text:
What is a focal copy number variation?
Often, genetics studies, especially genome wide ones, talk about "focal copy number variations" in genes or regions of the chromosome. I know what a copy number variation is. What does "focal" mean, exactly?
Are there non-focal CNVs? What are they? Where did the term "focal" originate? Is there a specific paper that coined (and hopefully unambiguously defined) the term?
A search for "focal copy number variation" on Google Scholar should turn up plenty of papers about it. The GISTIC algorithm is a popular computational method for finding putative CNVs- so information about this algorithm may have some clues.
A documentation text for one GISTIC implementation on the Broad Institute's website states the following:

(8) Broad or Focal: Identifies whether the region reaches significance due
  primarily to broad events (called “broad”), focal events (called “focal”), or
  independently significant broad and focal events (called “both”).

You could probably even call an aneuploidy (variation in chromosome number) a CNV. So that’s pretty large-scale.

A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next.
From: the NIH Glossary

Focal CNVs are regions of repeated genetic information that only span a small proportion  (<25%) of the chromosome arm (although this does not seem to be a consistent rule), and can contain few genes. CNVs greater than this are termed either 'large-scale' or 'broad'.

Here are some relevant papers I came across (no doubt there are more);
This paper is about a program (VarScan2) the authors have made to robustly detect somatic mutations and CNVs;

To identify SCNAs [somatic copy number alterations], VarScan 2 compares Q20 (base quality >=20) read depths between tumor and normal samples for contiguous regions of coverage ... Therefore, we apply a circular binary segmentation (CBS) algorithm (Seshan and Olshen 2010) to delineate segments by copy number and identify significant change-points. A subsequent joining procedure merged adjacent segments of similar copy number and classified them as either large-scale (>25% of chromosome arm) or focal events.
From: Koboldt D, et al, 2012.

I continued searching, as I wondered whether this was a standard definition, or just one used by the authors.
This paper is reporting bacterial genes that drive focal chromosomal aberrations, but do not give a great definition (as it seem quite arbitrary to me);

Many of these [chromosomal] aberrations concern large chromosomal regions, which makes it difficult to identify actual driver genes. Increased resolution has led to the detection of focal chromosomal aberrations, defined as 3 Mb or smaller in size [5–8]. Inherent to their size, focal aberrations contain a small number of genes, facilitating driver gene identification
From: Brosens R, et al, 2010.

This extract is from one of the studies referenced by the previous paper (when they mention their definition of focal CNVs). This paper is about CNVs in different tumour cells;

Primary tumors contain varying proportions of nonneoplastic cells thereby obscuring focal amplifications, defined by the increased copy number of a small region of the genome, from simple gains of whole chromosome arms.
From: Leary RJ, et al, 2008.


text:
Equation for accurate prediction of PCR yield
It is a cliche of freshman biology labs to point out that "every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount". However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 grams of DNA. This is clearly absurd and not the case.
Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an upper bound - but even so, a very uninformative one), and in practice, yields will fall far short of it because:

Every single duplex of DNA does not denature at each cycle
Primers do not bind to every single molecule of DNA at each cycle
Not every DNA strand gets bound by a polymerase at every cycle
Not every polymerase that binds manages to complete the entire product in time in every cycle
The reaction inhibits itself by depleting dNTPs
The heat denatures the reaction by degrading enzyme

In fact, cursory examination of qPCR output often follows saturation kinetics:

Mathematical methods for modeling qPCR are obviously well developed.
My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?
For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).

An expected efficiency for a typical PCR is 80%, meaning each cycle multiplies the copy number of the targeted DNA sequence 1.58 times.
Firstly, it makes more sense to refer to the amount of DNA in a polymerase chain reaction in terms of copy number or in terms of moles; the number of DNA molecules of interest is what the reaction is operating on, and the mass of product generated is a function of the length of the product (and, to a lesser degree, on the composition of the product).
The following discussion is sourced from this URL: https://www.csun.edu/~hcbio027/biotechnology/lec3/pcr/p.htm
According to Perkin-Elemer, copy-number amplification of 100,000 fold of the targeted sequence of DNA can be expected from a PCR with 0.1 ng of Lambda phage DNA (a well-characterized and standard DNA isolate) in a 100 µL reaction with > 25 cycles of denaturation, annealing, and extension.
In the above 100,000-fold amplification example, if the targeted amplicon were to be 500 bp in length, the estimated molecular-weight of duplex DNA of 500bp is 325,000 g/mol (based an average base-pair having a molecular mass of 650 g/mol).
The Lamdba Phage genome is 42,502 base-pairs in length.
42,502 bp × 650 grams/mol/bp = 2.762×10^7 grams/mol.
0.1 ng Lambda DNA -> 0.1×10^-9 grams.
0.1×10^-9 g ÷ 2.762×10^7 g/mol = 3.619 × 10^-18 moles.
3.619 × 10^-18 moles × NA (Avogradro's Number) = 2.179×10^6 copies, or 2,179,000 copies.
2.179×10^6 copies × 100,000 = 2.179×10^11 copies.
2.179×10^11 copies ÷ NA × 325,000 g/mol = 1.176×10^-7 grams of sequence.
1.176×10^-7 grams is equal to 0.117 µg or 117 ng.
An amplification yield of 100,000x after 25 cycles would mean at each cycle 1 template would yield 1.58 templates for the next round of synthesis.
How was this calculated? If c is the number of copies made per round of synthesis, then:
c^25 = 100,000 = 10^5
so c^5 = 10
and so 5(log c) = log 10 = 1
so log c = 0.2 and c = 1.58 (approximately)

(Or you could calculate the 25th root of 100,000 on a calculator, if you prefer.)

If we obtain 1.58 copies instead of the theoretical maximum of 2 copies, then the efficiency of the reaction could be said to be 79% (because 1.58/2.00 = 0.79).
One reason this calculation is important is that a slight loss of efficiency is magnified through the amplification. A reaction may appear to have not worked if the efficiency drops (in each cycle) by just a few percent. Optimization is critically important in the polymerase chain reaction.

Here is a useful website for calculating the molecular mass and number of copies of double-stranded DNA molecules based on their length in base-pairs. http://cels.uri.edu/gsc/cndna.html

The equation is correct, but there's an additional asymptotic limit to a maximum concentration of product depending on the starting concentration of NTPs, template and primer pairs in solution too.

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text:
How does heat shock transformation work?
What exactly happens when competent cells like DH5ɑ are heatshocked with DNA present? How does the DNA get inside the cells?
Specifically, why are all the steps necessary? What if you heatshock right after adding DNA? What if you don't put on ice after heatshock? What does the calcium chloride do? What actually happens when cells are "competent"? What governs transformation efficiency (besides obvious things like amount of DNA or cells)?
To make it clear what I'm talking about, I use a protocol like the following:

Take cells out of -80C and thaw on ice for 5 min.
Add 1 ul (~500 ng) plasmid DNA to 50 ul cells, mix gently with pipette tip.
Leave on ice for 30 min.
Put in 42C water bath for 45 sec.
Put on ice for 10 min.
Add 950 ul LB, put in 37C for 1 hour.
Spread 300 ul of the culture on LB-agar plates with appropriate selection.

I usually get thousands of colonies from this (in fact, often 1:10 or 1:100 dilution is necessary so I can actually get isolated colonies). Even if I skip the outgrowth, I still get hundreds.
I don't have my competent cell protocol, but basically I use that one rubidium chloride that everyone uses: DH5ɑ cells are washed with some buffers, suspended in a solution with CaCl2 and RbCl, then frozen in liquid nitrogen. I never actually measured, but usually the concentration of cells in the frozen aliquots is about 10 times as many as you would get from an overnight liquid culture (they are spun down and resuspended in a small volume).

I think it is still true that no-one knows "exactly" what happens. There is a piece of received wisdom that by growing cells at 37C then shocking them at 42C, the membrane becomes more fluid (true) and this helps DNA to cross this barrier. If anyone writes an answer with evidence for this I for one will be very interested.

@AlanBoyd I have heard many scientists also claim that nobody knows. I have always found it bizarre. How can such a simple, popular technique not be well understood? Are the experimental techniques to study it not available? Or does nobody bother because they think even if they figure it out, nobody will cite it or care?

I also learned/was told the same mechanism is responsible for E. coli transformation as written by Alan Boyd. This paper (Large-volume transformation with high-throughput efficiency chemically competent cells. Focus 20:2 (1998)) seems to get referenced a lot about the procedure; however, I do not know if the study offers any mechanistic explanation of heat-shock based E. coli transformation as I cannot seem to be able to access/find it.

Can't be sure about this but natural competence is affected by environmental stress.. May be it is the same case with chemically induced competence. See this post.

Heat shock transformation alters membrane fluidity creating pores:

A sudden increase in temperature creates pores in the plasma membrane of the bacteria and allows for plasmid DNA to enter the bacterial cell.

Reference: Journal of Visualized Experiments. Bacterial Transformation: The Heat Shock Method. 2014. http://www.jove.com/science-education/5059/bacterial-transformation-the-heat-shock-method

The change in temperature alters the fluidity of the semi-crystalline membrane state achieved at 0oC thus allowing the DNA molecule to enter the cell through the zone of adhesion.

Reference: Anh-Hue T. Tu. Transformation of Escherichia coli Made Competent by Calcium Chloride Protocol. 2008-2013. American Society for Microbiology

... heat-pulse (0 degrees C42 degrees C) step of the standard transformation procedure had lowered considerably outer membrane fluidity of cells. The decrease in fluidity was caused by release of lipids from cell surface to extra-cellular medium. A subsequent cold-shock (42 degrees C0 degrees C) to the cells raised the fluidity further to its original value and this was caused by release of membrane proteins to extra-cellular medium.

