text:
Why is AUG the initiation codon?
Is there any reason why AUG is the initiation codon?
Can’t translation start with different codons?

I have removed the following line from the original "Why is there a need for an initiation codon ?" and posted as a separate question. This has not been answered here, so there seems no harm done to any answers, and by doing this one is giving a chance for that part to be considered on its own merits. It is also in keepting with SE policy on not posting multiple questions in one, although I understand the original poster feeling that they are part and parcel of the same thing.

I have now posted the separate question here: https://biology.stackexchange.com/questions/82444/why-did-translation-develop-a-specific-codon-for-initiation.

A good question (if a little mixed up on transcription vs. translation!)
AUG is not always the start codon, but whatever the codon is it will always code for Methionine (or fMet, but still a variation on Met), even if the codon codes for a different amino acid otherwise. A  separate transfer RNA (tRNAi, the initiator tRNA) is used for the arrangement of this first step, guided by eIF2 [in eukarya].
In this respect it's less a question of "why AUG" than "why this specific initiator tRNA", the answer being that it's got certain sequence elements and modifications that distinguish it from the elongating tRNAs which bind elongation factors and hence are targeted to the ribosomal A and B sites instead of the ribosomal P site (with function being dependent on form, basically it's shaped to set up transcription rather than to elongate an existing nascent chain polypeptide).

"Identity elements appear to finely tune the structure of the initiator tRNA, and growing evidence suggests that the body of the tRNA is involved in transmitting the signal that the start codon has been found to the rest of the pre-initiation complex." — Kolitz and Lorsch, 2010

The other start codons are just from natural chemical variation (or evolution, whichever way you want to look at it) giving rise to different codon-recognising protein shapes.
The machinery for starting translation works, and as such is "conserved" - evolution has kept it, and that's why it is always the same codon (more or less). Archaea have a very similar shaped tRNAi acceptor stem, and is an equally good ligand, which shows how ancient the system is and gives an idea of how fundamentally difficult it must be for an organism to change a system like this through mutation (3.5 billion years of evolution can't be wrong! etc. haha).
Not to just gloss over the part where I said that non-AUG codons get used too (in yeast and mammalian cells), the following is from a study in which it was found changing 1 (and only 1) of the AUG bases still permitted translation initiation:

"Naturally occurring misrecognition indicates that discriminating two base-paired near-cognate codons from the perfect three-base-paired AUG
  codon is subject to mistakes. Mutations in translation
  initiation factors, such as eIF1 and eIF2b, further increase the levels of these mistakes.
Two base-pairing interactions between non-AUG codons and the anticodon of
  the Met-tRNAi are sufﬁcient to trigger translation initiation, suggesting that wild-type eIF1 plays a role in
  monitoring proper base-pairing interactions when scanning for the AUG start site. It would be predicted that
  the Met-tRNAi, not a cognate tRNA matching an individual non-AUG codon, is used in translation initiation at these non-AUG start codons.
The translation initiation complex will bind only the Met-tRNAi as
  opposed to other tRNAs because Met-tRNAi has unique
  sequence and structural features that allow it to be
  loaded onto eIF2 of the ternary complex and enable it
  to ﬁt into the P site of the ribosome" — Maduzia et al, 2010

Basically the consensus is that it's not really possible to say why the methionine codon, "it's just a structural thing", which is a bit of a circular argument really.

perhaps usage of methionine might have a metabolic reason. Methionine is an essential amino acid and is important for methyltransferases (SAM). So it might be vaguely possible that using Met for initiation is a metabolic checkpoint.

@WYSIWYG: it looks like it all has to do with translation initiation efficiency.

From recent empirical research (Wang et al., 2018) on eukaryotes, basically the non-AUG start codons have context-dependent [translation initiation] efficiency, while AUG is a "sure thing", i.e. the nucleotides surrounding it have little impact on its efficiency.

There are some theoretical biochem explanations for this, which I'll just quote as-is:

We demonstrated that non-AUG codons are more dependent on their surrounding nucleotide sequence context than AUG codons. Base pairing between an AUG start codon and anticodon of the initiator tRNA along with interactions between the scanning ribosome and the nucleotides surrounding the start codon (e.g., the interaction between Arg55 of eukaryotic initiation factor 2a and the -3 position [...]) cause the preinitiation complex to shift from an open conformation to a closed conformation so that translation initiation can occur. Most preinitiation complexes undergo translation initiation when they encounter an AUG start codon whether it is an efficient or inefficient context because the strong interaction between the codon and anticodon provide enough energy to drive the conformational shift. However, mismatches between a non-AUG start codon and the anticodon reduce the binding energy from the codon and anticodon. Therefore, the contributions from interactions between the preinitiation complex and the ‘context nucleotides’ likely become more significant and necessary. We also showed that sequence context, specifically the +4 position, affects the efficiency of each non-AUG start codon differently. The observed differential effect of the +4 position demonstrates that sequence properties can have codon-specific effects on TIS efficiency. It is possible that there are other properties with codon-specific effects. Furthermore, differences in these properties between reporters may explain why some previous studies have identified GUG or ACG as the most efficient non-AUG start codon [...] while others are in agreement with our findings [...].

Also pointed out in the paper, in some corner cases (specific sequences) a sequence containing a non-AUG codon can be "as efficient as" another sequence that contains an AUG. (From the box plot it looks to me like some non-AUG sequences have better efficiency than some AUG sequences, but the paper phrases it as "as good as".)

Anyway, this inversion of efficiency only happen in on some specific sequences. On average over all sequences, AUG has the best efficiency.

If we go [farther back in evolutionary time] to prokaryotes, a similar study of all potential starting codons has been done on E.coli in 2017. The picture is a little bit different in the sense that while AUG is still ahead in terms of efficiency, but together with GUG and UUG does form a cluster of its own, well ahead of the rest.

The standard explanation for this that I found in a review is that AUG, GUG and UUG are all decoded by fMet-tRNAfMet. (Also given in an answer here, based on an older review.) Actually the older review does offer tiny bit more insight:

AUG is the most common initiator codon because it forms the most stable interaction with the CAU anticodon in fMet-tRNA

Of course, one could equivalently ask how comes this enzyme co-evolved with the start codons (that it decodes). But I haven't found an answer to that. I'm probably going to ask that as a separate question.

You fail to mention that this analysis only applies to eukaryotes, where the selection of the initiation codon is very different from that in prokaryotes, which utilize Shine and Dalgarno sequences that interact with rRNA. It is therefore difficult to see how this can be a basic answer to the question.

@David: it did occur to me that before AUG was strongly selected in eukaryotes it was probably somewhat more weakly selected in prokaryotes. But I couldn't find a study along the lines of this one for prokaryotes. Perhaps there are well-known theoretical considerations that answer that part... which I'm sure you'd like to share as an answer.

@David: silly me, there actually is a (2017) paper like that https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397182/

@David: aren't both papers the accepted answer quotes about eukaryotes?

I have now provided the sort of answer that I think addresses the question, although the ideas in it are not mine — I'm recounting someone else's idea. I think your remark about AUG and the met-tRNA anticodon begs the question. We know that as AUG in the genetic code is methionine. But why was methionine chosen in evolution as the initiating amino acid? I don't think the paper you discusses address this. They are concerned with contemporary evolved initiating tRNA and its interaction with mRNA.

First of all, it is the coding sequence, the open reading frame (ORF), and not the gene that starts with an AUG. Also, there are actually quite a few ORFs that start with different initiation codons, they are just the exceptions rather than the norm.
As for the need, you can think of START and STOP codons as punctuation. The AUG is read like the first (capital) letter of a sentence (if you will allow me to stretch the definition of punctuation a little). Read up on the process of translation, the ribosome  will attach to the mRNA molecule which includes UTRs, it uses the AUG codon as an indication that it should now start translating.
UTRs are the untranslated regions and often contain regulatory sequences that can control translation. However, these should not be in the final protein product so the cellular machinery needs a way of knowing where the UTR ends and the coding sequence begins.

I could not understand the first line.Please help.

@biogirl I think lmmx explained it perfectly but a gene consists of much more than the protein coding transcript. Genes typically include promoters, enhancers, various splicing signals, introns etc. AUG (usually) marks the start of translation, the sequence that codes for proteins it does not mark the start of the gene.

The transcript certainly does not start with AUG. It is the *reading-frame" or the protein-coding region of the mRNA that starts with AUG.

@David oh good grief! I can't believe I wrote that. And I edited this answer yesterday and still managed not to notice! This is my field, for crying out loud! Thanks for the heads up; fixed now.

Forgiven. I’m writing a paper on protein structure at the moment and just before sending it to a colleague discovered a couple of places where I had written “base pair” instead of “hydrogen bond”.

Interpretation of the Question
There are two questions here. The one about alternative start codons is factual and has been well answered by Louis Maddox. The other is an evolutionary question which I would recast as

“Why was methionine selected as the initiating amino acid?”

Like Louis Maddox I would have said that this was almost impossible to answer. However, it turns out that there is at least one hypothesis — perhaps related to the comments on Maddox’s answer — so I feel it useful to present and discuss it.
The Regulatory Hypothesis for methionine as initiator
This hypothesis was presented by Bhattacharyyaa and Varshney in a paper in RNA Biology (2016).  (A personal or institutional subscription may be required for access to the full version.) Their argument can be summarized as:

Methionine does not perform a role in proteins that other aliphatic
amino acid side-chains could not, and is one of the rarest of amino
acids in proteins.
The synthesis of methionine has the highest metabolic cost among
amino acids
The synthesis of methionine (and N-formyl methionine) depends on
one-carbon metabolism.
Hence its adoption as an initiator of translation could have been
to ensure that protein synthesis only occurred when there was
sufficient energy in the cell for one-carbon metabolism, and, by
implication, for protein synthesis itself.
In addition, the requirement for S-adenosyl methionine for the
methylation of rRNA and certain tRNAs would represent a specific
coupling to other components of protein synthesis.

