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.

*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.

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.

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.

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?

botany - Why do the sick and unhealthy trees leaf out first in spring?

Trees that have been dormant over the winter exist on nutrients stored in their roots during fall. When a tree has been damaged or diseased, it may not have been able to store enough nutrients before winter, or may not have enough stored to heal the damage/disease. If the damaged/diseased tree has depleted its winter root stores, it must leaf out (earlier than others of its species) and resume photosynthesis in order to have enough energy to attempt healing itself.

coordinate - Declination change due to precession

I'm not absolutely sure if it is correct, but I use information from this site: http://star-www.st-and.ac.uk/~fv/webnotes/chapt9a.htm

And I convert equatorial coordinates (RA = α, Dec = δ) to ecliptic coordinates (λ, β) using this formula.

sin(β) = sin(δ) cos(ε) - cos(δ) sin(ε) sin(α)

cos(λ) cos(β) = cos(α) cos(δ)

ε = Axial tilt (23,5°)

I know that due to precession only λ changes (β remains same for ecliptic coordinates). So I add the angle of precession to the λ. Then I convert the new λ and β back to the equatorial coordinates.

sin(δ) = sin(β) cos(ε) + cos(β) sin(ε) sin(λ)

cos(λ) cos(β) = cos(α) cos(δ)

codon usage - How are the various classes of E coli genes determined?

I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 possible codons. A factorial cluster analysis (the categorical, multi-variate equivalent of principle component analysis) was run on these vectors, condensing 61 dimensions down to 2 dimensions. Now that the data complexity has been reduced to 2D, it is more manageable for a k-means algorithm to partition the data. In the end, the genes were clustered into 3 orthogonal groups (classes I, II and III, with 502, 191 and 89 CDS, respectively).

Only after the authors clustered the gene set were they able to go back and look at the canonical definitions of each gene. It so happened, fortuitously, that each class of the genes had a strong bias for subsets of cellular function (eg, metabolism, protein biosynthesis, transport). They did not use proteome data, but they were able to define the role for a large number of these genes based on the body of literature at the time.

Astronomy Jokes - Astronomy Meta

Three astronomers go out for dinner at a conference - an optical astronomer, an X-ray astronomer and a neutrino astrophysicist.

Incredibly, when the soup arrives, they all have a fly swimming about in it.

The optical astronomer uses his spoon to flip the fly out, splashing a lot of soup all over the table in the process.

The X-ray astronomer carefully fishes out the fly with his spoon, picks out the fly and drops the remaining soup from the spoon back into the bowl.

The neutrino astronomer does the same, but taps the fly vigorously, shouting "spit it out, spit out"!

astrophotography - Disc of the milky way

It's dust!

The black band is not absence of stars, but rather clouds of gas and dust — a significant component of almost all galaxies — which block the light of background stars and luminous gas.

In the image, you see both individual stars, scattered all over, and the distinctive bright band of the Milky Way, most of the stars of which are so far away that they blend together. Most of the dust is in the plane of the Milky Way. The individual stars are closer to us than the bright band and the dust clouds, so what you see is the billions of stars in the Milky Way band, some of the light of which is blocked by dust, and then on top of this you see a few 1000s individual stars that are closer.

The components of galaxies

Galaxies consist of roughly 85% dark matter and 15% normal ("baryonic") matter. By far, most of the normal matter is hydrogen and helium, some of which is locked up in stars, and some of it in huge gas clouds, sometimes glowing (the pink clouds you see in the Milky Way image are probably hydrogen clouds being excited by the hard UV radiation from hot and massive stars, subsequently emitting H$alpha$ light). A small fraction (1–2%) of the normal matter are heavier elements, by astronomers lazily referred to as "metals". Roughly 2/3 of the metals are in the gas phase, but the remaining 1/3 has depleted into dust grains, e.g. silicates and soot. This dust is mixed with the gas clouds and often become dense enough that they block light of stars.

A strong wavelength dependence of the dust's extinction properties

However, dust scatters and absorbs light with short wavelengths (such as blue and UV) much more efficiently than long wavelengths (such as red and infrared). So while it may effectively block visual and UV light, infrared light passes more or less unhindered. For instance, if you look at the molecular cloud Barnard 68 in red and near-infrared, it looks black (left in the image below), but if you look farther out in the infrared, you can actually see the background stars (right below):

^{Image taken from ESO.}

Dark matter

Dark matter cannot be seen. It's… well, dark. It interacts with normal matter and light only through gravity. That means that if you could place a lump of dark matter in front of a star (you can't, really), you wouldn't block its light. It would pass right through. If the lump were big enough, it might gravitationally deflect the light, so the background star would look distorted to you, as would a lump of normal matter (e.g. a black hole).

orbit - Capturing Ceres - Astronomy

It's not possible to "slightly" change it's orbit unless you have a very very long time to wait. When Orbits get in synch with large bodies like Jupiter, for example, then Jupiter can give a tiny tug to Ceres each orbit and if positioned just right, it might nudge Ceres towards the inner solar-system, but only over millions, if not tens of millions of years. That's the slow way.

