere is usally somewhere between 0.5 and 1 per airmass. (Petrova et al. 2012; Lemmon et al. 2014) and is nearly wavelength independent. This corresponds to a reduction in flux to between 37% and 60% of its value above the atmosphere. This compares to a typical optical (V-band) extinction of around 0.1 magnitude at a good site on Earth, which allows 90% of the flux through. There are times when it can be much worse than this on Mars.



This means that the limiting magnitude on Mars would be somewhere between 0.44 and 0.96 magnitudes brighter than it is on a dark site on Earth and that all the stars would be fainter by these values.



As a rough guide to the effect this has I took the Hipparcos catalogue and made a frequency histogram of V-magnitude of the stars. If we define a Hipparcos magnitude of 6 as the limit you can see from a good dark site on Earth, then you would see 4559 stars (that's over the whole of the sky in both hemispheres). If that limit was reduced to 5.56 or 5.04, then this number decreases to 2745 or 1560 respectively. Thus there would be a reduction in the number of stars you could see by typically between a factor of 1.66 and 2.92.

Saturday, 29 August 2009

solar system - What wavelength to best detect the "9th planet"?

There are two basic ways to detect such an object. First is to detect it through reflected sunlight. Second is from the heat that it produces. We already know that the reflected light of such an object likely would be around a 16.5 magnitude. To determine the infrared, we have to estimate the temperature



The temperature very much depends on the composition. For simplicity, let's assume a composition similar to Earth, and was created about the same time as the rest of the Solar System. These assumptions may not prove to be valid, but they are among the possibilities discussed. Earth's internal heat, in fact, is at least 50% from radioactive decay, according to Scientific America. Of course, that's the internal heat only, not all of that will make it to the surface.



This proposed planet is somewhat akin to a "Rogue Planet", where a small disk of gas collapsed into a planet without a star, or were ejected from their host system. A fair bit also depends on if there is a sizable moon of the object. If so, then tidal heating would dramatically increase the temperature of the object. Any such determination can't be made without observation, but it is possible. An atmosphere would also help to keep the planet from freezing. A paper for detecting rogue planets comes from Abbott and Switzer. They hypothesis that a 3.5 Earth Mass object could be detected if it comes within 1000 AU, specifically in the far infrared, with a surface temperature of about 50 K.



Bottom line, it would probably be wise to try to detect both in the far infrared, as well as the visible, although it might be difficult to detect, even then. Given parallax as the primary means of motion, the detection should be done at several points in Earth's orbit, probably the same spot should be searched about 90 days apart to give the maximum opportunity to move, as parallax would only be visible if the motion of the Earth was perpendicular to the location of the object.

Friday, 28 August 2009

biochemistry - Why 22 amino acids instead of 64?

With only 2 nucleotides per codon, a codon could only encode 16 amino acids (actually just 15, because you need at least one stop codon), which isn't enough to encode the 20 acids we require (actually 21). So 3 is the bare minimum. (Of course another option would have been to introduce two new nucleotides, but evidence suggests that just using 3 nucleotides per codon was easier)



Nature has a tendency to minimize everything (except entropy :D). And apparently evolution selected those who understand that:




Simplicity is the ultimate sophistication.
- Leonardo da Vinci



Perfection is finally attained not when there is no longer anything to add, but when there is no longer anything to take away.
- Antoine de Saint Exupéry




It's rather safe to assume that the 20 acids we use are the bare minimum we require to function and that's why we don't have more.
Ultimately, RNA/DNA is there to store amino acid sequences. So the number of nucleotides in a codon is determined by the number of acids that need to be encoded and not the other way round.

Thursday, 27 August 2009

molecular biology - What is the fastest way to build an alanine scanning library?

The fastest will change as time passes and better technologies are developed.



I think the fastest method existing at the moment is Shotgun Mutagenesis (provided by Integral Molecular Inc).



This does not employ any new method of doing that. They just provide a set of plasmids, that has all the possible mutations. The set itself is generated by automated DNA synthesis.



