human biology - Relationship between our microbiome and personalized nutrition

does the microbiome affect food metabolism?

Most definitely (and not surprisingly). The Arumugam paper [1] notes that

The drivers of [enterotype 1] seem to derive energy primarily from carbohydrates and proteins through fermentation, … because genes encoding enzymes involved in the degradation of these substrates (galactosidases, hexosaminidases, proteases) along with glycolysis and pentose phosphate pathways are enriched in this enterotype […]

Enterotype 2 … is enriched in Prevotella … and the co-occurring Desulfovibrio, which can act in synergy to degrade mucin glycoproteins present in the mucosal layer of the gut […]

Enterotype 3 is […] enriched in membrane transporters, mostly of sugars, indicating the efficient binding of mucin and its subsequent hydrolysis as well as uptake of the resulting simple sugars by these genera. […]

The enriched genera indicate that enterotypes use different routes to generate energy from fermentable substrates available in the colon, reminiscent of a potential specialization in ecological niches or guilds. In addition to the conversion of complex carbohydrates into absorbable substrates, the gut microbiota is also beneficial to the human host by producing vitamins. Although all the vitamin metabolism pathways are represented in all samples, enterotypes 1 and 2 were enriched in biosynthesis of different vitamins […]

[All emphasis mine.]

is the food that we eat affecting the microbiome?

Yes, just as certainly. I don’t have a publication handy but it should be obvious that our food influences our gut microbiome – in the extreme case, it can kill it (consider antibiotics side effects).

[1] Manimozhiyan Arumuga, Jeroen Raes & al., Enterotypes of the human gut microbiome, Nature 473, 174–180, May 2011.

molecular biology - What's the state of the art in designing and creating your own life forms?

The problem is of course very complex so take my answers as simplifications.

Most transgenesis so far has been done on unicellular beings (bacteria, yeast), which we can change as much as we want fairly "easily", plants, insects and some mammals. Notably, for the latter case, mice are the species which has been used the most for transgenesis, as they are cheap (compared to, say, using pigs), do not take lots of space, have big litters and a quick reproductive cycle (~20 days). Aside from mice we've seen GFP rats, pigs, dogs, cats, sheep and probably there is more, but I will mostly restrict my answers to mice (as far as I know there are big technical difficulties in applying transgenics procedures to something bigger than a mouse, but to be honest I could not explain you the details on this as I have never done it).

What features can be easily inserted into almost any organism easily?

Well, essentially, it is easy to give rise to monogenic traits (i.e. traits that depend on a single gene). Generally speaking, when you want to have more traits, or need more than 1 gene to have the trait you create single transgenics and then breed them together.

So, if your phenotype depends on the presence of gene A and B you will generate a (mouse) line expressing A, one expressing B, you breed them together and, if you are lucky, a part of the pups will be expressing both.

Next, I imagine that to design and create an artificial life-form will consist of three steps: 1. Figure out which proteins will give rise to those feaures, 2. Design a genome that will express those proteins in the right quantities and 3. Implant that genome into a cell and actually let the being grow.
Is the above sequence of steps correct, or am I missing something?

No, that is not how it is done!

There has been, to my knowledge, only one (very impressive) attempt to do that, a project led by Craig Venter at Celera Genomics. The project resulted in the creation of the first synthetic life form, named Mycoplasma laboratorium (see also the original paper on Science). Doing this for a multicellular being is, presently, science-fiction.

What normally you would do is to insert or remove just the piece of DNA you need in the genome.

There are different approaches to do that: for instance, you can start from embryonic stem cells, from fertilized oocytes or from spermatozoa.

This is the general process for making a transgenic mouse:

Source: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TransgenicAnimals.html

Now, depending on how you inject your gene you can distinguish between transgenics and knock-in mice. In a transgenic mouse you insert the gene somewhere in the genome and, although there are method to understand where it ended up you generally do not know.
Knock-in animals, instead, target a specific region of the genome. This is usually used in order to change an existing gene, to improve its function or to remove its function (knock-out animals). This process, called gene targeting relies on the biological process called homologous recombination.

So, why don't we just synthesize a new genome each time?
Aside from Venter's dream, the process would:

1. have incredibly high cost


2. be extremely complicated technically


3. be extremely long (mostly for reason 2)


4. suffer from the problem that there is so much we do not know about genome regulation in a bacteria, let alone in a mouse! You have to think that the genome is not just a series of genes one after another: there is a big part of regulatory regions that define things like the 3D form of the genome, which determines when and how much genes are accessible for transcription, when and where they are activated and so on. Also, more and more attention is now drawn to something called epigenetics marks, modifications of the DNA, or its associated proteins that can also modulate its transcription.

What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)

Quick answer: no you cannot.

1. Health authorities will be not very happy if you start to produce transgenic organisms in your garage


2. The sole cost of the reagents which you will need to create the transgene will be >$500. You would then need various machines (e.g. a thermocycler, probably a spectrophotometer, a hood, etc etc.).