There's no fast way to move Ceres into an earth orbit without exerting a significant force on it. Orbits are largely stable and to change an orbit that much would requires a serious amount of force.

My math isn't always right, but Ceres orbits the sun at 17.9 KM per S and the earth orbits the sun at about 30 KM/S - now, you might think you need to speed Ceres up, but actually the opposite, it needs to be slowed down to fall into a lower orbit and the amount it needs to be slowed down (My math would be long and clumsy), but the actual deceleration needed is about 1/2 of that velocity difference - so imagine how much energy you'd need to move an object nearly 1,000 KM from side to side, made of ice and rock, twice as dense as water (mass of about a billion billion tons) and you need to accelerate that (decelerate it) oh about 5-6 KM per second (20,000 Kilometers per hour).

Now, a lot of energy could be saved by dropping Ceres to a fly-by near mars and then doing a gravity assist, and then, using earth's gravity as well to help capture it into an orbit around the earth. Mars weighs about 700 times what Ceres weighs, so the effect on Mars would be pretty tiny (all bets are off for Mars' 2 tiny moons though). But at minimum, you still need to decelerate Ceres by about 3 KPS (10-11,000 KPH), and at a billion billion tons that's a ungodly amount of energy, unless you're willing to do it very very slowly, perhaps or by finding a fuel source on Ceres to generate some kind of thrust or moving it so that it's in proper synch with Jupiter so that it gets a small kick towards the sun every so often, (see Mercury/Jupiter resonance below)

http://en.wikipedia.org/wiki/Stability_of_the_Solar_System#Mercury.E2.80.93Jupiter_1:1_resonance

I love ideas like this by the way. Ceres would be a nice source of water Though in an earth's orbit it would lose it's water over time to solar wind, so it would be a trade-off moving it closer. Might be better to leave it where it is.

As to your 2nd question, Ceres weighs about 1/80th the mass of the moon. It's not massive enough to "mess up" any planets in the solar system, though if it crashed into the earth for example, it would "mess up" life on the earth big time, but it wouldn't significantly change the earth's orbit. It would change the earth's orbit a little, but only a tiny bit.

gravity - What would happen if Jupiter and Earth were at the same distance as the Moon is from Earth?

That's no good idea. Earth wouldn't necessarily fall into Jupiter in the short run, provided it orbits Jupiter fast enough (within about 1.7 days), and on a circular orbit, but we would risk to collide with Io, destroy it by tidal forces, or change its orbit heavily.
The other Galilean moons would get out of sync and change their orbits over time.

Tides would be severe on Earth, not just limited to oceans, but also for "solid" ground, as long as Earth isn't tidally locked. This would result in severe earth quakes and volcanism.

Our days would be dim due to the distance to the sun. After tidal locking of Earth and ejection/destruction of Io the tides as heat source would be lost, oceans would freeze, temperature would fall to about -160°C mean temperature. During the polar night oxygen would probably condense from the atmosphere and form lakes, may be even nitrogen. By this atmospheric pressure would drop.

Since Spock is smart enough to know these consequences in advance, he wouldn't do it.

observation - How Would a Neutron Star Actually Appear?

I can kind of give an answer, but I welcome correction.

I was wondering how a pulsar would appear to a human being, in visible
light

It wouldn't look like much in the visible light spectrum unless there was a significant nebula, then we might see the effect of the pulsar on the nebula, but not the pulsar itself. X-rays and radio waves aren't visible, and if the pulsar wasn't directed at us, we wouldn't see it pass through empty space.

Neutron Stars are generally too hot for us to see. If one was to cool down significantly, to maybe 10 or 20 thousand degrees on the surface, then it might glow visibly blue and look like the brightest star in the sky, still just a point in the sky, but the brighest point in the sky at 1 AU.

But mostly they're too hot to glow in visible light.

