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What are the "stars" we see after a bump on the head?
Sorry  if this might appear funny. When I close my eyes for a longer time, and suddenly open  it, I see some twinkling white small circles, and when i concentrate on anyone of them it disappears, as if the image is falling on the blind spot.
This also happens when I am struck on my head sometimes accidentally. I would see thousands of tiny objects floating. What are these and why they appear shiny ?

i think they are randomly triggered neural impulses in the retina or optical nerve.

"Seeing stars", or as it formally is called, "phosphene", is caused by stimulation of the visual cortex or retina by causes other than light hitting the retina.
http://www.oubliette.org.uk/Three.html

Wikipedia on it's own is a poor reference, try following their sources back to find something less fluid :)

@RoryM Ok, I don't know what you mean with "something less fluid" but I've added the source that seems most complete on the subject, although that source is also based on other sources, IDK if that's ok? P.S: I tought that puting a wiki article would count as a good reference cause they are required to have "reliable" sources backing up their text...

Hi Jo,  Wikipedia can change every day, there's no guarantee that a reference to wikipedia will remain accurate if the source article is changed.  Of course, you can say that about virtually any online source but Wikipedia in particular is prone to this.  Ideally, you should look at peer-reviewed sources, however the source you now link seems a comprehensive review, therefore I will reverse my downvote.

@RoryM, I do not mean to imply that Wikipedia carries more weight as reference than proper sources, but I'd like to point out that it is possible to link to a specific revision of an article. Under Toolbox, you can find the article's Permanent link, which will always redirect to the revision you were viewing.


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What actually happens when my leg 'falls asleep'?
Most people have experienced the temporary loss of feeling and tingling in their leg resulting from sitting in an abnormal position for a short while. Usually you get a loss of feeling in your leg while it is being compressed/constricted at some point and then the tingling sensation as the pressure is removed. But what is actually happening? I understand the the blood vessels are probably constricted from the pressure, but how does this lead to loss of feeling and later the strange tingling sensation? Are there any other things that extended compression on the leg does to cause this? What exactly are the requirements to get the sensation of a one's leg or other limb falling tingling in that manner?

Whilst it's not particularly academic or explanatory, this article does give you a basic explanation in layman's terms: http://health.howstuffworks.com/human-body/parts/question552.htm  -  I too would be interested to know the details, though.

This happens to arms, too. It hapens to my arms a lot during a sleep. I have feeling nerves are involved here not blood vessels.

Your circulation is being cut off when this occurs.

related: http://biology.stackexchange.com/q/16032/10198

The feeling you describe is called "paresthesia," and according to the NINDS info page, it happens "when sustained pressure is placed on a nerve."

Yes, a phenomenon also dubbed "saturday night palsy" when you nursed the bottle a little too closely ;-)

Does a choked blood supply play a part?

@atichnyu Blood flow can cause similar tingling sensations but I don't think they're otherwise related.

updated NINDS link

The explanation in the link Polynomial posted is essentially correct.
Whenever there is a reduced or blocked blood supply (ischaemia) to your extremities, the 'five P's' can occur: pulselessness, pain, pallor (colour), paresthesia (numbness) and paralysis (or weakness).(1).
The numbness and weakness happen after the blood flow have been reduced for a particularly prolonged period.
Cells in our body require a blood supply to stay alive (think about a stroke or heart attack for example). So a reduced supply can cause them to function abnormally or after a time (depending on the cell or tissue type) die.
So with a 'sleeping leg', staying in an awkward or particular position where arterial blood supply is blocked or reduced to the leg, the muscle, nerve tissue etc all lack supply hence causing sensory disturbance and weakness.
The possible buildup of metabolites could also contribute to the symptoms (pain).
Hope that helps!

Miller's Anaesthesia - Miller.

The linked explanation talks about squeezed nerves, and not about blocked blood supply. So I'm afraid your answer is actually incorrect: the arterial blood supply isn't blocked!

Check out the 3rd paragraph in that article Biocs - "This pressure can also squeeze arteries, stopping them from carrying nutrients to body cells."

The article states: "The pressure squeezes nerve pathways" and "This pressure can also squeeze arteries". Your answer does not mention nerves at all, whereas the article gives most weight to nerves.

Cheers Biocs. Good point. I haven't found an academic source in any of the textbooks or material I have access to regarding the nerve nerve compression mentioned in the article. I'll check it out and edit it accordingly.

I wouldn't recommend deletion of an answer just because it is not exactly what the OP is looking for. The information might be of use to others.

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conservation of C-peptide sequence in the guinea pig
Where can I compare the C-peptide sequence of guinea pig with human or mouse?
I am also interested in finding whether the guinea pig has insulin 1 and 2 to know whether I could use an anti-C-peptide 1 and 2?

Dou you want to compare protein or DNA sequences?

I would like to compare the protein sequence (amino acid sequence) to know wether I could use anti C-peptide that reacts for human to detected  C-peptide or proinsulin in guinea pig pancreas

Do a BLASTP with the human and mouse protein sequences to ascertain similarity between the sequences

and where can I find the protein sequence? is there a database?

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How can you identify if a person is homozygous for a certain allele?
I've been thinking about starting a small private research project. In this project I need to find out whether a person is homozygous for a certain allele. The reason for this is that I'm really trying to find out whether has a mutation that makes him/her not produce this chemokine. Thus I need to identify in an easy way which people are "normal", which people have the mutation in one chromosome, and which people have the mutation in both. About 1% of the population have the mutation in both chromosomes.
A primer would AFAIK not be able to differ between the heterozygous and the "normal" people.
Do anyone know how to approach this?

you could use a test cross but that might get complicated :)

I don't think I have time to breed humans ;)

You could use a 3-primers strategy, where you have a common primer, one that only amplifies the mutant allele and one that only amplifies the wt. This may or may not be feasable depending on the type of mutation.
DNA from het people will amplify both product, while homozygous will only amplify one (wt or mutant).
Of course then, linking the mutation of a gene to the lack of a chemokine is not necessarily straightforward.
To be honest, however, I would use a different approach: take people who don't produce the chemokine, and people who do (simply by dosing the chemokine in the blood). Now sequence the gene in the two groups and look for mutations.

Yeah, that's a smart approach. But I don't think (= don't know if) the nonfunctional gene will look the same in all individuals. Since it's a missense/nonsense mutation, it probably doesn't have a clear characteristic. Anyway, good point! +1

@Pedery: well, then wouldn't the sequencing be the best strategy in that case? Do you have any information whatsoever on the mutation or its product?

Not at the moment. Right now I'm trying to get an overview. Sequencing would not really be an option cause I want to make this into a super easy testing-kit, one that would need no expensive machinery and would get a test result from a mere droplet of blood. But indeed, your answer was helpful. If I don't get any better answers, I'll mark yours as accepted.

Btw, what would be the purpose of the common primer? If you have the two other primers, they will still tell you all the information you need, right?

Nope, you need two primers for doing a PCR amplification. If you only have a primer that goes on the mutant allele and one that goes on the wt you will have no way of amplifying anything, as the two will never bind on the same DNA.

Ah, got it. I was thinking in sets of two primers per allele as one primer.


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Which virus capsids consist of only one type of capsid protein?
The Tobacco Mosaic Virus (TMV) capsid consists of many copies of one protein (http://www.rcsb.org/pdb/101/motm.do?momID=109).
Which other viral capsids consist of only one kind of coat protein?
Does each copy of the protein in these also have the same tertiary structure?

Interestingly, the fact that viruses might be made up of repeating subunits was a hypothesis by the famous Watson and Crick in 1956.
A useful resource for this is the Viral Zone website maintained at by the ExPASy bioinformatics system. It contains an easily browsable and human interpretable list of viral families and their characteristics. In particular, you can "browse by virion" which will show you different structural classifications of viruses; make sure to look at all the different genetic classes of viruses (single-strand RNA, double-strand RNA, DNA, etc).
From my preliminary investigation, it appears that many capsids are composed of only a single subunit; in addition to TMV, some other examples I found are the totiviridae family of viruses which infect single-celled eukaryotes such as Giardia lamblia, the human-infecting astroviridae and calciviridae families, and (as far as I can tell) the Heptatitis B virus. It also appears that Dengue virus has a single capsid protein.
As for the tertiary structure of capsid subunits, you might find this review of interest. Basically, due to symmetries in the shape of icosahedra (or helices or other geometric shapes adopted by capsids), you can argue that the structure of subunits in certain symmetrical parts of the capsid has to be the same (because they are copies of the same protein and, by positional symmetry, they have to be experiencing the same forces). When there are asymmetries in the structure of the icosahedron, then it is often hypothesized that there exists a state of "quasi-equivalence;" that is, the deviation from symmetry is small enough that the tertiary structure of each subunit is not affected very much. The review goes into these points in much greater detail.


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Main methods used to predict functional annotations in GO
Can someone provide me some information about the main method used to predict the inferred electronic annotations in Gene Ontology?

This is an interesting question but I suspect that it’s better suited on biostars.org

Thank you for the suggestion, i'll try there. If i obtain answers i will re-post here.

I believe the most common source of electronic annotations comes from analysis of peptide sequences.  A collection of InterPro to GO mappings were created manually and can generate GO annotations.  DNA binding domains of transcription factors would be given "DNA binding" GO annotations say.
This method has its flaws - if the domain detected has evolved away from the function used for the Interpro to GO listing, there is a potential for error in this method.