3. I personally don't have a clue how one creates a transgenic plant, but I suspect it is not much easier than an animal. And definitely you don't want a mouse colony in your garage, do you?

An easy experiment you can do is extracting (fairly unpurified) DNA with stuff you have at home. More than that it gets really complicated.

the sun - Are we sure solar cycle is not related to the orbit of Jupiter?

The barycenter of the Solar System is the effect which should be considered physically. Although dominated by Jupiter other planets have substantial effect too, moving the Sun, with 99+% of all mass in the Solar System, around by entire Solar radii (700,000 km). Illustrated here

The diagram below I happened to stumble upon here. It shows the distance of the barycenter of the Solar System from the center of the Sun over time, with years on the circle. For some reason it spans from year 1773 to 1851. The peaks in the clover curve are regularly separated by about a sunspot cycle, or rather a bit longer. I suppose that the pattern of 2 big and 1 small sequential bulbs there reflects that Jupiter's and Saturn's orbital periods are about 3:1.

As StephenG says, that is just a numerological hint or coincidence, not an explanation. Another example is that the rotational period of the Sun is roughly similar to the orbital period of the Moon around Earth, with a similar error, but no one imagines any connection there.

It is however known that hot Jupiters, giant planets near stars, cause large starspots which rotate along with the planet's orbit. And the relatively tiny moons of Jupiter cause visible spots in the planetary aurora. Actually, the Sun causes an auroral "Jupiter spot"! So there are physics around which under certain conditions create sunspot-like effects.

Diagram: Barycenter distance from the Sun's center over time

Hubble image:The aurora on a pole of Jupiter in UV

star formation - Can dark matter decrease the Jeans length?

This is an area of active research. The current Cold Dark Matter (CDM) paradigm predicts bottom-up formation of halos, whereby smaller halos coalesce in to the larger halos we observe indirectly today through X-ray measurements of clusters. This suggests that small dark matter halos wouldn't survive to the present day.

There has been research in to the possibility of mini haloes surviving, but interactions with dense baryonic structures, such as stars, as well as streaming by an irregular galactic potential tend to wipe out any small overdensities in the distribution.

However, if such mini haloes did exist in the early universe they could have contributed to the collapse of primordial gas to form Population III stars. Simulations have been carried out to investigate such a model, with Population III stellar masses comparable to those expected $(sim100 Modot)$.

Why did the sensitive plant (Mimosa pudica) evolve its leaf-closing mechanism?

There are many reasons why Mimosa pudica (More commonly now referred to as the TickleMe Plant) may have evolved it's leave- closing mechanism. I have observed the movement when insects have landed on my plants. The insects apprear to be frightened by the movement as they do move on rather quickly when the plant collapses. The movement of the TickleMe Plant also occurs when the sun sets or if I place the plant in a dark room. This may be a way to reduce water loss by transpiration as the leaves fold down upon each other. Another reason for the leave movement may be to expose the few thorns found on adult plants. This could be another warning for herbivores to stay away. In cold weather TickleMe Plants will close their leaves as well, could this be a way to maintain its body temperature. All in all, this is the most amazing house plant and I am always learning new things about this plant and its beautiful cotton candy like TickleMe Plant pink flowers.

zoology - Can someone identify this bird?

It looks like a passerine bird, but I can't really tell the species without seeing the whole body. As for what to do with it, your best course of action is to leave it alone. Trust me. Once placed tissue paper over a pigeon's eggs to keep them warm, and the mother crushed them when she landed on the nest because she didn't see the eggs.

If there are eggs in the nest, try noting down what color they are. Passerines have colored eggs.

Why do objects burn when they enter earth's atmosphere?

You'll often hear that it's because of friction, but that's often not the main factor. For larger objects it's more likely the pressure they create.

In both cases the reason is the enormous speed, often tens of kilometers per second. When a larger object enters the atmosphere at these speed the air in front of it gets compressed so much that it becomes extremely hot. (Think of pumping up a tire; you're also compressing air and you can feel the valve becoming hot.) The compressed air will often disintegrate the object in the air, and then the debris may burn because of the heat. This is exactly what happened to the asteroid above Russia last year: it exploded with an enormous flash in the air, and left little traces on the ground.

This happens on other planets as well, if they have a sufficiently dense atmosphere. In 1994 the comet Shoemaker-Levy crashed into Jupiter. It disintegrated before entering Jupiter's atmosphere due to the strong gravitation, but when the fragments entered the atmosphere they could easily be seen lighting up as they burned up.

edit
Remember the Space Shuttle? It had heat resistant tiles on the bottom of the craft to protect it from burning when it entered the atmosphere, even though its speed is only a fraction of a meteorite's speed when that enters the atmosphere.
During the last launch of the Space Shuttle Columbia some material from the external fuel tank damaged this heat shield, and upon re-entry the heat and the highly pressurized air under the craft could enter it, causing the craft to disintegrate and kill all crew.

human biology - Why does hair turn grey or white, and why does it happen later for some?

Each individuals hair colour is determined by the particular pigment they produce (called melanin - the same stuff in your skin that makes you tan).