Reference: Panja S, Aich P, Jana B, Basu T. How does plasmid DNA penetrate cell membranes in artificial transformation process of Escherichia coli? Mol. Membr. Biol. 2008 Aug;25(5):411-22. doi: 10.1080/09687680802187765. PubMed PMID: 18651316.

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text:
What are the Gateway clonase enzymes?
The Gateway cloning system utilizes what Life Technologies refers to as "Clonase enzyme mix" to catalyze the BP and LR reactions.
What is in this enzyme mix? Is there a sequence for them?

I would imagine that if they're not listed on the datasheet, you're not going to be able to find out what they are...

@MattDMo The manual (publication number MAN0000282) does mention that they are "Int, Xis, IHF". Are these actual genes? I would expect they are engineered further, but do the native genes not work at all?

@Superbest they are recombinases. Usually the enzymes that are used in the lab are engineered to some extent, for better stability and efficacy.

The prototypes for these proteins are:
the bacteriophage λ proteins Int and Xis, required for, respectively the integration and excision of prophages. They are, as mentioned by @WYSIWYG, recombinases.

Genetic map of bacteriophage λ (source of image)
the original Ihf (integrative/integration host factor) was identified as an E. coli protein required for prophage integration.
As you might expect Int and Xis proteins occur in many phage genomes, and in integrated prophages in bacterial genomes, and Ihf, because it is involved in bacterial DNA replication, is ubiquitous. I imagine the actual source of the proteins used by Life Technologies could be a trade secret.


text:
Do tall people have more cells?
Within a single species, how does the relative number of cells in the body relate to the relative size of the organism?
Let's say we take two humans, one of them is 6 feet tall and the other one is 5 feet tall.  They have similar BMI, age, physical condition, genetic background (aside from height) and are the same sex.
Does the tall one have more cells? Or does he have bigger cells?
PS: Ideally, answers should be backed up by appropriate sources.
PPS: While I'm grateful to everyone for the very nice answers I got, I should point out that I'm waiting for an answer which includes references to accept it.

In retrospect, I have presented a false dichotomy. As jarlemag has pointed out, a tall person may have neither more cells nor bigger cells - their height (or size, see discussion in buzrw's answer) may be due to more non-cellular mass (eg. more ECM).

This is really the most fundamental concept of Cell Biology, so good question. If you look at the size of a any cell from a whale and compare it to the size of any of cells from a mouse, they are in fact quite similar, despite the extreme difference in the overall size of the organisms they are from. There is a reason why cells are small, and it has to do with the fact that they survive based on their ability to absorb enough nutrients from their environment. As a cell gets larger it needs more to survive (because it has a bigger mass). A bigger cell has also has a larger surface area around it (so it can absorb more nutrients).
HOWEVER, there gets to be a point where the mass of the cell is too large for the surface area to compensate for. Mathematically this is shown by what is called the "surface-area-to-volume ratio". Basically, it states that as a a sphere gets larger, the volume increases at a higher RATE than the surface area. So there is a reason cells get only so big, the 60's horror movie The Blob was not scientifically accurate, a single-cell that large (the blob) would not have enough surface area to absorb enough nutrients to sustain itself. Taller (or bigger) people have more cells (not bigger ones) than others.
Effects of osmotic pressure can alter cell size slightly.
When you are talking about taller individuals, you are (I think) really meaning larger people, people with a higher mass. And yes, they have more cells.
Another topic of Cell Biology you may want to explore is apoptosis. Let's say you have two individuals both 180 lbs. one of them is 5' tall and the other 7'. Both these individuals have the same number of cells, but the taller one has a higher percentage of them in the superior and inferior regions of the body. It is the process of apoptosis that sculps an organisms shape.

You are correct that I, in effect, meant "larger people", because I specified that their BMI is similar.

+1 sounds like a good answer for the cell biologist that I am NOT. You may add some elements about how (and why) cell size varies from one species to another. This article also might be of interest.

@Remi.b I'm not sure if that paper applies to my question per se, but it was a fascinating read! Thank you.

Well written, but I have 2 issues. 1. I can't imagine that 2 individuals of the same mass always have the same number of cells! Intracellular "stuff" (e.g. proteins & other macromolecules) varies b/w cell types -- think about adipose with a "full" vacuole vs RBCs. 2. Your post does not address extracellular "stuff" -- either space or non-cellular material (e.g. H2O) -- which could account for greater body size (both space and mass) . I know it's an old post, but please add some citations; otherwise I have to downvote as a "sounds good but probably isn't true" post. Thanks

Not sure it is proven, but this paper makes use of the assumption: West et al, PNAS 99:2473, http://www.pnas.org/content/99/suppl_1/2473.full
Btw, this paper may be relevant for you as it focuses on the metabolic activity, which is not quite propotional to body mass (power 3/4: it's growing slower)

With respect to the relationship between body mass and metabolic rate: https://biology.stackexchange.com/questions/25912/statistical-method-for-characterizing-the-relationship-between-body-mass-and-met/66659#66659

The taller person has more cells. Most cells can only lengthen up to a certain point. Whilst the neuronal cells will be longer and likely some others, the rest of the cells will just be of larger number.

Just to play the devil's advocate, are there actually any sources that confirm this? Couldn't it also be that tall people have the same number of cells, but with more extracellular matrix and larger spacing between the cells?

@jarlemag That's a very good point (which I originally missed); I added a comment to my question to clarify.


text:
What is a suicide plasmid?
What is a suicide plasmid?
Example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737453/ mentions a "suicide vector". See also http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/plasmids/allele-exchange.html which also mentions them.

While the answer to this is quite straightforward (see mine below), finding a source is less so. I will accept an answer which provides an appropriate reference for the definition.

Check out this page - it has a long discussion of suicide vectors, and from the note at the bottom it was adapted from a published source.

As can be inferred from the Shanks et al. paper linked in the question: In molecular biology, "suicide plasmid" is a term that refers to a plasmid which is replication incompetent.*
Plasmids normally bear a sequence called "origin of replication" Ori which marks the plasmid for replication by the host cell. Plasmids that lack this Ori will not be replicated during cell division, and will become diluted away and/or degraded after a few generations. Hence the name: The plasmid will "commit suicide" by promptly becoming eliminated from the population of DNA molecules inside each cell.
Note that because not all Oris are universal, the same exact plasmid may be a normal vector in one species (eg. E. coli) and a suicide vector in another species (eg. P. aeruginosa) - which is logical: If a vector can't replicate in any species at all, how do you produce this vector in the first place? (there are ways, but they are laborious)

*: I am unable to find an authoritative source for this definition. The other two paragraphs are common knowledge.


text:
How do I put on a labcoat?
Let's assume I am wearing a labcoat for two reasons:

Prevent the various bacteria, proteins, skin cells and substances on my clothes and my skin from contaminating my experiments.
Prevent various dangerous things from the experiment getting on me, and ruining my clothes or endangering my health (eg. toxic chemicals, pathogenic bacteria, ecotropic virus, etc)

A labcoat is an imperfect, but valuable barrier against such hazards. Perhaps a droplet of some Nasty Substance™ ends up flying towards my arm, but instead of getting on my exposed skin, hits my labcoat.
However, what happens when I take off my labcoat? My gloves, which have just been in contact with lots of Nasty Substance™, go through the sleeves of the coat, possibly smearing the substance all over the inside of the fabric. When I put on the coat again the next day, now my skin is in contact with these smears.
I could remove my gloves before taking off the labcoat, to avoid this smearing. But this time, I have to touch the labcoat with my bare hands as I remove it. Remember the Nasty Substance™ that was stopped when it splattered on the outside of the fabric instead of my skin? What if I know end up touching that?
I know that for truly dangerous conditions, there is specialized equipment and detailed procedure. Even at BSL2+, traditionally disposable labcoats are required, rendering the issue somewhat irrelevant. So let's assume the highest level below that, BSL2, as the context for answers.
In short, what is the correct way of putting on and taking off gloves and non-disposable labcoat when working in BSL2 conditions?

I use a labcoat when working with RNA or Iodine-125. I always do labcoat first, then gloves. When taking the coat off, I remove gloves first, then labcoat. This is usually sufficient, but if you're working with stuff nasty enough to matter, the coat won't provide protection for long. If it's acid, get the coat off ASAP before it soaks through. If it's biological you probably should have been working in BSL3 or 4 conditions. If you're working with something bad enough that a few drops on your labcoat will hurt you, your labcoat is not proper protection.

Wear two sets of gloves.  First, use nitrile gloves, not latex for this. 4mm or thicker is a specification I would recommend to avoid tearing.  Latex will bind too well to itself and tear easily with increased friction etc (same logic behind not using two condoms).  Also, use a coat with an elastic cuff on the sleeve.
So here's the breakdown

Put on first set of gloves
Put on coat over gloves.  Decon if needed for application.
Put on second set of gloves.
Science
Take off second set of gloves.
Decon as needed for your health
Take off coat
Take off first set of gloves

I can find sources for this, but I've been doing ABSL2 and BSL3 for a while, and they always go through this in safety training.
Edit: My internal nagging to site got the better of me, so some examples that recommend double gloving:
http://oehs.vcu.edu/chemical/labsafe/perchloricacid.pdf
https://extranet.fhcrc.org/EN/sections/ehs/hamm/chap3/section6.html
http://orsp.umich.edu/policies/um/committees/BRRC/ADDITIONAL_PRACTICES_revised_8_7_14.pdf
http://ehs.columbia.edu/carcmutguide.html
I could go on, but I think you get the idea.