So if you don't have a DNA synthesizer with you then simply order the kit from the company.

Wednesday, 26 August 2009

microbiology - How to understand influenza strain designations?

The sub-type is named for the broad classes of the hemagglutinin (HA) or neuraminidase (NA) surface proteins sticking through the viral envelope. There are 16 HA sub-types (designated H1 - H16) and 9 NA sub-types (designated N1 - N9). All of the possible combinations of these influenza A subtypes infect birds, but only those containing the H1, H2, H3, H5, H7 and H9 and the N1, N2 and N7 surface proteins infect humans, and of these, so far, only H1, H2, H3 and N1 and N2 do so to any extent.



Read more: http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses

Tuesday, 25 August 2009

neuroscience - Is it possible for any animals today to have more than one brain?

To some degree the answer depends on your definition of what counts as a brain.



Bilaterally symmetrical organisms tend to have some level of cephalization, which involves the concentration of sensory and inter-neurons at one end of the organism (the head).



This aggregation of neurons at the head is typically more complex than aggregations of neurons elsewhere in the body and so it gets designated as a brain whereas the others are designated as ganglia (if they are outside the central nervous system or nuclei if they are within the central nervous system).



In vertebrates, cephalization is very well developed so the brain is typically much more complex than the ganglia (although the enteric nervous system is pretty awesome, its not the brain). However in many invertebrates, the ganglia at the head of the organism (its brain) is not much more complex than the other ganglia around the body.



For this reason, many invertebrates can survive decapitation (at least for a while) and some like the flat worm, can famously survive and regenerate their head after decapitation.

Monday, 24 August 2009

spectra - Reference for broader spectral lines?

Both potassium (766.5+769.9 nm) and sodium (818.3+819.4 nm) have strong resonance lines (doublets) in this part of the spectrum. There are also the calcium triplet lines at 849.8+854.2+866.2 nm.



These are the strongest atomic absorption lines seen in the spectra of solar-type stars or cooler at 700-900 nm.



A more specific answer would require the spectral type of the star.



To do something more general and/or extensive you would need to get hold of a good line list (a line list alone cannot easily tell you which lines will appear strongest in a stellar spectrum) and a spectral synthesis programme like SME or MOOG.

Sunday, 23 August 2009

Moon's orbit around the Sun


What is the reason for this difference between assumed and actual path variation?




Even your second image isn't correct. Imagine zooming in on a small portion of the Moon's orbit about the Sun, for example, one full moon to the next, with the Sun zoomed out of the picture. Now imagine drawing a line segment from one outer cusp (full moon) to the next. In both of your images, that line segment crosses outside of the curve. In other words, both of your curves are concave.



Compare that to the he Moon's orbit about the Sun. This is a convex curve. If you pick any two points on that curve and draw a line segment between them, the entirety of that segment will be on or inside the curve. The reason the Moon's orbit about the Sun is convex is because the gravitational force exerted by the Sun on the Moon is more than twice than exerted by the Earth on the Moon. The orbit would be concave if the Moon was closer to the Earth than 259000 km (about 40.6 Earth radii). Since the Moon orbits at about 385000 km (about 60.4 Earth radii), the Moon's orbit about the Sun is convex.



Whether the orbit of a moon about the Sun is non-simple (first image in the question), simple/concave (second image in the question), or simple/convex (Moon's orbit about the Sun), the deviations from an ellipse are tiny. With regard to the Earth-Moon system, the deviations are so very small that at the plotted resolution (288x288 pixels), the orbits of the Earth, the Earth-Moon barycenter, and the Moon about the Sun will be right on top of one another. The reason the variations are so small (less than one pixel at 288x288 pixels) is because of the huge ratio of the size of Earth/Moon orbit about the Sun compared to the size of the Moon's orbit about the Earth.