As the body ages this pigment (produced by the melanonocytes - cells that reside in the hair follicle) is produced less and less, until the hair is no longer coloured, and appears grey.

This is unique to each individual because it is a genetic (and therefore highly heritable) trait. Because it is in no way linked to mortality there is no selection pressure against greying hair.

The reason that the pigment is not longer produced is the gradual depletion of the stem-cell pool with age. This is common to many tissues, hair follicles being just one. As the 'pool' of stem cells is depleted, the melanocytes are no longer replaced as frequently, and thus less pigment is produced as we age.

the sun - Why do stars become red giants?

The destiny of a star basically depends upon its mass.
All its activities variety depends upon its mass.
If a star's core has a mass that is below the Chandraseckhar limit ($Msim1.4M_{sun}$), then is destined to die as a white dwarf (or, actually, as a black dwarf in the end).
The composition of the white dwarf, also depends upon the original mass of the star. Different masses will lead to different compositions.
More precisely, the more massive is the star, the heavier are the elements composing the final object.
This is because more mass means more gravitational potential energy

$dU = - frac{GM(r)dm}{r}$

that in turns can be converted into heat.

The hydrogen nuclear fusion starts, for the proton-proton reaction(that is the dominant process for Sun-like stars) at around $10^7 K$. This is the value that allows the particles to overcome their coulombian barrier (i.e., to fuse).
After the hydrogen fusion, when the most of the core is composed by helium, then of course the hydrogen fusion can't happen anymore. The core starts to collapse, and heats itself. For a Sun-like star, there is enough mass to compress up to a level that heats the core enough to start the He burning. But that is all. When also the Helium is converted into Carbon, the star has not enough mass to compress again up to a level that starts another nuclear fusion reaction. This is why the core nuclear reactions stop. For the shell burning question, it is important to understand two things: $(1)$ the shell structure of a star is only an approximation, and $(2)$ there is a gradient of temperature within Sun-like stars, that means that (besides the corona) the temperature increases when you go from the outside to the core. Now, if the core is compressed and became so hot to burn helium, the shell "outside" the core (that in a onion-like schema was within the radius of the previous hydrogen burning core), is still hot enough to burn hydrogen. The size of the helium-burning core is smaller than the hydrogen-burning core (this is compression by definition). The shell has still enough hydrogen, and contemporary is deep enough inside the star (that means high temperature), to allow nuclear fusion of hydrogen.
If the star was more massive, more things could happen, like heavier elements core fusion, and more and more burning shells.

Take a look at these:
Ref 1, Ref 2.

Ref 3 for some numbers too.

cosmology - could dark energy be a force coming from the hyperspace outside the universe?

Nobody really has any idea what "dark energy" is. But there is a principle known as Occam's razor. It can be expressed in various ways, for example "When an observation can be explained in many ways, the one with fewest assumptions should be used."

To explain the properties of dark energy as being due to changing pressure of hyperspace, requires the assumption that "hyperspace" exists, that it has a property that pressurizes the universe, that this "pressure" is changing, and that affects the rate of expansion of the universe.

There are other hypothesis: a cosmological constant, or a as yet undiscovered force field. None have much observational evidence, but have the benefit of requiring fewer assumptions.

As Rob mentioned what you describe is similar to "brane cosmology", in which the universe is embedded in a higher dimensional space. These could influence our space, by controlling the scale of a cosmological constant, making it small, but non-zero. As with much of string theory, the experimenters are well behind the theorists.

universe - Is it possible to create an artificial Black Hole?

It is thought likely that black holes would produce Hawking radiation and evaporate. We can't yet describe the end products of an evaporating black hole, and space is too warm to detect Hawking radiation anywhere. There are some recent new ideas regarding complementarity that are difficult to reach a decision on as well.

Hawking seems to be pulling away from the black hole concept recently. I don't know what to make of that.

Regarding particle colliders: every few years some team gets into the general news cycle with an announcement about detections that resemble particular models of black hole behavior. Miscommunication tends to produce journalism about real black holes being created. Now there may be developing interest in the possibility of the galactic core lighting up. Maybe that would lead to better journalism.

Eclipse -- Solar and Lunar

Eclipses are a temporal alignment of the 3 bodies mentioned. Because those bodies are in constant relative motion -- and you have to be in the right location relative to that alignment to experience it (at least for solar eclipses) -- not everyone gets to see them.

In particular, to view a solar eclipse, you need to be somewhere "in line" with the line from 1) the center of the earth to 2) the moon to 3) the sun ... Of course, moon's shadow on the earth is not just a point on the earth but a circle, so you don't have to be precisely "in line", but close (within a few dozen miles, but you can do this computation yourself if you know the diameter of the earth, moon and sun). The circular shadow that crosses the surface of the earth moves in time (as the moon revolves around the earth and as the earth moves about the sun) so different places see it at different times. Finally, when the eclipse is over, it means that the moon's shadow has moved off the earth's surface and back out into space (where it is +99% of the time).