I would say that double gloves are overkill for BSL2. Above that level I would agree, but they are causing some problems and inconveniences, too. So I would do lab coat first, then gloves and vice versa. And make sure that you put the lab coat in the laundry regulary or when something get spilled on it. It is also a good idea to have some (probably older) clothes in the lab available for changing if necessary.

@Chris I agree it's a bit overkill, but it is the correct way to handle the scenario described.  It can also be used in BSL2 conditions where there are chemical concerns on top of biological ones.  I think the "I'm worried about a drop" scenario is only likely to be an issue with chemical concerns (but is actually unlikely altogether).  I would be curious to know if there are more users of BSL3 and higher or chemicals which require double gloves. I lean towards chemical, but that's just a guess.

I would say it really depends on the chemicals. Chloroform breaks through almost all gloves used in the typical biology/biochemistry lab, phenol gives a little more time.

The National Academies Press publishes reports on lab safety http://www.nap.edu/search/?term=Lab+safety PDF downloads are free. Chapter 1 of Safe Science; Promoting a Culture of Safety in Academic Chemical Research reads like the script for a horror movie of what can and does go wrong in and academic lab setting.


text:
What is the difference between second and third generation sequencing
I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to make sure that I understand it correctly.

Is second generation sequencing the same as next generation sequencing?
Is Sanger sequencing the first generation?
As of today, is there any commercial 3rd generation sequencing technology in use (or is it still in development)?

If there is any paper reference that could explain all of the above then it would be really great.

More recent related question: https://biology.stackexchange.com/questions/105101/what-is-the-difference-between-4th-generation-sequencing-and-ngs

I'm assuming you mean DNA sequencing (excluding things like RNA-seq).
Is Sanger sequencing the first generation?
From Metzker 2010:

The automated Sanger method is considered as a "first-generation" technology

Some of the technology that was in development when this review was written is no longer in development, but this is still an excellent review and a great place to start.
Is second generation sequencing the same as next generation sequencing?
Also from Metzker 2010:

and newer methods are referred to as next-generation sequencing (NGS).

The "newer methods" in the review are:

Emulsion PCR based like Roche/454
Solid phase amplification like Illumina/Solexa
Single molecule like Helicos BioSciences and Pacific Biosciences

As of today, is there any commercial 3rd generation sequencing technology in use (or is it still in development)?
The development of single molecule methods (third item in the above list) has historically taken longer than the other two, so sometimes they are referred to as third generation. However, note how Metzker above considers them all "next-gen".
A recent paper from PacBio itself makes the distinction of halting:

Second-generation sequencing (SGS): Sequencing of an ensemble of DNA molecules with wash-and-scan techniques.
Third-generation sequencing (TGS): Sequencing single DNA molecules without the need to halt between read steps (whether enzymatic or otherwise).

Ultimately, I think the "generations" are more useful to make the "Sanger vs. Not Sanger" distinction. Sanger sequencing is very different than next-gen in terms of what kind of experiment you can do and what sort of data you obtain.
Past that, the number of a generation is more of a marketing term. For instance, at the bottom of the PacBio paper:

Conflict of Interest statement. All authors are employees of Pacific Biosciences and own stock in the company.

In practice, PacBio competes with second generation platforms. It is in their interest to say their technology is on "another level" compared to what's available on the market, but in practice, this is debatable.
Anyhow, to answer your question:

There is a technology in use and commercially available which has been referred to as third gen (PacBio)
There was a technology in development that falls under most definitions of third gen (Helicos), which went bankrupt in 2012
There is a technology in development (ON MinION) that is single-molecule based and was introduced after PacBio, so if PacBio is third generations, so is MinION (although the MinION is apparently very different from PacBio)

Oxford Nanopore shipped MinIONs to a some researchers a few weeks ago.

@5heikki I was actually unfamiliar with MinION. Does it count as third-gen? Feel free to edit my answer and add it (or submit your own).

In my opinion referring to Sanger sequencing as 'first generation' is historically incorrect. Maxam-Gilbert sequencing preceded it and produced lots of useful results - see Addendum in my answer here: http://biology.stackexchange.com/questions/17598/how-was-restriction-site-of-ecori-sequenced/17603#17603

Ultimately we, as scientists, shouldn't get hung up on the exact use of this terminology since it is clearly now just part of marketing the latest advance in sequencing technology.

@AlanBoyd Strictly saying, it is not about precedence: the distinction between the first generation and the next generation is in terms of throughput. In this respect both Maxam-Gilbert and Sanger belong to the same class of methods.

@har-wadim thanks, I hadn't thought of it like that. What increase in throughput constitutes a generation?

@AlanBoyd I am regrettably not well informed about the history of sequencing technologies past the last decade. I think you have a good point, edits to my question are welcome.

An increase in throughput to discern between different generations is not true for second vs third generation sequencing (PacBio has the advantage of generating long reads but at a throughput lower than that of the second-generation sequencers: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-699 )

The sanger sequencing and Maxam-Gilbert sequencing methods are considered the first generation sequencing methods. Next generation sequencing is a term used to refer to the sequencing methods that came after those two methods offering high throughput sequencing. Therefore, second and third generation sequencing are collectively called next generation sequencing.

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text:
Transverse diffusion of lipids in red blood cells
The membrane of a human erythrocyte has polarity:

Phosphatidylethanolamine and phosphatidylserine are predominantly on the inner side.
Phosphatidylcholine and sphingomyelin are predominantly on the outer side.

Although these can diffuse in the lipid bilayer, they stay on only one side of it. How is this sidedness preserved?

Looks like a homework question. I would start by looking up flippases.

I need answer to this Question urgently Kindly plz help me..

flippases, and polarity is in many cell types, not just erythrocytes.

There are two reasons for the asymmetry for the lipid composition of membranes in cells usually.
The first which was mentioned by @Superbest is proteins which are called 'flippases' which describes three broad categories of proteins which facilitate the translocation of the lipids through the membrane, despite the fact that they all have polar or even charged head groups.
This is not really an answer to your question here though - they will have little to do with asymmetry of lipids in erythrocytes I think because the these proteins will only allow lipid diffusion to equilibrium on either side of the membrane.  To force an energetically unfavorable mixture of lipids they would require the use of energy.  While some lipid translocases can force the composition to change against the equilibrium, these seem to require ATP and human erythrocytes do not have mitochondria.
The second, probably better answer is that the lipid composition of a membrane at equilibrium is dictated by of the curvature of the membrane.  The outside of a membrane takes lipids with larger head groups and shorter or fewer chains, the interior will compose more of lipids with smaller head groups and longer and more aliphatic chains.
This capacity of a lipid to take up a greater volume in its head group vs its non-polar end is called its 'intrinsic curvature'.
Erythrocytes have some cytoskeletal structures such as ankyrins which give the cell its characteristic curvy 'dented lozenge' shape, which must also drive some of the lipid composition in some parts of the cell.

Erythrocytes still perform glycolysis for ATP generation.


text:
What are these strings used to describe animals?
For example, what's a $dt^{sz}$ hamster? (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/).
What's a Rgs9-Cre/+;gtROSA/+ mouse? (http://www.sciencedirect.com/science/article/pii/S2212877813000719)

Those describe the genotype of an animal (or plant, virus etc.).
The nomenclature can be very varied and domain-specific, but for those two examples:
$dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred during breeding, without specific human intervention) which gives predisposition to seizures.
They are described in this paper:
Spontaneous seizures: a new mutation in Syrian golden hamsters. - Yoon et al. - J Hered 1976

SPONTANEOUS motor seizures with tonic muscle spasms and severe paralytic states have been observed in inbred line BIO® 86.93 of Syrian hamsters
  (Mesocricetus auratus auratus). These animals had been inbred for 23 generations and maintained by Bio-Research Consultants. The seizures, which last from 2 to 5 hours, can be precipitated by mild stress, and occur in
  animals between the ages of 30 days and 60 days. Breeding tests have shown that the condition is transmitted as a simple recessive; accordingly, the gene symbol
  sz is proposed for this condition.

The lowercase indicates that the mutation is recessive that is, you need to have two copies of the mutation to see its effect (its phenotype).
dt comes from dystopia, another symptom of the mutation.
As for Rgs9-Cre/+;gtROSA/+ mouse, the genotype is a bit more complex.
Whenever you see /+ it means that the animal is heterozygous, that is, it only carries one copy of that specific gene.
For instance these are transgenic animals producing the bacterial protein Cre under the Rgs9 promoter. A promoter is a sequence of DNA that controls the expression of a certain gene. In this case the DNA sequence for the promoter of the gene Rgs9 was attached to the DNA sequence for Cre. This new construct was then inserted into the genome of the mouse.
The result is a mouse in which the cells that normally transcribe the Rgs9 gene also produce Cre.
This mouse line was then crossed with a reporter mouse line called gtROSA26, which expresses a certain protein called $\beta$-galactosidase in a Cre-dependent manner.
The gene for the galactosidase is present in all the cells, but only where Cre is present (in our case the Rgs9 positive cells) it will be transcribed.
Eventually the crossing leads to the expression of $\beta$-galactosidase in Rgs9 positive cells.
$\beta$-galactosidase has the nice property that it can change the colour of certain chemicals to blue, which allows to easily visualize the cells that produce it. This can help you answer questions like: "where is the Rgs9 gene transcribed?".
Wikipedia has a neat page on Gene nomenclature with lots of links to nomenclature guidelines.

These strings are specific genotypes of these animals. They often denominate mutations or transgenes.
For the hamster $dt^{sz}$ stands for dystopic, the sz comes from the first denomination of this symptoms as seizure. See here for a brief explanation.
For the mouse you have both alleles named: Rgs9-cre is a transgene, + in this context always stands for the wildtype. So this mouse has one allele of the transgene Rgs9-cre while the other allele is wildtype for it. Transgene constructs with the cre-recombinase can be inserted into the genome upon induction, which is a useful tool to modify genes. This needs to be done in mice which harbour the gtROSA transgene, which denominates a specific genetic background for the mice.
See here for more details:

"Promoter traps in embryonic stem cells: a genetic screen to
identify and mutate developmental genes in mice."
Identification and targeting of the ROSA26 locus in human embryonic
stem cells.