What you might see from 1 AU from a Neutron Star could be the accretion disk. Matter that falls into a Neutron Star gets very hot and the energy if impact is far greater than the energy of fission, so as matter gets close to the Neutron star and spirals in, you're probably talking x-rays and gamma rays, but you might see a visibly glowing accretion disk at some distance out, perhaps in a gradually decaying orbit. In effect, what you could see would depend on what's around the Neutron star than it would depend on the star itself.

As I understand, the pulsar's beam is projected from the star's
magnetic poles rather than rotational poles, which are not necessarily
in line with each other. Given that pulsars rotate extremely quickly
and the beam could be visible across vast distances - such as if it
were shining through the pulsar's nebula - would it appear as a
straight line, curved line or perhaps a cone

The problem here is, you can't see the beam. You see light as it's pointed towards you, you can't see a light beam in space (even if it's visible light).

You can see a beam not pointed at you in the atmosphere because of reflection off dust and water molecules in the air.

(see little picture)

In space, matter is far more spread out. It's true that a pulsar can light up part of a nebula, though the nebula may also glow on it's own anyway (I'm not 100% sure on that), but a Nebula is very large and very spread out. To see it from the naked eye, I don't think you'd see much other than perhaps a large glow.

If you could see a pulsar beam, it takes light 8 minutes to for light to travel 1 AU, and a pulsar can rotate hundreds of times, perhaps thousands of times in 8 minutes, so if you could actually see the beam, it would be enormously curved, like a spiral. The light itself would travel in a straight line but since the source of the light was rapidly rotating it would appear like this (picture below), if there was sufficient material for the light to reflect off of (which there probably wouldn't be, not within 1 AU).

In reality, it would look nothing like that, but if you could see the the beam, that's what it would look like. What that spiral looks like from a single point is a pulsar, off, on, off, on, off, on, etc.

Also, the light never travels in a spiral, it travels in a direct line away from the Pulsar, but like the water spiral here, which falls down in a straight line, but it looks like it falls in a spiral (if that makes sense).

Given the incredible density of neutron stars and their small physical
sizes, would the night sky be visibly distorted to the point where
(for example) just after sunset on a hypothetical planet, one could
possibly observe other planets near or behind the star that would
otherwise be blocked by it?

Well, for starters, without a sun there, planets would probably not be visible. If the Neutron Star glowed brightly due to a hot accretion disk you couldn't see anything behind it cause the brightness of it would make seeing light bent around it pale by comparison.

Now if the Neutron star was dark, to our eyes, then we could see gravity lensing around it, but stars, not planets cause planets would be dark. (The moon would be very dark too, visible more by what it blocks than what it shines). The lensing would be quite small however. Visible lensing would only be a few times the diameter of the Neutron star, maybe 100 miles across, which, 93 million miles away is really tiny. You might see some odd warping of a star here or there when properly lined up, but to see any interesting visible lensing you'd need a pretty powerful telescope.

Given their small surface areas, would a neutron star still appear as
luminous as say, the Sun, at a similar distance? How close would you
have to get to a neutron star for its apparent magnitude to match the
Sun's from Earth?

Kind of touched on this above. The Neutron Star can give off a lot of energy in it's pulsar beam, but it's mostly x-rays, not visible light. How bright it is would depend on how much material is falling into it at the time, so there's no right answer to how close the Earth would need to be to have equal brightness. It's a different kind of brightness too, mostly not visible light. But there's no way to answer that question cause it depends on too many things.

When a Neutron star is just formed (which usually happens after a supernova so there's enormous energy released), but when the star just forms, it's maybe 12-15 miles in diameter but it's surface temperature can be (guessing) perhaps a billion degrees, though it cools very quickly. A very young Neutron Star might emit more energy to our sun, though much of it would be in Neutrinos that would largely pass through the Earth. But that level of energy output wouldn't last long. It would cool down to about a million degrees within a few years. Source.

bacteriology - Why does ampicillin in solution turn yellow?

I have a universal tube with 10 mg mL-1 ampicillin. When I got it, it was supposed to be sterile. It was opened for approximately 20 minutes for an experiment and has since been standing around sealed for a good month now.

Within the last couple weeks, it has gradually turned yellow. Right now the colour is faint, with a green-ish tint.

Why would it turn yellow? I know NADH is yellow, so that was my first guess. But I couldn't exaplain why ampicillin would cause NADH to accumulate, so I discarded that.

Side info: Ampicillin acts on bacterial cell walls, maybe that might help.

biochemistry - How would one calculate the availability of nucleotides to an enzyme?