For lunar eclipses, you only have to be able to view the moon (at night and during the period of eclipse of course). That means if you can see the moon (about 1/2 the surface of the earth can see the moon at any time) you'll see the eclipse! This is because the entire earth is casting the shadow on the moon and when you can see the moon, by definition, you are on the side of the earth that is casting the shadow and hence in position to see that shadow transit the moon.

Again: all these effects are temporal since the earth/moon system is moving constantly (relative to the sun).

Eclipses of Jupiter's Moon during Retrograde motion

The fact that eclipses are either "early", "on time" or "late" only depend on the distance between Jupiter and the Earth. Since the speed of light is not infinite, a longer distance means a longer delay between the actual eclipse and the time it is observed from Earth.

For superior planets, retrograde motion occurs around opposition, at a time when the distance between the planet and the Earth is minimal. So you should expect eclipses to appear early during retrograde motion. But note that the early eclipses are not a consequence of retrograde motion: they are both consequences of keplerian motion.

amateur observing - International Space Station

To a first-order approximation, the ISS (as all satellites do), orbits in a fixed plane around the planet. As the orbital period is about 90 minutes, and observational conditions that allow viewing usually last longer than that, you might expect that if you could see it at one time, you would be able to in the future.

There are two major effects that change the relationship of the orbit with respect to twilight locations on the earth. The first is the orbit of the earth around the sun. If the plane of the orbit were fixed, this would change where the orbit encountered twilight with a yearly cycle.

The stronger effect though is precession. At the altitude of the ISS, the non-spherical mass of the earth causes the plane of rotation to move (about 5 degrees a day). So it takes a bit more than 2 months to precess all the way back around. Depending on your latitude, you should have two good periods of viewing during the full precession.

This means that for periods of weeks or so, the ISS will be passing overhead during unobservable times (middle of the day/middle of the night). As the orbit continues to precess, it will begin to pass overhead closer to twilight and you'll have opportunities for viewing based on the specifics of the orbit.

galaxy - Halpha velocity fields of spirals falling into a cluster

What kind of impact would you expect ram pressure stripping / tidal interactions / harassment / interactions with the cluster potential (etc!) to have on the h-alpha velocity fields of infalling spiral galaxies?
What I mean is, how easy is it to detect such processes at work, and how are you able to distinguish between these different mechanisms (using also h-alpha intensity maps, rotation curves, optical morphologies if available).

Cheers!

galaxy - How does the concept of a universe with no center work?

When we talk about the universe, we are really talking about one of two things:

• The observable universe, which is everything we can possibly see.


• The Universe, which is everything that has ever existed, currently exists, and will exist.

The observable universe has its own center, usually the Earth. It is a spherical region of everything that we can see, essentially anything whose light has reached us. We usually refer to this when we say things like "there are $10^{86}$ atoms in the universe."

In reality, everyone has their own observable universe, and it can change depending on where you are. An exoplanet far away has its own observable universe, and can receive light from different places. Essentially, you are the center of your own observable universe.

I assume you're talking about the latter, though. The Universe (notice the capital "U") is all of space and time and its contents. Anything that has existed, will exist, and currently exists is part of it.

The Universe is thought to be infinitely large, so it can't have a center. The center of something is the point equidistance from the edges, but if something spans infinitely long, it would just keep going. It wouldn't have an edge, and thus it wouldn't have a center. You couldn't find the point equidistant from the edges if it just spans infinitely.

You might ask, "then where did the Big Bang start? Surely it must've been the center of the Universe, right?" Well, you can say the Big Bang happened everywhere. Before the Big Bang, matter filled most of the Universe's emptiness. It was essentially dense, and so got extremely hot to the point where no hadrons could form.

It is thought that this temperature caused space itself to expand. Essentially, more space was created in between all the matter, until everything was able to cool down. This is what we call the Big Bang. It didn't happen at a certain point, but rather it happened everywhere.

EDIT: I understand your confusion. Let me just clear some common misconceptions:

The Universe is not like a ball. Rather, you can think of it like a flat grid, and its "expansion" just means that the distances between objects on the grid are getting larger. In essence, more space is being created between the objects. That's what we mean by expansion — that objects are moving away from each other, since more space is being created between them.

Here's an easy analogy: imagine you are walking your dog. Suddenly, the ground begins expanding between you. You and your dog will separated and continue receding away from each other.

That's essentially happening everywhere: space is expanding between everything, so we are drifting away from other galaxies. The Universe is infinite, and we can constantly drift apart from other objects because space is being created in between us. Here's a GIF I made that might help you get it:

You can see how the galaxies drift apart as the space between them increases. And this happens everywhere in the Universe. So let's keep that in mind and clear up the Big Bang.

The Big Bang did not happen at a single point, nor did the Universe begin at a single point. The Universe is, and has always been, infinite. The Big Bang was just when the Universe's expansion really began — that is, when objects started drifting away from each other. The Universe was still infinite, but there was less space between the matter.