Thank you! Do you have any suggested books/articles/material for me to read as a primer to this material? I need to be familiar with this stuff to be working in a research lab.


text:
Why don't warts caused by HPV spread to the whole body?
My son had a plantar wart on his foot, which (as I understand it) is caused by a virus which only infects skin cells. Once in the skin cell the virus replicates, but when attacked by the immune system prompts the growth of a hard, thick layer of skin (callus). Warts are caused by a HPV.
Given the wart has infected a skin cell, and skin cells are next to each other in a great big sheet covering the entire human body, why is it that we don't become completely covered in wart?  I assume that it's not the immune system keeping the wart at bay, because the original wart isn't defeated and we can get other spot infections elsewhere.

The Wikipedia page you link to says that they are self-limiting, although it doesn't say why.

actually there is a person who was completely covered with warts; not as a homogeneous sheet, though. Watched the video on youtube.

Plantar warts grow deep into the skin and slowly [1]. It is a common thing for warts to multiply [1], but because of the slow growth speed, their symptoms [2] and the self clear-up [1] they can't end up by covering the entire skin surface of a previously healthy person.
There are cases of generalized warts in patients with immune deficiency like hypogammaglobulinaemia, impairment of cell mediated immunity [3]. The immune system plays an important role in limiting warts. There is also a case of generalized facial warts in a patient with no other known medical condition [4].
References:

American College of Foot and Ankle Surgeons, Plantar Wart (Verruca Plantaris)
MAYO Clinic, Diseases and Conditions - Plantar warts.
Reid TM, Fraser NG, Kernohan IR. Generalized warts and immune deficiency. Br. J. Dermatol. 1976 Nov;95(5):559-64. PubMed PMID: 1086679.
Semon H. Papillomatosis: Generalized Facial Warts. Proc. R. Soc. Med. 1935 Dec;29(2):90. PubMed PMID: 19990539.

Your reference for "self clear-up" only indicates that this is a possibility, not a certainty, and doesn't discuss the mechanism. "Generalized warts and immune deficiency" was informative, and suggests that https://en.wikipedia.org/wiki/Antigenic_variation is the cause of subsequent infections.


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Cancer growth and cell division
I am confused about the prerequisites for cell division and cancer.
Which of the following is necessary for the cell cycle to progress?

Hormones
Growth factor
Cyclins
Cyclin dependent kinases

Which of the following is essential for cancer proliferation?

Growth factors
Signalling molecules
DNA replication
A control mechanism

How do the cell cycle and cancer relate to each other?

Hi!These are homework questions and you MUST show at least some effort to answer them and do tell us specifically where you are confused.

@biogirl I swear they are not homewark, these are questions I want to know the answers in order to know where is the confusing part , please help me

Biogirl I am waiting for you :(

Its okay. .they looked homework :) try Googling cdk and cell division. ..

Do you actually understand all the terms in the options ?

Maybe :/ . Ok I will try then correct my answer If I wrong , I think the cyclic is the answer for first Q

Cuz hormones are form of growth fectors , and cyclic is essential cuz it will activate CDK

Growth factor is the answer for second Q , cuz they will stimulate other cell to divide . .  Am I wrong ?

See my answer ask if you still do not understand any part.

Please do not post homework questions verbatim on this site. Asking for homework help is fine, but this isn't your free biology tutor - questions must be phrased so that they are interesting and useful to many future visitors. I will edit yours accordingly.

There is a wide continuum from "cancer" in the sense of uncontrolled cell division (this could include even things like 2-3 extra cells making an imperceptible, microscopic bulge in your colon) to cancer in the sense of huge lumps of meat growing on your body and killing you painfully within X months. For the latter kind, many "stages" of "evolution" must be completed by "the cancer" (forgive the excessive quotes, but the terminology is a bit nuanced here). For a better idea of the nature of cancer, you could start by reading The Hallmarks of Cancer (and reading about it).

Which of the following is always present in the cell cycle?

There are eukaryotic cells like yeast which can be cultured in a medium containing only nutrients. Because these are unicellular organisms, there's no reason to expect that they have any growth factors or hormones or extrinsic signal like that (there's a caveat that often even unicellular organism can signal each other, but I believe there are also many that don't). All eukaryotic cells that divide have a cell cycle, so these cells also have it.
Therefore, hormones and growth factors cannot be required for the cell cycle. Cyclins and Cdks are a fundamental part of virtually any cell cycle ever seen by science, so you could say they are necessary (though I think it is conceivable that an organism could exist which progresses its cell cycle using proteins completely divergent from known cyclins and Cdks, but then again).

Which of the following is essential in cancer growth and division?

Without DNA replication, you obviously cannot make more cells, so that is necessary.
There are cancer kinds which are dependent on growth factors (perhaps they make their own growth factor) but there are also cancer which simply jam the receptor active, so that they can grow even without the factor. This is discussed in The Hallmarks of Cancer.
Signalling molecules (assuming that extracellular signaling is meant, because if you start taking away signalling molecules inside the cell like IP3, obviously you can break the cell to the point it won't divide) is just a superset of growth factors; same arguments apply because growth factors are the most potent "signalling molecules".
Control mechanism is also "obviously unnecessary" and "obviously necessary". Cancer is uncontrolled division, so if there was control, the cancer wouldn't be there in the first place, duh. But obviously cancer cells also control their own division to some extent - they still have a coherent cell cycle and so on.

Ultimately, the key to understanding cancer is being cognizant of "perspectives".
"The body" (actually the wild-type genome) has a certain plan in mind for what each cell should do, and to that end, it has programmed the cells here to divide so many times in so and so fashion and the cells there to not divide unless this event happens and so forth. If those cells are mutated, and that programming is disrupted, they may divide in ways the body "does not want" (ie. they create tissue which has not been evolutionary selected for over previous generations), so from the body's point of view the cancer is indeed out of control.
On the other hand, the cancer is almost like its own separate organism - for one, it certainly has a different DNA than you, as it has mutated. It undergoes Darwinian evolution and becomes gradually more adept at surviving and spreading inside your body. So from the cancer's point of view, the cancer cells are indeed quite well-controlled, with the goal of that control being to divide as much as possible.

Cyclin dependent kinase is the answer for the first question. Cyclin concentration increases during m phase and falls in g1 s and g2 phase as it is degraded. Cdk is always present in the cell but gets activated during m phase, when cyclin is present. (cyclin dependent)
Cancer cells do not require growth factors to stimulate cell division. They have mutations which disrupts the normal cell cycle regulation. Now can you think what should be the answer ?


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Finding exons in DNA problem

My attempt:  I looked for the TACs because I thought this would be AUG in mRNA and ultimately Methionine (the start codon). But apparently, that's not how you do this problem.  Im confused because the answer (shown in red) doesn't have any TACs and the boxes seem to start at random places.  I am also confused as to why my professor drew a box around both strands.  I thought only one strand at a time was turned into mRNA?
UPDATE:  It has occured to me that the entire strand is transcribed and then the introns are removed.  So I know why not to look for the TACs.  But now, how can I identify the exons?

look at the polyA which is added after transcription and follow 3'-->5'. The first nucleotide after the polyA is a G then G then A. Can you find back them in the DNA? Yes? As soon as you find a correspondance between the RNA and the DNA you are in the last exon. When the correspondance is lost, you are in a intron, when the correspondance get back, you are in the following exon.

After an RNA has been transcribed, in eukaryotes it is spliced before it leaves the nucleus. This means that parts of the RNA are removed (called introns) and the ends are capped. The parts left over in the mature mRNA after removing the introns are called exons.
The mRNA does not have to start with a start codon. There can be sequences before and after the bit which actually gets translated.
Yes, only one strand of DNA is transcribed into RNA. When you look at the mature mRNA below, read the first few bases and try to find their complements in the original DNA because this is where they were transcribed from. UCAUG is transcribed from the DNA AGTAC (with TCATG on the opposite side).
Now you look for the end of the mRNA. Bear in mind that all the A's are the poly-A tail which is added during splicing and determines how long the mRNA will persist in the cytoplasm. So you look for CUAGG in the original DNA, which must be transcribed from GATCC (with CTAGG on the opposite strand).
As you can see, that's exactly where the two red boxes start and end.
Now since the mRNA you see here is mature (indicated by the poly-A tail and the 5'-cap), that means introns have already been taken out. So any bases that you can see in the DNA between the start and end that we just found but not in the mRNA must have been an intron. Or the other way round: all the bases that are in the mRNA which you can also find in the DNA must be exons.
You will notice that exactly the bit that isn't in the red boxes doesn't appear in the mRNA anymore. Or: All of the mRNA is in the red boxes. The sequence is interrupted by a short bit which you can't find in the mRNA anymore - so this must be an intron.


text:
PCR amplification and error propagation
Say I have one dsDNA that undergoes normal PCR (where amplification is exponential).  If there is a mistake, say a G is swapped for an A during the 2nd round of replication, what percentage of the final DNA will have the mistake if there are 12 more rounds?
I was talking to my teacher about this today.  I say 33%, my teacher said 12.5%.

I will format it to .ppt as soon as I have more time! If something is not readable, please let me know!
I have to point out several things:

The fraction of incorrect DNA molecules does not depend on the number of cycles (as long as the number of cycles is higher than 2).
There is one exception: if the mutation occurs outside of the region to be amplified (for example at the 4th molecule, downstream of the region of interest), the total number of wrong DNA molecules will be 0.