Those backward loops in your first image don't happen for any object orbiting the Earth. That would require an orbital velocity about the Earth greater than the Earth's orbital velocity about the Sun. The Earth's orbital velocity about the Sun is about 30 km/sec, considerably more than the orbital velocity of an object in low Earth orbit is about 7.8 km/sec.




Has this path been like this since the formation of the Moon?




No. The Moon formed at four to six Earth radii, far less than the 40.6 Earth radii figure cited above. The Moon's orbit initially looked like your second image.




Do Natural Satellites of other planets also follow the same orbit around the Sun?




The massive planets are much further from the Sun than is the Earth and are much more massive than is the Earth. The orbits of most of the moons of Jupiter about the Sun are concave rather than convex. Only the outermost moons of Jupiter have convex orbits about the Sun. A few of Jupiter's innermost moons (Metis, Adrastea, Amalthea, Thebe, Io, and Europa) exhibit the retrograde motion depicted in your first image.



With regard to moons whose orbit about the Sun is convex, the distances that correspond to the 259000 km value for the Earth are 129000 km for Mars, 24.1 million kilometers for Jupiter, 24.2 million kilometers for Saturn, 19.0 million kilometers for Uranus, and 32.3 million kilometers for Neptune. Both of Mars' moons orbit close-in. However, all four of the giant planets have moons whose semi-major axis orbit fall outside the corresponding limit.

solar - Linear limb darkening coefficient, u

I was wondering if anyone knew of any resources to understand the linear limb darkening coefficient, $u$. That is to say, how the $theta$-dependent coefficient $u$ (or sometimes $b_{nu}$) varies with wavelength and with stellar effective temperature.



I've looked at a number of sources, such as Schwarzschild (1906), Milne (1921) and my own lecture notes and others, but nothing on this coefficient? Does anyone know where to even start looking for information of the properties of $u$?

Saturday, 22 August 2009

imaging - Calculating the Diameter of Jupiter through Image

I was trying to calculate the diameter of Jupiter from a picture I took of it. Here's the information I was able to get that I needed to calculate the diameter:




Focal Length of Telescope: 1.2 m



Multiplier for Barlow Lens: 2x



Camera CCD (Sensor) dimensions: 14.8 x 22.2 (mm)




I found the diameter to be 135 pixels in my image. Here's what I did:



begin{align}
f_e &= text{Focal Length $cdot$ Barlow Multiplier}\
&= 1.2 cdot 2\
&= 2.4
end{align}



Then, to calculate the field of view:



$$text{Field of View} = frac{text{Sensor Size}}{f_e} cdot frac{180}{pi}$$



Where the sensor size is the length in millimetres of the size of the camera CCD (I used the horizontal axis, or the longer side, to get the 135 pixels, meaning that I'd use 22.2 mm), and the second fraction is there solely to convert radians into degrees. Substituting my values, I got:



begin{align}
text{Field of View} &= frac{0.0222}{2.4} cdot frac{180}{pi}\
&= 0.53^circ
end{align}



As my entire image is 4271.8 pixels wide, and I know the angular field of view, I used ratios to get the field of view of the 135-pixelled Jupiter to be $theta = 0.017^circ$.



Then, using basic trigonometry, I was able to calculate the radius of jupiter:



$$tan left(frac{theta}{2}right) = frac{text{Radius of Jupiter}}{text{Distance to Jupiter}}$$



The photo was taken on March 22, 2016 - Wolfram Alpha gives 667.6 million as the distance to Jupiter on that day:



$$tan left(frac{0.017^circ}{2}right) = frac{text{Radius of Jupiter}}{667.6 cdot 10^6}$$



$$therefore text{Radius of Jupiter} = 97 577 mathrm{km}$$



Googling the radius of Jupiter gives $69 911 mathrm{km}$ as the result. Is there any reason why my value is so significantly off? Anything wrong with my procedure, anything I'm missing? I was not able to to upload this image I took as the file size was too large, however, the image does not lack clarity and I am completely stumped as to why my result is off by such a significant amount.



