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When DNA is at its uncondensed form, what can it do?
I think it can do two things:

The cell may be duplicating the genome during S phase.
The cell may be transcribing the DNA into mRNA.

Question: Can the two activities occur at the same time or one at a time? In other words, are cells efficient multi-taskers?

At least in bacteria they can. In optimal conditions, E. coli divides itself about once every 20-30 minutes. Wich is more important, the replication time of its genome is about 40-50 minutes. That means that, in exponential phase, E. coli has at least two active replication bubbles. Since the density of ribosomes must be more or less constant, aswell that the new cells needs to synthetise peptidoglycan and other cell components, that means that replication and transcription occurs simultanously. If not, ribosomes, enzimes, tRNAs and mRNAs would be diluded in every replication event.
In eukarya I see no reason of why that shouldn't be possible. The formation of chromatin is not a random event and some specific proteins are required during short periods of time during some steps of mitosis, so it's logic to assume that some specific parts are not compacted or that transcriptional activity can occur even in chromatin.
The specific region that is duplicating itself in a given time will probably be unable to transcribe, because the polymerase complex is pretty big and they need to open the double helix, and that. But this is somehow like children playing in the train tracks. Once the train aproaches, the children stay apart, and they continue again when the train has gone.


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What is an explanation of the dual role of calcium hydroxide in teeth?
Calcium hydroxide induces dentine formation in permanent teeth, while it causes resorption of tooth in deciduous teeth. How is this dual role explained?

For more than 70 years calcium hydroxide has played a major role in endodontic therapy, although many of its functions are now being taken over by the recently introduced material MTA. Calcium hydroxide may be used to preserve the vital pulp if infection and bleeding are controlled; to repair root fractures, perforations, open apices and root resorptions [1].
Calcium ions released from calcium hydroxide stimulates fibronectin synthesis in dental pulp cells. Fibronectin might induce the differentiation of dental pulp cells to mineralized tissue forming cells that are the main cells to form dentine bridges, via contact with cells [2].
Calcium hydroxide ($Ca(OH)_2$) is known to cause internal resorption in the deciduous dentition. Though this has been attributed to chronic inflammation and odontoclasts, the exact mechanism has not been elucidated. $Ca(OH)_2$-induced odontoclastogenesis could be multifactorial. Odontoclasts may result from fusion of cells of monocyte/macrophage series either due to inflammatory mediators or through stimulation by stromal odontoblasts / fibroblasts. Pre-existing progenitor cells of primary tooth pulp because of their inherent propensity may transform into odontoclasts [3].

References:

Carrotte P. Endodontics: Part 9. Calcium hydroxide, root resorption, endo-perio lesions. Br Dent J. 2004 Dec 25;197(12):735-43. doi: 10.1038/sj.bdj.4811897. PubMed PMID: 15608732.

Mizuno M, Banzai Y. Calcium ion release from calcium hydroxide stimulated fibronectin gene expression in dental pulp cells and the differentiation of dental pulp cells to mineralized tissue forming cells by fibronectin. Int Endod J. 2008 Nov;41(11):933-8. doi: 10.1111/j.1365-2591.2008.01420.x. PubMed PMID: 19133082.

Ravi G R, Subramanyam R V. Calcium hydroxide-induced resorption of deciduous teeth: A possible explanation. Dent Hypotheses [serial online] 2012 [cited 2014 Jun 7];3:90-4.

Teeth are made of calcium hydroxyl apatite: $(Ca_5(PO_4)_3 OH)$, which can be transformed by fluoride ions into the much harder calcium fluor apatite $(Ca_5(PO_4)_3 F)$.

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Why do rodents' teeth continue to grow?
Why do rodents' teeth continue to grow? Enamel formation and/or root formation continue throughout rodents' lives.
What's the mechanism that causes this?

humans may be a tad unusual because their teeth don't continue to grow...

The article "Dental Anatomy of Rabbits and Rodents" (Crossley et al. 2010) provides a basic review of rodent teeth, as there are over 1700 species.  But, in general, the teeth are constant replaced due to abrasion.
What the mechanism is for continual dental growth in rodents are, in part, discussed in the article "Tooth organogenesis and regeneration" (Thesleff and Tummers), where they state

During the cap and bell stages the lateral sides of the epithelial bud start enveloping the underlying dental mesenchyme, and from this point onwards the leading edge of the epithelium is called the cervical loop. The basal epithelial cell layer of the loop bordering the dental papilla is known as the inner enamel epithelium and the part facing the dental follicle is known as the outer enamel epithelium. The core of the loop is populated by loosely arranged stellate reticulum cells and a thin layer of stratum intermedium cells facing the inner enamel epithelium This cervical loop structure is maintained in continuously growing teeth and constitutes the epithelial part of the adult stem cell niche (Harada et al., 1999; Tummers and Thesleff, 2003: Tummers and Thesleff, 2008)

authors: Никита Литовка

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Examples of references for mathematical approaches in bioinformatics that are applicable to linguistics?
Do you have any classic references for mathematical approaches in bioinformatics that are applicable to linguistics (or vice versa)?
EDIT
I am mainly interested in approaches to reconstruct the history of languages, the rate of language mutation, phylogenies of languages, etc.

An approach to do what exactly? The question is too vague to answer.

@fileunderwater,approaches to construct history of language,the rate of language mutation,the phylegen,etc.

I'm interested in whether you've crossposted this question on Linguistics SE. I wonder if you'd get different or similar answers.

@Oreotrephes,sorry,I have not crossposted this question on Linguistics SE.I think I will get no answer,since my other question and answers on the Linguistics usually get downvoted,very interesting.Of course,there are some persons standing up for my answer.

Strange – I hope these answers help you at least get started!