Your teacher is indeed correct.
In the first round you would get two identical molecules of the dsDNA.
In the second round you would get 3 identical molecules and one molecular with an A substituted for a G in one of the strands.  ie.
No error (3 of the 4 molecules):
------G-------
------C-------

One mismatch (1 of the 4 molecules):
------A-------
------C-------

So there are a total of 8 strands of DNA after the second round and one of those strands has the mismatch.  1 / 8 = 0.125 = 12.5%
In round 3 you would have 8 dsDNA molecules and only one of those 8 dsDNA molecules would have the mismatch.


text:
What causes tree lines?
There is an area of where there is a distinct line of only trees on one side and only shrubs on the other (right next to each other). What could cause this?
My attempt: I said there could be a difference in sunlight, but I'm not sure.

could you describe this a bit more?  my first thought is 'landscaping'...

I doubt you are referring to http://en.wikipedia.org/wiki/Tree_line

There are a bunch of possible answers;

On my own property I have such a line.  Turned out it was an old fence line.  One side was farmed intensely for 90 years, the other side left in bush.  The farmed soil is enough different that it doesn't grow good trees.  Even the grass is different.
Another place I have an abrupt line of willows.  That one turns out to be water level from the local creek.
A third one has an abrubt chaange in types of grass.  That one is caused by a clay seam coming to the surface.  Uphill the surface soil is sandy.  Water hits the clay, and moves downhill, coming out at the grass line.
I've seen another one, in the mountains, that I think is due to cold air drainage.  The valley floor and 20 feet up the sides are bush.  I think the cold air settles and kills young trees.


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What dragonfly is this?
I photographed a dragonfly but can't really identify the species using http://www.libellen.tv/. Are there any other resources I could use?
The pictures were taken in early June, around 11:00 next to a lake at 1700 meters above sea level. The pictures were taken in the Alps in Austria.

This does nothing to answer the question, but I'd like to formally register my jealousy of your ability to wander through the Alps in late spring taking pictures of dragonflies.

This is Libellula quadrimaculata, which is a common and very widespread species (North America, Europe, Asia at least). This is based on the relatively wide and flat abdomen (hard to judge due to the angle though), which suggests Libellula, brown/golden colour and a brownish wingbase. The main problem I have with the pictures (which makes my suggestion more uncertain) is that it is really hard to see the wingspots in your pictures, due to sun glare. Libellula quadrimaculata is one of the few European species that has four wing-spots (hence the english name Four-spotted chaser), which is why the wing-spots are important to see. However, I think I see hints of wing-spots at the middle of the wing (greyish patches on the top picture), which suggests four spots on each wing pair.
Edit
The distinctive four spots vary greatly in size among individuals and though small they are clearly present. The yellowish tint in the wings and the hairy thorax are also distinctive. The shining wings suggest this individual just emerged (from its larval stadium).  Colors may be less distinctive in these young individuals.
There are no similair species.

(picture from wikipedia)
More pictures of the species can be found here

I would consider myself an expert on European dragonflies and can verify this is libellula quadrimaculata.


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Aren't current explanations for the evolution of human cooperation a little too reductionist?
Lately, I've become a believer in the limits of reductionist explanations especially in areas like complex systems and biology. So, without wasting any more time, I'll get to my question..
Whenever we think of something like cooperation, the most common explanation that comes up is that of genetic fitness. It is said that evolution would have selected for psychological mechanisms of cooperation because it is beneficial in a society in which reciprocity is possible. You scratch my back, and I scratch yours. Add to the mix the ability to name names, and reputation becomes a kind of proxy signal for fitness.
Now, the major problem I have with this is does it all have to boil down to fitness? Can't it be a phenomenon that is culture-specific? Different cultures go to different lengths to help a stranger. Yet, we all share the same evolutionary history. This seems like a strong indicator that cooperation can't be reduced to one's genetic or reputational fitness alone. Should the study of cooperation be handed off to the anthropologists?

All animals are not humans ! So handing over to anthropologists - Bad option !

Sorry, I should have been more specific that I meant human altruism.

Ok! then I completely agree with you. Human altruism is  far more complex than other animal altruism. (I also suggest that you edit your question to be more specific)

You have to define altrusim here.  In evolutionary biology altruism often refers to an evolutionary adaptation where some individuals in a species are unable to reproduce, supporting a breeding caste.  e.g. ants and bees. Humans do not do this. I think you are actually thinking of what biologists call Cooperation.

Inclusive fitness proponents will tell you that this explanation is completely wrong, by they way (without being an expert, I tend to agree).

There are many various model used in order to explain evolution of cooperation. Here is a small list:

kin selection
group selection (levels of selection)
lineage selection
Reciprocity

direct
indirect
network

Memetics

People from many different background study social evolution including

mathematicians
biologists
philosophers
computer scientists
paleontologists
…

Social evolution is studied through fundamental science (using mathematical modelling and computer simulation) or by looking for common trait among species that are very social. For example, it seems that having a high extrinsic mortality rate "helps" a species evolving altruistic behaviors. Or sex determination mechanism such as haplo-diploidy seem to be important too. There are many experimental studies on human behavior too.
The field you referenced to ("Can't it be a phenomenon that is culture-specific") is called memetics. A meme (named by analogy with the word gene) is a cultural unit which reproduces according to their "memetic fitness" and mutates. There are lots of computer simulations on the subject and there are several empirical observations such as the evolution of a joke.
I think that none of the field we manage to think it would help explaining the evolution of cooperation is neglected. There are several articles who investigate the co-evolution between genes and memes. I don't know any of them who focused on the question of altruism. I have to confess that I have never read any article who considered the combined effects of several models from several fields in the study of altruism. But I don't think we have a sufficient level of understanding of each field in order to combine these models. For example, it's been argued that kin selection and group selection is actually the same process.

Interesting question!
I think that in terms of 'tribal' fitness, altruism would be strongly selected for, as communities would tend to be quite small (relative to, say, a town today). In modern civilization cultures have developed differing levels of altruism, but I imagine this is a result of upbringing rather than inherent differences in tendency toward altruistic actions.
So in my opinion you cannot rule out altruism being selected for because it is clearly an advantage (in terms of survival / fitness) in smaller communities - we just don't live in that kind of society any more; people don't have to be altruistic to get by, and this kind of mind-set can 'evolve' culturally, outside genetics. But on the whole I would still argue that most people are inclined toward altruism - ether because they feel naturally inclined to help others, or feel that by helping others some benefit (such a reputation) would be bestowed upon them (the former may be the same as the latter, but at an unconscious level).


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What is the essential benefit of center-surround organization of retinal ganglion cells?
I am trying to understand the significance of the overlapping on-center off-surround and off-center on-surround organization of the retinal ganglion cells, also called center-surround organization. What is the advantage of such an organization from the point of view of vision?
To highlight the point of the question, wouldn't it be computationally and organizationally easier to simply have the retinal ganglion cells arranged in a non-overlapping fashion, and without the center-surround ability? Then there would be a straightforward correspondence between the incoming spots of light and the firing of adjacent neurons in the optic nerve.

EDIT:
I just realized this question is two-fold in nature.

Why the center surround organization?
Why is there an overlap?

I think the answer by Bryan deals well with the first question, but doesn't quite touch upon the reason for the high degree of overlap.
I admit the question is worded in an slightly ambiguous way.

You are assuming that light comes in perfectly in spots, and that the purpose of vision is to replicate a "bitmap" of the incoming light. This would actually be very inefficient computationally.
In reality, vision relies on detecting salient features. Imagine a simple scene, maybe like this one:

Most of the white space of the wall is pretty uninteresting: you have no need to really process that information besides knowing it's one solid area. What is interesting in the image, if you are trying to understand the space your are occupying, is to see the edge between the floor and the wall. In fact, that's what really tells you this is a wall and a floor: if you only had the upper 1/4 of the image, you would just have a white box: you wouldn't know if this is a floor, a wall, a ceiling, the paint on someones car. The edge between the floor and wall gives you the needed context.
Lets think about how center-surround organization would respond to this image. In the whole blank white space, white light is hitting both the center and the surround: these cancel and there is little response. However, imagine what happens for an on-center off-surround cell right at the edge with the floor. That cell is getting white at its on-center, but only on about half of it's off-surround: the other half of the off-surround instead gets the darker wood floor. This cell would therefore respond to the imbalance in the average surround vs average center!
You can then combine many of this circular receptive fields to detect straight edges, like this:

From https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Perception
Note: the LGN (thalamus) receptive fields are very similar to the retinal ganglion cell receptive fields. In V1, primary visual cortex, these receptive fields are added together to make "simple cells" which respond to edges.
I think this picture comes closest to answering your question about how overlapping receptive fields can be useful.
This image from the Wikipedia page on receptive fields shows what you get when you put a scene through a center-surround filter: note how all the edges are emphasized!
Other benefits: this type of detector works well over a range of light levels, for example different steps of gray will appear the same, even though the pixel intensity varies a lot. This way, you get similar responses to edges in both a dark and light room. These detectors also help to sharpen images. Note that computer vision uses some of these same strategies as well!
What if you wanted to detect spots of dark instead of spots of light? We often think of eyes as being "light detectors" but they are just as appropriately described as "dark detectors." Imagine you are a rodent looking up at the sky, for example: an important, salient stimulus for you might be a dark spot where a hawk is blocking light from the sky. Therefore, having an off-center, on-surround type of cell is just as useful as the opposite (and indeed, the retina contains both types of retinal ganglion cells).

It is interesting that you mentioned computational inefficiency in your second sentence. Do you think the lack of center-surround org. is the reason why deep neural nets take so many training samples before they work well?