[Methionine synthesis — from Berg et al., Section 24.2.7]
Comments
A difficulty I personally have with this hypothesis is that I would expect a mechanism to evolve first, with regulation only appearing later. One possible way round this would be if methionine had displaced a similarly hydrophobic amino acid such as norleucine from the early genetic code, as suggested by Alvarez-Carreño
et al..  Before this, one would assume that initiation did not take place at a specific codon, as discussed in relation to another SE Biology question.

[Formylation of Methionine — from Berg et al., Figure 29.21]


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What is the advantage of the way eukaryotes initiate translation?
The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ?
Edit : I specifically want to know why eukaryotic ribosome first attaches to tRNA and then to mRNA but prokaryotic ribosome can do this in either order. Is there any advantage of the former ?

Is there any aspect in particular you are interested in?  Such as Shine-Dalgarno versus Kozak, or what?

@Amory Edited the question !

As far as I understand it (and I'll preface this by saying that initiation is not my strongest point), but prokaryotes utilize the beautiful AGGAGG Shine-Dalgarno sequence.  Usually around 8bp upstream of the start codon, it is this sequence that the prokaryotic ribosome seeks out to initiate translation.  It does this through a complementary region in the 3' sequence of the ribosomal RNA.  Upon complementary binding, the ribosome and mRNA are correctly bound.  Convenient!
In eukaryotes, however, there is no consensus SD sequence, so a different mechanism must be used; the complex of 40S and Methionine tRNA serves this purpose.  The two together scan the mRNA, looking for an AUG start codon which the tRNA is complementary to.  This eventually brings the full ribosome (40S + 60S) together to start translation.

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How does GTP help in the step of codon recognition?
The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step.
How does GTP do so ?

GTP based structural changes (even motor actions) are very common in biological systems. For e.g. G-proteins, Rab-GTPase (vesicular transport), Ran-GTPase (Nuclear export/import).
So all these GTP-bound proteins make use of an intrinsic or assisted GTPase activity to convert GTP to GDP. This conversion causes change in the structure of the associated protein. Going back to the GTP bound form requires proteins called GEF (Guanine nucleotide Exchange Factors).
So in the case of translation elongation, the elongation factor is a GTPase which changes confirmation upon GTP hydrolysis. This confirmational change twists the tRNA so that the bound amino acid moves closer to the peptidyl-transferase center (if P-site is in the left then the amino acid is bound to the rightward CCA tail of tRNA. The twist causes the amino acid to move leftwards- towards the P-site).
You can refer books like Genes by Lewin for details.

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Is there any use of CO₂ in human body?
We all know CO₂ as a waste product of metabolism . Does CO₂ have any helpful role , apart from having a role in pH of blood ?

Yes. CO2 regulates blood pH by acting as a buffer by its interconversion to carbonic acid by the enzime carbonic anhidrase

@TomD , the enzyme in q. has the largest turn-over number/rate...

Is there anything that could be made of H2CO3?

Before I restrict the answer to human metabolism, I recon it is important to mention that
CO2 is the source of the carbon atoms of glucose in photosynthesis (in the Calvin cycle). [In photosynthesis CO2 is 'fixed'].
Even with the above restriction, I am certain I  cannnot do justice to every helpful aspect of CO2 in mammalian metabolism, and I'll restrict myself to just one area that came to mind on reading your question: the requirement for carbon dioxide (in the form of bicarbonate) for fatty acid biosynthesis (FAS) and, in a bit more general sense, mammalian/bacterial biotin-dependent carboxylation reactions. Depeding on other contributions, I might be able to extend this a bit later.
Salih Wakil showed that CO2 is an absolute requiement for fatty acid biosynthesis, but carbon atoms from CO2 do not appear in the fatty acid product.
We now know that FAS begins with the carboxylation of acetyl-CoA to malonyl-CoA, catalyzed by the enzyme acetyl-CoA carboxylase. Acetyl-CoA, ATP and bicarbonate are the substrates for this enzyme, and malonyl-CoA is a key product. One of the many interesting properties of this enzyme is that it contains biotin, which (in this case) may be considered a carrier of 'active' CO2.
This explains the requriement for carbon dioxide but why no carbon from CO2 in the final product?
It is now known that in subsequent FAS reactions, a derivative of malonyl-CoA condenses with a derivative of acetyl-CoA (I am simplifying here) to give a four-carbon compound with loss of CO2.
Thus, carbon dioxide (in the form of bicarbonate) is an obligate requiement for mammalian fatty acid biosynthesis, but no CO2-derived carbon is incorporated into fatty acids.
Carbon dioxide is also required for oxaloacetate formation from pyruvate. This reaction may be though of a method of 'filling up' a key Krebs Cycle intermediate (a  so-called anapleurotic reaction).  The enzyme here is pyruvate carboxylase and the substrates for the reaction are pyruvate, bicarbonate and ATP, with oxaloacetate being a key product.  This enzyme also contains biotin and (like acetyl CoA carboxylase), CO2 becomes covalently bound to biotin during the reaction cycle.
Pyruvate-CoA carboxylase was discovered by Harland.G Wood and C. Werkman in bacteria (See here for a good reference on the early work on pyruvate carboxylase). Its discovery was very controversial because at the time it was thought that animal/bacterial cells could not 'fix' CO2; that is it was though that CO2 is only 'fixed' in photosynthesis.  This discovery disproved that piece of dogmatism.
A third enzyme that requires CO2  as substrate (in the form of bicarbonate) is propionyl-CoA carboxylase.  This enzyme occurs in mitochondria and functions in odd-chain fatty acid metabolism.  It also contains biotin.
I have concentrated on some biochemical aspects of your question.  The three enzymes mentioned, acety-CoA carboxylase, pyruvate carboxylase and propionyl-CoA carboxylase all require CO2 in the form of bicarbonate as substrate, all contain biotin, and (as far as I am aware) all play very central roles in mammalian metabolism.  (They also all require ATP as substrate).
Of the many interesting aspects of biotin, I'll mention just one.  Egg white contains a protein, avidin, which binds biotin very, very tightly.  In fact the biotin-avidin interaction is one of the strongest non-covalent interactions known.  As far as I am aware, no-one knows the function of avidin in egg white.  Some bacteria contain a similar  (but evolutionarily unrelated) protein called streptavidin. No one knows the function of steptavidin either (again, as far as I am aware).
The original Wood & Werkman paper: was published in the the Biochemical Journal in 1936
The utilisation of CO2 in the dissimilation of glycerol by the propionic acid bacteria.
Harland Goff Wood and Chester Hamlin Werkman.
Biochemical Journal, Volume 30, January 1936, pp 48-53

"acety-CoA carboxylase, pyruvate carboxylase and propionyl-CoA carboxylase all require CO2 in the form of bicarbonate" - None of the three uses H2CO2 from the blood made by carbonic anhidrase?

Some additional points about role of bicarbonate (which is directly formed from carbon dioxide as described by TomD):

Helps is neutralizing the acidic chyme when it enters intestine.
Formation of shells in invertebrates and eggshells in birds and reptiles. Shells are formed by deposition of calcite (calcium carbonate) which primarily happens by increased bicarbonate and calcium secretion.
Bicarbonate is also important for chloride transport (Anion exchange). In RBCs it happens through Band3

To add my 2 cents worth: Breathing rate and depth is regulated by chemoreceptors in the medulla in the brainstem. These chemoreceptors primarily respond to pH of the blood, but the pH is for an important part determined by the CO2/HCO3- equilibrium as explained by @TomD. Essentially it is the increase in CO2 that is sensed by the medulla and which increases breathing frequency and the depth of inhalation. See this web page about respiratory control.


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How to Diagnose this hepatitis A, B and C case?
Male patient who is working in the hospital and may be infected with contaminated blood had hepatitis
with genome IA 5 years ago. His hepatitis A at that time was confirmed with the rise of anti.HAV IgM and
later with anti-HAV IgG type antibodies. His wife is known to have antibodies against C hepatitits. The
patient had icteric illness in about three weeks ago. Which are the best indicators in
diagnosing his hepatitis?
Right answer is: Detection of HBsAg and anti-HCV antibodies.
I think this is because

to check if he has hepatitis B by HBsAg
to check if he has HepC by the antibody

Serum antigen of HB tells us about the levels of IgM and IgG.
If vaccinated, then IgG should be positive, I think?
What does HBsAg tell you?
Why do we need to detect anti-HCV?
If they are found, what does it mean?
I think that then it means if found that he does not have hepatitis C then.

The last sentence of the question doesn't make it clear what's being asked. But it seems to be asking: What version of Hepatitis did he get from the contaminated blood?
To that end...

Serum antigen of HB tells us about the levels of IgM and IgG. If vaccinated, then IgG should be positive, I think? What does HBsAg tell you?

HBsAg gives you the knowledge of whether or not there's an acute infection of Hep-B. Hep-B IgM antibodies indicate an acute infection, whilst IgG antibodies would show up due to his previous exposure/immunization. If the patient has Hep-B IgM, the icteric illness was probably a re-infection of Hep-B.

Why do we need to detect anti-HCV? If they are found, what does it mean? I think that then it means if found that he does not have hepatitis C then.

That would my assumption as well.
You run the HBsAg and can get two outcomes: IgM(+)/IgG(+) or IgM(-)/IgG(+). The former indicates the icteric illness was probably a reinfection of Hep-B.
You run the anti-HCV and get two outcomes: (+) or (-). The former indicates a present infection, the latter indicates no Hep-C.
What might throw you off is the wife's anti-HepC antibodies. If she was formerly infected and infected the patient (or vice versa) then you'd expect to find a (+) anti-HCV result.
I might come back to this after thinking on it a bit more, but that's the best I have for now.