You can refer the IEA documentation maintained by GO consortium to get an idea about the automatically assigned evidence codes using IEA. Also please note that IEA is different from Computational Analysis Evidence Codes

ISS: Inferred from Sequence or Structural Similarity
ISO: Inferred from Sequence Orthology
ISA: Inferred from Sequence Alignment
ISM: Inferred from Sequence Model
IGC: Inferred from Genomic Context
IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
RCA: inferred from Reviewed Computational Analysis


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How are antibodies designed?
Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.
This ability is harnessed as a tool in research to purify target structures in the cell (e.g. in chromatin immunoprecipitation, ChIP).
Now let’s say that I’ve identified an interesting target structure (such as a particular transcription factor) and I want to design an antibody to use in ChIP against said target. How would I go about producing such an antibody, taking into account that it should be both highly sensitive and specific?

Don't know enough about synthetic antibody design to give a complete answer, but this could be a good start: http://www.nature.com/nbt/journal/v25/n10/abs/nbt1336.html

Do you really mean "synthetic"? The mammalian immune system is pretty good at generating antibodies that are highly sensitive and specific - how about going the traditional route and making monoclonal antibodies? I note that the paper cited by nico describes the improvement in vitro of an existing antibody, not one designed de novo.

@Alan I didn’t. Nico added that word. I was actually interested in in vivo route. I think nico also meant the same (I wasn’t even aware that there was another route) and simply wanted to stress that they are designed.

Oh, sorry for the confusion @Konrad, I thought you were talking about completely synthetic antibodies (i.e. designed in silico) rather than the traditional "inject an animal with the antigen and then purify" way. I guess the design word tricked me into that.

@Konrad, I'm still not sure what level you are coming into this at. At risk of insulting you: here at the Pierce website [ http://www.pierce-antibodies.com/custom-antibodies/monoclonal-antibody-development.cfm ] is a good summary of the approaches that are usually taken. I have no connection to this company, they are just one of many  who offer a custom service. If you wanted to improve the antibody in vitro it would be necessary to clone the gene from the hybridoma cell line.

If you Google this doi [10.1093/protein/gzs024] you will get to a very recent review on Computer-aided antibody design in the journal Protein Engineering, Design & Selection.

@Alan I was actually talking about the monoclonal antibody design described in your previous link. The description there is quite good (mind writing up an answer?) although I’d wish for more detail in steps 1 & 2 … (there’s also a nice Wikipedia article but it’s less concise and not as well suited for an answer here, I think).

I worked for a long time at a leading high-quality antibody company, so I'll try and share some of my experiences with you. The process of making a highly specific antibody (I'll focus on monoclonals) has three important parts - antigen design and immunization, cloning and subcloning, and screening/validation. Each part is crucial on its own, and the better one is performed, the higher your chances of success downstream become.
In order for an antibody to work, it needs to bind specifically to its target. I won't get into all the specifics here, as there is a good open literature on antigen design, but basically you need something that will promote a strong immune response in the host, give you a variety of clones to choose from, and be specific - it shouldn't bind other targets besides your protein of interest. There are lots of factors to consider, including antigenicity, solubility, ease of production (for immunizing and screening), steric considerations (does another protein or nucleic acid obscure the target site in vivo?), and others. Antigens can be roughly divided into two types - peptides (typically less than 20 or 30 amino acids) and proteins or protein fragments. You will most likely want to try several antigens to maximize your probability of success. After the antigen is synthesized and purified, you need to come up with an immunization schedule for priming and boosting the animal(s), then determine when and how to test them (screening), and at what time and how to harvest it for the monoclonal process.
The cloning process then comes next. Clones can be generated by a variety of methods, some widely available, such as the various hybridoma methods, and some proprietary to individual companies. My former company employed a mix of both, depending on the species of animal, using some really cool in-house tech that was constantly being improved and expanded upon. These processes are very dependent on the quality of materials being used and the expertise of the cloners. The input B cells (which make the antibodies) need to have been harvested, treated, and stored according to a set of precise steps to allow for the highest number of viable clones. Once the immortalized cells have been obtained (after fusion with the myeloma partner cells in the hybridoma process, for example) they are diluted to a pre-determined cell count and plated in 96-well plates and allowed to recover and grow for a time, during which they are secreting antibodies into the medium. This media is then tested quickly (before the cells overgrow the well), and positive wells are diluted out to (hopefully) single-cell suspensions and subcloned, or frozen down for later. The first testing is frequently by ELISA using the immunizing antigen, although depending on your application of interest it may be by high-throughput screening via flow cytometry, immunohistochemistry, or immunofluorescence. After the initial testing, subsequent steps of subcloning and re-testing can occur at a more measured pace, as the cells can be frozen indefinitely after generating sufficient quantities of antibodies in the supernatant.
This is where the quality of your screening program comes in. Your assays need to be well-designed, robust, well-documented and performed, and have appropriate positive and negative controls so that you can truly tell whether a certain clone is of interest, or performs better than an existing product. This means controlled conditions, standardized reagents and protocols, and a high degree of repeatability from assay to assay. Also, the appropriateness of your controls cannot be emphasized enough. Do you have a knockout or non-expressing sample for comparison, or a way of looking at baseline vs. induced or inhibited activity? For ChIP, unless you have a good control antibody and primer pair for your gene of interest, how will you know if the assay works? You may get a great result doing a straight immunoprecipitation-Western blot, but still not pull down DNA-bound protein. If your ChIP method doesn't produce clean DNA, you may never get binding. And if you don't have appropriate data analysis protocols in place with multiple replicate wells, you may waste time chasing noise instead of specific signal. Additionally, along with testing all your clones, you also need to titrate them to determine the optimal working concentration. I've seen a lot of antibodies that look like crap when you first test the supe, but diluted 100 or 1000X they are clean, specific, and still strong. Be patient, testing is a lot of work and requires a ton of repetition to confirm your results, but it'll be well worth it in the end.
Finally, after all this is done, you hopefully have a great clone that does what you want it to do, and better than anything else out there. You now need to decide what you're going to do with it, because if you're an academic lab and publish with it, the world will come knocking at your door. Don't slack off at the end and decide 100 ml of supernatant will be enough to last forever - save the clones and put them in a cell bank, or try to get a commercialization deal with a manufacturing company so you don't have to do all the work!
I hope this helps, please let me know if you have any additional questions or concerns.

Very nice. However, where I’m still lacking understanding is the very first step, before the cloning process: how do you synthesise an antibody that binds to a target antigen?

Konrad - are you asking about how the immune system makes a specific antibody to a certain antigen, or how you could design a de novo antibody by computer?

@MattDMo I know how the immune system does it. I was unclear of how you get from your choice antigen to a tailored antibody. KT8’s answer covers that (i.e. you do it by exposing an animal to your antigen and let its immune system do the work for you).

@Konrad, that is the most straightforward way to go. However, there is now technology available that allows you to design very specific antibodies using libraries of antibody sequences. When the animal has started producing an immune response to the antigen, each activated mature B cell only makes one particular "clone." Using http://en.wikipedia.org/wiki/Next-generation_sequencing#Next-generation_methods you can harvest B cells and sequence the binding region of the antibody. These can then be recombined in silico and new recombinant monoclonal antibodies produced and tested.

Do you need the entire animal for step one?

@TheEnvironmentalist sorry, just saw your comment. The B cells are harvested from the spleen, but because the spleen is an essential organ, you need to euthanize the host animal. Depending on your process, you may save frozen splenocytes to do multiple rounds of immortalization and cloning.

Answering Konrad's comment, you produce the peptide or protein of interest using bacteria or chemically synthesize them (chemical synthesis generally only work for short peptide chains. After which, you get a lot of side products). This peptide or protein of your interest serves as your antigen. You inject this antigen into mouse or rabbit. The animal's immune system will naturally mount an immune response to produce antibodies against it. The B cells which are responsible for producing those antibodies can then be harvested. After which, you basically follow the protocol Matt stated.
You could, of course, also choose to just directly isolate the serum of the animal and purify it. However, this leads to the production of polyclonal antibodies which can be less specific than a monoclonal antibody.

Where in the organism are the B cells harvested from?


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How crowded is the bacterial cell?
I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in vivo. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue?
Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?

The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]
The concentrations of your substrate in respect to your enzyme are generally fairly analogous to in vitro studies compared to in vivo studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases that is true and errors can be corrected for using PEG to imitate the crowding effect. And yes, people have begun to look at the question [2]
However, for larger macromolecules like DNA and chromosomes that do see effects from subdiffusive transport, the molecules don't obey diffusive random-wal behavior [3]. The classic model system is the lac repressor which exhibits non-diffusive kinetics due to its interactions with DNA.

http://www.ncbi.nlm.nih.gov/pubmed/1748995
http://www.ncbi.nlm.nih.gov/pubmed/21237136
http://prl.aps.org/abstract/PRL/v104/i23/e238102
http://www.ncbi.nlm.nih.gov/pubmed/7317363

Composition of E. coli (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other
Protein concentration is about 100 mg/ml or 3 mM. From the size of an E. coli cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.
Diffusion coefficient for an "average" protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an E. coli. For reference, a small metabolite in water diffuses about 30-100x faster.
Reference: Cell 141:1262, Key Numbers in Biology

For a great visualization of the macromolecules inside the cell, check out David Goodsell's illustrations.  He tries to reproduce the protein and DNA density within the cell to show how things might be in vivo.  Really great stuff.
The answer is - its very concentrated.  Compare the density of the cell to that of a typical crystallized protein, which is I believe 0.8 g/ml of protein.
http://mgl.scripps.edu/people/goodsell/


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Could we transmit smells electronically?
We can encode sound and images in radio waves and send them, but presumably there's some physiological reason that we can't easily make a picture or video of a smell. Could we realistically break smells down into "primary scents", in analogy with "primary colors" and encode the information for easy reproduction?