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Do neurons have agency with respect to modulation of spike timings?
I am aware of the mechanism of Spike Timing Dependent Plasticity (STDP) and its ability to cause Long Term Potentiation (LTP) and Long Term Depression (LTD). So far, I've been viewing neurons as input-output devices. However, there seems to be a problem with approximating neurons this way. If all they do is sum the inputs and produce an output, then it seems as if LTP and LTD as caused by STDP would be purely a function of the inputs from the environment. This would leave animals without any meaningful agency.
I would be much more comfortable with the idea that neurons actively try to optimize some parameters by competing with each other, perhaps by varying the timing of their spikes. Is this picture consistent with neuro-scientific findings?

I don't have time to look into this and form a proper answer, but if I were to guess at an answer, with regards to each individual neuron, they don't really have any 'agency', other than differences between their proteins, ion channel expression etc. However across a network of neurons, there would be some correlation of activity that drove patterns of excitation/inhibition that could be considered agency. You might look into developmental spontaneous activity that is important for formation of sensory circuits in the visual and audio systems to see if that fits with your idea.


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Genetic networks vs genetic architectures?
What is the difference between the terms genetic network and genetic architecture? I've heard both in a variety of contexts used by different people, so I am interested in what people think they mean, other than what is described in Wikipedia:
Genetic architecture refers to the underlying genetic basis of a phenotypic trait
Genetic regulatory network (GRN) is a collection of DNA segments in a cell which interact with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.
EDIT: so what I take from the answers so far is that a genetic network is the molecular wiring of all the interacting loci, whereas genetic architecture describes the phenotypic consequence(s) one would be able to see from that network. Then, trying to bring the two definitions together, if we would assume we knew all the molecular details of a genetic network, we would only need to add the other factors in the model, such as environmental perturbations, to end up with the description of the genetic architecture, right?

You can think of a genetic network as a network of interacting genes, turning each other on and off based on complex relationships and external stimuli. A genetic network is typically characterized in terms of graph theory--connectivity, density, etc.
The term genetic architecture, on the other hand, typically refers to a trait or phenotype and the characteristics of the gene(s) that contribute to that phenotype (this is what the Wikipedia article means by genotype-phenotype mapping). Characterization of a phenotype's genetic architecture involves describing how the phenotype(s) is/are related to the genotype(s). For example, for a particular trait or set of traits, is there a one-to-one relationship between gene and trait? Or do multiple genes contribute to a single trait? Or are multiple traits affected by changes in a single gene? The relevant terminology is discussed briefly in the Wikipedia article: polygeny, pleiotropy, etc.

Ok so what I take from your answers is that a genetic network is the molecular wiring of all the interacting loci, whereas genetic architecture is the phenotypic consequence(s) one would be able to see from that network. Then, trying to bring the two definitions together, if we would assume we knew all the molecular details of a genetic network, we would only need to add the other factors in the model, such as environmental perturbations, to end up with the description of the genetic architecture, right?

@130490868091234 You can characterize the genetic architecture without knowing much about the details of the molecular wiring. But yes, understanding how the molecular details of genetic networks influence important observable traits is one of the grand challenges of integrative systems biology.

As I understand it "gene network" refers to functional 'pathways' that a gene is involved in. For instance there is an extensive gene network around the p53 tumour suppressor - many different gene-products regulate and are regulated by p53, which make up this particular network. These interactions are often visualized using flow-chart-like diagrams, with the stimuli at the top, and the 'outcome' of the network of interactions at the bottom.
Genetic architecture refers to the actual structure of the gene itself. For instance, the coding sequence length, the intron:exon ratio, the 5' and 3' UTR lengths, are all traits relating to genetic architecture.
You have presumably already read the Wiki pages so I've given you my take on the meanings, as I understand them in a general manner - this may well differ from others.

I think you may have confused the term genetic architecture with gene structure.

Determining gene structure is one of the primary goals of genome annotation. See http://en.wikipedia.org/wiki/Genome_project#Genome_annotation. This description of gene annotation is a bit narrow, but it gets the basic idea across.


text:
circularizing DNA molecules?
I have been reading about next-generation sequencing technologies that can sequence long reads. Even though the origin of my question is sequencing technologies, the question I am asking is about the basics of DNA biochemistry.
One of the issues in manipulating DNA samples seems to be the ability to circularize long linear DNA molecules into circular DNA molecules. What are the technical challenges of circularising DNA molecules longer than 50Kbp?

sorry i mistook 50kb as 50bp.. If you are referring to Moleculo then it still has to undergo the HiSeq type of sequencing. I guess splitting the genome just makes the assembly easier.. Can you indicate the references which quote the 50kbp limit.. Ilumina says it is 10kbp..

I am not sure if it is a limit of input or ease of protocol/assembly.. Because it is not impossible to clone 50-100kb in plasmids.. Is circularization an essential step?  Illumina doesn't explain the process in detail.

From Illumina LRS FAQ: "Long reads are generated by creating one or several libraries from an individual sample, depending on each sample type. To create a library, genomic DNA is first fragmented to approximately 10 kilobases (Kb). Next, these fragments are clonally amplified, sheared, and labeled with a unique index. The fragments are then sequenced using Illumina technology. The short sequence reads originating from each molecule are assembled separately into synthetic long reads using proprietary algorithms, resulting in a full sequence of each long fragment."

@WYSIWYG, I clarified my question. Although I want to know about DNA circularization because of my interest in next-generation sequencing, my question is not about next-gen.

For ligation of a linear molecule to occur, the two ends must come together at the active site of the DNA ligase. In a simple molecular cloning experiment the aim is usually to avoid recircularisation of a cut plasmid vector, and instead to get a new fragment of DNA inserted into the vector. However because the ends of the linearised circular plasmid are tethered together (by being ends of the same molecule) they are more likely to encounter each other than they are to encounter the end of an incoming fragment. This is usually overcome, in part, by increasing the relative concentration of the target fragment.
If you are aiming to recircularise a long fragment then the opposite effect will come into play: the ends of individual long molecules will be much more independent and so the end of another molecule will be likely to compete successfully for ligation. In theory this effect could be overcome by reducing the DNA concentration, but I assume that this is impractical for other reasons.

thanks for your answer, which is very clear and something that didn't occur to me before. I have a follow-up question in a new post.

http://biology.stackexchange.com/q/15737/658


text:
effect of background selection on promoter regions compared to distant enhancers?
Has anyone looked at the effect of background selection on the levels of conservation of promoter regions compared to distant enhancers? Do promoter regions have a higher conservation due to background selection from nearby genes compared to more distant enhancer regions?
My attempts to google for this only gave me a 2004 Drosophila paper on a few genes survey:
http://mbe.oxfordjournals.org/content/21/2/374.full
I am wondering if this has been looked at before or if there are any other relevant bits of genetics one should consider first.
EDIT: a bit more of explanation into the hypothesis below, and a reference that could be useful:
Let's start supposing a region near a coding gene that can gain regulatory potential via a new point mutation or small translocation. This new regulatory potential needs to be positively selected after it appears, or it will gradually accumulate more mutations and disappear. But if the region is close enough to the coding gene, recombination rate between the region and the nearby gene body will be low, proportional to their distance. If the gene body is assumed under selective constraint, there will be a hitchhiking effect of the nearby regulatory region by the gene nearby. The background levels of mutation on the regulatory region are then going to be lower (lower background mutation) than in a region that is not near a gene under strong selective constraint. So one way of explaining why close promoter/enhancer regions are more conserved than distant enhancer regions would simply be due to linkage.
A second part of the hypothesis would be about the presence or absence of recombination hotspots in upstream regions of a coding region: if nearby promoter/enhancers are kept via linkage to the closest gene, unbiased measures of cross-over (e.g. PRDM9 experiments in mouse testis) should indicate if there is an increased linkage of functional genomic blocks, like enhancer/promoter/gene blocks (Hi-C, 4C, 3C data), whereas if recombination doesn't play a role, regulatory blocks wouldn't necessarily be kept in the same haplotype block.

So are you suggesting that negative selection (natural selection against a trait) may be stronger on enhancers that are more distant for the gene itself? I haven't seen any, but will keep an eye out! This would probably be a (relatively) simple and interesting bioinformatic/phylogenetic analysis given a proper framework. I expect it will very much depend on which gene/promotion mechanism you are looking at - unless the question is 'any'?


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DIY extraction and long term storage of human DNA sample?
What is the recommended DIY way of extracting and long term storing of human DNA samples to store at home and send for sequencing in years time? Considerations:

Sample material: cheek swab, hair, blood?
Extraction: which detergent, alcohol?
Storage: freezer? what temperature?