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What is Growing on These Tree Leaves? (Image)
I found a seemingly diseased tree when I was out playing tennis yesterday... What is growing on this tree leaf? Is this a disease? If so, is it contagious? I have zero knowledge in botany, but I'm curious about what is happening to these trees. :)

I'm just wondering if you still play tennis in that location to confirm if you see any Juniperous virginiana (eastern red cedar) nearby.

This is actually not a gall as other answers have suggested.
This is likely a fungus called Cedar-apple rust (Gymnosporangium juniperi-virginianae).
The fungus only thrives in the presence of both Juniperus virginiana (Eastern red cedar) and apple (Malus spp.) trees.
The leaf in the picture belongs to some species of the apple genus and the growths are aecia of G. juniperi-virginianae. You can read about this interesting fungi through Rutger's Plant & Pest Advisory here.
You can see a picture of the fungi here, and I've included Sabrina Tirpak's (Rutgers PDL) photo of its aecia below:
http://plant-pest-advisory.rutgers.edu/3859/
Below is a visual of the telia of the rust fungus on J. virginiana:

 (Photo source: Ada Hayden Herbarium)

What a fascinating organism!

Right?! I've never seen the tentacled glob that grows on the Juniper

That's so cool :)

Briefly, these look like insect galls; which are reactions of plant tissue caused by parasitic insects (often wasps) laying eggs inside the leaf. I'm sure someone can answer in more detail, though!
Cf. How do plant galls form?

Would the tree die because of this? Most of its leaves are growing "insect galls"...

I imagine that it depends on the galling species and tree species, but most leaf galls don't hurt trees

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Can we remove impacted teeth by key hole surgery?
Can we remove impacted teeth by key hole surgery, rather than an open technique, like lithotripsy?

Could you add some additional context to your question, such as what you know, why you are interested, etc.? It's not clear what you are seeking beyond a yes or no answer.

The impacted tooth is partially or fully enclosed in the bone. Even if accessed by a drill hole to reach the tooth. The tooth is too hard to be cut up into smaller sections with any of the conventional equipments available through an endoscope.
Tooth is a composite of three highly organized, mineralised tissues. The bulk of the tooth is formed by dentin and has around 30% organic content almost similar to that of bone. A large part of the organic content is collagen a tough fibre. Where as kidney stones etc are aggregates of minerals etc and are much more susceptible for pulverisation by shock waves from a lithotripter.
Besides an impacted tooth is either partially of fully inclosed in bone. So that too rules out the use of a lithotripter.


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Why are certain baby (water)fowl yellow?
Why are e.g. ducklings, goslings, turkey and chicken chicks (partly) yellow?
What is the chemistry background to this? What compounds from the egg cause this to happen?
What is the evolutionary background to this? How could it help the bird to survive?
While domestication has led to selection of all-white adult birds and thus more common all-yellow babies, why does an all-yellow baby become an all-white adult, in terms of biochemistry?

Most wild ducklings are not yellow as far as I know, but in more "helpful" colors. Chicken ducklings emerged from selective breeding, no need for them be able to mimic their environment.

Wild ducklings, like these baby Mallard ducks, are in fact typically only partly yellow:

Photo by TheBrockenInaGlory via Wikimedia Commons, used under the CC-By-SA 3.0 license.
While I'm no expert, I would guess that the mottled yellow-brown coloring of the juveniles is, at least partially, protective coloration, just like the somewhat similar pattern on the adult female's feathers.  While it may appear conspicuous on open water, ducks in their natural habitat will often seek shelter among reeds and other vegetation, where the irregular pattern of light and shadow would create a very effective camouflage for the ducklings.
As for the all-yellow ducklings of domestic ducks, these presumably arose via elimination of the darker parts of the coloring as a result of selective breeding, perhaps as a side effect of artificial selection for the white adult plumage found in many domestic ducks today.
Specifically, according to a recent study of domestic duck genetics, it appears that the all-white plumage of domestic Pekin ducks is caused by a single recessive mutation to the MITF gene, which regulates melanin production.  The mutation, when homozygous, causes the normal melanin production pathway in the skin to be almost entirely shut off, so that the adult plumage is pure white regardless of what other plumage color genes the bird may be carrying (a fact apparently known for a long time from cross-breeding experiments, even though the specific mutation behind this effect was not determined until recently).
Apparently, however, the yellow base pigmentation in young ducklings is not affected by the MITF mutation, and thus appears even in individuals homozygous for it.  Presumably this is because the yellow color is produced via some other pathway, which is active in young ducks but gets shut off as they develop their adult plumage.  The brown pigmentation pattern overlaid on top of it in wild-type ducklings, however, is controlled by MITF, and thus fails to appear in ducklings with two copies of the mutated version of the gene, leaving their juvenile plumage pure yellow.
As far as I can tell, the specific reason why the yellow pigmentation in ducklings is not controlled by the MITF gene still remains unknown.  Or, if it is known, my Google search skills were not good enough to find it.

Good to know that they're still alarmingly cute with their natural colourings though!

Still doesn't give any specific answer to the chemistry of why a bird that will be white as an adult, is yellow as a baby. That is what I'd like to know.

@ArcaneEngineer: I did some Googling, and found a recent study that sheds some light on the genetic mechanism behind the white/yellow coloring of domestic ducks. It would seem that the adult plumage color and the brown plumage patterns in wild-type ducklings are controlled by the same gene, which is disabled by a mutation in white domestic ducks. The yellow base color in ducklings is apparently not controlled by this gene, though, so the ducklings end up yellow instead of white. No idea why that is so, though.

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How did the genetic code evolve?
The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is coded by 6 codons, tryptophan is coded only by one codon.
[I am aware that the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last base that does not affect the amino-acid that is encoded.]
I therefore do not think that the genetic code can be entirely be explained by “it happened to occur that way the first time” (at the origin of life or in the last universal common ancestor) “and it never changed”.
So, my questions are:

Why are some amino acids coded by a several codons while others are coded only by one or two?
Specifically, why is methionine coded by only one codon — AUG — which has also to serve as a start signal?
In general, how (by what mechanisms, selective pressures) has the genetic code evolved to give this pattern of redundancies?

This is an area of ongoing research, and I don't think you'll get a great answer. There are some ideas about the early evolution of the code, and there is some variation among extant life, but it is hard to say how it evolves because it evolves so rarely.

This question (actually two questions) allows only speculative answers, and is not likely to find one here, given the complexity of any serious argument. However it has been popular and so there is little point in suggesting it be closed. Instead I have tidied it up and tightened it up, without changing the essential question(s).

This question is closely related, and the fascinating link posted by @JohnSmith is a good read.
In short, with a four-base system, and a codon size of 1, you get four possible amino acids.  Silly system.  A codon size of 2 gives 16.  Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids.  Codons of size 3 gives 64 - plenty of room to work with and it covers all your forseeable amino acids, and then some, without being too wasteful.
The redundancy, known as degeneracy, is pretty straightforward.  There's room to expand, and any redundancy/degeneracy will only reduce the likelihood of errors.  That's a huge benefit.  For some amino acids, the first two bases are enough.  That third position can be quite tolerant to mutation, which is very beneficial to organisms.  It appears to be even more fine-tuned, to the degree that redundancy often not only reduces the likelihood of mutation but also reduces the damage caused when a base does mutate.  Swapping a hydrophobic AA for another hydrophobic one is less likely to cause aberrant protein function, and anything with a U in the middle is probably hydrophobic.  Convenient!  I'll also note that, while it's not perfect or even a significant correlation, the more popular amino acids tend to get more redundancy; tryptophan is traditionally the least common AA.
Finally, there are a few non-proteinogenic amino acids, so, as the linked question/answer above points out, maybe in the future there will be more amino acids.

This fails to answer any of the three questions posed.

It seems that duplicate codons make translation more robust and resistant to translational misreading. There are four theories that explain existence of duplicate codons:

Stereochemical theory
Coevolution theory
Error minimization theory
Frozen accident hypothesis

They are not mutually exclusive and “Origin and evolution of the genetic code: the universal enigma” paper attempts to reconcile them:

Mathematical analysis of the structure and possible evolutionary
  trajectories of the code shows that it is highly robust to
  translational misreading but there are numerous more robust codes, so
  the standard code potentially could evolve from a random code via a
  short sequence of codon series reassignments. Thus, much of the
  evolution that led to the standard code could be a combination of
  frozen accident with selection for error minimization although
  contributions from coevolution of the code with metabolic pathways and
  weak affinities between amino acids and nucleotide triplets cannot be
  ruled out. However, such scenarios for the code evolution are based on
  formal schemes whose relevance to the actual primordial evolution is
  uncertain. A real understanding of the code origin and evolution is
  likely to be attainable only in conjunction with a credible scenario
  for the evolution of the coding principle itself and the translation
  system.

From my understanding the idea is that codons are grouped by selection for physico-chemical properties of corresponding amino-acids so a random one nucleotide mutation wouldn't change properties or a corresponding amino-acids too dramatic.

Some elements of response to your question.
First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on minor tRNA (while the ribosome waits for the proper tRNA). This may have very important impact on the folding of proteins (see for instance this paper: http://dx.doi.org/10.1371/journal.pone.0002189). Having several codons for common amino-acids may actually be a powerful fine-tuning too for the folding of proteins.
Second, as in some cases (splicing, selenocysteine insertion, what else ?), the secondary structure of the mRNA produced is extremely important, the organisms must be able to tweak the sequence of RNA to leave room for that to happen, and that can only happen if there are lots of amino acids for which there is latitude to tweak the produced mRNA sequence.
Third, it is false that the genetic code is universal. There are some evolutions of the genetic code, see for instance the specific case of methionine in mitochondria: http://dx.doi.org/10.1073/pnas.0802779105.

This fails to answer any of the three questions posed.


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Axial skeletal system
I was curious about a fact given in my biology textbook as to why the Japanese have  3 pairs o floating ribs unlike the rest who have just two?