@Oreotrephes,thank you,and I have browsed the articles every one recommended,to tell you the truth,some results are too interesting to be true.Is this interesting? I think some researchers are eager to find something interesting

There are a number of more recent papers dealing with phylogenetic methods in reconstructing language history as well, including work by Colin Renfrew and Quentin Atkinson.
Here are two recent high-profile papers. Unfortunately, both are still behind paywalls, but even reading the list of papers they cite / that cite them would be a great way to answer your question.

 Bouchard-Côté A, Hall D, Griffiths TL, Klein D. 2013. Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences 110: 4224–4229.
 Gray RD, Drummond AJ, Greenhill SJ. 2009. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323: 479–483.

Maybe not quite as high-profile, but available online, one of my classmates did his (superb) undergraduate thesis as a Biology/Linguistics double major in exactly this topic. I think it could be a very useful place to start, although there have certainly been developments in the field in the last six years:

 Saunders, A. 2006. Linguistic Phylogenetics of the Austronesian Family: a performance review of methods adapted from biology.

See also the wikipedia page Quantitative Comparative Linguistics, this Stanford how-to, and this interesting article Linguistic Phylogenies Are Not the Same as Biological Phylogenies.

Branching processes (from probability theory) were originally developed to study the extinction of family names (Galton-Watson process), but are also used to study biological extinction and general evolutionary processes. One example that applies ideas from branching processes and phylogenetic methods to reconstruct ancient languanges can be found in Forster & Toth (2003). The basic concepts of branching processes can be found in most textbooks on probability theory, but a classic reference is Harris 1963 (pdf).
This is maybe not exactly what you are after but should be related to your question.


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Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?
I'm thinking of the human genome specifically, but more general answers are welcome.
As RNA polymerase moves along the DNA helix it follows a single strand.  The two DNA strands are unwound locally by a helicase enzyme. However, after some distance, I imagine that either the polymerase must move around the axis of the DNA OR the DNA must somehow be rotated along it's length to relieve the twisting by the polymerase.
I can't quite understand how the DNA is free to rotate, being part of a very long molecule. However the other option is also causing me a problem: the growing (nascent) mRNA can be tens of thousands of bases long while still attached to the RNA polymerase and the DNA template.  If the RNA polymerase follows the helix of the DNA, does it also drag the full transcript around with it?

My bounty is prompted by watching this WEHI animation, where the first sequence ignores the need for rotation and shows both the RNA polymerase and the DNA as lacking any rotation. The second sequence shows the DNA as spinning and the RNA polymerase as static. Is the second sequence accurate or also an approximation of reality? How does the DNA accommodate tens of thousands of revolutions required for long sequences?

I'm not sure the question makes much sense. Whether an object is 'rotating' or not, needs to be discussed in relation to a common frame of reference or to another object. An enzyme (like a polymerase) is much smaller than a chromosome, by many orders of magnitude. The DNA is flexible, of course, and requires bending, twisting, and other local configuration changes to function. But, again, a chromosome is a huge molecule! Is like asking if a passenger (polymerase) is moving, or if it's the train (chromosome) what is moving. Clearly both are moving, but at different temporal and spatial scales.

@TumbiSapichu the bottom line is that the RNA polymerase must rotate with respect to the DNA. The obvious frame of reference is the solvent they are both suspended in. If the polymerase rotates w.r.t. the solvent then the RNA that it outputs will end up wound around the DNA - is it? If not, then the polymerase must have been stationary and the DNA was the one rotating w.r.t. the solvent. The question is which is it, and if it's the latter, how does the DNA accommodate such twisting, being a very long molecule.

Both the DNA and the RNA polymerase complexes moves along the DNA molecule like it was a track. While the new mRNA is big, it would never be as big as the whole genome, so the reference point is the DNA molecule. Plus, the functioning of the movement of this enzymes is quite similar to other proteins that move "climbing" long polymers, such as actin polymers or microtubules.
One of the theoretical models that describes the movement of this kind of proteins is the model of rectified thermal diffusion, based on Richard Feynman's idea of the Brownian ratchet. A Brownian ratchet is a device that allows the conversion of Brownian random movements into a directional force.
http://en.wikipedia.org/wiki/Brownian_ratchet
The polymerases consume ATP, which enable them to suffer cyclic conformational changes (one change per ATP consumed), which allows the complex to attach to the molecule and detach. Once the complex has detached, by simple diffusion it moves in a random direction. Then, it attaches again. If the movement has occurred in the right sense, it will stay where it ended, while if it has gone in the wrong sense it will return to its previous position. As only a few movements are allowed, the complex will only move in that sense, even if the motor force is random.
I don't know exactly what conformational changes occurs in the RNA polymerase, but this general process seems to apply to almost any motile protein, including those enzymes that travel across polymers. Since the motor force is simple diffusion, and since the mRNA molecule doesn't need to "travel" with the polymerase (it just floats joined to it, but doesn't "pull"), I think there isn't any trouble with this.

I'm thinking more of the topology of strands of RNA and DNA. What happens to the mRNA/DNA as the polymerase moves around the spiral of the DNA?

mRNA are single-stranded, so they don't have problems with supercoiling. RNA polymerase complex carry helicase and topoisomerase activity in order to relax the DNA, because it needs to separate both strands of the DNA and because the movement changes the coiling in the DNA, as they cause positive supercoiling in front of the enzime and negative supercoiling behind. The wikipedia article is pretty good: http://en.wikipedia.org/wiki/RNA_polymerase

I think he is asking a different question. At some point the RNA should be wound around the DNA if the RNAP is spinning around the DNA.