Any help will be greatly appreciated, thanks in advance.

supermassive black hole - Can an SMBH recycle dark matter into energy?

The accretion of dark matter by a black hole is possible, but difficult. Unless its trajectory takes it into the black hole, then it will simply approach the black hole, speed up and then escape again, since non-interacting dark matter cannot dissipate energy in any way.



Presuming a black hole did accrete the dark matter then the energy possessed by the dark matter would become part of the rest mass energy of the black hole. So yes, the black hole would grow. Not sure what you mean by recycle the energy. Energy is always recycled (conserved). If you mean can the black hole lose its rest mass energy? I suppose it may do via Hawking radiation, but this is vanishingly small for a SMBH. The dark matter will also carry angular momentum into the BH and there are ways that this rotational energy can be extracted (e.g. the Penrose process https://en.m.wikipedia.org/wiki/Penrose_process ).

Friday, 21 August 2009

vision - How do we know the brain flips images projected on the retina back around?

The basis of this question is a common misconception, and unfortunately the accepted answer by @CHM is also based on this common misconception. The misconception is based on the homunculus falacy and the tendency for people to think that the image that lands on the retina is somehow 'assembled' and presented for something (the 'consciousness') to view. This is not the case.



As the comment by @mgkrebbs expains, there is no orientation (up or down) in the brain, there is only neural firing. The infromation of the visual scene is distributed over the brain, and information does not have physical properties like orientation. Although as @nico pointed out the neurons that process the information do have a spatial structure that mimics that of the retina, this is a topological property (i.e. simuli that are close on the retina are processes by neurons that are close in V1) and such a topological property does not induce an orientation.



The root of the problem is really that the question "How do we know the brain flips images projected on the retina back around?" is a pseudo-question. Although it is grammatically well-formed, it makes no semantic sense. When the image is 'in the' (i.e. being processed by the) brain it no longer has physical properties like orientation. Thus you cannot ask if it has been flipped or not.

human anatomy - Reproduction and defecation

The cloaca, which is the common opening of the urinary, excretory, and reproductive systems, is present in birds as well as in non-avian reptiles (and thus presumably dinosaurs), amphibians, and monotremes (e.g., duck-billed platypus). To answer your first question, yes, this condition does seem to be universal for those groups mentioned above.



To answer your second question, evolutionary history is as good a reason as I can think of. The cloacal system has worked well enough for >350 million years (in the case of amphibians).

Wednesday, 19 August 2009

general relativity - are modern flat earthers still believe the earth is flat not round?

I saw a video in youtube and read few articles about how flat earthers believed that earth is actually flat but not round. They even presented facts about how everything which is true right now is true in their cases too.



But after so many technologies, so many space missions how do they still believe earth is flat like this society : https://en.wikipedia.org/wiki/Modern_flat_Earth_societies

Tuesday, 18 August 2009

botany - (How) does coppicing fundamentally alter tree growth?

According to Deckmyn et al (2004), the primary effect of coppice management is that the fraction of total biomass in roots is relatively higher after coppicing, and that a substantial fraction of carbon in roots (~20% of root mass) is reallocated aboveground to support shoot growth in the spring following coppicing.



Because of this large re-allocation, coppiced plants are able to grow more rapidly (and reach canopy closure sooner), than seedlings (Ceulemans et al 1996) it is important to consider that canopy closure (maximum leaf area index) occurrs more rapidly after coppicing




Deckman et al, 2004 Poplar growth and yield in short rotation coppice: model simulations using the process model SECRETS. Biomass and Bioenergy doi:10.1016/S0961-9534(03)00121-1



Ceulemans et al, 1996. A comparison among eucalypt, poplar and willow characteristics with particular reference to a coppice, growth-modelling approach Original Research Article
Biomass and Bioenergy, Volume 11, Issues 2–3, Pages 215-231 doi:10.1016/0961-9534(96)00035-9

Monday, 17 August 2009

What is the last nuclear reaction in a binary system before supernova?