This density caused the Universe to get extremely hot and expand. So here, space itself was distorted and began to expand. More and more space was created between the matter, and still is now (although now it is mainly due to dark energy instead of heat).

light - When stars explode why can we still see them?

Because we are not moving at the speed of light.

From our point of view, light travels at the speed of light, and so events on a distant star are not visible until the light reaches us.

From the point of view of the photon, the universe is 2 dimensional (it is flattened by infinite Lorentz contraction) and there is no passing of time (infinite time dialation). The star and you are at the same point. Photons have a weird point of view.

Fortunately we don't have to worry about that, because we have mass and so we are not moving at the speeed of light. We have a 3d universe and we have a dimension of time. Thank Higgs we have mass!

telescope - Diameter of Astronomical Object Using Magnification

You could use your image to estimate the angular size of Jupiter that night. To find the actual diameter of Jupiter you would also need to know the distance that Jupiter is from Earth, and since Jupiter and Earth are both orbiting the sun, this distance changes.

You can find the distance with software (Eg Stellarium) or using Nasa's Horizons web interface (You will need to use the column labeled "delta" which gives distance in astronomical units). To find the diameter you will need to do some trigonometry. (Diameter = distance $times$ angular size in radians)

Alternatively you could use the published Diameter of Jupiter (70000km) and use your observations to calculate the distance.

To calculate the distance to Jupiter without knowing it's diameter requires more than a single observation. You will need to have:

1. A long enough series of observations to establish the orbital period and elements of Jupiter.


2. Knowledge of Kepler's laws of planetary motion


3. Knowledge of the distance of Earth from the sun, and to get this you can fund a expedition to the South Pacific during a transit of Venus.


4. A sharp pencil to do all the maths.

I'm being a little glib... The point is that it took more than 150 years of research between the broad acceptance of heliocentric solar system, and our knowledge of its scale, or the actual sizes of planets.

asteroids - Has someone ever captured footage of the collision of a meteoroid and a meteoroid?

It's a Needle in a Haysta... In The Pacific Ocean

Sometimes galaxies' gravities catch each other and they slowly merge. Even with billions of stars and planets merging with billions of other stars and planets, its theorized that almost no collisions take place. Point being that although it does happen:

• Space is mostly "empty" and statistical odds of collision are close to nil


• Unlike planets, astroids often have complex trajectories that aren't shared with other solid bodies (two asteroids very rarely even have a similar route, like planets and moons do)


• Humanity's ability to monitor the night sky is limited. We see very little of what happens out there.

Sorry to say but I think you're unlikely to find what you're looking for!

Next Best Bet:

Try Googling asteroid belt collisions? Or collisions in planet's rings? Those areas are rocks and ice, so a collision might be similar to an asteroid/asteroid collision.

No two asteroid collisions would be alike anyhow. They would vary widely. If one is huge and one relatively small, that collision would be very different from a collision where they were the same size. Or head on versus rear-ending, etc. So, you've got some artistic freedom for your video game.

Lastly, you could Google collisions of asteroids that hurdled into terrestrial planets or moons without atmospheres. Watching a collision with Earth or Titan does you no good because the atmosphere changes the dynamic of the impact.

Just remember to think of the physics. If the two sides colliding are well lit, there shouldn't be ice. Well-lit means the sun likely melted the ice. The ice is on the dark side and in the crevasses.

extremophiles - What is the most heat-tolerant organism?

I'd add that biochemically speaking, animals and microorganisms from thermal vents tend to have a higher GC content in their genomes, which makes it more thermostable.

All of the proteins are adapted to work at higher temperature. There are a higher number of salt bridges and specific hydrogen bonds in the proteins to stabilize them - more arginines, more glutamic acids, etc. While this reference says that Cysteine is less common, I imagine anything which is not in a reducing environment will have more disulfide bonds - e.g. for proteins on the cell surface.

Sulferous deep sea vents would tend to be reducing as is the inside of the cell, but maybe in the case of fresh hot water spring extemophiles this may be the case.

Reference:
http://peds.oxfordjournals.org/content/13/3/179.full

space time - How could universe inflate itself out of the very dense and curved early spacetime? Could it happen in a black hole too?

Great question! Sorry for this huge response, and it might not be a satisfying answer, but it'll address your questions.

Sadly, as with most of astronomy, the Big Bang is surrounded in mystery. It is one of the biggest uncertainties out there, and you'll come to this realization if you've researched it enough.

Most of what we can get out of the Big Bang is through extrapolation. If we observe the expansion of the Universe, we can presume that at one point, there was far less space between all the matter in the Universe. This is where things begin to break down, though.

Through General Relativity — which explains our modern understanding of gravity — and our extrapolation, we would reach the phenomena you're describing; the entire Universe would have originated as an infintely small point (called a singularity) singularity, from which matter was incredibly hot.

However, General Relativity begins to break down at those levels, since its equations cannot explain the conditions of such a universe accurately. For one, as you hint at, an infinite density and potentially infinite mass would likely have an infinitely strong gravity.