The partial answer by Miguel helped a lot but I needed to go and read about the extra part that I was missing: Topoisomerases.
The DNA is unwound beneath the RNA polymerase, which causes supercoiling in front and behind.  For long transcripts to proceed, the current theory is that the DNA template has to be cut, unwound and re-ligated and that this is performed by Topoisomerases.
This raises the questions as to how often the DNA gets cut and re-ligated during active transcription and does this produce a noticeable effect (i.e. mutation)?

There is an alternative view that polymerases are sort of DNA motors that move DNA while they themselves remain static. I cannot find that reference now but I read this ~5 years back in a Nature Reviews article. The notion of transcription and replication factories also fits this model.
Highly transcribed regions do have a higher propensity to acquire mutations [1].
Although I am not sure about it but sequence composition of genes might also have a role. The pitch of the helix along with other physical parameters are dependent on sequence composition. It has been shown that geneic regions have different composition compared to non-transcribed regions (geneic regions have higher GC content [2].

I would have to agree that the "transcription factories" (several RNA Polymerases and some other proteins combined) attract DNA and transcription factors, and then start transcription while they remain static.  One such factory can actually transcribe many genes at once.
Most books and online sources still describe the Polymerase as moving along the DNA and carrying out transcription, but this has been proven wrong.
source:
http://www.ncbi.nlm.nih.gov/pubmed/8799830
can't find the article on Nature either, but I heard about it too.

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Why do our eyes "wrap" hue from UV to IR?
On the high-wavelength side of things, we see almost-infrared as reddish, with a slight tinge of magenta. On the low side, we see violet fading into the same magenta color. Why is that?
You can see it clearly on any hue chart. There's an unbroken flow from one to the other, even though the wavelengths are literally as far apart as they can be while still remaining visible.
I understand that color vision is limited due to several biological factors(cone receptivity, absorption, etc), but why do the colors on both side fade into each other? Is it just our brain making things "neat" and continuous?

Basically.  You are most likely looking at the electromagnetic spectrum, which is linear and conveniently makes sense... except for magenta.
Colors as we perceive them are additive and made up of Red, Green, and Blue; this is opposed to subtractive color we learned about while finger-painting in kindergarten (Red, Yellow, Blue).  The three types of cones in our eyes each are sensitive to one of these colors, and it is from the combinations of Red, Green, and Blue that we see all the colors we see.  Yellow, for example, is when the red and green cones are both stimulated.  Purple/violet is from red and blue stimulated together.  This is the single special case, as you point out, because red and blue are at opposite sides of the spectrum from each other.  Our brain has two options:

Use the color smack-dab in the middle aka Green
Make a new one as if they wrapped around

Green is far away and already taken, so our brain intelligently invents Magenta.  This produces, instead of a linear EM spectra, a circular color wheel that looks very intuitive.

I understand RGB(software developer), and I see what you mean about a red/blue mix needing an invented color, but what about (almost) pure infrared? With a (strong) very-near IR laser, you'd expect it to appear as red, but it still gets closer to magenta as wavelength increases, even though there shouldn't be any blue/violet light to mix. For example, in a very dark room, I can see my TV remote IR led, and it is definitely not just "red".

TV remotes are often not pure IR.  At that level, the long tail of the faint visible colors can be enough to stimulate a color; you are not seeing the IR being rapidly sent.  Some cameras (my laptop does it) will show IR, often as a neat little purple.  That's a good test to see what you're not seeing.

Yes, playing with my camera is what led me to the question, since even there they pick it up as some shade of purple, depending on hardware. I think the bit about the faint visible colors is the primary answer.

@Geobits yes, I have noticed this in my UV-camera image sensor observations

this is really easy to answer.
this is a chart of the light activation of the light sensitive cells in the human eye.

see that little blip up on the tail end of the red cone, that minor ranges means the extreme blue end of the spectrum activates blue cones but also has a chance to activate red cones. That is why you can sometimes see magenta tinges in bluest of blue light. There is also a sensitive issue as blue cones are the least sensitive of our cones so it requires a stronger blue light source to activate it than the equivalent light on other cones, since red is more sensitive a strong blue and a weak red source will blend to about equal as far as our eyes are concerned so at the bluest end of the spectrum, where the blue activation is at its weakest it does not take much to activate the blue and red "blip" equally meaning all sources at that extreme end blend into magenta.
Also magenta itself is not actually part of the spectrum, it can be produced in two ways, the first I discussed above, hitting the far end of that little blip perfectly. The second and most common requires light from two disparate and different parts of the spectrum in other words not a single wavelength. It is blue light and red light without green light, it is not a real color but an artifact of how our eyes see light. Your cones can't tell how they are activated just that they are. Yellow and cyan (and every other common human color)on the other hand can be produced by a single wavelength, which may or may not activate multiple types of cones.
You can find more information here

The question has an invalid premise. Namely, that the UV light looks like magenta/purple. It is not the case. While it it true that approaching UV end the perceived color becomes more purple (because the red protoreceptors have a second maximum there), moving further to the UV area (which is possible if the eye has the lens removed), makes the perceived color more whitish/light blue because the green receptor also has a second maximum there (somewhat further than the red one).
I do not know why the IR has magenta color though. It could be because of not pure source. Try using a hot piece of metal to see if it becomes more purple as it cools, I think it does not.

The photo-detectors of the eye don't detect a linear spectrum... they detect three colors. The amplitudes of the three colors are mixed a bit similar to a color wheel.

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Telomere elongation methods?
What sort of telomere elongation methods are there currently?
Would this stop aging? (edit: No, probably)
I couldn't turn up anything good on google. I was thinking that maybe you could sequence the telomeres, trim them all at a certain point, and then engineer a polymerase molecule to extend from that same point. Is this how it's done?

It would be simpler to simply activate telomerase genes or insert them using some vector virus. However, telomerase is a key component in the process of tumoral transformation. Basically, if you don't let cells die they will stack mutations until they become tumoral.