I guess it depends on the type of Supernovae.



Type 1a supernovae are produced by a white dwarf star orbiting a companion close enough that matter transfers from the companion to the surface of the white dwarf.



Assuming only your star system of a 3M star and 6M star, the 6M star would become a white dwarf star first. At the end of it's life, it would have been furiously converting hydrogen to helium, and helium to carbon via the C-N-O cycle and the triple alpha process (C-N-O being dominant in stars above 1.3M sol). The highest reaction in this stars main sequence lifetime would have been the creation of oxygen, but oxygen is a catalyst in the C-N-O cycle, and therefore the last probable reaction in the star would be that of Helium in some form of shell burning in the outer core (more on that next).



The white dwarf, while orbting the companion, may siphon off hydrogen from the surface of the donor star. This hydrogen will accumulate evenly over the surface of the dwarf star, slowly growing the mass of the dwarf. Also, the hydrogen will be shell-burned into helium during this time increasing the density.



If sufficient mass can be accumulated, then the carbon within the white dwarf can ignite in a runaway reaction - literally blowing the entire star apart. These supernovae produce every element up to Nickel (Ni-56).

Sunday, 16 August 2009

Identify this object - Astronomy

Most likely it's Jupiter. According to the software I use to run my telescope and plan my observations, Jupiter rose at about 6:40 pm and set the following day at about 8:30 am. It would have been about -2.6 magnitude ,making it the brightest natural object in the sky that night. It, of course, rose in the east and would have traveled in an arc across the sky that dipped a little south.



It could also have been Betelgeuse, or even Sirius (for Sirius, it would probably need to be fairly low in the sky when the picture was taken to account for the color). But my best guess is still Jupiter.

human biology - Does testosterone increase female sexual behavior?

Although male testes are responsible for huge testosterone secretion, testosterone can be produced by other organs both in males and females. So, women do have testosterone. Similarly, estrogen is also produced in men and not only in women. In addition, both sexes produce the androgen and the estrogen receptors, so endogeneous or external testosterone will be active in women. Among other things, testosterone supplementation have been shown to be useful in clinical studies conducted on women suffering from hypoactive sexual desire.



Woodis et al., Pharmacotherapy. 2012 Jan;32(1):38-53. doi: 10.1002/PHAR.1004.

Friday, 14 August 2009

human biology - What portions of the brain have drastic changes in activation when we "sense" someone is there?

First of all one should tell that one can attribute the activation of certain brain zones with some indepent events only when the activation takes place along the signal input (receptors, sensory pathways towards the cortex and the sensory areas in cortex) or motor action (=output) (along the motox cortex => motor neuron => target organ). Those zones in brain are also termed as primary ones, for there is a clear mapping between the event/action and the activity here.



In case of your "sneak feeling" as you describe in your post, there seems to be more not the sensory input from some unknown type of receptor, but rather a subconscious processing of the complete sensory input that reveals some potential danger and is percepted as a kind of "smell of danger". Since this processing happens in secondary zones and can be well distributed throughout the whole brain, there is no possibility to find a single focus with high activity change here (in my opinion, of course) -- those changes in activity are beyond the measuring/imaging capabilities of modern examination methods.



Possible sensory inputs here might include (but not limited to):



  1. Optical (some shades, moving asyncronously etc).

  2. Acustic (some sneaking sounds, normally disguised by the background sound).

  3. Air move, air stream blocking sense etc (tactile feeling).

So, everything you suggest might apply here.

Thursday, 13 August 2009

star - How to cool down a moon?

Assuming the major heat input is from the star (the gas giant may also radiate significant IR) then you could seed clouds or freeze the water in order to increase the albedo.



Alternatively, you could increase the radiative efficiency by somehow painting the side of the moon facing away from the star black. Tricky, as no doubt this hemisphere changes with time quite rapidly.



If tidal heating from the gas giant is significant then you need to get the moon into a wider orbit!