Any ideas?

sorry for not understand your question before

If you have access to a centrifuge, either spin columns or phenol:chloroform will give very pure, high-quality DNA. Even with dirty methods, you can re-extract the product several times, to sacrifice yield for purity. Just be very clean. Whatever method you use should remove salts and proteins, which are the major contaminants. I won't go too much into how to extract DNA, as that's a whole separate question - but the most important thing is that purer is better.
You should resuspend in Tris-EDTA. Tris buffer maintains pH at slightly acidic (best for DNA) and EDTA chelates metal ions which can catalyze oxidative damage of DNA. Very pure distilled water works too, but if you get contaminants they will do more damage.
Afterwards you can store the DNA for quite some time provided it's frozen. At -20C you can store DNA for years. It may not be perfect quality when you pull it out a decade later, but most of it will be good, and I'm sure it will be okay if you use a good sequencing method (and I'm sure sequencing technology will advance more in 10 years than the degradation of your DNA). The good news is that you can simply store it in your freezer, and it will be okay. -20C particularly is not hugely important, you can probably get away with -10C or so - the crucial thing is for it to be frozen, not liquid (this vastly reduces diffusion).
If you want to do it like a pro, you would put it under -80C. This is considered very safe for multiple years. You can do even better by precipitating it with ethanol, and then storing at -80C. In my opinion, this -80C is overkill - DNA is fine, for the most part, stored at -20C and even 4C, especially if you work reasonably clean and contamination-free. If you had some extremely valuable, very sensitive DNA, sure, do the -80. But just personal sequencing/genotyping? Just extract a bit extra DNA  (a couple micrograms).
The really safe method is liquid nitrogen, which stops practically all chemical activity. Higher temperatures are too cold for most DNA-damaging reactions to proceed at a significant rate, but the molecules still move around. At -200C, they stop dead. But, once again, overkill unless you are saving very critical DNA for centuries later.
Source.
Three simple things I can recommend that are less obvious: First, do not handle your sample with hands, even gloved. Use some kind of plastic tweezers. Hands are warm and will locally warm up the sample. I would go as far as to put the sample tube in another box so that there is no direct contact. Second, avoid freeze/thawing. Whatever your storage system is, make sure it is very reliable. Third, wrap it in something opaque, to minimize light exposure.
Note as per Chris's comments: Always consult the MSDS of the substances you work with and take appropriate safety precautions! Always make sure to receive proper training before working with hazardous materials, and never purchase illegal contraband without appropriate authorization!

Please do not use Phenol/Chloroform outside of safe cabinets. This is nothing you want to do at home as especially Phenol is highly dangerous.

@Chris Always consult the MSDS of the substances you work with and take appropriate safety precautions!

That's right, but you need proper training as well. Reading about safety precautions alone won't help. Additionally I don't think private persons will be able to order phenol.

Would a safe organic solvent like a vegetable oil be hydrophobic enough to remove the proteins and cell debris from a DNA prep?

@user137 Doubt it. Phenol is needed to denature the proteins.

@Superbest In this procedure for getting DNA from an onion, they just use shampoo or laundry detergent to lyse the cells and free the DNA. I suppose that could denature and remove proteins, but I don't think this protocol is designed for high quality DNA extraction.


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How and when did a dedicated immune system evolve?
I have recently been doing a lot of research into the interplay between the innate and adaptive immune systems in humans, and mammalian laboratory models. This has led to my reading some interesting information on the immune response in insects;

Insects have a highly efficient immune system.  In response to a bacterial attack, their fat body (the equivalent of the liver in mammals) synthesizes a whole range of peptides with an antibacterial and antifungal effect.

This fascinated me, as the clear inference is that there are no ‘dedicated’ immune cells, but that adipose tissue has far more diverse functions that I had realized.
I have done a little more reading, and also looked at plant immune systems, which seems far more analogous to those in insects than mammals;

Plants, unlike mammals, lack mobile defender cells and a somatic adaptive immune system. Instead, they rely on the innate immunity of each cell and on systemic signals emanating from infection sites.
  (Jones, 2006)

My questions relates to the need of an adaptive immune response in mammals. The immune systems in insects and plants - a more 'systemic' immunity due to the lack of dedicated/mobile immune cells - seems much simpler.
Given that evolution works incrementally (there are no 'jumps' - for instance, going from a non-dedicated immune system, to a dedicated immune system), I would hypothesise that organisms less distantly related to insects and plants may have tissues with duel functions (similar to insects?), but that specialize further as immune cells until gradually (down the evolutionary tree) a complex and specific immune system emerges. (This is complicated by the fact that our immune systems do have multiple roles - e.g. tissue remodelling, but I wasn't going to go into that here. Feel free in your answers if it is necessary!).
My overall curiosity can be summarized as 2 questions;

What are the possible reasons why a dedicated and immensely complex immune system evolved in some lineages of organism?
Is there any evidence of 'half-way' organisms, and about what ecological time-frame might the dedicated immune system have developed?

Immunity has probably evolved more than once as it is completely necessary for survival.  You might even argue that defenses such as antibiotics and predatory behavior are immune defenses for single celled creatures.
As you point out, plants have a different immune system than animals do.  Insects do too.  They don't have innate immune memory which many animals have, where pools of cells embody the immune response to a specific antigen.  (i.e. encode for a specific immunoglobin or a tCell Receptor variant).
I found this reference that this appears to be the collective property of jawed vertebrates.  Even so, there are many late innovations in the immune system, where reptilian and mammalian immune responses vary substantially.
Its not clear to me whether other animals have the insect system. Animals that branched off before insect lines such as radiates probably have their own way of dealing with immune response.  That's just a guess though.

As you guessed, the immune system as we think of it in humans has evolved incrementally over hundreds of millions of years.  The components that most people think of as "immune system" (T cells, B cells, antibodies) arose in sharks, around 400 million years ago. Lampreys and hagfish, which split off from the rest of the vertebrate lineage before sharks developed their adaptive immune system, have parallel solutions to the problem that are mostly independent but that involve some evolutionarily related structures.
The "innate" immune system is much more ancient.  Humans and other vertebrates share parts of the innate immune system with insects and more evolutionarily diverse organisms, so these arose well over 500 million years ago.
The topic is reasonably well understood and far too broad to discuss in any detail here.  I've written a couple of summaries elsewhere:

Same trip, different routes: Lamprey immunity (links to 12 publications)
Sea urchin immune systems (links to 3 publications)

Here are some review articles:

Design principles of adaptive immune systems
The evolution and genetics of innate immunity
Mice, men and the relatives: cross-species studies underpin innate immunity
Pioneering immunology: insect style

Immunology is a bio-chemical and nebulous concept, however it's equally complicated as the nervous, structural and circulatory morphology and chemistry. You can compare the immune system complexity to visible complexity that evolved in animals, from simple spiral and pattern shells, to metameric (repetitive segment) shells with a small amount of articulations like crabs and experimental Archean animals, to highly articulated shrimp and scorpions, and then to thousands of complex scales with specialized points and stings, which even become an endoskeleton. The evolution of the first muscled and articulated endoskeletons is as confusing as the immune system but it also happened gradually, before there were bony fish there were cartilaginous ones like sharks. In the same way, the immune system has evolved in strange steps from simple to highly complex and made of many pieces.
Bacteria have kinds of immune systems to protect against viruses, which consist  simply of DNA tricks to randomly re-arrange it's DNA and so neutralize the dangerous virus DNA which is copied within them and inherit new genes without making virii... If you want to go a step up from that in evolution complexity, then study immunology of worms and immunity of sponges.
The battle between bacteria and bacteria-eating viruses has been going on for millions of years, with viruses attempting to replicate themselves by -- in one approach -- invading bacteria cells and integrating themselves into the chromosomes of the bacteria. When this happens a bacterium makes a copy of its chromosome, which includes the virus particle. The virus then can choose at a later time to replicate itself, killing the bacterium -- similar to a ticking time bomb, Wood says.
However, things can go radically wrong for the virus because of random but abundant mutations that occur within the chromosome of the bacterium. Having already integrated itself into the bacterium's chromosome, the virus is subject to mutation as well, and some of these mutations, Wood explains, render the virus unable to replicate and kill the bacterium.
With this new diverse blend of genetic material, Wood says, a bacterium not only overcomes the virus' lethal intentions but also flourishes at a greater rate than similar bacteria that have not incorporated viral DNA.


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Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?
[Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe.  I'm not interested in debating creationism.]
According to Wikipedia[1]:

In Darwin’s Black Box (Behe 1996) I claimed that the bacterial
  flagellum was irreducibly complex and so required deliberate
  intelligent design. The flip side of this claim is that the flagellum
  can’t be produced by natural selection acting on random mutation, or
  any other unintelligent process. To falsify such a claim, a scientist
  could go into the laboratory, place a bacterial species lacking a
  flagellum under some selective pressure (for mobility, say), grow it
  for ten thousand generations, and see if a flagellum--or any equally
  complex system--was produced. If that happened, my claims would be
  neatly disproven.

[emphasis mine.]
As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications).  [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity[2].]  This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).

Question: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?

Experiments reproducing steps in evolution seem to turn out much easier than I would have expected a priori, e.g. reproductive isolation of fruit flies[3], experimental evolution of multicellularity[4], so perhaps Behe's experiment would also be surprisingly easy to implement.
References:

Wikipedia: Michael Behe
 Blocker A, Komoriya K, Aizawa S-I. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.
 Dodd DMB. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.
 Ratcliff WC, Denison RF, Borrello M, Travisano M. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.

Behe has no concept of the time scales involved: (Douglas Adams, replace space with time)Space is big. You just won't believe how vastly, hugely, mind- bogglingly big it is. I mean, you may think it's a long way down the road to the chemist's, but that's just peanuts to space.

still thanks for asking this question! its the sort of mental exercise that should be done more often.

The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and that it could not have arisen by natural selection. This is theoretically falsifiable, but the experiment he proposed does not provide a good dichotomy - there is a very large chance that he is wrong but over the experimental term of 10,000 or 10,000,000 generations, the flagellum might not arise.
The absence of the flagellum in the experiment is the most likely scenario, and doesn't either support or falsify his claim. It took evolutionary time, something on the order of 1010+ generations, to arise the first time (according to the consensus claim); we could not expect similar complexity to arise for the same purpose under conditions of directed evolution. That's a terrible experimental design: huge resource input, huge likelihood of no result.
To be clear: it is technically feasible, but not a good experiment. He proposed it because he knew that nobody would do it (because it's a bad idea).

Hmm... yes, if we replayed the tape of life, we would see a lot of generations, but (I would expect that) most of them did not contribute towards the evolution of the flagellum (nor its precursors).  Through artificial selection, the number of generations required in the lab should be far less than in nature.  [PS. I don't mean to sound unappreciative of your answer.]