I'm confused. I thought the issue with telomere length wasn't that it effects the longevity of the cell, but its ability to reproduce and have its offspring reproduce etc. So then wouldn't longer telomeres just let you have healthy cell reproduction in old age?

It isn't as simple. Many of the things that seems to cause aging are also defenses against cancer, like telomer lenght limitation (wich prevents cells to suffer too much mutations), DNA repair systems, and autoimmunity. For instance, you could overexpress any of those mechanisms in order to prevent cancer, but they lead to accelerated aging, and the opposite is also true. While it is still a polemic topic, it seems that animals have to choose between lifespan and cancer.

I wonder if you activated telomerase in naked mole rats how long they would live. (they have cell density detection that kills all cancer, I've read)

Telomerase will not cause the tumor cells grow faster or live longer because these cells already have their own version of telomerase and adding it to them causes nothing. But healthy cells of the body will take the advantage of having telomerase around them and with a repaired and longer telomerase cancer killer and cancer detector cells will do their job much better thus tumors will be removed with younger cells trying to fight them.


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Does a blood transfusion cure disease?
Does transferring blood between two people also transfer all the white blood cells?
Why can't AIDS victims with low t-cell count just get blood transfusions till they have more t-cells? Why can't someone who's over a cold give blood to someone with a cold to cure them? I know this is silly, but I really want to know why this won't work.

Don't know if this qualifies as a disease, but have you heard of the experiment that supposedly slowed down ageing by transfusing blood from young to old mice?
It was a normal transfusion, consisting just of RBCs as described by @Amory, and apparently, there was something in the young blood that decreased in concentration as the mice aged.
See here and here for more info.

Wow, that's some sci fi stuff. I assume it will lead to a dystopian future where everyone is Elizabeth Bathory - https://en.wikipedia.org/wiki/Elizabeth_B%C3%A1thory

Isnt't that the new WBCs will get infected again with  HIV already present in the patient? As well; blood cells are continuously being synthesized as well old-blood cells are dying after certain stage. So even if blood transfusion not done... all of us are continuously using  a bit new blood.

t-cells do not last forever, the victims would need constant transfusion.

Not really no.  Most blood transfusions we think about are red blood cells or platelets, which don't have the immune function you're asking for.  That's a good thing.  Usually, if there are white blood cells in the transfused blood, the host's immune system will recognize them as foreign and destroy them.  Remember, your cells all look like foreign invaders to my cells; blood transfusions of red blood cells are carefully matched to limit negative reactions.  There is also a process called transfusion-associated graft versus host disease in which the donor white blood cells will attack the host cells; this mainly occurs in immune-compromised individuals, but GvHD is definitely something to avoid.  Blood transfusions are usually filtered and irradiated to remove, among other things, white blood cells.
That being said, people are beginning to use white blood cells as treatment.  A new therapy being studied heavily for all sorts of diseases, from cancer to HIV, is to take the hosts own white blood cells and grow them up in the lab to select for the strongest and most effective cells.  The researchers then wipe out the individual's immune system and give them a dose of their own, super-powered white blood cells, hoping that works.
Sometimes it kind of does.  They've also been trying a new system, similar to what you propose, using bone marrow.  They had a huge success with an HIV-positive individual now referred to as "the Berlin patient."  They gave him a marrow transfusion which would produce HIV-immune white blood cells and replaced his immune system.  He was and is effectively cured of HIV/AIDS.

Wow interesting! But why do they have to wipe out the host's immune system before injecting the "super white blood cells" that they grew?
Also why can parts of the body be transplanted without (usually) being destroyed like the white blood cells? Are blood cells more scrutinized by the native white ones?

@CornSmith To answer your first question, it's usually a numbers game.  No matter how many cells the researchers can grow your body is probably producing more.  A virus like HIV, for example, infects T-cells, so if 5% are super-charged but 95% are still susceptible...

As for your second question, all transplants are hugely scrutinized, far more than red blood cells.  We distinguish our own tissues from foreign ones using the MHC antigens, and they're very difficult to match perfectly; siblings, for example, have only a one-in-four chance of matching up.  If there's any difference, there will be an immune reaction.  In most cases, there will be some attack, which is why people can reject transplants (in the worst cases) and why almost everyone receiving a donation takes immune-suppressors.  It's better to have a liver.


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Is there any definition of complexity about gene and protein according their function?
Sorry for such a question,if it is too naive.
Is there any definition of complexity about gene and protein according their function?If so,what is the relation between them?

Could you explain a bit more about what you are asking?  What do you mean by "definition of complexity according to their function?"

@Amory,like what the protein play

Proteins and genes usually are classified in superfamilies and families acording with its inner structure (mainly its domain organization). Domains are parts of the protein with its own 3D structure that usually have their own function and acts more or less in an independent manner.
However, this doesn't talk very much about their complexity. Myoglobin and hemoglobin, for instance, are very related proteins and thus are classified in the same family. However, hemoglobin forms tetramers, while myoglobin is a single molecule. It's not unheard that very close-related proteins may differ in their association with other proteins, polymeration pattern, addition of new domains, etc. Very similar poteins may have very different functions, i.e. catalyzing similar reaction in opposite directions or in very different pathways, or acting in different parts of the cell or the organism.
In biology, it is desirable for any classification to be based in evolutionary criteria, since not only it is a more neutral and unbiased way to classify biological things, but also provide information about the origin and structure of those. You could classify proteins by their structure, number of motifs, number of domains, number of different domains, size, function (in fact, there is a very useful and widely used classification for enzymes), etc; and you could classify the genes according to its number of exons, structure of its promoter/enhancer, policystronic or not, etc. However, this classification will usually prove itself to be inferior to an evolutionary classification.