There is no place for such infinities in a proper mathematical description of the universe, and at that point, Einstein's equations — the basis for predicting the evolution of the cosmos — collapse. These equations provide us with unreliable results and we run into some of the problems you are describing.

Quantum mechanics is more fit for such small scales, but it fails to explain how gravity acts and what its role was at the time. Thus, this tells us that QM and GR are necessarily incomplete. Their equations cannot describe the Big Bang singularity in its entirety, especially since GR (which deals with large, high-mass phenomena) and QM (which deals with small, low-mass phenomena) are incompatible and cannot describe small, high-mass phenomena.

Thus, we're left with a lot of unanswered questions: did the Big Bang create the Universe, or was it simply an event in the Universe's history? Why would the Universe be compressed to such a small scale? Would the idea of an infinitely dense Universe goes against the presumption of an infinite universe?

There has long been hope that these questions can be explained within a theory of quantum gravity. Quantum gravity attempts to unify general relativity and the concepts of quantum theory (QM and QFT). These hopes have recently taken on a more concrete shape, with the help of what is called loop quantum gravity, and its applications to cosmology.

Quantum gravity is still unproven and hypothetical. The infamous string theory also tries to unify GM and QFT, but is unfalsifiable. Thus, the Big Bang is a point in time that astronomers really know little about. It's unfortunate and surprising, but it's something physicist are trying to overcome.

amateur observing - A good place to start?

Find a local astronomy club; they will help you get started, learn the sky, and show you different types of equipment. Also, read "Turn Left At Orion", H.A. Rey's "A New Way to See Them" and "Find The Constellations" to learn the sky.

And get a pair of 10x50 binoculars. These are the best "telescope" (actually, two telescopes!) to start with: inexpensive, wide-field of view to find objects (anti-soda straw effect), and 100x the light gathering power of the naked eye.

acid base - Side reactions of NHS Chemistry

The reactivity of NHS activated esters has mostly been desribed quite anecdotically. They are susceptible to hydrolysis in water, the kinetics of which is dependent on the nature of the NHS activated group (ester vs carnonate vs carbamate) as well as on the pH of the reaction buffer¹, which is one way to show that primary amines are not the only nucleophile which can react with NHS-activated esters.

As for the chemical groups that have been observed to react with NHS activated esters, I did find a couple of examples upon looking up this issue. For instance, the Zenobi group have attempted a quite systematic study on the groups that can react with doubly NHS activated cross-linkers. Citing the abstract² :

As soon as additional cross-linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type-1 cross-link formation. The reactivity is highly dependent on the pH and on adjacent amino acids.

In an earlier work, the reactivity of a biotinylation NHS-ester based reagent was assessed on a single peptide, [D-Lys(6)]gonadotropin releasing hormone. A similar reactivity of -OH groups was observed, with in addition that of the arginine guanidinium group³:

In addition to the O-acylation of Ser(4) and Tyr(5) in this peptide, we have also identified a novel biotinylation of the Arg(8) side chain.

Other groups have also observed some reactivity with cysteins (sulfhydryl groups), but in a situation where the reagent is included within a ligand of the target protein. One can assume, as do the authors, that specific positionning of the ligand within the binding site can lead to binding with a cystein group^4,5.

From these earlier work, one cas conclude, in answer to your question that although primary amines are the most reactive group for NHS-ester derivatization, other groups present in peptide side-chains (-OH for tyrosine, serine, threonine, guanidinium for arginine and sulfhydryls for cysteins).

The last issue raised in the question remains that of the secondary amine groups. It is widely accepted that pH influences strongly the kinetics of NHS derivatization, mostly through protonation of the amine groups which cannot act as nucleophiles in protonated state. This has been put to use in controlling the buffer pH in order to favor N-terminal reaction vs lysine side chain reaction. Although, in my experience, it is not at all a straightforward experiment and it is highly dependent on the nature of the derivatization group. One could hypothesize that since secondary amines are more basic then primary amines, the reactivity of secondary amines towards NHS should be reduced compared to primary amines, but I have no experimental or litterature proof for this part of the answer.

Is it pure luck that the voyager 1 survived to travel beyond our solar system in interstellar space?

A thing works fine until something goes wrong.
As far as I can see, the main external risks of the voyage were the radiation belts of Jupiter and Saturn, but those were already survived by the Pioneer 10 and 11 missions. After the planetary fly-bys, there are close to nothing external affecting the spacecraft.
The important risks therefore lies in the potential failure of of one of the spacecraft’s subsystems:

Power
The power source of the Voyager missions was an RTG. This requires no moving parts, and the decay of radioactive isotopes is not dependent on any external factors. This will probably work just fine until the power level has decreased enough.

Computer hardware
A computer has multiple potential weaknesses, the most common ones being overheating and memory malfunction, like what happened on the Galileo mission.
Radiation in outer space will over time slowly degrade electronic components. Magnetic memory will over time degenerate anyway.
It seems like what eventually will likely cause the Voyagers to fail is their nearly four decade old electronics.