I could read this question more than one way. Are you talking about an enzyme in a cell or in a reaction in vitro? Kinetics and mechanical explanations can overlap, but are not entirely the same and are usually dealt with separately - kinetics with watching the rate of reactions in a tube and mechanism in a crystal structure or possibly Nuclear Magnetic Resonance.

Protein structures are usually static- you only get a time lapse snapshot of the reaction in most cases. kinetics allows you to see how fast these things go and can help you understand the order of binding when more than one component is needed for the reaction, etc.

The polymerase has a binding pocket where the template strand and the growing strand are used to build a double helix together. if the base being introduced does not form Watson Crick base pair bonds, the geometry of the reaction will not allow the base to be added to the growing strand.

Hope this helps? If I can make this clearer, can you drop me a comment and I'll revise...

biochemistry - Why does RNA adopt an A-form helix?

RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions.

_{From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by Richard Wheeler}

The preference of RNA for the different conformation is supposed to be caused by the 2'-OH, my question is now how exactly this favors the A-helix? Which interactions are important and cause RNA to adopt an A-form helix?

Could there be a -1 dimension?

Could we have a 0th dimension ? Could we have a -1th dimension ?

In the sense that a dimension number is a label, yes.

However we describe a space as having a given number of dimensions. In this sense a zero dimensional space would be a dimensionless nothing. A -1 dimensional space simply has no meaning in this sense and hence a -1 th dimension has no meaning.

Are we supporting the 2nd dimension, 1st dimensions existence by being part of the higher multiverse?

The dimensions are not related in that way. Again I'd suggest you let go of the view of individual dimensions and thing in terms of a space having a stated number of dimensions.

Finally, can fields inside our dimension (higgs field) interact with other dimensions? I am sure certain that we think gravity is a force interconnecting this "multiverse" together, if it even exists, but can our own particles and matter interact with dimensions completely different to us? Are we affecting other dimensions in this so called "multiverse"?

The dimensions, again, should not be thought of in this way. They are not things that interact with each other. I think you are mistakenly picking up this notion of interactions from the idea that space and time are linked in theoretical space-time models. But this "link" is really a description of the geometric properties of the space we use as our model and which incorporate time as a notional dimension. These are not interactions, but definitions of how that model of space is structured.

Even though this query makes absolutely no sense to me - I'm sure the second part of the question can be answered.

Note that an answer like "it makes no sense" would also be an answer. I think the problem here is that you are treating dimensions as things.

The "right" number of dimensions is a question that starts heated arguments among physicists. If better minds than mine can't agree I'd be loath to express an opinion. I'll go with whatever works for whatever system I need to model, and for an awful lot of purposes Newtonian still works fine.

human biology - How does protein help to cure wound?

Saying protein in general helps to heal wounds is a very far step. Different proteins are essential for nearly every process that happens anywhere in your body.

There is a range of proteins which is required specifically for wound healing. The first step of wound healing is blood clotting in order to close wounds. This uses several so-called clotting factors, all of which are proteins. Some of these help the platelets (small cells in the blood) stick to the walls of the blood vessels which have been damaged, others are responsible for forming a tight clot around them to make sure no more blood leaks out. Most clotting factors also require vitamin K for their production.

The next step is wound healing. This involves several cell types gathering at the wound and laying down what is called connective tissue, a network made mostly of proteins. Cells of the skin will need to replicate themselves in order to close the wound, and they will require lots of proteins for this.

Protein reaches all cells of the body from the intestines via the blood flow.

Eating a diet high in protein would surely not be a bad thing to do - your body needs it everywhere. But it is important that you consume it mixed with healthy amounts of carbohydrate (needed for energy) and fats (needed for many structures and hormones).

observation - What is the schedule for science runs of aLIGO (and VIRGO)?

Advanced LIGO seems to operate only intermittently. Is there a schedule for at what times it will be able to register new gravity waves? Even if no formal schedule is available, what main factors determine the scheduling?

I suppose VIRGO in Italy, to get started in 2016, will operate mostly simultaneously with aLIGO. Or would its design require another type of schedule?

planet - Why is the universe full of spinning objects?

It comes from angular momentum. Angular momentum is a conserved quantity of physics. That means that the sum of angular momentum of the universe is constant, even though some parts of the universe may transfer angular momentum to other parts.

We do not know the total amount of angular momentum of the universe, but from observations we know that it is not uniformly distributed. This explains why celestial objects rotate.

If the total amount of angular momentum of the universe would be zero it would be theoretically possible that rotation could cease in the future. However, nobody knows the ultimate fate of the universe, so this is purely speculative.

the sun - Does the Sun belong to a constellation?