The sunshade at the L1 point idea is widely discussed. Usually it is lenses that are considered, to avoid big problems with radiation pressure. I'm sure you could calculate some appropriate numbers to block a certain percentage of light in your system.

Wednesday, 12 August 2009

exoplanet - Can you assume atmosphere height for the purpose of surface pressure calculation?

Given that by definition of scale height an atmosphere thins by a factor of 1/e^x where x is elevation in terms of scale height multiples (See the table here: Definition of Scale Height), can we assume that the atmosphere is effectively non-existent at the elevation of 6H?



Density at elevation 6H
1/e^6 = ~0.00248 would mean about 0.2% of density at surface level



I know there is no real physical boundary but what I'm looking for is what is the assumed standard for simplifying calculations. Or is it just a bad idea to try and do it this way?



*This is a followup to another question:
How can you determine the initial volume of a planet's atmosphere?

Tuesday, 11 August 2009

Meaningful theories of the shape of the universe

Normally, when people say "the universe is infinite" they generally mean something like "the observable universe is locally flat, it is easy to assume that it is flat way beyond the observable universe, I don't know what lies beyond that, I won't talk about that, that is enough for practical purposes" (or any other proposition implying infinity in any direction and assumed for simplicity's sake while actually focussing on a small region of the space, the observable universe). So, "the universe is infinite" does not seriously mean that physical space goes on forever because this simply makes no sense at all, "infinite" is not a number, it is not a magnitude, it is not a property of real things (if you disagree with this premise please explain how the notion of infinity can be seriously applied to any direction of physical space, i.e. how you can seriously think to extend, sic et simpliciter, such a property of your mathematical model to the real world). (Personally I don't think this should be counted as a theory of the shape of the universe at all).



On the contrary, "the universe is finite and unbounded, compact, closed in all directions" is indeed a meaningful and in principle acceptable theory because it can be thought, described, discussed for what it actually implies. Of course, we don't know what lies beyond the observable universe but the idea of a compact universe makes sense and it seems to me this is the only meaningful explanation currently available of what "could" be (it is not necessarily the right, true explanation, of course).



Is there any other meaningful alternative (which can be thought, described, discussed)? Is there any alternative to the dichotomy "finite universe" vs "infinite universe"? Is there anybody out there working on models that overcome this dichotomy?

Sunday, 9 August 2009

human biology - Is telomere length a reliable measure of health/lifespan?

It would be reliable if we don't take into account the environment, and if we are comparing two genetically identical persons.



First, because there are many other factors that can cause genetic mutation and consequently shorten lifespan.
Second, giving an extreme example and not taking into account the environment and modern medicine, we cannot expect a hemophilic to have the same lifespan as a non-hemophilic.



More, not all the individuals have the exactly same rate of cell division thus, two persons with the same telomere length can have slightly distinct ages, and consequently die at different ages.



I would say, it is not 100% reliable since there are many other factors to take into account, but it could give a rough idea of lifespan

Saturday, 8 August 2009

human biology - Is a raised baseline between T and QRS normal in any ECG lead?

I am not sure if I understand your question correct. What I can see here is a clear ST depression, that might be indicative of myocardial ischemia/infarction. The underlying mechanism is the shortage of oxygen in myocytes leading to elevation of resting potential and slowing of the depolarization -- this accounts for the elevated baseline after T.



I am not at all an ECG expert, but I have seen the misplaces T-P segment many times while at medical school. It wasn't indicative for diagnosis, whereas all other segments were.



So, why are you worrying about this segment?

Are mass extinction events more likely during meteor showers / passing through comet debris?

This recent paper by Napier et al. indeed concludes that centaur comets break up into many pieces large enough to cause mass extinction events on Earth. Since objects orbit in the same way regardless of mass, I suppose that dangerously big comet debris are more common in meteor streams, and that major impacts are more common during meteor showers.