I guess ultimately you could say the reason is the nature of the sense you're trying to reproduce. While seeing, hearing and touch are all senses based on non-material physical phenomena (sound waves, light rays, forces), the sense of smell serves as a tool to sample gaseous chemicals. This is why it's so intimately connected to taste, which is sampling the chemicals in solid and liquid matter.

There are only three kinds of optical receptors in the eye, but more than 900 kinds of olfactory receptors. Thus you can encode pictures with the three primary colors, but there is no small set of primary scents.
To transmit a smell via "primary scents", you'd have to create an artificial nose that monitors the response of each of the olfactory receptors, and then at the other end release a chemical mixture that has the exact same response pattern. (You won't find a one-to-one mapping of chemical compound to receptor.)

I think this is only half the answer. Encoding > 900 different olfactory signals shouldn’t be too big a problem – just create a distinctive signature for each molecule. We have this already in chemistry databases. The problem is actually converting the electrical signal back to a chemical one, since the alternative, plugging directly into the nerves of the nose, would be slightly unpleasant.

@KonradRudolph did you see the 2nd paragraph? ;)

I believe creating mixes of 900 substances could be rather hard. OTOH, electronic neurostimulation - bypassing the receptors and stimulating their respective nerves directly would be more doable (if still difficult).

one question: just how specifically can one stimulate those receptors. The fact that any wavelength of light stimulates all three photoreceptors to some degree has the interesting consequence that it's impossible to mimic the full color space with 3 primary colors. I wonder if scents would have a similar limitation.

In expansion to biocs' excellent answer, I would like to highlight some practical limitations of this. Suppose we did manage to create a huge database of exact chemical mixtures which produce all smells recognisable by humans. You would still meet some complications:

The output device (analogous to headphones or screen) would either need to be able to produce those substances on demand or have a large enough stack of them.

The former would require a whole lab built into one device - even with our miniature technology this would probably end up rather large.
The latter would require you to regularly stock up on all of the substances. You could sell these in an all-in-one package (again size becomes a problem) or in smaller "smell sets" (possibly practicable - but it would take a long time until people would understand what this is about)

The "smell substances" have to get to your nose somehow. At the same time, you probably don't want them in the rest of the room: While sound boxes are no problem because sound disappears rather quickly after being produced, smell can stick around for longer. The solution would be an apparatus that you insert into your nose. Not very practical, but people might do it.

I can't think of more at the moment but there probably are :)

In my view, the reason we can't transmit smell is that we don't understand it. That is, we don't have a solid understanding of how odor information is coded, so it is hard to imagine how to build a system that could reproduce that information.
This is sometimes discussed in terms of a multi-dimensional "odor space," where each odor could be described by its location along each dimension. The problem is that we don't really know what any of the dimensions are. By contrast, we know that visual space can be described by the intensity of a set of colors in a two-dimensional plane; auditory space is described by frequency and amplitude. It is clear that odors are comprised of chemicals, but we don't yet know where those chemicals fit in odor space. Understanding the odor space is a prerequisite to building a system that could transmit messages from it.
Also, to a great extent, how to engineer a smell transmission system is only partly a biological question. For instance, a CMYK printing system does a fine job at generating images that our RGB photoreceptors understand just fine. A telephone wire can transmit sound without a care about how the cochlea actually works. Transmitted pictures and transmitted sounds work because they activate our photoreceptors and auditory hair cells in the same pattern that the original images and sounds would. We can build systems to do this because we understand the nature of the information sensory systems decode, and we don't need a really deep understanding of the physiology to do that. (Of course, I think figuring out that physiology is great fun, but that's another point.) That is, to build a smell system, it's probably not really necessary to know what every one of the many olfactory receptors does. That's a detail of the way the mammalian olfactory system evolved. The important thing is to understand the nature of odor information. Then it really may be theoretically feasible to create a system to transmit odors.

A smell capsule with primary smells, concentrated non runny oils that can be heated up by a code sent to the capsule Then it will release the code, a built in fan will blow it to you from pc or phone, on a pc it could be renewed, maybe plugged in to a usb, Ive been thinking about this lately an have come to the conclusion that a smell Capsule would only need a collection of smells, if you type out banana there is a code behind the keys for the letter to appear, i think a smell program will be needed so that if some one sends you a coded image of a banana from there smell program the soon as you receive it and click on it the code will activate the same code in your program and you will smell the banana i have no idea how many primary smells there are or even if you can mix them but a collection of most common smells will do the job till the primary and mixing is masted,  I believe a pc is missing the smell capability and it will come along just as many other things have, it would be great to smell the ocean while watching ships or even while sailing one on a simulator, a heating of a oil scent will do the job fine, A thin wire sitting in each concentrated thick scented oil and all the different oils in separate compartments with there individual codes inside a complex capsule and a fan to blow out the heated one that the thin wire heated up

Can you add some references?


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Does the word "polymorphism" refer to the gene, the phenotype, or both?
In genetics, does the word "polymorphism" properly refer to genes, to phenotypes, or both? For example, if there are two alleles that lead to differences in the structure of the D2 neuroreceptor, would I talk about "a polymorphism in the gene for the D2 neuroreceptor" or "a polymorphism in the D2 neuroreceptor"? I've seen both uses in the literature, but it's not my primary field, so I don't have a feel for whether one is more widely accepted.
Bonus question: is there a preference regarding "polymorphism of," "polymorphism in," and "polymorphism on"?

The term "polymorphism" itself is more generally defined as "the quality or state of existing in or assuming different forms" (Merriam-Webster dictionary). So I guess semantically, it would be correct to say that there is polymorphism in a gene that can occur in different allelic variants, or polymorphism in phenotype because of variant traits (such as sexual dimorphism).
However, when biologists today speak of polymorphisms, often they refer to variations at the level of individual nucleotides (single nucleotide polymorphisms or SNPs; some people use the terms polymorphism and SNP interchangeably). These SNPs have become popular for genotyping and for correlation with a variety of diseases or other observable phenotypes.
And regarding the bonus question, I think "polymorphism in" is the most correct usage--it's definitely the most widely used. For example, you could say "there is a polymorphism in nucleotide 257 of..." or simply "there is polymorphism in nucleotide 257 of..." or even "nucleotide 257 of ... exhibits polymorphism".

A difference in phenotypes might result from polymorphisms, but one doesn't refer to those differences as polymorphisms.


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Ultrasound during pregnancy
In a hospital I can see a long queue of pregnant women waiting for their turn for ultrasound.  Is it safe to go through the ultrasound during pregnancy, especially during last few weeks?
Is ultrasound really required?  What if it is not done? How does ultrasound affect baby?

As Luke points out, the ultrasound is very safe. However, in many cases it is not required. Typically by 20 weeks into the pregnancy, and sometimes earlier, a baby's sex can be determined by examining the genitals via ultrasound. My experience is that this is the most common reason for an ultrasound during pregnancy.
Of course if there are complications during the pregnancy, an ultrasound might be helpful to visualize the fetus and diagnose any problems. However there is no definite need for an ultrasound during the course of a normal pregnancy.

Nice. forgot there was a follow-up "why is it used" question when posting my answer!

The U.S. Food and Drug Administration (FDA) has the following information regarding the risks of ultrasound imaging;

Ultrasound imaging has been used for over 20 years and has an excellent safety record. It is non-ionizing radiation, so it does not have the same risks as x-rays or other types of ionizing radiation.
Even though there are no known risks of ultrasound imaging, it can produce effects on the body. When ultrasound enters the body, it heats the tissues slightly. In some cases, it can also produce small pockets of gas in body fluids or tissues (cavitation). The long-term effects of tissue heating and cavitation are not known.
Because of the particular concern for fetal exposures, national and international organizations have advocated prudent use of ultrasound imaging. Furthermore, the use of diagnostic ultrasound for non-medical purposes such as fetal keepsake videos has been discouraged.

FDA > Radiation Emitting Products > Medical Imaging > Ultrasound Imaging
Further information

I had a bit of a look through PubMed and Scopus for any papers relating to ultrasound risk, but didn't find any.

Radiation?! Ultrasound is sound is a pressure wave, while radiation means actual particles (including, but not limited to, light consisting of photons. I know you didn't write that yourself, but still this requires emphasis - ultrasound is not radiation

@TobiasKienzler that really didn't twig when I first read it, but you are correct. The FDA just lumps it in with other medical imaging (under Radiation Emitting Products). Presumably the blurb was written by a web-developer rather than someone involved with ultrasound...

I sure hope so - I wouldn't go as far as distrusting an actual doctor who claimed this, since it's a Physics detail that shouldn't taint the diagnosis, but still I'd be very careful with someone who claims false facts instead of simply admitting to not knowing for sure...

Ultrasound is just another techniques for medical imaging and it is very common to use radiation for imaging. Therefore the notice that this is not ionizing radiation might be important in this context. Besides, radiation is not limited  to particles emission only and can also be emission of waves, that ultrasound actually is.


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Why do we sweat after drinking water and running?
Why do we sweat after running?
Also we sweat sometime after drinking lots of water. Why it is so?
Can someone please enlighten me in this regard?

Exercise, such as running, increases muscle activity.  This increases the energy demand of these tissues, which increases the rate of cellular respiration.  Respiration releases heat as a by-product, therefore the body is hotter during and after exercise.
Sweating is a homoeostatic mechanism to keep core body temperature constant. It is a response to lower the body temperature. When the body becomes too hot, sweat is released onto the surface of the skin.  The water from the sweat then takes some of the excess heat energy from the body and uses it to evaporate.  Because water has a relatively large specific heat capacity a lot of heat can be carried away by this method.

But I sweat even after I lots of drinking water.... what could be the reason here?