Constellations are human constructs to make sense of the night sky. When you are trying to find your way around, it helps to "chunk" stars into patterns and assign those groupings names. When I want to point out a particular object in the sky (say Polaris, the North Star), I start by pointing out a familiar constellation (say Ursa Major, the Big Dipper). From there, I can tell my friend to follow this or that line to get them to look where I'm looking:

With the advent of computerized telescopes and large data sets, constellations are less important for professional astronomers. However, many stellar databases use Flamsteed or Bayer designations, which assign stars to constellations. In order to include all stars, the sky is divided into irregular regions that encompass the familiar constellations.

So, which constellations is the Sun assigned to? Well, from the perspective of someone on the Earth, the Sun moves through the constellations throughout the course of the year. Or rather, Sol moves through the region of the sky where some of the constellations would be seen if its light did not drown out distant stars. Our moon and the rest of the planets move through those same constellations. (The Greek phrase which gives us the word "planet" means "wandering star".)

The current position of the sun against the background of distant stars changes over the course of the year. (This is important for astrology.) It's a little easier to make sense of with a diagram:

So perhaps a better question is:

What constellation does the Sun belong to today?

Presumably an observer on an exoplanet would assign Sol to some constellation that is convenient from her perspective. But from our perspective within the Solar system our sun, moon, and planets are not part of any constellation.

Is there a good field methods book that covers terrestrial ecology?

In the past I have used Limnological Analysis by Wetzel and Likens and Methods in Stream Ecology edited by Hauer and Lamberti to develop labs and research methods for courses and projects with an aquatic focus.

These books detail the standard methods of lotic and lentic ecology with some emphasis on utilizing the methods in undergraduate or graduate level courses.

I am now developing a biogeochemistry course that is not limited to aquatic systems and I am looking for a summary of field methods for terrestrial systems.

Is there a book that summarizes terrestrial field ecology methods similar to Wetzel and Likens and Hauer and Lamberti?

cosmology - Is the Universe really expanding at an increasing rate?

I don't take this at face value because we should expect more distant
objects to have higher observed speeds and therefore higher observed
red-shifts.

That's true. That was the original Hubble discovery - the farther away things were, the faster they were moving away from us.

Here's why. Let's start with a model where the Universe expanded very
fast early on, but has been slowing down ever since due to gravity, as
one would normally expect.

Yes - that's what everybody thought following Hubble's discovery.

Remember that, the farther away a cosmic object is, the farther back
in the past we are observing it. An object 1,000 light years away, if
it's light is reaching us now, is being observed in its state that
existed 1,000 years ago. We are effectively looking through a time
machine.

This is not lost on Astrophysicists.

So if we observe a more distant object, we're observing an older state
of that object. Therefore, we are observing it at a time when the
Universe was expanding faster than it is now, so it has higher
red-shifts.

OK, 2 points. 2nd point first. The red-shift has to do with relative velocity, not speeding up or slowing down. Something can be more red-shifted and slowing down and something can be less red-shifted and speeding up, especially since the acceleration/deceleration is comparatively slow compared to the relative velocity.

and other point - lets keep in mind, we don't know what a galaxy 3 billion light years away is doing now. We can guess and we can run models, but we can only see what it's doing 3 billion years ago.

And isn't that what we observe today? The more distant the galaxy, the
higher its red-shift? This is not inconsistent with a "normal" model
where the expansion is slowing down due to gravity.

Yes, the more distant the galaxy the higher it's red-shift. But no, that's not inconsistent with expansion. That's what you'd see, expansion or contraction, because red-shift is just relative velocity.

What am I missing? Why are scientists trying to explain such things
with weird dark matter and dark energy that otherwise have never been
detected or found evidence of and aren't needed for any other model,
and in fact get in the way of our models of physics and quantum
dynamics?

A lot of these ideas are confusing. They're confusing to scientists too, especially when they were first discovered - so you're not alone.

Dark matter was observed because galaxies were behaving strangely. The stars in the outer arms of the galaxy were observed to be moving much too fast and faster than the stars more towards the middle of the galaxy and that made no sense. The galaxies also weighed too much and the only way to explain this was extra mass in kind of a halo around the galaxy, but this extra mass, also, didn't interact with electromagnetic waves like the mass here on earth does - so they called this extra mass (and there's a lot of it, more than there is regular mass), but since it's invisible, they called it "dark matter" and it's not dark like dirt or coal, it's dark as in - invisible. It's completely transparent to light, but it has mass and they still don't know what it is. They have some OK theories, but nothing definite.