Small meteoroidal fragments do have their trajectories changed by Solar heating and the Solar wind, but since Earth crossing centaur fragments seem to be cleared out within only thousands of years, there should be no major difference between the large and tiny objects' orbits.



It also seems as if mass extinctions might be caused by meteor showers depositing dust particles in the atmosphere. Suggested by Klekociuk et al.

space travel - What would the cost be of visiting an asteroid?

I'm trying to think through what the cost would be of an unmanned mission to a nearby asteroid. To me it seems like the high-level costs would be the fixed cost of the "spaceship" itself (including any scientific or mining equipment required to carry out the mission), the cost of getting into orbit which would depend on the ship mass, and the fuel to get there and return (which would be a function of fuel cost, ship mass, how fast you want to get there, and the mass of anything collected at the asteroid site that would be returned). Is there anywhere that this is discussed or has anyone thought this through further?

Wednesday, 5 August 2009

orbit - Two body transient solution

There is no transient part



In solving a linear ode y'' + ay' + by = f(x), one finds that the solution is the superimposition of a general solution of y''+ay'+by=0, and a particular solution of the ode. In the situation in which the ode represents damped harmonic motion, the general solution part is said to be transient. This is a particular solution to this ODE, and not a general technique for solving all differential equations, and does not apply to the ode that describes newtonian gravity.



However there is another way of solving the newtonian equations, in the case of a two body problem, and that is Kepler's laws of planetary motion. These give a complete solution, and there is not transient part. Given a body's initial state, you can immediately find it's orbit using Kepler's laws. The body will be in an elliptical orbit, and return to its starting point, having made one complete orbit.

dna sequencing - protocol for pulldown of DNA breakpoints?

The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.



I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:



you could detect them with a tiling array. - that's an micro array which has an oligomer every 40 bp or so of the genome. The array could be used in a CHP experiment that detects the same proteins as in this paper.



Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right. This sounds noisy though.



On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep. if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply.



any of these sound like a good bit of work :)

Tuesday, 4 August 2009

Shadows of Light = Space or Dark Matter?


You cannot have dark without light.




Not true in the case of dark matter (for the general case, see below). Dark matter is called "dark" because it appears that it doesn't absorb or emit electromagnetic radiation - light! It can interact with light via gravitational lensing, but dark matter particles have no electromagnetic charge (we think) and so are considered "dark".




The only thing faster than light is dark (i.e. shadows)




This is true, as the video explains.




Does this make "dark matter" mere shadows of extremely bright objects?




This is the meat of the question, and the answer is a clear "no". First, any "bright objects", while capable of casting a shadow of something else, will emit electromagnetic radiation.



Okay, so why can't there just be non-extremely luminous objects casting a shadow? One reason is that the dark matter simply isn't where these shadows should be. Many galaxies have a dark matter halo that extends far beyond the galactic plane. Any light sources emitting light (that is then shadowed) would have to be on the opposite side of the galactic disk. This is simply not the case.



The second, more convincing, reason is that dark matter has mass. In fact, that's the reason the idea was first conceived (to account for anomalies in galactic rotation curves)! Shadows don't have mass; therefore, dark matter cannot be explained by shadows.




Is that also why it has to get dark before we can really see the majority of stars (subjective experience)?




No. I don't know for sure, but I believe that that's because the Sun's light is still blocking out the light of distant stars.[citation needed]




Addendum after edit to question




Can you provide sources for your claims?




I think that they're pretty well sourced! The first section can easily be checked via Wikipedia (which I assumed you had seen). The rest seems to be well-sourced, too (aside from the last bit, which is, admittedly, unsourced but only tangential).




Also I didn't say you can't have DARK MATTER without Light , I said you can't have Dark, as in Darkness. I think you're getting hung up on Dark Matter which is a big part of my question, but not the entire question.




Okay, I may have misinterpreted this.



Darkness is, by definition, the absence of light (electromagnetic radiation). So no, you don't have to have light for there to be darkness.