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What is the lowest intensity threshold of light for photosynthesis in any species?
Recently, I was reading the question "Photosynthesis - light intensity, particularly the answer, that states that different species require different intensity of light.  My question is what is the lowest threshold of light intensity for photosynthesis of any species?
Specifically, how have that species adapted to take full advantage of the low intensity?

So you are asking about light needed for photosynthesis to take place, not the light intensity needed to sustain the plant? Since photosynthesis is an interaction between chlorophyll and single photons I would assume that photosynthetic reactions could take place with just single photons of suitable wavelength (i.e. at the limit of defining light intensity), but to measure this might be extremely hard in practice. The article Photosynthesis in the Abyss indicates that this might be the case, saying ...

@fileunderwater thank you for that!  That is the kind of information I am after - and that is an amazing example.

Reposted comment as answer since you found it interesting, and to make it more visible.

Disclaimer: photosynthesis is not my field of expertise.
I assume you are asking about the amount of light needed for photosynthesis to take place, not the light intensity needed to sustain the plant? Since photosynthesis is an interaction between chlorophyll and single photons I would assume that photosynthetic reactions could take place with just single photons of suitable wavelength (i.e. at the limit of defining light intensity), but to measure this might be extremely hard in practice. The article Photosynthesis in the Abyss indicates that this might be the case, saying that in deep sea environments "A single molecule of bacteriochlorophyll receives a single photon only about once every 8 hours" (see also this popular science article). The conditions for deep sea photosynthesis is described in Beatty et al. (2005), which report photosynthesis by green sulfur bacteria at hydrothermal vents, where the only source of light is geothermal radiation.
However, as stated earlier, photosynthesis is not my subject field so I do not know how credible this information is.

The answer was great, the additional references are brilliant.

@UV-D Would be great with an answer from somebody working actively with photosynthesis though as a complement, e.g. some comparative results on how different species cope with low-light conditions.


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Do invasive species cause long-term damage to ecosystems they invade?
Growing up in the U.S., I was warned at various times of the dire consequences of a variety of introduced pests (usually insects).
Japanese beetles, gypsy moths, and most recently the brown marmorated stink bug are all introduced pests that, at various times, were described as serious threats to our ecology.
These threats aren't confined to arthropods, either.  The giant African land snail is causing a stir in Florida (indeed, Florida seems to suffer from an excessive variety of introduced species.
"Lack of native predators" is frequently cited as the primary reason many invasive species are considered such a risk to the ecology.
I understand that these introduced species can place tremendous pressure on native species that fill similar ecological niches, and may even push these species out of the region due to competition for food and habitat.  However, do the overall ecologies that these species are introduced to adjust over long periods of time?
The numbers of Japanese beetles and gypsy moths don't seem anywhere as high as when I was a child.  Has the ecosystem adjusted, or has the overpopulation self-corrected as the species ran low on food through over-consumption?  Or are the populations still just as problematic now as they were 30 years ago, and I just am not seeing the bigger picture?
What is the long-term impact that we've seen from invasive, introduced species?  Is there a significant difference on the long-term impact between introduced flora, arthropods, or mammals?

You may also be interested in the classic example of rabbits in Australia.

Good question, and I'm excited to read some good answers. I'd guess just as an idea that introduced species have fundamental effects on ecosystems when the native species that they detrimentally affect are community structuring species, eg. Emerald Ash Borer in an Ash woodland.

Oh, and Homo sapiens are a pretty seriously destructive / transformative invasive species, I suppose.

This is extremely broad and a little vague. It may help to break it up, or at least specificy the exact issues you are interested in. What do you mean by "damage"? That they drive out any other species? That they reduce productivity? That they reduce species richness? That they reduce the aesthetic value of the landscape?

It might also help to define what you meant by "ecosystem". If we consider the intestinal tract of a human as a microbial ecosystem, it's rather straightforward to show that invasive species cause long-term damage, by killing the host.

@EpiGrad I assumed it was pretty obvious from the context, and the commonly accepted use of the phrase "invasive species", that this question isn't asking "can diseases kill people".

@Beofett I used an extreme example, but it's never the less useful to make sure your question is bounded by scope and time, because it changes the answer.

@EpiGrad Given the notable lack of answers after 3 months, I'm not sure that it would be beneficial to draw lines that would exclude valid potential answers because they defined key concepts slightly differently than any (wholly arbitrary) boundaries I might add (e.g. I don't want to define "long-term" as 30 years, and thereby miss answers involving research on 25 year impact). If there were an over-abundance of answers, I might be inclined to agree that further refinement of scope could help, but I think this question is pretty clear in its intent as-is, as highlighted by the examples I cite.

It is maybe worthwhile adding, that if you take an other wildly spread definition of "invasive species" the question becomes circular (at least if we drop the "long-term"): Wikipedia e.g which takes it's definition from the GB non-native species secreteriat defines invasive species as: "a plant or animal that is not native to a specific location (an introduced species); and has a tendency to spread, which is believed to cause damage to the environment, human economy and/or human health"

The answer really depends on how you think of invasive.  One extreme answer is to say that all things are relative, and that the concepts of local and invasive are all relative.  This matters to a certain extent because ecologists draw a fuzzy line between invasive and naturalized.  You could start with some basic species that we all think of as either good, local, or neutral.  Take the earthworm.  Most people think of it as a common native species, but the earthworm is actually an invasive species that has radically changed much of North America that came over with the Europeans.  Similarly, brown trout are also invasive, coming to the US in the 1800's.
As far as why invasive species succeed, it's still an open question.  What you reference is the enemy release hypothesis, but there are others such as disturbance, diversity of the new community, and just the traits.  Here's a good review of biological invasions and a second one.
To answer your question about adapting, I wouldn't trust your memory. It's important to keep in mind that most likely your memory is flawed, and you are only observing a very limited number samples with an incomplete sampling methodology.  For instance gypsy moths undergo wild population fluctuations, and have for over 100 years.  How well do ecosystems bounce back from invasions depends on lots of factors.  Often time the ecosystem can survive, but the some species won't.  An easy example would be Norther Hardwood forests.  Chestnuts (extirpated by an invasive fungus)are mostly gone from the wild, but the forest persists, as well as many of the species that rely on them.  So in part the answer to your question depends on scale.  The forest survived, but an individual species was nearly destroyed.
Ecological economists have tried to put a value on the destruction that invasive species have caused too.