Now, dark energy - think about the big bang and all matter flying apart - the galaxies twice as far are moving away twice as fast, BUT, as you said, because of gravity, we should see the galaxies that are twice as far moving away more than twice as fast, cause the nearer the galaxy, the more time it's had to slow down - aha, they thought, if we can compare the speed of the galaxies 4 billion light years away to the speed of the galaxies 2 billion light years away to the speed 1 billion light years - etc, etc and measure it all carefully, we can measure the rate at which gravity is slowing down the universe. - that makes sense right.

And with careful measurement of Type 1A supernovas, which temporarily outshine entire galaxies - with remarkable consistency (what they call a standard candle - a very bright standard candle, but a standard candle all the same) - with that, they thought they could measure the gravitational slow down of expansion - exactly what you're talking about.

The problem was, the measurements told them the opposite of what they expected to find. The measurements told them that the galaxies 2 billion light years away were traveling slightly more than half as fast as the galaxies 4 billion light years away, and so on. They checked this, cause it had to be wrong, then they re-checked it, and re-checked again and the only conclusion was, stuff out there is speeding up, not slowing down - cause that's what the telescopes tell us.

Dark energy wasn't a hair-brained scheme that mad scientists thunk up. It was an observed reality that nobody expected (well, cept just maybe for Einstein and his cosmological constant, but that's another story).

Dark energy's just a name anyway. They have to call it something, even if they're not sure what it is or how it works.

How bad could we reasonably expect a solar flare to impact earth, and what can be done to mitigate the impact?

Space Weather is the field within heliophysics that tries to understand this Sun-Earth relationship. When a Solar Flare occurs multiple things may happen and how it interacts with the Earth and our technology depend on different factors.

The first effect, the X-ray radiation produced by an Solar Flare affects the ionosphere and therefore the radio communications. This effect is almost immediate and there's no way to attenuate or prevent it. We can forecast the likelihood of a flare to happen on the day but still we don't have the knowledge enough to exactly predict when it will happen. The radiation from the flare it takes around 8 minutes to get to Earth, and at the time we see it the radio communications have already been affected. This effects mostly to VLF bands.

After a solar flare high energetic particles and coronal mass ejection could be produced, these two events have different effects on Earth and whether interacts with Earth or not depends on where it happens on the Sun and the properties of the solar wind at that time. High energetic particles (also known as Solar Energetic Particle events - SEPs) could arrive around 30 minutes after the flare happened, and Coronal Mass Ejections (CMEs) between 2 or 3 days. These times depends on the properties of the events, not all are the same.

CMEs could be somehow predicted, and are these the ones that could affect, between others, the power grid. It won't affect your computer. The reason of why it affects the power grids is due to a induced electric current happened by the interaction of the CME's magnetic field produces in the Earth's magnetic field. The electric current finds it easier to travel through the power grid than through the Earth itself (the cables are better conductors). In simple words, when that happens the electric grid "thinks" that there is an increase of demand and tries to compensate it generating more electricity and that can burn them - as it happened in Canada in 1989.

To reduce it effects there are a lot of engineering work around these systems and I'm not an expert in such topic to be able to explain them properly. However, a warning to the power grids of a couple of days in advance helps. The difficult bit is how to be exact in the forecasting. CMEs sometime are deflected by the solar wind and just a flank of it "touches" the Earth, other times small ones get accelerated and have a larger impact than expected. So, to be able to reduce the effects we need to have a better understanding of their origin and surroundings, understand their physics and be able to model what they are doing. There are few models out there (e.g., CCMC) but at the moment we need to keep researching to improve these further.

Answering to "how bad" a solar storm (not just a flare) can affect Earth is hard to quantified, in UK it has been classified as one of the highest priority natural hazards in the National Risk Register, and similarly in other countries. An event like Carrington's (the one you linked) could have a lot of impact in our current technological civilization and it's been estimated in many years and trillions of US dollars to restore the damage (see Royal Academy of Engineer report on Space weather).

Calculating Right Ascension and Declination from Latitude / Longitude / Time

I have a latitude / longitude / time of a location on Earth, I need to calculate the Right Ascension / Declination that's overhead at the time provided.

So far I've found out that Right Ascension is the same as the sidereal time for the location but I haven't found any information about declination.

I'm trying to set my overhead viewing location in the web portal of World Wide Telescope. It defaults to "now" but I want to show 10PM and there's no way (that I've found) to set time through the javascript interface. I can however set Right Ascension and Declination, hence my question.

space time - The multiverse spacetime paradox?