Manoeuvring
The probes needed propellant for changing attitude, as well as for trajectory corrections. Corrosive propellant staying in the tanks for years are a major cause of spacecraft failures. See for instance the Akatsuki probe. 

observation - Are there any galaxies which fell out of sight horizon due to cosmic expansion?

No. In fact the opposite is the case.

It is a common misbelief that galaxies receding faster than the speed of light are not visible to us. This is not the case; we easily see galaxies moving at superluminal velocities. This does not — as I think most people would think — contradict the theory relativity, since nothing travel through space faster than $c$.

We see "super-luminal" galaxies

The recession velocity $v_mathrm{rec}$ of a galaxy is given by Hubble's Law:
$$
v_mathrm{rec} = H_0 d,
$$
where $H_0 simeq 67.8,mathrm{km},mathrm{s}^{-1},mathrm{Mpc}^{-1}$ is the Hubble constant. This law implies that galaxies farther away than
$$
d_{v>c} = c/H_0 = 4400,mathrm{Mpc} = 14.4 , mathrm{Gly}
$$
recede faster than $c$ ("Gly" means giga-lightyears). Objects at this distance have a redshift of $zsimeq1.5$.

Consider a photon emitted from a distant galaxy (say, GN-z11 at redshift $z=11.1$) in the past, in the direction of the Milky Way. What special relativity tells us is that locally, the photon always travels through space at $v=c$. Initially, the photon thus increases it distance from GN-z11 at velocity $c$. However, even though the photon travels toward us, its distance to MW increases, due to the expansion of the Universe. As the photon increases its distance to GN-z11, the same expansion causes it to recede from GN-z11 at an ever-increasing velocity. Moreover, as it travels toward MW, it will slowly "overcome" the expansion until it reaches the point where $v_mathrm{rec} = c$. For an infinitesimally small period, it will stand will wrt. MW, after which it will begin to travel faster and faster as measured from MW. Eventually, its velocity — still in MW's reference frame — will reach $c$, at which point it will have reached MW.

Thus, even though GN-z11 and MW recede from each other at $v_mathrm{rec} = 2.2c$, we are still able to see it.

We see more and more distant galaxies

There is, however, a limit to how fast a galaxy visible to us can recede, given by the distance $d_mathrm{PH}$ that light has had the time to travel since the Universe was created. Light comes to us from all directions, so we're situated in the center of a sphere of radius $d_mathrm{PH}$. This sphere is called "the observable Universe", and its surface (which is not a physical thing) is called the particle horizon (hence the subscript "PH"). Galaxies at the particle horizon are receding at $v_mathrm{rec}simeq3.3c$.

As time goes by, light from ever-more-distant galaxies$^dagger$ will reach us; that is $d_mathrm{PH}$ increases. In other words, the observable Universe always increases in size, and no galaxy visible today will ever leave the observable Universe, no matter its speed.

However, since future observable galaxies will be more and more redshifted, their light will eventually shift out of the visible range and into longer and longer radiowaves. Furthermore, the time between each detected photon will increase, so they will be dimmer and dimmer, and thus in practice, they will disappear.

---

$^dagger$_{Note that since large distances also means looking back in time (since the light has spent a long time traveling), we actually don't see galaxies this far away, as they hadn't formed this early in history. We do however see the gas from which the galaxies were born, as far back as 380,000 years after Big Bang.}

Table of absolute magnitudes of stars by spectral type and photometric band

There are a couple of standard papers containing the table you want.

Kenyon & Hartmann (1995) http://adsabs.harvard.edu/abs/1995ApJS..101..117K

Table A5 contains many colours for stars as a function of spectral type. You need to combine this with something that gives absolute V magnitude along the main sequence, like that of Schmidt-Kaler (1982), which can be found online at
http://xoomer.virgilio.it/hrtrace/Sk.htm

An alternative, that has colours for both main sequence and pre main sequence stars (though the absolute magnitude of a PMS star is age-dependent) is found in Pecaut & Mamajek (2013).
http://arxiv.org/abs/1307.2657

Online table at
http://vizier.cfa.harvard.edu/viz-bin/VizieR-3?-source=J/ApJS/208/9/table5

gravitational waves - How to derive the redshift of GW150914?

That is a lot of questions, but I can take them in order:

It seems GW has Doppler shift too. There is a GW spectrum with emission or absorption lines like optical spectrum?

Yes, GW has Doppler shift too, as they are travelling at a finite speed, but no, there are no emission or absorption lines we can detect it from. In EM radiation those are caused by the fact that light is quantized, such that certain wavelengths can be absorbed or emitted by atoms. As far as we know, gravity is not quantized, or the effect is too small to be measured. Any irregularity in the signal is then going to be continuous, and not wavelength specific. Detecting a spectra in gravitational waves is unlikely, but would strengthen the theories of quantum gravity and the graviton.

people take their masses derived seriously?

The method for the mass estimate is described well by @Rob Jeffries, but an even simpler point can be made: There are no other ways to measure their mass more accurately.

What does a 100HZ GW mean?

Hertz is the frequency, 1/s. That is the number of waves per second. 100Hz is comparable to normal sound waves.