Because your textbook is probably worded poorly.
It appears that the Japanese (and several other ethnic groups) apparently have a higher proclivity for the 10th rib to be a true floating rib, but every ethnic group has the chance of having a floating 10th rib.
With that said, the one McGraw-Hill book cited in the Wiki article is the only source I've seen for this higher morphology rate. I, personally, wouldn't trust just one source, and (if true) the rate may not be much higher.


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What is the difference between "lineage restriction" and "differentiated" in terms of stem cell biology
Is there a subtle difference between these two concepts or are they basically the same thing? When I mean differentiated, I don't mean terminally differentiated.

lineage restricted stem cells are multipotent i.e they can give rise to only a few types of cells. Embryonic stem cell to hematopetic cell is also differentiation. Differentiation just means becoming into a specialized cell which can even be a lineage restricted multipotent stem cell.

So they are basically the same concept?

differentiation leads to lineage restriction

I agree with @WYSIWYG and add that I tend to see 'lineage restriction' usually as a function of assay conditions  (ie the precursor cell population could become X and Y but now the cell can only become X, so the cell is lineage restricted) whereas differentiation is a function of phenotype (i.e. looks more like maturing cell X than maturing cell Y).   But the concepts are clearly inter-related

When you look at the development of the embryo, at the beginning all cells are totipotent, meaning they can develop into any cell type of the body. This changes relatively fast by differentiation, which means that the totipotent cells develop into more specialized cell types, which then can not give rise to all cell types. So the different germ layers (meso, ecto- and endoderm) develop and from these all the cell types in our body. See the first figure for clarification (from here):

Lineage restriction means that you have a differentiated cell line, which can only further develop into cells of this line. So hematipoietic stem cells can only further develop into cells of the hematopietic line (lymphocytes, erythrocytes, basophiles and so on), like shown in the figure below (taken from here):


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Creating expression template from PCR: What annealing temperature to use?
I am creating a transcription template for expression in PURExpress and was confused about the annealing temperature to use.
I have two primers with the T7 promoter and an RBS on the forward primer and a termination sequence on the reverse primer.  The melting temperature of these primers are 84.4 and 83.8 degrees C.  The melting temperature of the regions that are complementary to the gene of interest I want to amplify by PCR are both about 65 degrees C.
What annealing temperature should I use a h?  Since at the beginning of the PCR reaction I will have mostly template that will have the complementary sequences of the primers binding to the GOI and not the 5' and 3' extensions.

It seems the answer, which may be context specific, is to use an annealing temperature about 5 degrees below the entire oligo melting temperature.  I did not get any bands at lower temperatures.

I have to add a comment that I asked PI who focus is synthetic biology, and that PI told me to use an annealing temperature 5 degrees below the melting temperature of the area of the primer that bind directly to the starting template.  I think the answer is somewhere in the middle.


text:
How does electroporation mediated recombination work?
For yeast and other organisms, DNA can be readily taken up into the cell naturally or through membrane disruption. What does applying a voltage to cells do exactly that allows more recombination to occur?

Electroporation is a fairly common way to introduce exogenous nucleic acids into cells. Its name essentially describes the process - an electric voltage potential is applied across a biological membrane, eventually leading to the production of conducting hydrophilic pores. The image below is from the Wikipedia page linked above, showing non-conducting (upper) hydrophobic and conducting (lower) hydrophilic pores. Depending on the voltage, membrane composition, and other factors, these pores can eventually "heal" and close back up, or join together and lead to the rupture of the cell.

Electroporation is used in the lab as a method of transfecting or transporting nucleic acids (usually DNA) into cells, to make them express genes they otherwise wouldn't, or to otherwise alter the genetic machinery. The transfected DNA can either remain in its own structure (such as a plasmid), or be incorporated (recombined) into the host genome, similar to what happens during a retrovirus infection. Whether or not this happens is dependent on the structure and sequence of the construct being introduced, not the method of introduction.
So, in reference to your question, electroporation doesn't do anything that directly allows more recombination to occur - all it is is a method of transportation. However, electroporation may allow for certain constructs to be introduced into the host more efficiently, or for a larger quantity of them to be introduced, leading to a greater transformation efficiency. Some cells, especially primary cells like neurons, for example, may only be transfected with any sort of efficiency with electroporation. However, electroporation can also have its down sides, as it can be rather stressful to the cells, and if the voltages and timing aren't properly adjusted can lead to high levels of cell death.


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What type of insect is this?
I'm naturally thinking this is a bee, but I cannot find it anywhere in any insect identifiers. I caught this picture on top of my doorway, it's about 1 1/2 inches in length, and its torso seems to be coated in a layer of hair, and the rest of its body is narrow. The thick layer of hair may or may not be accurate, I didn't want to get too close to it, but that's how it appeared at least.

What is this?
PS - Found in Kentucky, and I'm not sure why one pic shows wings and the other one doesn't...

Well I can suggest why the wings are not seen in two of the pictures. From the shadows it is obvious you have not used the flash. Under natural low light the shutter remains open for a longer time and any movement of the wings will blur it. In the third picture you must have got when the wings were not moving.

Well I was using a camera phone

It's a red-footed robber fly, check out those lateral stripes and the red/yellow leg segments

From the general body plan, it looks like it's probably a robber fly. Here's a page of specifically Kentucky robber flies – it's possible yours could be a Bearded Robber Fly.

That looks about right

It is most certainly a Robber Fly. I would agree with Oreotrephes that it is a Bearded. I can't seem to find anything closer.

My first idea as well, but the picture is probably to unclear for a certain species determination.

Yes, I would say that is a bearded robber fly. Robber flies are similar to dragonflies in that they catch prey by catching it in midair. They will attack mostly bees, wasps, and hornets, and I have seen many catching bumblebees in the wild. I have even seen some sit near a yellow jacket nest and catch a hornet when it comes out. They suck out the juices of their prey with a proboscis using methods similar to spiders. They will also bite when handled, as I have found out through experience.

It is commonly called as "Robber fly" or "assassin fly". Scientifically it is "Asilidae" of the order "Diptera" and it is a fast attacking predator mostly preying on grasshopper nymphs and damsel flies. It is strongly built for kill.
http://www.robberflies.info/keyger/htmle/didpic.html

Can you provide some references for your answer? Please read the help for this site, in particular here where you can know how to write a good answer.

http://en.wikipedia.org/wiki/Asilidae

Also posting a separate image of your ID is important to allow other usres assess your answer


text:
Is there any natural blue rose?
I had recently read an article that the possibility of having natural blue rose is extremely rare because of the absence of delphinidin in most roses. Are all blue roses just a product of cross-breeding?

Wikipedia article on blue roses has a pretty comprehensive explanation.

There are no roses (that is, flowers of genus Rosa species) that naturally express a "true" blue color. Through cross-breeding, there are lilac-mauve rose horticultural varieties ("Blue Nile","Blue Moon","Lady X", etc.), and through genetic engineering (actually inserting delphinidin-producing genes) there are mauve-lavender varieties ("Applause"). The insertion of delphinidin-producing genes did not yield blue colour roses as hoped is due to the acidity of the rose petals, which itself changed the delphinidin blue to mauve-lavender instead. The next breakthrough will be to switch off the acidity of the rose petals to create a true blue rose.
More info
Wikipedia article Blue Rose gives good coverage.
Here's a nice scientific bibliography of rose pigments with some good information on blues.


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Why is there sperm mitochondrial suicide?
The mitochondria in the sperm are digested upon entry into the egg, making mDNA inheritance exclusively female. What is the advantage of this? Wouldn't some male mDNA be beneficial because of the advantages of (at least a little) sexual reproduction?
Reference:
"Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission" (behind paywall, here's a ScienceDaily article discussing the results).
Edit:
Both answers seem valid but it is hard to quantify the relative costs.

cant be sure about this but sperm mitochondria have the main purpose of fuelling the sperm movement. There is a likelihood that these mitochondria have developed some mutation because of this excessive respiratory load.

Maternal inheritance of mitochondrial DNA is very well conserved, although some species, such as some mussels, show paternal inheritance.  As for why or what the advantage is, some of it is due to basic logistics: sperm cells have ~100-1000 mitochondria, egg cells have 105-106, so male contributions are largely washed out.  Plus, most mitochondria in sperm are toward the tail, which does not always or necessarily get inside the egg.
For a more selection-based mechanism of the actual destruction, think about what sperm do.  They are small packets of energy that do nothing but race until they die.  That's it.  Energy production, which occurs in the mitochondria, produces reactive oxygen that can damage genomes.  The mt-genome in the egg is far less likely to be damaged.
Additionally, I might look to chromosome uniformity.  Heteroplasmy does occur now and again, and it's not usually a good thing.  Mitochondria are very important, so it makes sense to have an all-or-nothing approach, lest any deleterious genomes persist.

The mainstream theory, I believe, is that it's a way of avoiding the inevitable destructive (organismal fitness-lowering) competition that the two parents' mitochondria would otherwise be in.
From Austin Burst and Robert Trivers' book Genes in Conflict (p. 146):

Selfish mitochondrial genomes... have
  a replication advantage over normal mitochondrial genomes in
  within-organism selection, but they lose out in conventional
  among-organism selection... Therefore, if a population is polymorphic for 2 mitochondrial types, one more selfish than the other, a nuclear gene that somehow reduces the efficacy of the within-individual selection will tend to become associated with the less selfish type, and so can increase in frequency due to among-organism selection.. That is, there will be selection for nuclear genes that modify mitochondrial behavior so as to reduce the efficacy of within-organism selection (just as there is selection on nuclear genes to suppress drive at unlinked loci)...
An even better way to limit within-organism mitochondrial selection is
  to ensure that only one parent transmits mitochondria to the next
  generation - that is, to impose uniparental inheritance...

I think the implication is that uniparental inheritance on the mtDNA, is imposed by adaptations acting in the interest of the nDNA. Without uniparental inheritance, within-cell selection on mitochondria would drive them to replicate faster than is optimal from the rest of the cell's (and the nDNA's) perspective.
Apparently this theory also plays a role in answering Fisher's question, from the preface to The Genetical Theory of Natural Selection:

No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?