Also, are you claiming that all darkness in space is dark matter? I don't like to assume but for scientific purposes (not an accredited scientist) would we not agree that the measures made on dark matter were on a sample, and not the entire universe?




I never said that, but you did. Your original question asked if dark matter could be shadows. The answer is no.




So to further question this, do shadows not exist in space?




They exist. Any object blocking a light source casts a shadow:





This happens to have been used in the video, so it shouldn't be new to you.

Monday, 3 August 2009

the sun - When was the nearest star discovered?

When historically did we realize that the Sun is a star, like all the others?



An answer was posted, then the question was put on hold. I would like to answer:
If indeed someone asserted that the Sun was a star 2500 years ago, that is rather humbling. That it took until about 100 years ago for it to be proven is even more humbling!



People level a lot of claims against science and scientists. But if a field of knowledge takes over 100 generations to prove a true statement, perhaps they have a right to criticize. So, I think that science needs to do a better job of proving its theories. Either that, or people need to have more common sense, not to recognize something that has been staring billions of people in the face for all time. Perhaps, we should all be a bit more humble about the state of knowledge, even in obvious areas?



Maybe if we had taken the people who proposed this fact, and the concept of atoms, seriously at the time, we would be on our way to other stars by now instead of still having only visited that big white thing nearby (forgot the name just now) and that not for the past 40 years.

distances - How do astronomer measures the size of any celestial objects?

The main tool to measure the diameter of a star is interferometry combined with a parallax-based distance measurement - a brief review by Kervella (2008) might be useful. The principles behind interferometry are described here.



Interferometry involves measuring the light from a star using two (or more) telescopes that are separated by some distance. Together, the signals from these telescopes can be combined to give an angular resolution that can be (in the best circumstances) equivalent to a telescope with a diameter equal to the telescope separation. These measurements give the angular size of the star, which must then be multiplied by their distances to get a physical diameter.



One of the most successful experiments is the Chara array, which has yielded diameters for many nearby stars. Precisions can be as good as a few percent, but more usually 10% and of order 100 (predominantly nearby) stars have had their radii measured in this way.



A second main direct technique is to use eclipsing binary systems. The measured light curve can be used in an almost model-independent way to estimate the radii of the two stars involved. Of course most eclipsing binaries are close pairs with short orbital periods and with orbital inclinations that allow us to see the eclipse. They are therefore highly prized objects. Radii can be measured with precisions of 1%. A reasonably complete catalogue of the $sim 100$ known eclipsing binaries with precise radii can be found here.



Another technique is lunar occultation. The passage of a star behind the limb of the moon results in a changing diffraction pattern that can be used to estimate the angular size of the star. Again a distance is required to convert this into an actual diameter.



More distant stars are inaccessible - their angular diameters are simply too small. At the moment only indirect estimates of their radii are possible. For example, if we were to assume that a star radiates as a blackbody, then its luminosity ($L$), radius ($R$) and temperature ($T$) are related by Stefan's law.
$$ L = 4pi R^2 sigma T^4,$$
where $sigma$ is the Stefan constant. If the star has a measured flux at the Earth and we know how far away it is, then $L$ can be estimated. If we take a spectrum and estimate its temperature, then the equation above can be rearranged to give the radius in terms of the measured luminosity and temperature. Real stars are more complicated than blackbodies, but the principle is the same.



Neither of the above techniques can work for black holes, and the sizes (event horizon or Schwarzschild radius) of black holes have not yet been directly measured. The physics of a black hole is relatively simple(!) and so there is a direct relationship between their Schwarzschild radii and their masses (modified somewhat by rotation). Basically it is 3 km multiplied by the mass in solar units. Therefore a measurement of the black hole mass gives its "radius". The masses of black holes are measured by looking at the motions of stars and gas around them and applying our knowledge of how gravity works.

Saturday, 1 August 2009

human biology - How many, and how severe, are known single gene polymorphisms for obesity?

MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see Thorleifsson et al. (2009), Elks et al. (2010) and Willer (2009)