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Hibernation, Metabolism and Aging
People are beginning to seriously research space travel applications of therapeutic hypothermia, specifically for reducing metabolism and stress on humans traveling to Mars.
It seems that as you decrease the temperature, the metabolism decreases. My question is regarding the relationship between ageing and metabolism. Do we have any data that answers the question if lowered metabolism also lowers the rate of ageing?
I'm wondering if these hypothetical astronauts going to Mars are actually losing 6 months of their lifespan in an unconscious state, or is their ageing rate being lowered as well? And by how much?
For the sake of simplicity, let's ignore the effects of radiation on ageing during the travel.

Therapeutic hypothermia certainly is an extremely useful short-term treatment for hypoxic and ischaemic injury to tissues (caused by loss of blood flow and/or oxygen) and is part of the protocol for treating people in intensive care who have had out of hospital cardiac or respiratory arrest as well as being used during heart surgery in cardiopulmonary bypass. In addition there is currently research into treating people who have just had heart attacks and strokes, both conditions where there is acute loss of blood flow due to a clot.
However, there is little evidence as regards use of chronic (long term) hypothermia to prevent aging. While severe hypothermia does suppress cellular respiration and slow down metabolism and bodily function, it also often causes other abnormalities such as:

Disturbances in cardiac conduction that can lead to cardiac arrest
Markedly reduced blood flow to skin and limbs which can lead to tissue death in fingers, toes, etc.
Clotting dysfunction (haemorrhage if there is any injury)
Pulmonary oedema - fluid in the lungs causing inability to oxygenate and/or ventilate the blood
Increase in infections

There is, however, quite a lot more evidence in regards to slowing down cell ageing from oxidative stress using diet energy restriction and this has been replicated in rodents.
In other words, there really isn't any good evidence at this stage in regards to long term hypothermia, but currently, given the high risks of cardiac dysfunction and death, without invasive monitoring and intervention (such as in an ICU) it is not feasible.

Interesting. But your last paragraph suggests that invasive monitoring and intervention could perhaps help to achieve long term hypothermia? can you give a little bit more detail on what you are thinking?

At a minimum you'd need a way to feed the person and dispose of waste- without introducing infection (a major risk of catheters and long term intravenous lines), as well as pacing wires or a defibrillator. You would also probably need a way to monitor blood test results and treat any problems with peripheral circulation and lung problems. Certainly too complex to be automated.


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What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)
What tests could be run to test the purity and type of HCG?
We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide and can use a contracted lab to perform tests but due to my academic background I have no clue which tests to request to determine the purity and type of the raw powder. The following is what we should be receiving from the labs in China.
Product Description
CAS Number: 9002-61-3
pI = 2.951
Extinction Coefficient: EmM = 3.88 (278nm)2
Synonym: Choriogonin, hCG
The molecular weight is approximately 37.9 kDa (with
approximately 31% carbohydrate by weight). The
theoretical molecular weight is 37.9 kDa based on the
native form, which contains 2 subunits. The α subunit
has a molecular weight of 14.9 kDa of which
approximately 10.2 kDa is for the polypeptide and
approximately 4.7 kDa for the carbohydrate. The
β subunit has a molecular weight of 23 kDa of which
approximately 16.0 kDa is for the polypeptide and
approximately 7.0 kDa is for the carbohydrate.3,
To answer Mad Scientists Question, the peptide is "supposed" to be CGA (1081) for use on humans. This is why it is so important for us to find a test that can define the qualities of the raw peptide.

What exactly do you want to do with it afterwards? The level of purity and the kind of contamination that would be acceptable is very different if you do some in vitro experiments or if you do in vivo experiments in animals, not to speak of giving it to humans.

A quick way could be a size analysis via a gel permeation chromatography, if you have access to this equipment.

A monograph from a pharmacopeia gives a good starting point for active pharmaceutical ingredient characterization. AFAIK there is no monograph for hCG nor your actual peptide of interest, but there is one for FSH (here for the european pharmacopeia monograph), which shares a subunit with CGA, meaning that modifications of it could suffice (though validating these modification will be a good amount of work, and will depend on the ultimate use for the peptide).
First, it is necessary to stress that even if the compound passes all assays, it would still be unsuitable for human use. It may be acceptable for animal experimentation. This is because the pharmacopoeia assumes a context where you have a non-adversarial relationship with your supplier, such that statement like "up to XX% remaining impurities" is an acceptable standard as the synthesis route & typical impurities are known. However, buying peptides from a random Chinese seller with no transparency on process is likely an adversarial situation.
Some keys to read the monograph:

Compound followed by the letter R ("water R", "glycine R"): these compounds have their own monograph. You could assay them accordingly, but for this use case understanding the R as "analytical grade" is possibly good enough.
"Follitropin CRS": chemical reference substance, a reference standard powder of follitropin obtained through reliable means (typically through EDQM for pharmaceutical purpose). Here also, substituting for an analytical grade standard from a reputable chemical seller could work.
Method followed with three numbers ("Bacterial endotoxins (2.6.14)"): reference a method monograph found in the given chapter/section. Apply methodology as described in the referenced text.