@gpuguy Do you mean you sweat after exercise even if you drink water? Or do you mean that at rest, in a cool room when one wouldn't usually sweat, you drink a lot of water and then begin to sweat?

i meant: "that at rest, in a cool room when one wouldn't usually sweat, you drink a lot of water and then begin to sweat?" (especially some time after having dinner/lunch)

If the meal you eat is hot, you will get some heat and if your body will consider it as excessive heat, it will try to get rid of some by making you sweat.
Drinking water and sweating after a meal may be coincidentally related and probably caused by hot meal rather than water. A side note: When you are dehydrated, you sweat less and when well hydrated you can sweat "normally," but drinking water by itself does not stimulate sweating.
Some people with "reactive hypoglycemia" can sweat and get anxious after meals. In this case, after a meal, food passes through the stomach rapidly to the small intestine, where glucose from the food is quickly absorbed and raises blood glucose level considerably. This triggers excessive insulin release that allows quick uptake of glucose by the cells resulting in drop of blood glucose under the normal level (hypoglycemia). This triggers the release of adrenaline, which breaks down some glycogen from the liver to produce glucose. Adrenaline also triggers sweating.
Certain underlying neurological conditions (not necessary diseases), such as increased tonus of the vagal nerve (that supplies the gut) can make you sweet more in certain circumstances.
A meal can be a "stress" (psychological or physical) which can trigger the release of adrenaline, which makes you sweat (just like in anxiety from any cause).

Sources:
Diaphoresis (excessive sweating) Ehealthstar.com
Reactive hypoglycemia Mayo Clinic


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Effect of spaying on the female cat organism and health
Veterinarians often recommend spaying a female cat if the owner does not want her to have kittens. What does biology know about the effect of spaying on female cats' organism and health (apart from lack of fertility, of course)?

From the standpoint of the skeletal system, spaying is definitely not good for her health. Removal of the ovaries mimics what happens at menopause, when circulating estrogen levels fall. Estrogen is necessary for maintenance of bone mineralization. Without estrogen, bones start to demineralize (the same process that happens in human females after menopause, leading to osteoporosis).
Then again, some animals, if they do not get pregnant, will cycle indefinitely until they get anemic and die. Ferrets are an example. So it's better to have these spayed.

"Then again, some animals, if they do get pregnant, will cycle indefinitely until they get anemic" - did you mean "if they don't get pregnant"?

Do these animals include cats? I've heard that cats go in heat more often than dogs.

I asked something similar: https://biology.stackexchange.com/questions/70223/cat-pregnancy-vs-cancer-risk


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What does the term 'bioavailability' mean?
From what I've read,

Bioavailability is the degree to which food nutrients are available
  for absorption and utilization in the body.

How would you explain this with an example?

Bioavailability is a concept which applies to nutrients and drugs which pass through first-pass metabolism, i.e. orally (and to some extent nasally) consumed substances. Anything absorbed in the gut first passes through the liver before reaching the rest of the circulation, and both the gut and liver may metabolise it to some extent. The liver in specific has the powerful Cytochrome P450 system, a huge variety of enzymes to break down all sorts of substances, although in some cases it can actually produce more active or even toxic forms instead of breaking them down.
This can lead to drastic reductions in the amount available in the systemic circulation after oral administration. E.g. propanolol (a beta blocker) needs to be given in 100mg doses orally while intravenously (avoiding first-pass metabolism) only 5mg are needed.

Why is the bioavailability of drugs more important than the bioavailability of nutrients?

An unfortunate choice of words, you are right. I'll adjust that :)

Bioavailability is also used in plant biology with a similar meaning; the amount of a substance (nutrient) that can be absorbed by the plant. For example a soil can contain a lot of Phosporus, but only a small part is bioavailable.

IMPORTANT:  In addition first-pass metabolism, bioavailability also accounts for any hindrance of absorption through the gut wall due to limitations in solubility or permeability of drugs or nutrients (see BCS classification of oral drugs)


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Small worm living in some kind of cocoon, what are these animals?
I am curious what animal is this. It is/lives inside some kind of cocoon, about 1 cm in length. They are attached to walls and to the ceiling, but sometimes they fall off. Inside the structure there is a small worm that can come out at both ends alternatingly. It can then hold on to the ground to move the cocoon around. They are said to feed on paper.

Related: Can you Identify this Creature?

This little dude is not a Caddisfly, but a true moth,  Tinea pellionella, a case making clothing moth.  Confusing because they do resemble caddisfly larvae cocoons more so than those of their own family (Tineidae).  Sort blurb Here:

"The brown-headed larva spins a silken case that is open at both ends. The case in the above image is covered with fine sand and debris, and superficially resembles a caddisfly case. The flattened case is about 10-11 mm long (3/8 to 1/2 inch). When crawling, the larva's head, thorax, and three pairs of legs protrude out of the case, and drag it along. According to Internet sources, the larva feeds on a variety of material, including hair, fur, silk, felt, feathers, woolen clothing, upholstered furniture and carpets. It apparently prefers darkness and soiled clothing, and is not fond of synthetic fabrics, such as nylon and polyesters."

This is probably caterpillar of one of the moth species from family Psychidae. They larvae looks like Trichoptera larvae and builds similar cases out of silk and material found in nearby surroundings. In contrast to Trichoptera, Psychidae caterpillars don't live in water, and some of them inhabit stones and walls, where they feed on lichens.

This is a wild stab in the dark, so downvote me as you see fit: Caddis fly larvae (Insect Order Trichoptera). I thought caddis larvae were aquatic though.

You are correct that caddis larvae are aquatic - thus these are not caddis larvae.


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How reversible is DAT upregulation from long-term ADHD medication use?
A mechanism for ADHD stimulant medication tolerance has now been found. See http://neurosciencenews.com/adhd-medication-patient-brains-adapt-dat/.
Here's the thing though: what exactly is the "signal" that the body uses to interpret whether or not it needs to upregulate the amount of DAT (dopamine transporter) that exist? Is it a dopamine-based signal  that somehow then gets carried to a transcription factor that gets carried to the nucleus for additional transcription?

http://www.longecity.org/forum/topic/54091-how-reversible-is-dat-receptor-upregulation-from-long-term-adhd-medication-use/

First the boring (but most important part) looking at the study:
It is important to critique the study design FIRST to see what kind of information we can actually obtain from this study. This is a meta-analysis of cross-sectional studies (meaning there is no record of change over time) that include a variety of age ranges of ADHD patients (some on treatment, some not) who were compared with age, gender and IQ-matched non-ADHD people to measure DAT levels in the stratum measured with PET and SPECT.
What they found:
There were very heterogeneous results from all the studies, there was no statistically significant difference between DAT in ADHD and normal (note that they use the word "trends"). The only thing statistically significant that they found was that there was a wide spread of DAT in the ADHD population, and that exposure to treatment accounted for half of this spread (variance).
What can we say about this?
This is not a very conclusive study, but studies like this are often necessary to merit doing higher resource intensive studies.  This study did not reach statistical significance in it's primary outcome, and on further search was able to only find a single outcome of significance. My summary of this would be: maybe this could represent a method of medication tolerance.
To answer your question
If hypothetically this was the cause and I had to make up a possible method of transcription control, I would say something similar to your answer. I would guess there is some transcription factor that is inhibited by dopamine in the cell. When there isn't dopamine (b/c it is being blocked from returning), it would somehow become active and start transcribing the gene for DAT.
Disclaimer
I am not a neurobiologist, this is my opinion after reading the article. Feel free to add to my comments

Reference:
Fusar-Poli, P., Rubia, K., Rossi, G., Sartori, G., & Balottin, U. (2012). Striatal dopamine transporter alterations in ADHD: pathophysiology or adaptation to psychostimulants? A meta-analysis. American Journal of Psychiatry, 169(3), 264-272.[Link]

Do they speculate a possible mechanism within the body of the paper?  Quoting that would strengthen the answer.


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Could hydrogen replace oxygen in cellular respiration?
I was wondering what oxygen actually does in the body. I have seen a few answers to other questions that involve the electron chain and I am really not sure what that is. So I was wondering what oxygen does and could hydrogen do the same thing as a substitute?

Thanks for the clarifying edit @MadScientist. I would rescind my vote to close the question if I could, but alas...http://meta.stackexchange.com/questions/915/can-we-have-the-ability-to-rescind-a-close-vote-before-it-closes.

