telescope - How useful are filters for spotting nebulae?

With an 8" scope, a filter will very likely give you better results than observing without a filter. Although a filter does block light, the crucial aspect is that a filter increases contrast (by blocking light pollution and extraneous wavelengths of light more than the nebula), thereby allowing you to spot low contrast diffuse nebulae (like IC59 and IC1318) much more easily. This is in fact more critical for visual observation than for photography because it is possible to increase contract in post-production with photography. You will find that visual astronomers go to great lengths to increase contrast--baffling, flocking, premium mirrors, etc.

Light pollution filters are broadband, meaning they allow all light except light emitted by streetlights. From darker skies (like bortle 4.5), this will not give dramatic results. I would recommend using an OIII filter to start with. The OIII filter is a narrowband filter, meaning it cuts all light except at a very narrow wavelength range from ionized oxygen. Very often OIII filters make the difference between being able to see an object and not being able to see it, even from very dark skies. As an excellent test of the OIII filter, check out the Veil Nebula too; from your skies, this object would be rather difficult without an OIII but rather stunning with an OIII filter.

solar system - What is the future of our universe?

What is the future of our universe?

Like StephenG said, nobody knows for sure. But we do have confidence that the universe is expanding, and we also have confidence that the expansion is speeding up. So extrapolating from that, the future looks cold and lonely and bleak. A bit like life for the older generation!

Is the universe heading towards a Big Freeze, a Big Rip, a Big Crunch or a Big Bounce? Or is it part of an infinitely recurring cyclic model?

I'd say the Big Crunch and the Big Bounce are out. The universe didn't contract when it was small and dense. Instead it expanded, and that expansion is increasing. So it looks like we're in for a Big Freeze. However I wouldn't rule out a Big Rip of sorts. Have a look at page 5 of this paper where Milgrom mentions the strength of space. Then think of the balloon analogy, but make it a bubble-gum balloon, in vacuum.

^{Image courtesy of the one-minute astronomer}.

The skin gets thinner and the balloon expands, then the skin gets even weaker, so the balloon expands even faster, and so on. Bubble-gum bubbles sometimes end badly, and there's something about this article by Phil Plait that strikes a chord.

Or is it part of an infinitely recurring cyclic model?

I don't know. I have no evidence to suggest that there's any kind of recycling going on, and I can't think of mechanism by which this might occur. I have of course read about "conformal cyclic cosmology", but I just don't buy it, along with other stuff from Penrose.

galaxy - How much of the Milky Way is visible to the naked eye from earth?

At any one time, an average observer can see about 2,500 stars in a clear dark sky. Note that eyesight varies and sharp-eyed individuals may be able to see a half-magnitude dimmer stars than the average eye (apparent magnitude is a scale in which each integer is $2.51$ ($100^{0.2}$) times brighter or dimmer than the next consecutive integer.) A very dark sky may enable magnitude $+7.5$ or even $+8$ stars to be seen, but in a typical "dark" non-urban sky the limit is often $+5.5$ to $+6.5$.

Supernovae can potentially be seen as far as 13 billion light-years (ly) away, essentially from the 'edge' of our observable universe. So, it's not saying much to say that a supernova might be seen across a distance of 100,000 ly.

Some types of supernovae can be over $-22$ in absolute magnitude — where absolute magnitude is defined as their apparent magnitude if they were observed from a 32.6 ly distance (to be honest, I'm not sure if supernovae absolute brightness is defined in exactly this same way). By way of comparison, the Sun's abs. mag. is $+4.8$ (lower numbers indicate brighter stars).

Because of the dust and interstellar medium, the possible distance we can see is just a small fraction of the size of the Milky Way. In reality, few stars are bright enough to be seen over 400 ly away. Deneb which has an estimated distance of 2,600 ly (but may be as close as 1,550 ly, the large uncertainty is due to its variation in brightness). Only 6 visible stars are thought to be farther from us than 1,000 ly.

So, to sum up, looking inwards into the Milky Way, our visibility is very restricted to the nearest 1,000–2,000 ly (while the MW disk's radius is 50,000 to 90,000 ly and we're about 27,000 ly on this side of center, but only the brightest stars are visible from more than about 400 ly away.

While looking away, we can see the Andromeda Galaxy (but not its individual stars) which is 2,500,000 ly from us. In other words, most people blame dust for the poor visibility, but that's mostly only relevant for telescopes. For us, our limited eye-sight is the real barrier (not to mention the dearth of really dark skies).

evolution - Why do eukaryotic organisms have introns in their DNA?

Prokaryotes can't have introns, because they have transcription coupled to translation. They don't have time/space for that, since intron splicing will stop the coupling. Eukaryotes evolved the nucleus, where splicing can be done. The ancestor of eukaryotes that developed the nucleus could afford more variability (because of introns) than species without it, so they had a greater fitness.

Bacteria can't afford high complexity compartmentalization, a process that requires a lot of available energy per gene, a eukaryotic cell can have tens, hundreds or even thousands of mitochondria that have similar energy output to a bacterial cell, while having a genome about 100-500 times smaller (16 kb of a human mitochondria compared to 4.000 kb for a E. coli cell).

I hope that clarifies your doubts, and you can see that this is a debatable answer.

Sorry for my bad English.

Sources:

Lane & Martin 2010.

Martin 2011

bioinformatics - When does BLAST fail to align 2 DNA sequences?

I am not sure I understand BLAST correctly.

When using BLAST in DNA and protein, they are different. There is a threshold T in protein "seeding" step, which means the seeding sequence is not perfectly matched. However, it seems there is no T in seeding step and we are looking for perfect match and extend them to neighbouring sequence.

So, if there is no word length 5 exact match between these 2 sequence, BLAST will fail.

Is ours the first universe?

It is very hard to tell whether we are in a unique Universe. The difficulty is the closer we attempt to probe in the fractions of a nano second after the Big Bang our current forumlations of Gravity and the three our fundamental forces do not work. So it is very hard to tell whether our Universe is unique.

However, with all that said, my own personal belief is that our Universe is not unique. The estimated time for random quantum fluctuations to generate a new Big Bang as quoted in the page that you have referred to is an UNIMAGINELY large time scale.

My question I will pose back to you is, how could we ever tell we are a unique Universe, or part of a collection of Universes?

evolution - How do we know that dinosaurs were related to lizards and/or birds?

In general the answer is always the same: you construct a phylogenetic tree. In order to locate different species on this tree in relation to each other, you use various features to compare which species are more similar to each other than others.

The best way of doing this is by comparing their DNA sequence, especially orthologous genes (i.e. genes common to the species compared).

Unfortunately, genetic sequences usually aren’t available for extinct species. You can still compare homologous features though. For instance, the class of mammals are all characterised by the possession of mammary glands. Similarly, all vertebrates have a vertebral column and all aves are feathered, warm-blooded, egg-laying vertebrates.

The collection of many such features from fossile records allows the creation of more or less detailed phylogenies. The Wikipedia explanation mentions several transitional fossil forms which trace the evolution from dinosaurs to modern birds via several intermediates. All of the inferences are based on anatomical resemblance.

This may sound weak evidence but in fact anatomical homology has proved to be sufficiently accurate in constructing other phylogenies, where we have been able to verify the correctness using genome comparison data. So while there is much uncertainty about the precise branching point of birds from dinosaurs (or maybe archosaurs), there is near-certainty that the common ancestor of birds and dinosaurs was, in fact, an archosaur.