To adapt the assays to your peptide of interest, you need to understand which parts are specific to follitropin (and should be modified), and which applied to gonadotrophin-like peptides in general. For instance, for isoelectric focusing, the running conditions (pH, catholyte/anolyte) will be adequate, but the follitropin reference will be replaced with a CGA reference. On the contrary, the selective cleavage of peptide bonds assays is specific to the peptide, and will need extensive rework.


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What is a "mechanistic study"?
I believe a "mechanistic study" means a study where a medicinal product is being used but the purpose of the study is to investigate the patient or disease, not the medicinal product.
How does this differ from any other type of study?  What is the purpose of this study?  Why would we not be interested in the medicinal product?
Please provide a very simple example that a non-scientist could understand.

A mechanistic study aims to uncover a mechanism. It can be a mechanism of the disease (exactly how does the disease do damage to the body), or a mechanism of a drug (exactly how does the drug prevent or repair the damage) that is being investigated.
Understanding mechanism, be it mechanism of disease or mechanism of the drug, is very important toward targeted improvements of treatments, as opposed to trying lots and lots of compounds, hoping that someday we'll find one that's better.
Non-mechanistic studies involving drugs aim to show that the drug provides a clinically relevant health benefit over competing treatments, or to determine the safe dosage of a drug. At that point, the mechanism of action of a drug is known to a reasonably large extent.
In short, there are many different things that need to be known for drugs to reach the market. Mechanism is one of them.

"There are many different things that need to be known for drugs for each the market. Mechanism is one of them." This is incorrect according to the regulatory authorities I'm familiar with. The standard is safe and effective. Many drugs have been approved before we understood anything about their mechanism of action (e.g., Lithium). Some we still don't understand much about (e.g., Levetiracetam).


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Is there any database with RNA classification?
I am looking for a database that would provide classification of various types of RNA - information about its structure, function, etc.

Probably http://scor.berkeley.edu/

Rfam is a database about RNA families, similar to Pfam (wich is for proteins). I think it's what you're looking for.
http://rfam.sanger.ac.uk/search
You could also enjoy miRbase, a database for micro RNAs: http://www.mirbase.org/
There are tRNA databases, too, like this one: http://trnadb.bioinf.uni-leipzig.de/
And this tool for predict RNA secondary structure (However, this kind of tools aren't as good as they proteinic counterpart): http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form


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Are biological systems engineered? They are often reverse engineered at a molecular level!!
Understanding biological systems, molecular biologists need to “reverse  engineer” them. Is this evidence that the systems were engineered to begin with?

No.
So I looked up a definition of 'reverse engineering'. Wikipedia states:

Reverse engineering is the process of discovering the technological principles of a device, object, or system through analysis of its structure, function, and operation. It often involves taking apart something (a mechanical device, electronic component, computer program, or biological, chemical, or organic matter) and analyzing its workings in detail to be used in maintenance, or to try to make a new device or program that does the same thing without using or simply duplicating (without understanding) the original.

How else are you suppose to study something? Anything?
I dont want to answer a question with a question so I will continue. If you are working with a complex system, you will need to study the individual pieces. Although it is helpful to sometimes to look at the system of a whole, doing that introduces many variables that makes it impossible to tell what is really going on.
Some will say you need to do this because biological systems are so complex and that this is 'evidence' for a creator. That is silly. I can agree that biological systems are complex, but that is not evidence for a creator. Complexity is not a good thing. I think sometimes people have a naive view of a cell that it is organized and everything works perfectly and there is precision in everything (or even a lot of things). But thats not true. It is messy. Cells are chaotic. They are a freshman's dorm room. I study splicing, a very complex process.  And I just read a paper where they looked at highly conserved transcripts with no known alternative isoforms. And what did they find? They found that in small amounts every exon was being spliced incorrectly. Sure, most of the time it was spliced correctly. They even called it high fidelity. But the gene they looked at had 5 exons. Consider that the largest gene in humans has over 300 exons, and if all of those are being spliced incorrectly, it adds up. If an exon is misspliced 1/1000 times, and you have 300 exons, that means 1/3 of your transcripts are not what you want. It adds up to a lot of wasted effort by the cell, and it certainly would be better if there was no splicing (or at least less) for large genes.
Thats just one example but you could literally pick any component of the cell and find inefficiency. Sure, 1/1000th is good accuracy fot splicing, but lets have some context. Since we are talking about designers, does anyone here use a watch (designed by mere mortals) that stops working one minute out of every thousand? A computer that shuts down randomly one minute of every thousand? Me either.
Is 'reverse engineering' evidence of a designer? No, its evidence that cells are a mess and we need to separate the noise from whatever it is we want to study.

No. We can reverse-engineer diamonds, or oil, or waves, or the sound of leaves in the wind. Neither of these were engineered. Thus, whether or not we can reverse-engineer something does not tell anything about the origin of the thing.

No. If I wanted to study the sun, I might build a space ship to take me there. Does that mean the sun was put in place by a space ship? I can study your knee using X-rays, does that mean you knee was made by X-rays? The fact that you can use method X to analyze object Y in no way implies that object Y was created using method X.
To take another example, think of balancing rocks like these:

If I were to "study" them I could make the "intelligent" decision (I am using intelligent in the freest possible sense of the word) to poke the thing to see if it is really balancing or otherwise attached. If I were to do so, I would be acting, to use @Jason's terminology, "as an engineer making intelligent interventions and not as a gambler throwing dice". I would choose the place to poke carefully, near the top perhaps, so that it would return a maximum of useful information (fall), I would not just push them randomly. Does that imply that the rock was placed by an intelligent designer?
To go back to your basic question. First of all, we do not "need" to reverse engineer systems in order to understand them, in fact, with very few exceptions, we can't reverse engineer biological systems (which is also taken as "evidence" for intelligent design by the way, in a wonderful example of screwed if you do, screwed if you don't). Most analyses of biological systems consist of observing them.
Anyway, even if we were to reverse engineer that does not in any way imply that the systems were engineered in the first place. That is like saying that if I see you walking down the road today, that implies that yesterday you walked backwards up the same road. If we were to successfully reverse engineer a biological system, that could imply that we are intelligent, but it would imply nothing of the existence of a creator of these systems, let alone the intelligence of such a being.