What does the frequency stand for in the binary system?

As two objects revolve around each other, they would make two waves per orbit,resulting in a double frequency of the system's rotation.

DO you think the team win a Nobel prize only after other facilities like LISA find GW again?

This is almost certainty ending in a Nobel prize, and they do not necessarily have to wait till after the results are confirmed by other experiments. That said, verification by peer researchers is one of the core principles of science.

observation - Color of planets

Here are some values found by taking the hue from images, and adjusting the brightness to fit the albedo:

Mercury #1a1a1a Yes it is really that dark

Venus #e6e6e6 or perhaps a bit darker

Earth tricky as it is a mix of colors, and changes over the year
seems to average out as about #2f6a69

Mars #993d00

Jupiter #b07f35

Saturn #b08f36

Uranus #5580aa

Neptune #366896

You might find these surprisingly dark. Planets look like bright dots against the dark sky

human biology - What is the effective relatedness of inbreeding?

The easiest and most simplistic way to look at it is to assume that the amount of genetic material halves each generation. On average, humans are about 0.1% to 0.15% different from each other, so in order to get that you'd need around $1/2^{10}=0.0976%$ and $1/2^9=0.1953%$. The exponent numbers $2^9$ and $2^{10}$ are 512 and 1024, respectively.

Armatus' Dawkins bit is almost word-for-word what he actually said:

By the time we get to third cousins, "we are getting down near the baseline probability that a particular gene possessed by A will be shared by any random individual taken from the population".

Dawkins was ball-parking that a bit, although he was really talking only about a specific gene. The inbreeding coefficient is properly defined as:

The probability that an individual carries two identical-by-descent alleles at a locus.

Which takes care of some of the fudging. With that in mind, though, within eight generations the odds are less than even you even share any genetic material with an ancestor/offspring. That's actually a mathematical analysis (with plenty of assumptions!) from the mid-80s but it's an interesting read: you can look up values for certain relations going back a bit. The answer will vary depending on the background "average" you care about. Europeans, for example, are particularly closely related.

Indeed, "[g]enetic variation is geographically structured, as expected from the partial isolation of human populations during much of their history." If you want a perhaps easier-to-read explanation of some of the math, I would suggest this 2006 review, in particular box 2. From that, a silly back-of-the-envelope calculation from 0.1% related gives a path of around 10 individuals, which is a little more distant than your third cousin.

astrophysics - What more could be learned from a rare astronomical event if we knew precisely when it would occur?

This is actually related to a question I recently asked on Worldbuilding, but seemed more appropriately asked here.

To keep this from being too broad in scope, let's assume that someone figured out the exact moment that Eta Carinae will go supernova (I wouldn't hold it against anyone if they suggested a more scientifically interesting event).

Due to this foreknowledge, we could point every telescope we have in its direction for the main event. Is there any science we know we could do/learn from this event that we wouldn't get by reacting to it after the fact? I know such an event would generate data for a century or more to come, but I'm interest in the moment of the explosion.

Somewhat related, is there anything we would/could do now to prepare for it if this event were going to happen today?

orbit - Why doesn't Earth's axis change during the year?

Picture the Earth as a small ball suspended in midair, not moving, although it's rotating on its axis. Unless forces are applied to it, absolutely nothing will happen. That's conservation of energy (or momentum; you can work with it either way). Earth will not spontaneously start moving in one direction because that would violate conservation of translational energy and conservation of linear momentum. If that did happen, energy would be gained out of nowhere.

For the same reason, Earth will not start tilting to one side. This is conservation of rotational kinetic energy and conservation of angular momentum at work. Savvy?

So, yep, Keith is spot-on. You'd need some sort of torque to turn the Earth's axis like that.

So why does the Earth's axis move over 26,000 years (it does, by the way, just not one cycle per year)? Just like with the tides, as well as how Earth's rotation is slowing down, it's primarily the tidal forces of the Moon and the Sun at work, although the other planets do make some contributions to the overall changes.

I can add in some math if you want, but be warned, I'm learning it myself, so it won't be explained as well as you might like.

The other planets obey the same laws as the Earth, so their axes should point in the same direction throughout the year, ignoring the effects of axial precession.

coordinate - Why is declination positive in the northern hemisphere?

After quite an extensive search of dictionaries and books on astronomical nomenclature I came across this article that has a comprehensive review of celestial coordinate systems. And upon reading page 84 (8/14) I came across the answer to your question.

It would appear that the reason declination is used, as opposed to inclination, is that declination was first interpreted as a "deviation from standard" not an inclination of angular distance from a given point as we know it today.

This "deviation from standard" was first used to describe the motion of the sun along the ecliptic that "deviated" from the then widely accepted notion of all heavenly bodies following the line of the equator. It goes into more detail in the article but it would appear that when translated from Greek to Latin and then Latin to Arabic, the precise meaning of the word changed and evolved so that now the term declination refers to the angular distance of any celestial body.

Source:http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1942PASP...54...77W&db_key=AST