No, hydrogen could not replace oxygen because it has entirely different characteristics. The most important one is probably its electronegativity - oxygen 'pulls' electrons much 'stronger' than hydrogen.
Basics: Reduction potential
Oxygen is the so-called terminal electron acceptor of the electron transport chain in eukaryotes. You can see "reduction potential" as a kind of stored "energy" which molecules have, similar to the power stored in batteries (very similar actually). To make this text a bit shorter I'll call it "RP" from now on.
One maybe confusing detail is that a substance with low RP has "more energy" than a substance with high RP, so it is the opposite way of thinking.
In very generalised terms, metabolism means that molecules with a low RP (glucose) are oxidised (burned) and turn into molecules with much higher RP (CO2). Coupled with this, a different molecule with very high RP (oxygen) is reduced and becomes a molecule with slightly lower RP (H2O). (You may have heard this before - it's called a redox reaction.) *
The important part is that the RP "released" by the oxidisation (burning) is larger than the RP "taken up" by the reduction. The surplus leaves as energy - heat and light if you just burn the glucose. This is a spontaneous process, meaning it will occur just by itself - even if it takes a long time if nobody drops a match on it.
The idea of metabolism is to let that process happen - but use as much of the energy it releases as possible. This works by not just letting it burn, but intercepting that burning process at different stages so that at each step a bit of the RP can be taken off and stored in something else. This "something else" is NAD which I'm sure you've encountered before. Each step that glucose is burned down, another bit of NADH is made, which then has a respectable reduction potential.
NADH (leaving out NADPH here which is a bit different) is channeled into a process called oxidative phosphorylation which retrieves the reduction potential in an actual form of energy.
Basics: Terminal electron acceptor
Finally, the reduction potential I've been talking about all the time is really just electrons, involved in bonds which are "happy" to react. Passing down the reduction potential as I've explained is really a passing down of electrons into more and more stable, less reactive bonds. That's why it's called "electron transport chain". At the end of oxidative phosphorylation, those electrons are dropped onto O2 and make it into H2O. That's why O2 is called the "terminal electron acceptor".
Why Hydrogen can't replace Oxygen
Now to come back to why hydrogen cannot perform oxygen's function in our body. We use glucose as our source of reduction power and oxygen as our terminal electron acceptor. O has a high electronegativity (3.5) so it pulls electrons strongly towards it. H's electronegativity is only 2.1, so it's much weaker. O as a terminal electron acceptor works because it pulls them much stronger than H when they bond, so an O-H bond is almost like giving oxygen an electron. In order for hydrogen gas (H2) to perform the same function, it would need to be possible to drop electrons onto hydrogen in a bond where it pulls them much stronger than the other partner. They do exist, and such compounds are called hydrides. But the catch is: unlike H2O, these are normally strong reducing agents, meaning that hydrogen would rather not be in that bond. This not a feasible option for cell respiration, at least in humans, because it requires a lot of RP input. Making oxygen into H2O does not require a lot, it's a very cheap electron acceptor.
I hope I was able to put this in understandable terms. Let me know if I need to clarify anything.
--
*It works with other molecules than glucose->CO2 / O2->H2O too, many prokaryotes do that and in fact that's how batteries work

Hahaha, what a blunder! I managed to let my lecturer's graphics mislead me. It shows a vertical reduction potential scale - but I didn't realise it's inverted with the lowest (most negative) at the top. I'll correct that of course, thanks!

I would say that while you could not just replace oxygen with hydrogen and expect life to just go on normally, it's possible for living things to be energetically provided for by H2 if it were found in the environment in enough plenty.  This is just speculation as Armatus points out metabolism does not work this way in animals, but I think that its quite possible a living organism could live off of H2 as an energy source.
Extremophiles can metabolize sulfur in underwater vents rather than oxygen.
In the soil, anoxic metabolisms reduce nitrogn gas to ammonia.
Photosynthesis uses light to reduce CO2 to glucose.  Atmospheric molecular oxygen is provided entirely by photosynthesis, and at one point there was little or none of it in the atmosphere and living things were found everywhere.  The glucose metabolism came after O2 appeared.
The main point is that H2 stores a reasonable amount of energy even if free oxygen is not available to drive the formation of water from another oxide, or even more exotic chemistry. There's not thermodynamic reason that it couldn't work and biology on earth has proven to be versatile in getting chemical energy wherever it needs to.
Its xenobiology and speculation, but I feel that if microorganisms evolved on a gas giant with a primarily hydrogen atmosphere, they could use the redox energy from H2, which is quite reactive even without O2 present.


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How fast do different organs turn over cells?
It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is the scale of change and especially, is it possible to measure and how fast do:
1) cells change
2) molecules change
3) atoms change
High, medium and max rate organ examples would be appreciated.

1) cell growth
You should look into chemotherapy and cancer medicine in general.  Because chemo is mostly effective because it kills fast dividing cells, this has been worked out reasonably well.  the 7-10 year number is not really correct, some cells are replaced a lot more slowly.
This is why hair often falls out in cancer treatment, because the follicle cells are growing quickly.  Neurons divide very slowly - if at all - and often are never replaced.  Fat cells are in between - probably replaced in the 7-10 year range.  Heart cells are replaced albeit quite slowly - less than 1% per year, which implies that many cells are with you your entire lifetime.
2) atoms/molecules change
The cell itself is in a continuous state of flux, but different parts of the cell, like cells in the body, change at different rates. Some proteins which make up the cell matrix or the DNA in the nucleus are replaced very rarely (through repair or rearrangement of the chromosome for instance) and most of the chromosome DNA is with the cell for the entire life of the cell.
Most proteins are labelled for degradation and are recycled after a few hours of function.  Metabolic compounds such as sugars or salt might drift in and out of the cell continuously, maybe turning over in an hour or so. Fats can be incorporated into the cell and last for years I think.

Is it possible to make/get a chart of different main organs and their turn over time?

For (1) it should be - oncologists probably have a lot of this information in their heads, and probably you can walk through a few textbooks and get some basic information.  there are always new kinds of cells to be discovered it seems though.


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Why human body cannot defend against HIV?
Some says that HIV destroy IRF3, and some says HIV overruns T-cells.

This question really needs some extra work, you can use more than one sentence.

There are two main components of the immune system that are involved: Antibodies and T-cells.
T-cells are responsible for activating white blood cells to help fight off infection. These are the cells the HIV infects. Antibodies bond to the HIV virus and try to neutralize them before they can infect more cells. Unfortunately as the HIV virus replicates, there is too much virus and not enough antibodies to neutralize.
When a T-cell becomes infected with HIV, the virus takes over and causes it to start replicating more HIV. This eventually causes the T-cell to die. So T-cells keep dying while HIV loads keep increasing. When enough T-cells die, the infected person is considered to have AIDS.
It is particularly difficult for the immune system to fight off HIV infection for a number of reasons, including the following:

HIV attacks the immune system itself, weakening its ability to fight back.
HIV replicates in large quantities that are more than the compromised immune system can handle.
HIV has the ability to mutate (change itself) very quickly, making it more difficult for the body to fight the infection.

So conclusion, our bodies can fight HIV for awhile. It's just a matter of time before the viral load outweighs the capabilities of our immune system.

For an understandable explanation: The human body can defend against HIV - hence why an HIV infection does not immediately develop AIDS, and in fact for a long time the virus cannot be detected in blood. This is because the immune response is keeping them down, but slowly the virus works its way through the cells, proliferates and kills more and more T cells, until the immune response is too weak. That's when AIDS develops.


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Question about SAM CIGAR string
My question is about the CIGAR specification.
The documentation states:
M 0 alignment match (can be a sequence match or mismatch)
I 1 insertion to the reference
Q1: If I have a CIGAR string 99M170661N26M, does that mean I have 99 matches. Can that also mean 99 mismatches? What about 98 matches and 1 mismatch? The specification states it could be a sequence match or mismatch.
Q2: Assuming I'm doing an RNA-seq experiment. In my CIGAR string 99M170661N26M, does that mean my read aligns to an intron which has 17066 bases? Can I think like: "I have a spliced read which aligns to two exons and an intron. I have 99 matches to my first exon and 26 matches to my second exon. I have 17066 matches to my intron."?
EDIT:
Can I get the number of matches in my read? Does that even make sense? For example, how do I know if I have 10 exact matches?

Q1: Yes, the CIGAR string operation 'M' means you can have both matches and mismatches. For example if you have a CIGAR string 10M, then you could have 10 bases that matched perfectly or you could have 5 matches and 5 mismatches. In this case, you have what are known as SNPs (or single nucleotide polymorphisms).
Q2: In your case, you have 99 matches, 170661 skipped regions in the reference genome, and 26 matches.
Q3: If you want to find out how many matches or mismatches there were, you'd have to take the reads from your SAM file, align them to their position in the reference genome, and compare them base pair by base pair to see if their nucleotides match. You can take advantage of the positional information found in field 4 of the alignment to accomplish this.
You can write your own code to accomplish this or use  something like Samtools, which I believe comes with a variant caller.

What does that skipped regions mean? In an RNA-seq experiment, can I interpret it as intron?

@Student T for mRNA yes

The MD optional flag gives more details regarding the alignment:

The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means
from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different
from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted
sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.

Don't know how to quote properly in a comment. I quoted footnote 10 of the current sam format specification (page 7).


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Why should we use the NA12878 dataset for benchmarking?
As far as I understand, the human genome sample called NA12878 provides high confidence variants for a human sample. It is being used as a benchmark for many genomic research projects.
Q: Why exactly the NA12878 is such a popular benchmark dataset? Just because we have a set of high confidence variants? But we can also get some high confidence variants from the 1000 Genome project. Does that have something to do with the sequencing technology? Anything to do with the sample itself? Why do we want to benchmark our experiments with NA12878?

It would be a good idea to explain abbreviations you use, so other people could understand them as well.

@Chris NA12878 is the name. It is not abbreviation of anything.

Still, your answer might be closed as unclear.

@Chris I know you are a mod, but I disagree. NA12878 is a very well known human sample, covered in many high quality papers. My question is about why it is a good benchmarking data set.

First: This has nothing to do with me being a mod. Then: It is well known to people from the field, but questions/answers here are expected to stand on their own without reading further literature.

@Chris I still disagree. This is like explaining DNA for any question related to genetics. Prior knowledge is assumed and required for most questions in this site. Anyway, I did give a brief introduction on what NA12878 is in my first sentence. The title and the question could be a potential useful resource for anyone googling NA128278.

No it isn't. I work with NA12878 daily, so I happen to recognize it, but that doesn't mean that everyone who could answer your question would know the code on sight. I have been working in genomics for almost 10 years now but didn't know what NA12878 was until last year when I started doing variant calling. More to the point, if another user, let alone a mod, suggests that your question could be clearer, why don't you just clarify instead of arguing? Obviously it seems clear to you, but equally obviously, it isn't so clear to everyone.

@terdon Chris is a mod, he could have just closed the question if he really believed it was inappropriate. Furthermore, a user who doesn't know what NA12878 will not be able to benefit from it. The question will benefit NA12878 users, and we know there're many. I did introduce NA12878 in the very first sentence. I ask because I don't understand NA12878 very well. I can't summarise something I don't really know. What else do you want?