Laurence Hurst and Bill Hamilton argue, in their paper Cytoplasmic Fusion and the Nature of Sexes (1992):

Binary mating types are proposed to arise in a three-stage process through selection of nuclear genes to minimize cytoplasmic gene conflict at the time of gamete fusion. In support of this view we argue that: (i) in systems with fusion of gametes, the mating type genes are typically binary and regulate cytoplasmic inheritance; (ii) binary sexes have evolved several times independently associated with fusion, although at least twice binary types have been lost, associated with a loss of fusion; further, in accordance with the theory are findings for isogamous species that (iii) close inbreeding may correlate with less than two sexes and biparental inheritance of cytoplasmic genes; and (iv) species with more than two sexes may have uniparental inheritance of cytoplasmic genes, be rare and be afflicted by deleterious cytoplasmic genes which attempt to pervert normal cytoplasmic genetics.


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Is it possible to suffer from hyperthermia by spending too much of time in the hot springs?
People may tend to spend time in a hot water spring. Is it possible to get hyperthermia (like a sun stroke) due to this?

You betcha!

We report a case of acute hepatic failure combined with disseminated
  intravascular coagulopathy, acute renal failure, and neurological
  deficit caused by heat stroke after bathing in a hot spring.

Generically, the term you're looking for is non-exertional heat stroke.


text:
Is there differences in components of saliva among species
Are there differences in the components of saliva among species? Also, do the functions of saliva differ between species?

Some functions stay the same. For instance, at least in mammals, saliva helps to lubricate food for swallowing, begins digestion of starches by amylases and provides a liquid medium in order for taste sensation to funciton. More broadly conserved in animals is the inclusion of antimicrobial peptides in the saliva that function as a primitive immune function to keep the oral cavity clear of harmful microbes.

This question should be narrowed down somewhat. Which species are you asking about?

It could be better answered if you specified which species you were interested in. Broadly from Wikipedia, snakes have venom, some swifts have gummy saliva to help in the building of nests, spiders produce their web from salivary glands etc. This is too broad a topic. The human salivary composition is found on the Wikipedia page I have linked. Salivary compositions can change with habits which have been detailed in this article. To compare, I am also providing the link to an article on the saliva composition of an assassin bug.

Not to nitpick, but venom is technically injected and is not a normal component of saliva. Toxins on the other hand are completely normal.

@leonardo wikipedia mentioned venomous saliva so i just put it in but u are right. Toxins would be right term to use

I think the answer is not very original or authoritative. Can you try to flesh it out a little? I agree that the question is broad, but I think you could put a little more into the answer.

@jmusser Thank you for your opinion. I will have a look at it as soon as I get some time.


text:
What determines the strength of a tree
What determines the strength of a tree. A morphologically strong looking tree found broken down at trunk. can we determine the strength/ life of a plant

Please define what you mean as 'strength' - what aspect are you thinking about?

I think it is fairy obvious what you are asking (what determines the strength of wood to bending/breaking - probably mainly against horizontal forces), but you should really clarify the Q. However, I think that the Q should be left open until the poster has at least had time to see the comments and rephrase the Q.

I was letting my fingers surfed in the internet about this question and found this interesting article : http://www.caves.org/section/vertical/nh/55/TreeAnchors.pdf
Your  question is too broad so I guess the link gives a general answer.
hope this helps


text:
What determines the size and shape of a cell?
What determines the size and shape of a cell? They differ at different tissues / organs/ species

Can you add some specifics to your question? Have you done any previous research, and are you particularly interested in a certain type of cells (eg bacteria, plant, animal tissue etc)?

Can confirm, this is the exact question that motivates my research interests, and I can tell you that even now this is far from a settled question, in pretty much any organism.

This is quite a hard to answer question.
There are different cell cycle molecules that, if mutated or knocked out, have shown to cause the cell to have a different shape or "overgrow" in size or not grow at all...
You might find some insight here.
There are lots of factors that influence cell size and shape, thus it is a very complex system to study. For example, cell shape is influenced by the cytoskeleton but also other factors.


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Tree census data for Sweden/Scandinavia?
Is anyone aware of any attempts to count or approximate the number of trees there are in Sweden or Scandinavia? I have a small popular science side project for which this would be useful

This site says 51 billion but there is no source http://www.sverigeturism.se/smorgasbord/smorgasbord/natrecspo/nature/forest.html

There are bit more specific statistics with forestry sites.

I would definatley look at data from Swedish National Forest Inventory (Riksskogstaxeringen). They have time series data of multiple variables (DBH, size classes, species, dead wood etc) from plots all over the country. Extrapolations based on these data should produce reasonable estimates of total tree count, and probably the most accurate one that can be obtained at the moment. As an example, this report (in swedish) includes graphs on trees/km$^2$ for different species and areas (page 17 ff), but this is only based on areas that can support productive forestry.

Did a bit of a search, but could not find any Scandinavian specific statistics; however, I did find European Commission Forestry Statistics page, within this site there are some stats by country.  Further, the website
About Forestry in Northern European countries  also has a few links to country based data.
I hope this helps.


text:
potency in preformed germ-line
In organism that have a preformed germ-line like Drosophila where germ cells are pre-allocated in the oocyte, are there technically no adult pluripotent stem cells since germ line cells can't be developed from somatic stem cells?

In almost all metazoa, the pro-germline cells get segregated from other stem cells at an early stage of development and they thrive and differentiate in their neighborhood. This is important in order to preserve the germline. This post provides some basic explanation.
However, even drosophila have adult multipotent stem cells and help in the formation of midgut as reported by this study.


text:
Why are human eye colours limited?
Related to the question What causes the colors we see in eyes?, I am wondering why human eyes are restricted in colour. Most common eye colours are blue, green and brown. Why not yellow, orange, purple, red and so on?
I am guessing this is related to the function of the iris and that other colours do not have the same effect on light absorbing or something like that.

I think the excellent answer in that thread http://biology.stackexchange.com/a/8984/3795 explains it reasonably well, it is to do with the melanin concentrations in the eye.  Are you after the optical properties of melanin?

@UV-D Even though that answer sort-of answers my question, it doesn't do so directly. There are certain proeprties to the colours blue, green and brown that explain their occurence. But why not other colours then?

I was going through and cleaning up some of my old answers when I came to this one.  Was there something else you were looking for in an answer?

There is only one main "coloring" agent, or pigment, in the eyes.  That pigment is melanin.  To a much lesser extent, at least in health individuals, you can have lipofuscin produced which gives a golden-amber color to the eyes.  It should be noted that lipofuscin is most likely produced because of oxidation damage/stress in your eye, and not something to be hoping for (Beatty et al has a good review of the subject (1)).
Indeed, lipofuscin in the eyes can be seen as a symptom to physicians, so for the rest of the answer I will only consider melanin, eumelanin and pheomelanin in particular, as the normative pigment in the iris.
To make additional colors, we would need to develop an additional pigment, and or modify eumelanin so that it produces different scattering properties.  So why do we have melanocytes in the eye producing melanin in the first place?
As much as we might consider it as a factor now, sexual selection was probably not the main pressure for having pigment in the eyes.  Instead UV protection almost assuredly is (2, 3).  Thus for another pigment to be selected for, it would probably need to do a better job protecting us vs. UV (also, further selection in humans is hampered by all kinds of things like behavior, medicine, and life span).
Eumelanin does a good job protecting us from UV (2, 3) and in fact does a better job than phenomelanin (4).  It seems incredibly unlikely that we would develop the necessary evolutionary pressure to have our pigment epithelium to produce a totally foreign pigment.
And that is what prevents us from naturally having a whole rainbow of colors in our iris.  One could conceivably engineer a better pigment, and have the genetic information needed to produce it delivered in gene therapy (I hate to think of people purposefully infecting their pigment epithelia).  I, for one, wouldn’t sign up for that.
(1) Beatty S. et al. The role of oxidative stress in the pathogenesis of age-related macular degeneration. Surv Ophthalmol. 2000 Sep-Oct;45(2):115-34.
(2) Hu DN. et al. Role of ocular melanin in ophthalmic physiology and pathology. Photochem Photobiol. 2008 May-Jun;84(3):639-44. doi: 10.1111/j.1751-1097.2008.00316.x. Epub 2008 Mar 8.
(3) Simon JD, Peles DN. The red and the black.  Acc Chem Res. 2010 Nov 16;43(11):1452-60. doi: 10.1021/ar100079y. Epub 2010 Aug 24.
(4) Hu DN et al. Uveal melanocytes, ocular pigment epithelium, and Müller cells in culture: in vitro toxicology. Int J Toxicol. 2002 Nov-Dec;21(6):465-72.


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What species have had their genomes sequenced/are being sequenced?
The human genome project released it's first complete genome nearly ten years ago. Since then many species have also been sequenced.
I am trying to find a list of completed (and possibly ongoing/initiated) projects sequencing other species along with some very basic summary data such as number of genes (divided amongst the sex chromosomes and autosomes), length of DNA, number of chromosomes etc.
This is for a presentation I am giving at a conference and would make a nice addition to my talk.

"ongoing/initiated" is data you just cannot collect. There are more sequencing projects ongoing at some university which have not been publicly mentioned (and often won't before they are finished) than I would be willing to count. I am involved in at least 2.

The GOLD database (Genomes Online DB) contains data on the sequencing status, and also some stats (number of chromosomes, genome size) -- but this extra data is not available for all species.

There are several lists on Wikipedia, for example for plants, bacteria and eucaryotes.

The Genome 10K project, in their words "aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus.". Here is their species list.

At NCBI, you can find a table with genome Information per organism.
For each organism, you can find the Kingdom, group and subgroup it belongs to, the size in Megabases, the number of chromosomes, organelles and plasmids (if present) and the number of assemblies.