It's true that directed evolution, by definition, is supposed to take a shortcut. But the likelihood of achieving the desired outcome is miniscule in this case, precisely because of the complexity of the organ. And whilst we might skip some of the non-contributory generations, we are talking many orders of magnitude difference between a human lifetime and evolutionary time. Previous directed evolution experiments have never achieved this. By a random evolutionary walk, we might see a simpler solution or none at all in human timescales in the lab.

On the other hand people who have tried looking for complex phenotypes have found interesting results.  These folks got a primitive multicelluar phenotype in about a month.  http://www.pnas.org/content/109/5/1595.long  It would not kill anyone to try a month long experiment for a few liters of culture.  While it would probably not produce a flagellum, its hard to believe that something would not happen.  Negative thinking never discovered anything. This one does not have to be expensive and could be done as a high school science project or in someone's basement.

You may be interested in this paper and a video that summarizes it. It seems to be made quite clear that 1) effectively all of the parts of the flagellum are not original to it, and 2) there is a reasonable evolutionary path (one involving only increment/refine steps) that could have been responsible for it.
The video mentions but doesn't describe experiments that were in support of the proposed model. I assume they might involve refinement or statistical issues of the environment, not the  whole-thing-at-once as Behe outlines. Obviously, if you can show that each step is independently adaptive, then the whole chain is shown to be possible evolutionarily, without trying to set up an experiment where you win the lottery n times simultaneously.
Personally I think the fact that the most awesome thing about the flagellum -- the rotation -- already exists in ATP synthase steals a lot of the flagellum's thunder. :)
Edit (Douglas S. Stones):  Following the above references led me to this paper:

M.J. Pallen, N.J. Matzke "From The Origin of Species to the origin of bacterial flagella" Nature Reviews Microbiology 4 (2006), 784-790. (pdf)

In this article the authors discuss the possibility of designing a lab experiment to reproduce (steps of) the evolution of the flagellum.

Scott Minnich speculated in his testimony that studies on flagellar
evolution need not be restricted to sequence analysis or theoretical
models, but that instead this topic could become the subject of
laboratory-based experimental studies. But obviously, one cannot
model millions of years of evolution in a few weeks or months.
So how
might such studies be conducted? One option might be to look back in
time. It is feasible to use phylogenetic analyses to reconstruct
plausible ancestral sequences of modern-day proteins, and then
synthesize and investigate these ancestral proteins. Proof of
principle for this approach has already been demonstrated on several
NF proteins[69–75]. Similar studies could recreate plausible ancestors
for various flagellar components (for example, the common ancestor of
flagellins and HAP3 proteins). These proteins could then be reproduced
in the laboratory in order to examine their properties (for example,
how well they self-assemble into filaments and what those filaments
look like).
An alternative, more radical, option would be to model
flagellar evolution prospectively, for example, by creating random or
minimally constrained libraries and then iteratively selecting
proteins that assemble into ever more sophisticated artificial
analogues of the flagellar filament.
Another experimental option might
be to investigate the environmental conditions that favour or
disfavour bacterial motility. The fundamental physics involved
(diffusion due to Brownian motion) is mathematically tractable, and
has already been used to predict, for example, that powered motility
is useless in very small bacteria[76,77].

[For readability, I've added some line breaks to the above.  There's too many cited references to list them all.]

[I'm answering my own question, but this seems too important not to include as an answer.]
A long-term E. coli evolution experiment (Wikipedia) was begun in February 1988 by Richard Lenski.  He took 12 initially identical populations of Escherichia coli, and let them grow, having now completed over 50,000 generations.
One striking observation made through this research, is that one sample of E. coli evolved the ability to metabolise citrate, which took over 30,000 generations (see Blount, Borland, Lenski, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli" PNAS (2008)).  This evolutionary step was achieved in a glucose-limited medium, thereby adding evolutionary pressure.  Moreover, their results suggest that a necessary "potentiating change" occurred at around 20,000 generations.
These results demonstrate that significant evolutionary change is possible to observe in the laboratory, and gives a feel for how long it might take for something as complicated as the flagellum.


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Can DNA & RNA be considered as nature's programming language?
The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA).
If after fertilization the DNA of the zygote could be genetically engineered to prevent complications occurring later in the life of that human being, it could become the ultimate medicine.
Also, we know that (in humans) only 2% of the genome encodes genes that are translated into proteins; is the rest required for function?
Can DNA & RNA be considered the ultimate blueprint of all living organisms?

Answers to your main question (the bold part at the end) will to a large extent "primarily opinion-based" (and speculative). The relationship between DNA/RNA and the functioning of organism is also a very broad topic. I think you should try to ask several narrowed down questions instead.

Will you answer my title as an yes or a no?

"...all other fields in Biology is just beating around the bush" - tsss...

Was literally just writing an answer :/ in my eyes there is nothing opinion-based about this (although the question could be phrased better): classical molecular biologay says DNA makes RNA makes Protein. Whilst this is true, less than 2% of the genome is protein-coding, with the rest coding for regulatory regions and non-coding RNA molecules (often with important functions of their own). So whilst in some respects DNA could be considered the 'code' for organisms, it is much more complicated than this: each cell of an organisms has the same genetics but different phenotypes, so clearly ...

... there is more at work than simply the DNA. This field of regulation and differentiation concerns epigenetics, which are modifications to the DNA that do not change the genetic sequence, and is to some degree hertiable. Therefore it is incorrect to say that DNA alone makes an organism, and it is incorrect to say that other fields of biology are just beating around the bush - there are many more factors at play than just the genetic code.

Hi @a.aniq I have made some edits to your question, to give you an idea of how a question might be structured (i.e. remove anything subjective - clarified meaning); but there are still massive assumptions that you made that I have left in - if you do a little research to clarify your own understanding and substantiate some of your assumptions with sources this question may qualify for re-opening and one of us can provide you with a much more detailed answer :)

@Luke You wanted to answer this question; would you convert your comments to an answer?

"Can DNA & RNA be considered as nature's programming language?" Yes. It is Turing complete.

This question can't be answered with a simple yes/no, but I would say that the analogy of DNA being the "code" used by cells is a reasonable one, if taken with a number of other considerations.
DNA function
When Watson and Crick first described the structure of DNA (being a double-stranded sequence  of the nucleotides Adenine, Cytosine, Guanine and Thymine) this led to what is known as the Central Dogma of Molecular Biology [1], which posits that DNA makes RNA makes Protein (figure from [2], as originally produced by Watson).

As you correctly point out, less than 2% of the genome is protein-coding, however our understanding of the rest of the genome is increasing manifold due to projects like ENCODE [3], which are discovering not only the "regulatory" regions that control the expression of protein-coding genes, but also the discovery of non-coding RNA's, many of which are totally uncharacterised [4].
The point of this section is to clarify that although only 2% of the genome codes for protein, it is incorrect to say the rest is "junk" or non-functional. The Central Dogma described above is now an outdated model - certainly some DNA makes RNA makes Protein, but not all; many RNA molecules are functional in their own right.
You could argue that proteins and non-coding RNA molecules are the product of "scripts" in the DNA that are run or performed by cells, although you are unlikely to find any genomic scientists talking in these terms.
Epigenetic control
Where the analogy breaks down is that all* the cells in an organism have the same genome, yet they are vastly different to one another. These differences are due to epigenetic processes, which are described as non-coding modifications to the DNA that affect expression of transcripts. A basic overview can be found here [5].
These modifications come in several forms and include:

DNA methylation

the addition of a methyl-group to cytosine nucleotides that can affect binding of transcription factors etc,

Histone modifications

DNA is actually a 3-dimensional structure, and is wrapped around proteins called histones, which wrap together to form chromatin and the characteristic chromosomal structure.

The availability of DNA to transcription factors is completely dependent on these modifications to the DNA, which are specific to individual cell types and prevent retinal cells, for instance, expressing liver enzymes. (Below figure from [6])

Overview
In short, genetics and the DNA sequence can certainly be thought of as the blueprint for an organism - changes to this sequence can profoundly affect phenotype - however it is too simplistic to imagine that the sequence alone provides all the information needed.
Not only are there many non-coding molecules essential for functioning in cells, there is exquisite control over expression by DNA modifications that do not affect the sequence of nucleotides and are essential for cellular differentiation.
The ENCODE (Encyclopedia of DNA elements) project [7] is making headway into the interpretation of the non-protein-coding elements of the DNA, but there is still a long way to go.

* not quite all, for instance B-cells have a hypervariable region to enrich antibodies for variation [8]

http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html
http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html
ENCODE Project Consortium, “The ENCODE (ENCyclopedia Of DNA Elements) Project.,” Science, vol. 306, pp. 636–640, 2004. PMID: 15499007
http://www.nature.com/encode/threads/non-coding-rna-characterization
http://www.whatisepigenetics.com/fundamentals/
http://www.eusem.com/main/CH/epi
http://www.genome.gov/encode/
http://www.anaptysbio.com/technology/somatic-hypermutation/

Quite a comprehensive answer :)

This is an excellent answer from the biology side (which is appropriate since this is a biology site), but perhaps more could be said from a CS perspective. In particular, I think it's important to distinguish between DNA's self-regulatory mechanisms (e.g. TATA boxes) and fully Turing-complete coding languages. There's a strong distinction, I think, between the epigenetic mechanisms necessary within organisms and the hardware capabilities used to run computer code, and this is probably most clear once it's recognized that DNA is very unlike Turing-complete computer languages.

I was somewhat busy all these days, and I didn't even imagine this question of mine would get such an elaborate answer. Thanks for answering my question.