It's not about closing, it's about making the question easier to understand. And nobody said it was inappropriate. The only thing inappropriate here is your reaction to a helpful suggestion telling you how to improve your question and increase your chances of getting an answer. You took it as criticism and started arguing when all you needed to do is provide a link as I just did. That way, people can click on it and see that you are referring to a DNA sequencing sample and can look up information about it.

@StudentT It's not about closing, this is something I would have done if I think a mod intervention is necessary. It is about improving the question and understandability, nothing else.

@StudentT jumping in here - you shouldn't start ranting, but be glad folks try to help. Also understand a little introduction is always nice. This site is not only about you you know. The best questions are relevant and interesting for the community at large. A short introductory sentence on NA12878 (what is it, why do you use it) may provide useful information for others such that they can actually learn from the question.

This might be helpful: NA12878 is part of the Illumina Platinum Genomes dataset.
https://www.illumina.com/platinumgenomes.html

@Chris, NA12878 is a 'known' reference genome in the variant/structural genomics world. The question really is what was this particular standard choosen over any other and it is valid. The name is the name though.

@Artem Great. Then why it is so complicated to add this information to the question?

So to clarify for people unfamiliar with NA12878, that's the sample identification for a particular Utah woman. Her parents are NA12891 and NA12892. In human variation data-sets that's what we are given to identify individuals, an ID, sex and population. All the other data is removed to protect patient privacy. So the question is why was NA12878 (this Utah woman) chosen as the reference patient in genomic analysis...
I don't know the real practical answer but from what I gather it's inertia.
I don't have a full history for her but I do know somethings which make her genome a good choice for a benchmark. NA12878 is a fairly old to geneticists and her DNA is included in multiple legacy projects, specifically HapMap.
She has a genetic disease (CYP2D6 mutation) which is probably what initially included her and her family genetic analysis. This is a better reason to study this genome in detail instead of it simply being someone famous (i.e. Venter).
She's Utah mormon (small founder population with extensive pedigree information), has 11 children (can do recombination/inheritance analysis). What this means is that a deep understanding of her genome will have applications to this population.
Her lymphoblastoid cell line GM12878 was included as tier-1 ENCODE cell of study. This means there's terabytes of epignomic data for her as well.
When I choose to do human genome analysis, NA12878 is the obvious choice because of how much data is already available, which also means more data is going to be available. Thus I think the answer is largely inertia.
Also consider it this way, if you're trying to say your pipeline or sequencing technology is better then other ones, and everyone uses NA12878 to benchmark their technology, then it's wise to also use NA12878 so the results can be comparable.


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What is the strand specificity of a reference genome?
It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue.
So here's to putting all those questions to rest.
Is the reference genome a positive or a negative strand? And why so.

Koustav. Thanks for your effort; it is quite commendable. IMO Q/A such as this which are intended to serve as a reference can be made a community wiki. It makes posts easily editable without much rep requirement; flipside is that you don't get reputation points. It is just a suggestion and it is up to you whether you want to do that or not.

Done! I didn't notice that option before!

@WYSIWYG — why is this question a community wiki? It is imprecise and based on a false assumption, as my answer makes clear.

@David The post sounded like a popular question for which an authoritative answer can be provided and therefore I proposed CW. BTW, the assumption is not entirely incorrect.

First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand.
For more background on the strand names here's a somewhat incorrect note from the wiki article under sense (molecular biology)

The strand names actually depend on which direction you are writing
  the sequence that contains the information for proteins (the "sense"
  information), not on which strand is on the top or bottom (that is
  arbitrary). The only real biological information that is important for
  labeling strands is the location of the 5' phosphate group and the 3'
  hydroxyl group because these ends determine the direction of
  transcription and translation. A sequence 5' CGCTAT 3' is equivalent
  to a sequence written 3' TATCGC 5' as long as the 5' and 3' ends are
  noted. If the ends are not labeled, convention is to assume that the
  sequence is written in the 5' to 3' direction. Watson strand refers to
  5' to 3' top strand (5' → 3'), whereas Crick strand refers to 5' to 3'
  bottom strand (3' ← 5').[4] Both Watson and Crick strands can be
  either sense or antisense strands depending on the gene whose
  sequences are displayed in the genome sequence database. For example,
  YEL021W, an alias of URA3 gene used in NCBI database, defines that
  this gene is located on the 21st open reading frame (ORF) from the
  centromere of the left arm (L) of Yeast (Y) chromosome number V (E),
  and that the expression coding strand is Watson strand (W). YKL074C
  defines the 74th ORF to the left of the centromere of chromosome XI
  and denotes coding strand from the Crick strand (C). Another confusing
  term referring to "Plus" and "Minus" strand is also widely used.
  Whatever the strand is a sense (positive) or antisense (negative), the
  default query sequence in NCBI BLAST alignment is "Plus" strand.

Although it is correct when it says

Watson = Sense = Plus Strands
Crick = Antisense = Negative Strands

A satisfactory answer/convention is provided/suggested in this PMC article covering the terminology of the Watson and Crick strands
Below are some interesting excerpts from the publication:

The earliest reference that we could find to the "Watson strand" and
  the "Crick strand" is somewhat tongue-in-cheek and comes from a pair
  of papers in 1967 by Wacław Szybalski and colleagues. They
  bound the two DNA strands of phage λ to the synthetic polynucleotide,
  poly(IG), which has an affinity to cytosine-rich regions. They then
  separated the two strands by density, which turned out to be
  determined by the amount of bound poly(IG). In a cesium-chloride
  density gradient, the strand with more bound poly(IG) was denser and
  heavier than its complement. Because the "dense" strand was
  cytosine-rich, Szybalski and colleagues called it the "C strand."
  Logically, thus, the complementary strand, which was guanine rich,
  should have been the "G strand." Instead, it was christened the "W
  strand."

So the authors note that the Strands started on their terminology journey with their roles reversed with the Crick strand specifying the heavy strand (with IG) and the Watson strand specifying the lighter one.
They also note that the present day terminology of the WC model is non-arbitratrily based on the current horizontal drawing convention where one strand is placed on top and the other at the bottom.
They also suggested a typical convention which is followed today. If it was due to their suggestion is a different matter altogether, but beyond the scope of this question.

Given the amount of effort already spent on standardizing such
  databases, and their influence on other disciplines, we feel that the
  genomic definition of Watson and Crick strands has the most mass
  behind it. Specifically, we find that the unambiguous usage of the
  Saccharomyces Genome Database to be the most useful. Under the first
  part of our proposal, the centromere is a reference point that divides
  a chromosome into two arms of unequal length. The chromosome is
  oriented so that shorter arm is on the left and the longer arm on the
  right. Furthermore, the top strand has its 5'-end at the left
  (short-arm) telomere and its 3'-end at the right (long-arm) telomere.
  This strand is the Watson strand. Similarly, the bottom strand has its
  5'-end at the right telomere and its 3' at the left telomere and is
  the Crick strand. We further propose that "top", "forward", and "plus"
  be used as synonyms for the Watson strand and "bottom", "reverse", and
  "minus" for the Crick strand.

and later on...

If it is ultimately impossible to distinguish Watson and Crick strands
  using biological properties, then we propose that Watson should refer
  to the stand arbitrarily used as a reference in a database (i.e. the
  "plus" stand) and the Crick strand should refer to its complement

But let's come back to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand.
Which suggests that the product originated from either the Watson (positive) or the Crick (negative) strands. For example, a read is actually the reverse complement of the product, but since you do a PCR step during you library preparation, that particular bit of information is lost and therefore the downstream analysis protocols tend to consider the entire loci any single product aligns to.
The difference between strand specific sequencing and non-strand specific sequencing are covered here.

The present state of this answer seems to confound terminology appropriate for gene-relative purposes with that appropriate for chromosome-relative purposes. Gene-relative uses Sense/Antisense (or Coding/Template), while chromosome-relative uses Forward/Reverse (or Plus/Minus).  A Forward strand will have both Sense and Antisense sequences on it.  See Bio_X2Y's answer here for an accurate and concise description.

I'm sorry I'd go further than @mgkrebbs and say both question and this answer are nonsense. I am not familar with Community wikis, but this should definitely not be some standard reference. I have written an answer explaining why.

The + and - is a bioinformatics classification. The reference sequence is by default the + and all the genes in the opposite orientation are annotated as -.
For linear eykaryotic chromosomes, the reference genome sequence is in the orientation of the chromosome (based on older cytogenetic assignment; usually the short arm is 5').
For prokaryotes, I guess the origin of replication is the beginning of the reference genome (Eisen et al, 2000).

I would replace "bioinformatics classification" by "data file designation". GenBank files and the like are human-readable, so they have strictly nothing to do with informatics, and I don't think there is any classification involved.

Answer
There is no such thing as a positive or negative strand for a genome (reference or otherwise), for the simple reason that the genomes of almost all organisms contain genes in both orientations, and hence each strand contains genes the sequence of which are in the sense and the anti-sense direction with respect to the mRNA.
The exception is single-stranded RNA viruses, where a single strand may act as the mRNA. This is where the ‘+’ and ‘–’ nomenclature is mainly used — to distinguish which strand is used in the virus genome.
I have previously addressed this topic in my answers to related questions about sequence direction in databases and reading frames.
Further Clarification: Where do reference genomes begin and on which strand?
To find the answer to this question you should look at the documentation in the database for the particular genome of interest. However, as far as I am aware, the following is generally true. (Others may be able to improve on this.)