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Is there variation of AT/CG ratio along species?
Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T.
But what about the ratio $\frac{nA+nT}{nC+nG}$?
Is there variation along species of this ratio that is higher than expected by random processes? If yes, what causes this variation?

That ratio is essentially, as WYSIWYG pointed out, called GC-content.  In actuality, GC-content is reported as $(G+C)/(A+C+G+T)$, converted to percent; i.e., what percent of the genome is G or C.
There is vast variation in GC-content, both amongst species and within a given species' own genome.  For example, in humans the first intron and exon are generally more GC-rich than following introns/exons.1  Genes themselves are often found in higher GC areas,2,11 in particular CpG islands are found near a large number of (mammalian) promoters.3
Across species, there can be a big difference.  Yeast and Arabidopsis are both around 35%4,5 whereas Plasmodium falciparum is around 24%;6 Carsonella are even lower, at around 16.5%.14  On the other hand, the plankton Emiliania huxleyi is around 65%7.  We can use these differences to study genomic history.  Bacteria often have genes from all over the place thanks to horizontal gene transfer, and GC-content can be used to differentiate between their own genes and those from horizontal gene transfer;8 a good example is the CRISPR-Cas system,9 even in a virus!10
Here's a list of a few things genomic GC-content is correlated with:15

genome size
whether the bacterium is free-living or not
the environment
aerobiosis
nitrogen utilization

In the lab, high GC-content often means a harder region to work with, as the presence of three instead of two bonds (between A and T) requires more energy to break;12 anything involving primers can be made more annoying, including (especially, to some) sequencing.  There is a theory that high GC-content would be an adaptation to high temperatures, to avoid DNA damage, but that is controversial.13,16,17,18

Yes that ratio varies and is generally referred to as GC-content which is expressed as percentage. Earlier, people used GC-content as one of the identifiers for a group of organisms.
Though there have been quite a few studies on the evolution and variation of GC-content, there is still no clear explanation for why certain organisms have a certain level of GC-content- it exerts no great bias on the protein composition though it is argued that it controls protein expression. Chemical mutability is higher for C->U and A->G because of deamination but this might not be the sole criterion. You may refer to this nice review for details.

Well. i read that review fully, just now. Though it is nice, it doesnt summarize everything. But you may find a lot of analysis on this topic. Plus A doesn't get deaminated to G. It becomes Inosine which can base pair with C and thus can be read as G.

GC-content varies greatly among prokaryots, and it is used as a taxonomic characteristic. It is specially elevated in extremophyles, such as halophiles and thermophyles, and it's thought to be an adaptation to high temperature and other chemical and physical stresses. GC bonds are stronger than AT, so it's supossed to acts as a protection agains denaturalizing agents.


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Smallest unit on which selection can act
Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also consider all sequences that affect the fitness even though they are not genes (even though the do not code for polypeptide). And theoretically, any sequence of DNA does have an effect on fitness because it influences the time and energy for DNA replication (although it might be negligible). The decision of considering the gene as the smallest unit of NS seems rather arbitrary to me. We might as well consider a group of genes or a given exon of even a smaller sequence.
Here are my questions:

What factors influence the minimal size of a sequence to be considered as a unit on which NS acts? Mutation rate, generation time, selection differential for this sequence, recombination rate, ...?
Could we consider a nucleotide as a unit of NS? Why?
How does the quasispecies model fit into the question of what is the smallest unit of NS? (for those interested, you will also find a very good explanation of this model in Martin Nowak's book called Evolutionnary Dynamic: exploring the equations of life)
Is it worth talking about that? Is this question biologically relevant? Or is it rather a question based on a choice of definition such as "Is a virus alive?"

As I asked several questions, let me know if I should split my post into several. Otherwise, please do not hesitate to answer only very partially to this post!
UPDATE
Terdon's answer makes sense to me. I should be a bit more accurate in the reas of my question.  I read The extended Phenotype from Richard Dawkins quite a long time ago and if I'm not mistaken, Dawkins says the following things
A unit on which selection acts has to be:

active
germ-line
replicator

A replicator has the 3 following properties:

fecundity
longevity
fidelity while being copied

Therefore for fidelity to be respected a unit of selection has to be a sequence which is not too long, so that it is not too often modified by recombination or mutation. He argues in this sense.
He also argues that nucleotides are not possible unit of selection. Indeed, it is hard to imagine a nucleotide being an active replicator. The word active means that it influences its not probability to be replicated. I don't think a nucleotide can do such a thing.
Unfortunately I don't have the book with me right now and I can't check what I have said, give you a citation nor a more accurate a reference. If anyone has some citations from this book, it will be welcome for the discussion!
Thank you!

Who considers the gene as the smallest unit? I have never come across that idea (at least not in a modern context) . For example, SNPs can be selected for/against. Also, gene does not mean protein-coding sequence. As a simple example, think of tRNA genes (let alone the more complex cases).

Plus a single SNP can destroy a functional gene (nonsense mutation). Frameshifts are also huge changes because of 1-2nt indels. So the minimum possible limit on size is 1nt.

@WYSIWYG heh, your comment came as I was writing my answer, frameshifts are exactly what I had in mind.

perhaps i had a telepathic perception .. lol

Yes, you're absolutely right for the gene definition! Thanks!

The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages.
To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is something relatively important like p53, the SNP in question will be lethal and will be selected against. So, to take your questions one by one:

What factors influence the minimal size of a sequence to be considered as a unit on which NS acts? Mutation rate, generation time, selection differential for this sequence, recombination rate, ...?

any sequence unit whose alteration can affect fitness is a candidate for NS.

Could we consider a nucleotide as a unit of NS? Why?

Yes, if it can affect fitness (which it can, see above) it can be selected for or against.

How does the quasispecies model fit into the question of what is the smallest unit of NS?

As far as I can tell, it is irrelevant. NS can act on any self-replicating entity as long as the process of replication can produce variation that can affect fitness. If I understand correctly, the quasispecies model simply posits a group of entities with a very very high mutational rate. However, the rate of mutation does not affect the smallest unit that NS can act on, as I said above, anything that can affect fitness will be subject to NS.

Is it worth talking about that? Is this question biologically relevant? Or is it rather a question based on a choice of definition such as "Is a virus alive?"
Yes, it is worth talking about it if you have the misconception that the smallest unit is a gene :). No, but seriously, it is an interesting concept and a very useful tool. The selfish gene hypothesis for example, helped us see the world of evolution in terms of sequences rather than species or individuals. NS did not change, our conception of it did.

These are all useful conceptual tools that allow us as scientists to understand complex questions. However, NS is not a directed or conscious process so it does not care or know what it acts on.

PS. Please do not confuse protein-coding sequences with genes. As I said in my comment, there are many genes that do not produce proteins (tRNA genes for example) and that was even before the waters were muddied in the past few years. The current definition of gene is something like:

any nucleotide sequence with a job to do

Read the ENCODE papers for a more technical definition or take this one from wikipedia:

A gene is a molecular unit of heredity of a living organism.

UPDATE: First of all, you have to remember that Dawkins wrote The Extended Phenotype more than 30 years ago, in a time when the only complete genomes available were those of a few viruses. The first bacterial genome was sequenced in the mid nineties and the first human genome draft human in 2000. It was a time when selection was seen as acting at the level of the individual, and the importance of genes was underestimated. Dawkins books were instrumental in bringing genes into the spotlight.
However, if he did argue that a nucleotide cannot be selected (I have not read this particular book) he was simply wrong. A nucleotide can indeed affect its chances of being replicated. Think about it, if you have a G at a given position in the genome, and that G is mutated to an A, then the chances of the original G being replicated are obviously very low. Therefore, the nucleotide 'affected' its chances of replication. Alternatively, a mutation of a single nucleotide in the promoter of a gene can also cause the entire gene not to be transcribed and, as I mentioned before, frameshift mutations can wreak havoc as well. All of these are down to single nucleotides.
In any case, our vision of what a gene is has changed enormously since Dawkins wrote his book, we understand the genome much better now, and we have realized that it is far more complex than originally believed. 30-year old literature about genes, even if written by such luminaries as Rihard Dawkins, should be taken with a pinch of salt today.

@terdon Thanks for your answer! I updated my question, you might want to have a look and react to it.

@Remi.b see my updated answer.


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When was the purpose of bone marrow discovered?
I'm currently reading William Cheselden's book Osteographia or The Anatomy of the Bones, which was published in 1733 (for the pretty pictures, naturally; not up to date anatomy). When he addresses the topic of bone marrow, he says,

Every cylindrical bone has a large middle cavity, which contains an oily marrow, and a great number of lesser cells towards their extremities, which contain a bloody marrow. [...] The bloody marrow is also found in all spongy cells of the bones. [...] The use of the first kind of marrow I imagine is to soften, and render less brittle, the harder fibres of bones near which it is seated; and that the other marrow is of the same use to the less compact fibres, which the more oily marrow might have made to soft; and that for this reason, there is less of the oily marrow, and more of the bloody in young bones than in old ones.

Which strikes me as completely incorrect -- though correct me if I'm wrong. So, when was the purpose of marrow in hematopoiesis discovered, and by whom?

Answer: In the late 1800s, by a few different guys building on each other.
I personally had no idea, but a little searching around found this little gem, which seems up our alley: The origins of bone marrow as the seedbed of our blood: from antiquity to the time of Osler.  It's only ten pages so definitely worth a read, but a few passages of note:

Neumann and Bizzozero... are credited with making the initial observations leading to the recognition of the marrow as the seat of blood formation... In his report published in October 1868, Neumann described the presence of nucleated red blood cells in the bone marrow sap of humans and rabbits by squeezing bone. He was the first to conclude that during postembryonic life, erythropoiesis was taking place in the marrow.

However, Neumann concluded erroneously that the proliferation of marrow cells occurred inside the blood vessels of the marrow; the concept of marrow sinusoids was not coined until Minot's description in 1901.