I'm not about to suggest that multiverse(s) do not exist, but merely that it is a fascinating, but highly speculative, topic. The Wikipedia article is a good start. From the wiki:

The structure of the multiverse, the nature of each universe within it and the relationships among the various constituent universes, depend on the specific multiverse hypothesis considered. Multiple universes have been hypothesized in cosmology, physics, astronomy, religion, philosophy, transpersonal psychology, and fiction, particularly in science fiction and fantasy. In these contexts, parallel universes are also called "alternate universes", "quantum universes", "interpenetrating dimensions", "parallel dimensions", "parallel worlds", "alternate realities", "alternate timelines", and "dimensional planes," among others.

From the way you phrase your question, you may want particularly to look at the sections on M-theory.

orbit - Do all planets rotate in the same direction in relation to each other?

In other words, does everything spin counterclockwise according to their axes (in relation to each other)? I suppose my question goes for stars, moons and other objects too.

But then again, all you have to do is look at any rotation upside down and it goes clockwise. So depending how you're looking at it, one could say everything rotates in the same direction whether they do or not. It's all a matter of perspective, right? And in space, there is no "right side up". Maybe my question is moot now that I think about it.

If we re-drew all of Earth's maps and globes upside down, New York or Sydney would be on the "west coast" and the Sun would rise in the "west" and set in the "east". Is it just by luck or maybe by the prominent early mapmakers, or that the majority of human population lives in the Northern Hemisphere, that it's given "dominance" on "top"? (I've heard that theory before)

Ugh. This is all so confusing.

distances - Do astronomers, in principle, have more information about older phenomena than younger?

There are more stars and galaxies but not necessarily more information.

You might choose to measure the information content in terms of photons received, in which case, for a given star/galaxy, this decreases as the inverse square of the distance, so the two effects cancel out.

Astronomy is a constant struggle with the tension between these two competing dependencies. As we look further, not only do we see more of particular types of object, but we also get to see examples of rare objects - i.e. the tails of the distributions. On the other hand as we expand our horizons, so our grasp of what is going on becomes increasingly blurred in terms of spatial, spectral and temporal resolution. It is for that reason that bigger and bigger telescopes are built!

The issue you raise concerning redshift is interesting. The co-moving volume versus look back time in any direction will not be a simple function (i.e. doesn't just go as the square of the lookback time) and depends critically on the adopted cosmological parameters.

There is of course a limit in any case. Once we get back to the microwave background at $z=1100$, then further probing backwards with electromagnetic radiation is stymied by the optically thick nature of the universe at early times.

space time - Could the Earth use gravitational lensing / bending of light to see it's own bottom?

Whimsical question. Similarly, you could reason that someone on a planet far, far away would be holding up a mirror, such that we could see our own reflected past again.

Unfortunately, both options are practically infeasible, even if the light would be undistorted and redirected perfectly towards us. Remember that (1) Earth is small, (2) the reflected signal is weak as it is, (3) any object capable of reflecting this back towards us would be a black hole, the closest of which is further away than most known exoplanets, and the signal falls of with $r^{2}$ with $r$ twice (!) the distance to the object doing this lensing.

Now, if we somehow were able to observe it anyway, it would be straightforward enough to estimate the look back time - the distance to the lens would presumably be fairly well known.

How bright it would have to be is not really a sensible question - there are too many variables in play for that (which (hypothetical future) telescope are we using, what are the observing conditions, how far away is the source, what kind of source are we talking about...). And at the end of the day, the brightness of your source is not even the biggest problem; finding a suitable lens is.

the sun - Will a Ball placed close to Sun fall into it?

The answer depends on the size and mass of the ball. It also depends on its ability to reflect light (albedo $A$), but let's forget that for a moment.

Pressure vs. gravity

Solar pressure decreases with $R^2$ (the inverse square law). At Earth, which is located at a distance of $1,mathrm{AU}$ from the Sun, we receive an irradiance $S_0 = 1361,mathrm{W},mathrm{m}^{-2}$. Since the momentum of a photon of energy $E$ is $p = E/c$, the pressure at a distance $R$ from the Sun is
$$
P = frac{S_0}{c(R/mathrm{AU})^2}.
$$
If the ball's radius is $r$, this pressure will exert a force
$$
F_gamma = pi r^2 P = frac{pi r^2 S_0}{c (R/mathrm{AU})^2}qquad(mathrm{away,from,the,Sun}).
$$
Meanwhile, if the ball's mass is $m$, the gravitational force exerted by the Sun on the ball is
$$
F_g = frac{G M_odot m}{R^2},qquad(mathrm{toward,the,Sun})
$$
where $G$ is the gravitational constant and $M_odot$ is the mass of the Sun.