In bacterial and plasmid genomes the sequence usually starts from the (single) origin of replication, proceeding in the direction in which replication occurs, written to the right of the origin. The strand represented in the database is the one starting with a 5′ end on the left at this origin.
In eukaryotic genomes that have been well studied there is a recognizable cytochemical assymetry of the chromosomes (in terms of banding of heterochromatin and, in some cases, ‘arms’) and there is a convention to designate one end ‘left’ and one ‘right’.  In the reference genomes the sequence starts from the conventially viewed left of the chromosome, presenting the DNA sequence of the strand that has the 5′ end. I provide an example of how Genbank indicates the ‘reverse’ directionality of genes using the term ‘complement’, below.
In single-stranded RNA viruses — where the ‘+’ and ‘–’ nomenclature is used — the sequence is of the ‘+’, starting at the 5′ end.

     gene            complement(11566..11952)
                     /locus_tag="YAL065C"
     CDS             complement(11566..11952)
                     /locus_tag="YAL065C"
                     /note="Yal065cp"
                     /codon_start=1
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /product="Putative protein of unknown function; has
                     homology to FLO1; possible pseudogene"
                     /protein_id="NP_009335.1"
                     /db_xref="SGD:S000001817"
                     /db_xref="GI:6319252"
                     /db_xref="GeneID:851232"
                     /translation="MNSATSETTTNTGAAETTTSTGAAETKTVVTSSISRFNHAETQT
                     ASATDVIGHSSSVVSVSETGNTKSLITSGLSTMSQQPRSTPASSIIGSSTASLEISTY
                     VGIANGLLTNNGISVFISTVLLAIVW"
     gene            12047..12427
                     /locus_tag="YAL064W-B"
                     /db_xref="GeneID:851233"
     CDS             12047..12427
                     /locus_tag="YAL064W-B"
                     /note="Yal064w-bp"
                     /codon_start=1
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /product="Fungal-specific protein of unknown function"
                     /protein_id="NP_009336.1"
                     /db_xref="SGD:S000002141"
                     /db_xref="GI:6319253"
                     /db_xref="GeneID:851233"
                     /translation="MAGEAVSEHTPDSQEVTVTSVVCCLDSVVEIGHHVVYSVVTPLI
                     VAVLIDTMAGEAVLEHTSDSQEEIVTTVVCSVVPLVCFVVSVVCFVISVVEIGHHVVY
                     SVVAPLTVTVAVETIAEEMDSVHT"
[Example of part of Genbank file (NC_001133) showing how directionality of two genes with opposite orientations is indicated using term ‘complement’.]
Postscript: Bioinformatics programs
As @WYSIWYG indicates in his answer, certain bioinformatics programs that produce tables of genes indicate their direction using ‘+’ or ‘–’ to indicate ‘left-to-right’ or ‘right-to-left’ respectively.

There is however a natural direction depending on the direction of replication.

@JackAidley — Direction of replication? This may hold for bacteria, but not for eukaryotes. But, although it wasn't strictly the question and the poster is long gone I'veadded something about where the "reference genomes" start from.

@WYSIWYG — I see your point that  + and – are used in the data files but the poster's question "Is the reference genome a positive?" clearly indicates that this is not what he meant, otherwise the answer is the trivial '+'. And the terms + strand and – strand were used in molecular virology before nucleic acid sequencing was invented, so although I have written programs to read GenBank files and am familiar with this designation, I never heard them refered to as + strand. The other answer also assumes that the poster is talking about "sense" strands, although he goes off on a tangent rather.

"...never heard them refered to as + strand..." I allegedly just have seen "minus" used by a data sheet (shown here on Stackexchange; I might be able to refer to) As  the minust strand is the template used in engeneering, data banks refer to minus-, not the "coding strand"/plus-strand?


text:
How do organoarsenics improve digestion efficiency in poultry?
It struck me as very surprising that these organoarsenic compound with structure looking not very compatible with living system is widely used as food additive to increase weight gain and improve food efficiency in poultry. I wonder what is the mechanism of action that causes the effects in these animals?
For instance, here is the structure of one particular additive - Roxarsone:

We used to treat a lot of poultry workers around here - before the plants closed down - for coccidial diarrhea. My guess (and why this is not posted as an answer) is that it's added for its anticoccidial actions. Coccidiosis - an intestinal parasite which decreases the effectiveness of ingested nutrients - is the most costly disease threat to poultry production.  Keep the poultry intestinal tract healthier => poultry do better. If it's more than this, I'm intrigued.


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Cancer biology: Can tumors form from cells that are genetically identical to non-cancerous cells?
Can a tumor begin to form without any genetic mutations? I'm specifically interested in a tumor which could later lead to cancer.

Very good question!  I'm not aware of any cancer type where the genome is completely intact. There are cancer types caused by viruses such as human papillomavirus, but also here viral sequences get inserted into the host cell genome.

Someone has initiated a close vote on this question. This is not a broad question. It's a very specific question that will simply rely on the right expert coming along and saying "No. It appears this is a prerequisite for cancerous growth. See review X.", "This is semantically how we define a cancer according to citation A", or "Yes there is a rare case of cancers that work this way. See wikipedia link." Where is the breadth there?

This is a very interesting question, and one that has been at the heart of cancer research for a long time. I think it separates into three issues.
Are there non-genetic mechanisms that can induce uncontrolled cell proliferation?
Yes, at least in experimental settings. There are many viruses that induce proliferation in its host cell, and viral genes / proteins have been identified that can disable the host cell's cell cycle regulation machinery. A well-studied example is the SV40 Large-T gene (from Simian Virus 40); this gene can be expressed in cells to cause cell proliferation in a transient, reversible manner, and it does so by interacting with host proteins, without causing genetic changes. See for example this article.
Can such genetically normal cells progress to form tumors?
It depends on what you mean by "tumor". To my knowledge, tumors large enough to be a serious medical problem are always found to be genetically altered in one way or another. There are plenty of viruses that cause tumors in humans, for example Epstein-Barr and papilloma (HPV) virus, but in all cases viral sequences are found integrated into the host genome. This may be because development of large tumors requires many cell division, and any non-genetic change that drives proliferation is likely to be lost on the way.
On the other hand, HPV virus frequently causes warts, which technically are small benign tumors. As far as I know, no genetic modification of the host cell is required for this to happen; rather, the virus replicates from its own separate DNA while simultaneously driving keratinocyte cell proliferation to cause these growths. So this example shows that small "tumors" can be formed without any genetic cause. Perhaps there is a limit on how large tumors can grow without genetic changes.
Can genetically normal cells form cancer, meaning a malignant (invasive) tumors?
No, as far as I know, this has never been observed. Large, malignant tumors without genetic changes are unlikely for the reasons above. There are cases of metastatic cancer where the primary tumor is so small that it cannot be located, but in these cases the metastatic cells are again genetically altered. Experimentally, it is possible to produce invasive behavior in cell lines by expressing oncogenes like ras, but these genes are mutated to begin with. Also, normal cells have mechanisms that detect such alterations, causing senescence, and they must first be inactivated by mutations. Transformation to an invasive phenotype is not usually caused by viruses, probably because it would give no advantage to the virus (unlike cell proliferation).
For more information, Robert Weinberg's Cancer textbook does a good job of discussing these issues. This article also provides a historical perspective of tumor virology with some interesting pointers.

Given the incidence rate of cancer, it is likely that usually multiple somewhat independent events have to occur, so that cancer forms (see the famous interpretation of the underlying data/thinking by Hanahan et Weinberg 2000 )
Epigenetic changes seem to be a likely factor contributing to cancer ( summary of an experiment, where they are also causal/inducing )
People have been suspecting, with good rationale, that the intrinsic variability of (bio)chemical reactions, which often only involve a small number of copies of the involved molecules, could contribute to cancer ( e.g.: Ansel et al. 2008 ). (Note: directly addressing this hypothesis for cancer by experiments would be quite difficult / perhaps-impossible)
None of the above should be seen as opposing the relevance of genetic mutations

I would go with NO for the simple reason: For a cell to become malignant (cancerous), cells need to break several barriers. One is to be able to activate telomerase, an enzyme that restores telomeres and enables infinite cell divisions.
Another important part is to be able to ignore apoptosis. This is programmed cell death. Specific cell signals lead to systematic chemical changes and cell death. So for cancer cells, it is important to be able to ignore this signal.
These are only two basic things, there are more, for a cell to become cancerous.
Changes to this will necessarily lead to change in DNA. However, I don't have direct proof and I don't work in this area.

In curosity to the above answer: I agree that in the situation of cancer, there are changes in DNA and genetic mutations are found in all types of cancers. I also agree that to become cancerous, a cell has to break several barriers and at some point one of the barriers are mutations in DNA. But, how does it prove that a cell cannot start proliferating at a faster rate due to for example: just metabolic changes? How is it necessary that a genetic mutation has to be there to start maybe a cell proliferating more which could further lead to a situation of tumor and further cancer.

Because there are several safety mechanisms, like those I mentioned. Even if cell did multiply much faster, it will sooner or later die due to all the errors after telomeres are depleted. And similarly, even if cells suddenly started multiply, signal for apoptosis could easily stop this attempt at revolution.

or some metabolic changes leads to start in proliferation and activation of oncogenes...leading to start accumulating more genetic mutations and being able to fight with all the barriers which can stop the tumor growth. I still do not agree why a genetic mutation have to be  a start for a cell to sense for over-multiplication or to start becoming cancerous. It is probably the sum of all...(start could be anything..genetic, metabolic or epigenetic).Ultimately changes at all levels of regulations are disturbed in cancer cells.

@Crazy in principle you are right --- in a single cell, uncontrolled cell proliferation can be caused by non-genetic mechanisms (notably by viruses). I think the main reason why (large) tumors always show genetic changes is because the alterations that drive proliferation must remain intact over many generations of cells.