It later says that, in the mid-1880s Osler stated

that there can be no doubt that nucleated red cells originate in the bone marrow...

It's actually a pretty interesting read, all in all, and like all of the best discoveries in science, it seems like a few people built on each others' work over the years, with a bunch sort of figuring it out around the same time.


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Why is the liver the only internal organ of the human body to regrow?
Related to my earlier question, "How does the human liver regrow?", am curious as to why the liver is the only major organ that has this capability?
Why is it that other major organs, such as the heart and lungs etc are not able to regrow in the same fashion?

Would you be opposed to changing "part" in your title to internal organ?  I believe that is what you mean.  Also, how would you consider the GI track in your clasification of major?

@AtlLED I am not opposed at all to any constructive edits, such as you suggest.  I am not 100% sure about the 'GI track'?

The GI, or gastrointestinal tract, is all the machinery that helps you eat and digest things. Esophagus, stomach, small and large intestines, that sort of thing.

@JeremyKemball thank you, I just did not know what GI stood for in this context.

@AtlLED yes, now thatI know what GI stands for, yes, (but isn't the GI track a system?)

Yes it is a system, but it includes many organs that are constantly "regrowing" but not in the sense I think you mean.  They "renew" might be a better way to think of it.

Maybe it is due to two factors:

The liver is one of the few solid non-tubular organs. If a tubular organ is damaged, all the layers that composes it must regenerate. This layers usually have different cell types, which is always nasty for regeneration since some of them may be formed by specialized tissue (for instance, myocytes are very difficult to regenerate. If the organ has a muscle layer, such as the esophagus, regeneration will be more difficult). Furthermore, damage in a tubular organ usually involves perforation, which will disrupt its function even if the injure isn't big.
Hepatocytes are pretty undifferentiated cells. They are basically enzymatic sacks with some vacuoles and mitochondrion, but they remain as your typical animal cell. They have a regular nucleus, they don't have any cytoskeletal adaptation and their vacuoles don't compose the most part of their cytoplasm (in a healthy liver). Cells with so little morphological specialization usually regenerate with no problem. Plus, the liver itself is constantly exposed to chemical damage due to toxins, drugs and other chemical compounds that may be present in the diet. This situation is special and don't apply for any other organs, with the exception of the kidneys (which, in fact is a very complicated tubular organ).

thank you for the answer! Do you have some references to add?

http://www.stembook.org/node/512  This is a complete article describing all the embrionic development of the liver and also has some information about liver regeneration. I hope that is enought.

I'm sure that the structure of the organ is important, but even so,  liver growth in the lab requires a scaffold and doesn't regenerate from cells alone.  I think the liver cells might regenerate more easily because of their role in detoxifying the blood - they probably die more frequently and need sometimes replacement even in segments of the organ.

It helps to think about why it's beneficial for an organ/tissue to regenerate. The liver is your main detoxifying organ. It does this by chemically modifying external (and internal) molecules to counter their possible bad effects or simply to be able to excrete them. This role brings liver cells in harms way. Take paracetamol for example. It is recognized as a foreign compound and detoxified mainly in the liver. If you overdose like many unfortunately do, liver cells are the first to die. So, to keep up your defenses the body has activated regeneration in liver cells but not in many other parts of the body that are more safely tucked away.
That said, many other organs and tissues in the body constantly regenerate too. The intestinal tract constantly produces new surface cells from stem cells that lie deeper down in the organ because it also is on the front lines just like liver cells. Something similar is true for the skin but of course skin and gut are both external organs and therefore closer to our environment. The liver is not far off, because it is among the first organs to receive blood from the intestine.
So even though it is possible to induce regeneration in many cells of our bodies artificially as induced pluripotent stem cells have shown, evolution has switched this on only in a few of our cell types which require more renewal than others, hepatocytes included.


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Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms?
From: http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf

Discard any infant formula remaining after a feeding. The mixture of infant formula with saliva provides an ideal breeding ground for disease-causing micro-organisms.

Why is this so? Doesn't Saliva contain anti-bacterial properties?

Doesn't Saliva contain anti-bacterial properties?

Yes, in particular some IgA antibodies and lysozyme, but there are also plenty, and I mean plenty of bacteria in your mouth at any given point; we do, after all, still have to brush our teeth!  In fact, animal (including human) bites should be treated lest they lead to sepsis.  Those bacteria would love all the magnificent nutrients in infant formula.  Contact with an infant's mouth will introduce bacteria to the formula, as will exposure to air, contact with your hand, and anything else it experiences.  As an example, in the past few years, there have been some cases (from China, I believe, someone correct me if I'm wrong) of formula contaminated with bacteria, which were more than happy to stick around.

Consider also that the neonatal immune system isn't yet fully working. In fact, one of the reasons breastfeeding is important is transfer of IgA from the mother. Even when antibody production starts after 4-6 months, they don't bind as well.
"In addition to quantitative differences in antibody production during early life versus adulthood, there are also qualitative differences. IgG and IgA responses to pathogens, although inducible, are relatively weak during the first year of life, being short-lived and of low avidity." (Jaspsen et al., 2006)

Whether infant formula or food for adult consumption - should be discarded if there is salivary contamination since there is universal presence of microorganisms in saliva. These act as culture media and the microorgnisms rapidly degrade the food, not to mention the selective overgrowth of pathogenic microorganisms.


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How are the correct tRNAs transported to the ribosome?
I have been trying to understand how the tRNA transporting the correct amino acid required by the ribosome reaches the ribosome. The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombard the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.
I can not imagine any other mechanism in the cell's cytoplasm that will somehow filter or push the correct tRNA+amino acid and move it towards the ribosome that needs it.
How do we explain this mystery?

The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.

Yup, basically.  This is an extremely cool figure showing the process. There are various elongation factors that aid the process, such as EF-Tu, which essentially waits until there is a good codon-anticodon match before hydrolyzing GTP and allowing the tRNA/amino acid to enter the ribosome.
This process can be particularly salient when you look at a concept such as codon-usage bias.  Certain tRNAs are more common in the cell, so if a given mRNA uses codons to match those tRNA instead of matching other degenerate but less common anti-codons, translation will occur faster.  This is more obvious in organisms such as E. coli where growth is paramount.

Apart from random movement, are there any other factors which move the tRNA near the ribosome, where the ones you mentioned take effect?


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Does Blood Loss Shorten Telomeres?
If blood loss necessitates immediate cell division to replace lost cells, does the increase in cell division correlate to shortening of telomeres? Does it further cause the Hayflick Limit to be reached sooner? Does blood loss accelerate apoptosis?

One that down votes should make a comment to inform the OP what goes wrong with its question.

while it may be true that blood cells themselves come from HSC, there are more things in the blood than just those cells.
Research such as http://www.telegraph.co.uk/health/9615779/Transfusion-of-young-blood-could-delay-onset-of-diseases-like-Alzheimers.html is showing that indeed higher than normal blood loss over a long period of time may then cause more rapid-than-normal cell division and premature aging. Something interesting along these lines: fasting for a day every few days is shown to increase lifespan, might be related to simply slowing cell division... we don't know.

Nope, nope, and nope.  A cursory glance over any page on hematopoesis will reveal that blood cells are replenished from HSC, hematopoetic stem cells, which are self-renewing stem cells.  Telomerase is activated in stem cells.

So what you are saying is that blood cells have no limit on cell divisions; and the telomere shortening theory does not apply to them? To which cells does it apply?

@Angelo Blood stem cells have no limit.  Stem cells theoretically have an indefinite potential to divide.  They express telomerase and are not subject to the Hayflick limit in the same way as other cells.


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The difference between "Hunger" and "Appetite"
When I am "hungry", I need something to eat physically. But what about "appetite"? I think it is a psychological phenomenon. Is that correct?

According to the website "Appetite vs. hunger", the difference is very similar to what you were saying:

Hunger is the need to eat.

Hunger is instinctive, it is the body's way of letting you know it needs sustenance.
and

Appetite is the desire to eat.

It is a coordination between the brain and the stomach, this is learned behaviour.
Some further information can be found in the article preview "The Biological Nature of Appetite" (Stellar, 1992)


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Estimation of number of species at an earlier time
The estimated number of species on Earth, as reported in this article is around 8.7 million. I am fascinated by how nature produces such a wide variety of species.
As per my understanding, many species have gone extinct, that is, were not able to adapt to changing conditions on Earth. Perhaps the number of species before few thousands of years were larger than today. Can we estimate the approximate number of species at a given point in the past, using available data?

Nice question.  It would be interesting to try and plot the extinction of species vs speciation of a new one.  I strongly doubt it's liner over time, even if you account for catastrophic extinction events.

according to the National Science Foundation press release"Species Have Come and Gone at Different Rates than Previously Believed" indeed show what Atl LED suggests, that the progression is not linear, with the study showing that:

The previously thought exponential increase in diversity is not there.

Further, there is the "Palaeobiology Database, that

seeks to provide researchers and the public with information about the entire fossil record.

The site also has links to further papers of the topic.


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What is it the most common reason for community acquired pneumonia?
This is a difficult question because there are many types of community-acquired pneumonia (CAP): typical acute, atypical acute and chronic.
Most common microorganisms are also different among different groups: children, adults, elderly, immunocompromised and people at risk of different diseases.
Some options:

Streptococcus pneumoniae
Hemophilus influenzae
Escherichia coli
Klebsiella pneumoniae
Pseudomonas aeruginosa
bronchiectasis
Chlamydia pneumoniae

Not any virus, since they are present in only about 20% of diseases.
Streptococcus pneumonia is probably a good choice.
What is the most common reason for community acquired pneumonia?

Are these being pulled from Medical Microbiology, and if so which edition?