Threshold for falling

The threshold for the ball falling into the Sun is found by equating the two oppositely directed forces:
$$
frac{pi r^2 S_0}{c (R/mathrm{AU})^2} = frac{G M_odot m}{R^2}.
$$
The first thing to notice is that $R$ cancels out; the reason being that flux density and gravity both follow the inverse square law. Second, re-arranging terms we see that the ball will fall if its mass per area is greater than this threshold (if I have calculated correctly):
$$
frac{m}{r^2} gtrsim frac{pi S_0}{c G M_odot } mathrm{AU}^2 simeq 2.4times10^{-4},mathrm{g},mathrm{cm}^{-2}.
$$
Now you can plug in your favorite numbers. You will find that for most macroscopic objects, such as a football, a rock, and even a sand grain, it will fall. On the other hand, small "balls" such as dust grains and atoms, will tend to be pushed away from the Sun. An example of a macroscopic object that won't fall is a solar sail which seeks to maximize area per mass.

For a given density, say $rho = 2.5,mathrm{g},mathrm{cm}^{-3}$ which is characteristic of rocky materials, you can also calculate the maximum size before it falls toward the Sun:
$$
r_mathrm{max} = frac{3}{4pirho} ,(2.4times10^{-4},mathrm{g},mathrm{cm}^{-2}) sim 0.1mathrm{-}1,mumathrm{m}.
$$

Albedo

The above calculations hold of all the radiation is absorbed by the object. If a fraction of it is reflected, the radiation will transfer more momentum to the object, and for a prefectly reflecting object, the radiation force will be roughly twice the amount above (the exact factor depends on the geometry of the object).

Extinction curves

It should be noted, though, that treating small particles as rigid spheres with a geometric cross section becomes imprecise when their size is comparable to wavelength of the light; rather, their absorption/scattering cross section should be treated quantum mechanically. In practice, extinction curves — i.e. the cross section as a function of the wavelength of the light for a given dust particle size distribution — are measured observationally by comparing the light from unobscured star with similar stars behind dust clouds, and subsequently fitted with various functional forms.

neuroscience - Does body mass have a bearing on reflex speed?

I went into this with the same assumptions that jello did, but I found two studies that had some interesting results.

Isojärvi (2010) found that in obese and under-exercised adults, physical fitness level predicted, among other things, a significant proportion of the variance of nerve conduction velocity and F-wave latency. So, these individuals may theoretically have a slower response to noxious stimuli.

While Type II diabetes is not always a result of obesity, there is often a high correlation between the two. Oltman (2005) found that, in "Zucker diabetic fatty" rats (an animal model of Type II diabetes), motor nerve conduction velocity in the sciatic was significantly slowed. This effect, too, would affect the rate with which an individual could withdraw a limb from a noxious stimuli.

So, I don't think that anatomical changes in the bodies of individuals who are obese would have any effect, but clearly there are physiological changes in the neurons of these individuals.

---

References:

Isojärvi H, Keinänen-Kiukaanniemi S, Kallio M, Kaikkonen K, Jämsä T, Korpelainen J, Korpelainen R. (2010). Exercise and fitness are related to peripheral nervous system function in overweight adults. Med Sci Sports Exerc. 42(7):1241-5.

Oltman CL, Coppey LJ, Gellett JS, Davidson EP, Lund DD, Yorek MA. (2005). Progression of vascular and neural dysfunction in sciatic nerves of Zucker diabetic fatty and Zucker rats. Am J Physiol Endocrinol Metab. 289(1):E113-22.

cosmology - Is parallel universe possible

As much as parallel universes go, there's a theory for this known as the Multiverse theory, part of the String theory.

In String theory, the Multiverse is a theory in which our universe is
not the only one; many universes exist parallel to each other. These
distinct universes within the multiverse theory are called parallel
universes.

There are cosmic inflation models that support this as said here in Wikipedia. A quote from there:

It's hard to build models of inflation that don't lead to a
multiverse. It's not impossible, so I think there's still certainly
research that needs to be done. But most models of inflation do lead
to a multiverse, and evidence for inflation will be pushing us in the
direction of taking [the idea of a] multiverse seriously. Alan Guth[7]

Now to address your point if we can ever know if a parallel universe exists exists.

Opinion: Possible but unlikely. I don't think that we are close to achieving this.