Endometriosis fits this definition.  In many ways endometriosis is like metastatic cancer.  Endometriosis is the movement of fragments of endometrial lining out of the uterus (prsumably via the fallopian tubes) to other sites in the body.  There these fragments implant and call in a vascular supply to feed them.  Endometriosis fragments usually cause trouble in the abdomen and pelvis but they can go anywhere, including skin, lung and the brain.  Metastasis is not an inappropriate name for this.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942279/
https://www.ncbi.nlm.nih.gov/pubmed/21195968
These fragments grow and stick things together (like intestines), causing the same sort of problems that cancer can cause in these sites.  They bleed with the menstrual cycle.  Endometriosis in the lung can cause hemoptysis.  The masses of endometrial tissue and the blood and fluid they accumulate can become endometriomas: benign tumors which are accumulations of tissues and blood which can be mistaken for cancerous tumors on imaging.
The endometrial tissues causing this are not mutant.  They are just in the wrong place.  Endometriosis can, however, give rise to a true cancer.  Clear cell carcinoma is known to form in deposits of endometriosis.

This is a fascinating answer! However, in reading one of the reviews you link, they say "there is evidence that endometriosis
has genetic alterations similar to some cancer types" with reference to this paper: https://www.ncbi.nlm.nih.gov/pubmed/11093061 - though I am not sure of the field's recent consensus on this.

P.S. I do not recommend a downvote on this answer, because it will be very relevant to someone interested in this question - but the caveat that we are not certain about genetic alterations is pretty important.


text:
To what extent is the genetic code more than just a code?
It is worth specifying the exact meaning of "code" in this question. A code is a map from one space to another space with which it has no algorithmic connection. Thus representing 321 as 0x141 is not an instance of a code, because there is an algorithm; but representing 321 as the letter Ł is a code (Unicode, in this case) because there is no intrinsic connection between the number and the symbol. The only way of knowing which number matches which symbol is to look it up in a book.
Popular presentations of the way cells work speak of the DNA/RNA code as a code. There is no algorithmic transcription of RNA to proteins. The transcription from codons to amino acids is a code which human beings interpret by looking it up in a table. Cellular machinery interprets it by the fact that GUN→Val transfer RNA is present in the cell but a GUN→Glu transfer RNA is not. During protein synthesis, each transfer RNA molecule, having acquired a molecule of its designated amino acid, pairs with the codon it is designed to pair with. The code table is thus defined by the set of tRNAs that happen to be floating around in the cell.
(There may well have been some over-simplifications in the above picture).
On the other hand, the DNA code is not a code in the sense that the DNA molecule (and still more RNA) is not a passive repository of code sequences but a reactive entity, and those reactions depend on the nucleotide sequence in a way different from the tRNA-mediated encoding. Coding regions; non-coding regions; long strings of single nucleotides; initiation sites; 3-D structure of the molecule – all these depend on the nucleotide sequences in a way separate from their role as codons.
This is why this is a "to what extent?" question.
A thought experiment
To the extent that the genetic code is a code, an experiment of this kind ought to be possible, and perhaps even not far from practicability. To the extent that the code isn't a code, it wouldn't work.

Elucidate the structure of GAU-to-Glu tRNA and GAA-to-Asp tRNA, neither of which exist in nature.
Synthesise RNA that codes for them and insert it into a suitable cell, making it a machine for synthesizing these two tRNAs. Manufacture a large quantity of these tRNAs.
Taking the DNA of a target cell (not necessarily the same species as before), replace the genes coding for GAU-to-Asp and GAA-to-Glu tRNA with genes coding for GAU-to-Glu tRNA and GAA-to-Asp tRNA. Such a cell would not live, since it would mistranscribe most of its proteins.
Before reinserting the DNA, make a copy of it, replacing every occurrence of GAT with GAA and every occurrence of GAA with GAT.
Just before reinserting the DNA, flood the cell with the new tRNAs manufactured in step 2. This changes the code.
Reinsert the DNA.

The cell should now be viable. Everywhere that GAT used to code for Asp in the original cell, GAA is now found; but since the only tRNA available to the synthesis process is GAA-to-Asp, this means that Asp is still inserted exactly where it should be inserted. The change in DNA sequence is exactly compensated for by the change in available tRNAs - that is, the change in the code.
Purpose of the thought experiment
On the one hand, postulate success. The modified cell, using a different genetic code from anything else on the planet, has the advantage of being immune to all viruses. Or will being immune to viruses turn out not to be an advantage after all? The modified cell will also be very much inbred, since it cannot exchange genetic material with anything else. Advantage, or disadvantage?
On the other hand, consider the possibility of failure. Failure would appear to be because GAT and GAA (or GAU and GAA) are subtly different in their chemical properties quite apart from their role as codons. DNA and RNA might adopt different conformations, ones sufficiently different to change the nature and kinetics of their reactions as macromolecules as opposed to information repositories.
Which brings us exactly to the title of this question. If the genetic code is a pure code, then the experiment will work - just as I could make a variant Intel x86 chip in which the code for Add does subtraction and the code for Subtract does addition, and compensate for it by modifying all my programs accordingly. To the extent that the code is more than a code, the experiment will work less well.
But to what extent?

The post was talking about messenger RNA and mRNA but could only make sense if transfer RNA and tRNA was meant, so I've edited the dozen plus instances.

See also: https://biology.stackexchange.com/questions/21918/are-the-dna-codon-mappings-arbitrary

You call it a thought experiment but something like this has actually been done. Not entirely similar as they don't switch 2, but still they replace a codon.
An overview: https://en.wikipedia.org/wiki/Expanded_genetic_code
Big thing: in the two articles leading up to this one they replaced all 314 UAG stop codons in E.coli K12 and used the now unused UAG codon for some fancy stuff: https://www.ncbi.nlm.nih.gov/pubmed/25607366

+1 for alternate uses of stop codons. This is a great example

Hasn’t your question already been answered by those organisms (and organelles) that have a different genetic code from the standard genetic code (originally known as ‘universal’)? Essentially they have performed the experiment for you by developing machinery to decode mRNA differently (transfer RNAs with appropriately different anticodon/amino-acid accepting ability — that’s what determine how the code is interpreted).
And I think DNA is a red herring here. The genetic code is a code to decipher information in regions of mRNA that specify proteins. It does not — and was never intended to — apply to anything else. Thus, it does not apply to the 5' and 3' untranslated regions of mRNAs, where there may be other combinations of nucleotides that are interpreted differently (e.g. ribosome-binding sequences in prokaryotes, polyA-addition signals in eukaryotes). Use of a modified (T for U) genetic code is only used with DNA to make predictions about regions that specify the protein-encoding parts of mRNAs (i.e. whether they can, and if so, what the amino acid sequence of the protein will be).
[Apologies if you were aware of all this molecular biological background and I have misunderstood your argument.]

On one hand, designing an experiment which would kill (and resurrect) a cell is not possible: once a cell malfunctions, it's likely damaged beyond repair.  However, other than that I don't think this experiment kind of cannot actually be done. You would just have to simultaneously expose different cultures (grown in the same conditions) to different inserted DNA or RNA. This would include exposures you would predict cause both cell death and survival or growth and "control" exposures you know would kill or spare cells. This is done routinely with bacteria, yeast, and mammalian cancer cells.
Depending on your interpretation of a "true code" this would be testable. Clearly a DNA ATG maps to AUG in a particularly well defined way. mRNA AUG is also decoded to Met but the mechanism here is important: the tRNA is a "decoding" class of molecules, these have a complementary recognition site for an mRNA codon, e.g, UAC, and a binding site for an amino acid such as Met on the other end. These decoding molecules are otherwise identical in structures and interchangeable, indeed there are some bacterial species that use "non-canonical" decoding tRNAs different to other species and "genetic re-coding" where additional amino acids or frameshifts are encoded by our STOP codons.
I don't know if tRNA here fits your analogy as an algorithm or compiler but evolution has produced a vast range of exceptions we could test the genetic "code" on. Basically we work with a table that we're familiar with and some bacteria use a different one with additional amino acids like selenocysteine. Recent experiments have even added DNA/RNA bases not occurring in nature and "non-canonical" amino acids not used in naturally occurring cells, others are attempting synthetic biology to engineer their own cells as you've proposed.
However, it's worth noting gene expression isn't a simple one-to-one mapping. The amount and variant of gene expression is also important, many regulatory sequences affect expression of DNA, splicing of mRNA, or ribosomal binding. Once a protein is produced it is often cleaved, phosphorylated, or glycosylated and can form complexes with identical or different proteins. Whether the "exon" DNA encodes a "raw" protein sequence is intriguing and as much as I would hypothesise that DNA to protein is a true code, in the context of a complex biological system other factors beyond the raw sequence affect gene function.


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Strange Black-Brown Insect Identification
Interesting Insect from Singapore. Around 0.5cm. Has 2 tiny pinchers at its tail. Insect is black for most part.
Please zoom in on scotch tape:

That is an earwig. https://en.m.wikipedia.org/wiki/Earwig

This is an earwig, an insect in the order Dermaptera that has notably robust cerci.

 Credit: Ron Yeo
Note that the name comes from an old wives' tale about these insects crawling into people's ears. They don't:

Earwigs do get their name from the belief that they climb into human ears while individuals are asleep, however, this belief is fortunately untrue

Based on the sexing rules indicated here, your specimen's relatively straight cerci might be an indication that you found a female.
Earwigs are found worldwide, and with about 2000 species (source), it'll be difficult to narrow this down to species. If you can get access to a local dichotomous key or other accurate insect ID guide, you might be able to narrow further.

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