I cannot find this from my edition. I do not know which edition of the book it is, but its cover is this: https://dl.dropboxusercontent.com/u/62073194/Screen%20Shot%202013-08-29%20at%2011.18.58%20AM.png

You are right in that there are several ways to split down CAP, and plenty of different pathogens to look at.  But then we are looking for the most common.  Pnumonia is most common in children and adults over the age of 75 (or 65 depending on who's counting).  Luckily there are plenty of good reviews for both populations.
From the pediatric side we have Iroh Tam PY(1):

Pneumonia occurs more often in early childhood than at any other age,
with the exception of adults older than 75 years, and kills more
children than any other disease worldwide

As far as pathogens:

Streptococcus pneumoniae and Haemophilus influenzae type b (Hib) have
been characterized as 2 bacteria predominately responsible for cases
of fatal pneumonia in children.  However, widespread introduction
of Hib and pneumococcal conjugate vaccines has led to significant
declines, especially of Hib, although Streptococcus pneumoniae is
still the predominant bacteria isolated from bacterial CAP in
children.  There is increasing recognition of the prevalence of mixed
bacterial and viral infections, which have been documented in 23% to
33% of cases of pneumonia.

Then we move to the geriatric side of things with Falcone et al (2):

Common pathogens include H. influenzae, enteric gram-negative bacilli,
the atypical organisms, S. aureus, Pseudomonas aeruginosa, and M.
catarrhalis, although the relative prevalence of each tends to vary
among studies. Among elderly individuals with aspiration pneumonia,
gram-negative bacilli are the predominate organisms (49 %), followed
by anaerobic bacteria (16 %) and S. aureus (12 %).

Though I should note, having done them myself, getting accurate cultures is difficult, and viral levels a very likely to be under reported because of handling and skill.

For example, in different prospective studies in which the
microbiologic etiology of CAP was systematically sought in the
elderly, a definite or presumptive pathogen was often reported in <60
% of the patients. (2)

And again in children:

There are 2 main challenges in the diagnosis of CAP: the first is the
definition of CAP, particularly in young children, in whom bacterial
and viral infections can occur with similar frequencies, and in whom
overdiagnosis of mild symptoms and signs may lead to unnecessary
antibiotic use; the second is the identification of a causative pathogen, which is frequently impractical and inadequate in children, and
in whom the failure to isolate an organism can result in unnecessary
antibiotic use. (1)

Taking into account more global sources, I'm actually thinking Hib infection has dropped more due to vaccination than I gave it credit for, putting my bet on S. pneumoniae, and showing my regional experience may not be representative (3, 4, 5, 6).
(1) Iroh Tam PY. Approach to common bacterial infections: community-acquired pneumonia. Pediatr Clin North Am. 2013 Apr;60(2):437-53. doi: 10.1016/j.pcl.2012.12.009. Epub 2013 Jan 12
(2) Falcone M. et al. Pneumonia in frail older patients: an up to date. Intern Emerg Med. 2012 Oct;7(5):415-24. Epub 2012 Jun 12.
(3) Brown JS. Community-acquired pneumonia. Clin Med. 2012 Dec;12(6):538-43.
(4) Kurutepe S, Ecemiş T, Ozgen A, Biçmen C, Celik P, Aktoğu Özkan S, Sürücüoğlu S. [Investigation of bacterial etiology with conventional and multiplex PCR methods in adult patients with community-acquired pneumonia]. Mikrobiyol Bul. 2012 Oct;46(4):523-31.
(5) Tao LL, Hu BJ, He LX, Wei L, Xie HM, Wang BQ, Li HY, Chen XH, Zhou CM, Deng WW. Etiology and antimicrobial resistance of community-acquired pneumonia in adult patients in China. Chin Med J (Engl). 2012 Sep;125(17):2967-72.
(6) Capelastegui A, España PP, Bilbao A, Gamazo J, Medel F, Salgado J, Gorostiaga I, Lopez de Goicoechea MJ, Gorordo I, Esteban C, Altube L, Quintana JM; Poblational Study of Pneumonia (PSoP) Group. Etiology of community-acquired pneumonia in a population-based study: link between etiology and patients characteristics, process-of-care, clinical evolution and outcomes.  BMC Infect Dis. 2012 Jun 12;12:134. doi: 10.1186/1471-2334-12-134.

I had a question in exam where Chlamydia pneumoniae was the most common reason for CAP in the situation. I cannot remember the situation. Can you think any situation where Chlamydia is the most common pathogen?

@Masi The only possible thought is a-typical with myco ruled out.  Another possibility is with a sub-section of patients who develop low risk CAP.  If you look at any of the sources I posted world wide, not one of them found C. pneumoniae as most common.


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Can the colour of skin change with age
Can the colour of skin change with age? Can a dark skinned person become fair or vice versa?  Can Melanocyte production vary?

Vitiligo is a loss of skin pigmentation that causes patches of lighter skin as the immune system attacks melanocytes. It can eventually progress to cover the entire body.
Edit:
Ongenae, K., Van Geel, N. and Naeyaert, J.-M. (2003), Evidence for an Autoimmune Pathogenesis of Vitiligo. Pigment Cell Research, 16: 90–100. doi: 10.1034/j.1600-0749.2003.00023.x

Do you have a reference or 2 for your answer?

There are all sorts of things that can stimulate melanocytes, most notably UV rays (ie from the Sun).  So yes, melanogenesis can very over age and exposure to the Sun.  Young infants often are lacking build ups of melanin in their skin, eyes, and hair, which is why these things darken with age.
There are other more pathogenic ways to change melanogenesis, including malnutrition, but UV exposure this health common way.

Could you dial back your pigmentation campaign a little? What you are doing is fine but it is generating a hell of a lot of review jobs, and bringing all these old questions to the front page. Please try to only make a few such edits per day.

@terdon I'm done.  Sorry, I didn't think about resurrecting old questions to the front page.  I did find an unanswered one I want to go back and answer.  I won't go through them all at once again.

Hey, no worries, you are actively improving the site, just try and avoid too many consecutive edits like that :). Answering is fine mind you, newly answered questions should be on the front page.


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Can retroviral delivery systems "overwrite" genes?
As the question states, what are the limits of retroviral genetic delivery systems?
Are they limited to adding additional gene sequences to a cell, or can they actually overwrite specified segments of DNA?
Or, more aptly described, can they remove one segment of DNA, and insert a new segment (whether the same or different length) in the spot where the old segment used to be?

To me "overwriting" seems to imply limited memory (e.g. based on using computer memory as a metaphor for DNA), while changes in DNA are due to deletion, insertion and single base mutations (substitutions). Chromosomal translocations are another case (as deletion->insertion).

Well, I am a programmer, so that is the first metaphor that comes to mind for me.  :)  . I'll reword and clarify a bit.

Retroviruses, such as HIV, have a genome that is composed of RNA.  Once inside the host cell, that RNA is reverse-transcribed into DNA; it is that DNA which is inserted into the host genome.  All retroviral genomes are integrated through insertion; there is never any replacement.
Some retroviruses do, however, disrupt normal gene function.  Mouse mammary tumor virus (MMTV) or Human T-lymphotropic viurs (HTLV) will often insert inside or near host genes termed "oncogenes," that, when disrupted, can lead to cancer formation.1,2  Viruses could cause up to 15% of cancers in humans.3  So, no actual genetic replacement, but there can definitely be genetic disruption and a deleterious functional change.
This ability, to insert new genes, has recently been touted as a new way to cure many diseases.  Here's the most recent case, where the researchers used a retroviral backbone to insert a functional gene into some children; i.e., genetic engineering (Side note: Every time you see an article saying how scientists used HIV to cure a disease or something, this is what they mean.  It's akin to calling dental X-rays "giant death lasers that fight cavities.").  With luck we will get better and better at it, but right now it's only successful in limited cases for very specific diseases; massive genetic engineering of humans is still far off (unless you count bone marrow transplants).

Nice answer, but a few references (especially for the removal function) would be great.

A friend is telling me about genetics research she has worked on regarding treating Huntington's disease, but that a true cure would be hard because it's genetic. So not being a geneticist, the first thing came to mind was well, use a retrovirus to deliver a cure. Would an RV be able to add code then which 'disrupts' the faulty genes, and add new code which does what the bad ones should've been doing?

@fileunderwater I added a few references, in particular a solid review.  It's not a particularly new concept so there's plenty out there.

@eidylon I tried to answer your question a bit, pointing to some research people are currently doing.  GE on that scale is still a long ways away but it's amazing the strides we're making right now.

Just to give a simpler example of what Amory has explained. Viruses can overwrite existing information, just not the way you would think if coming from the world of computers.
As already mentioned, viruses have the ability to insert their genetic information into the host's genome. They do this by essentially cutting the host DNA open and inserting themselves between the cuts. This insertion can disrupt a gene, thereby, in a sense, overwriting it.
To take a simple metaphor, consider the following sentence (a "gene"):

Hello, my name is Bob.

If I were to insert a new sequence of characters into that sentence, it's meaning would be lost:

Hellalkehfgawpif galsdhfblasud hyflaishbflaegfvlhD BFHDFLHFEiDBFKHDBfo, my name is Bob

While the original sentence is still there so it has not been overwritten in the strictest sense of the term, the information it contains has now been lost to the cell so the result is the same.


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Can we identify an individual from their palm lines
Can we identify an individual from their palm lines. Is there any uniqueness for palm lines among family members ?

as someone with a passing interest in biometrics - I think this is a good question.

It was tricky searching for this through the morass of palmistry sites.  But, in the field of biometrics, I found the article "Palm Print Recognition", which states that (bolding mine):

Because fingerprints and palms have both uniqueness and permanence..

it has been used for identification the same as fingerprints. The only reason it is not as widespread as fingerprints is largely due to logistics such as computer processing.

Studies show correlations between palm primary lines and lip lines and palatal rugae patterns.Familial uniqueness should be there.

Welcome to Biology Stack Exchange.  This isn't really a full answer at the moment, however you can [edit] it to add more details - for example which studies show this?