In regular engineering one begins with a plan to construct a machine that serves a
given function and then builds the machine according to plan. In reverse
engineering, by contrast, one starts with a finished machine and tries to determine
what its purpose is and how it was constructed.
Scott Minnich, a University of
Idaho molecular biologist and prominent proponent of intelligent design, will
often remark in his public lectures that the only way for biologists to understand
the workings of the cell is to approach its various systems as a reverse engineer.
Thus the molecular biologist may take a functioning system in the cell, perturb it,
see how the cell behaves differently to infer the system’s function. Alternatively,
the molecular biologist may interfere at various points in the system’s self assembly to determine how the system is constructed.
In all such cases, the molecular biologist acts as an engineer making intelligent interventions and not as a gambler throwing dice. If we need the science of engineering to understand biological systems, then it wouldn't be a stupid bet that the systems are themselves designed.

do you have references to support this?

With all due respect, this is really a ridiculous argument. An intelligent designer may or may not exist. The fact that we study systems by making intelligent choices however, only implies that we are intelligent, not their designer.


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While someone's ears pops with pressure, can he/she hear other sound at the same time?
I know that after or before someone's ears pops because of pressure changes, he/she can hear the sound such as laughter. But can these two things ("her ears popped with pressure" and "she can hear the laughter") happen at the same time?

Yes, of course they can. What happens when your ears feel 'full' like on an aeroplane is that the air pressure in the middle ear is different from the air pressure outside. When you 'pop' your ears, you push open the Eustachian tubes that connect the middle ear to the throat and make the pressure equal. No matter what the air pressure, the air still conducts sounds. The difference is that your ear drum moves a bit less if the middle ear pressure and outside pressure is different, thus why sound is muffled before you pop your ears.

the air still conducts sounds---yeah, that's the key, thank you ! can we hear a sound like a "pop" when we pop our ears?

Sort of! it's kind of similar to the noise you hear when you swallow saliva as well as a gentle 'popping' feeling and relief.

aha!I see. and if the pressure of inside and outside is highly imbalanced, then the sound of a "pop" will not be gentle, and will be like a really "pop", right?

@Lincoln I guess so?

maybe having an extreme experience like this will know it...but the one will be deaf, right?...

@Lincoln well usually if the pressure on either side is different your hearing is a bit muffled. If there is an extreme pressure difference (from a combination of Eustachian tube blockage, infection & air travel, or more commonly a momentary difference caused by a huge sound like an explosion) your eardrum will burst. This is called 'barotrauma'

@Lincoln no problem! I'm guessing you've never felt your ears pop?

yeah, being seen through by you...  (hope you understand what i am saying... pardon my my bad english...not a native speaker).


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Are there any open plant databases (database/library/collection), containing species information and pictures?
I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?

What about EOL?

Large online floras have the advantage of not only having details and often photographs and illustrations, but also being (more or less) definitive, that is, botanists will refer to them.
See my answer here for links to examples, and also for some of the problems with using floras (e.g. not easily downloadable).

They really need to release a database version of Mabberley's Plant Book

1. DELTA identification program key. (DELTA – DEscription Language for TAxonomy).
http://delta-intkey.com/ , http://delta-intkey.com/angio/ , https://florabase.dpaw.wa.gov.au/help/keys/intkey_tutorial.pdf
2.  FloraBase.
https://florabase.dpaw.wa.gov.au/ (Australian Database).
3. Royal Botanic Garden (England) and Kew Herbarium 's Database.
http://www.kew.org/, http://epic.kew.org/index.htm http://www.kew.org/science/tropamerica/ikey.htm,
4. Actkey, maintained by Harvard University Herbarium
http://huh.harvard.edu/pages/herbaria
https://web.archive.org/web/20170809022620/http://www.millersville.edu/biology/courses/471/4_471_Brach_Song_2005.pdf
5. Taxacom, an E-mail server for discussion on systematics of living-systems. Monitored by University of Kansas
http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom (Taxacom main page)
http://mailman.nhm.ku.edu/pipermail/taxacom/ (Taxacom Archive)
http://taxacom.markmail.org/ (Post- Search engine)
6. Angiosperm Phylogeny Website, under Missouri Botanic Garden.
http://www.mobot.org/MOBOT/research/APweb/

Source: Plant Systematics- Theory and Practice, 2nd Edition, by Gurcharan Singh, Oxford and IBH Publishing House New Delhi

The United States Department of Agriculture have a plant database (http://plants.usda.gov) where you can download search results and checklists. Look at their download page. However, I think that you can only download text (no pics), and it mostly (only?) contain plants found in the US. I have not used the download functionality myself, so I do not know anything about flexibility or interface.


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Are there any enzymes synthesised by humans that specifically catalyse the hydrolysis of non-cyclic Imides?
Imides or dicarbonyl amides are an interesting class of compounds that includes the pharmaceuticals thalidomide, aniracetam and a few other drugs. These compounds, however, are cyclic and I'm wondering whether there's an enzyme found in the human body that specifically catalyses the degradation of non-cyclic imides. I'm thinking that fatty acid amide hydrolase (FAAH) may catalyse the hydrolysis of non-cyclic imides at least as a minor metabolic pathway.


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How can fresh cavities form at the margins of sliver amalgam fillings on teeth?
Silver amalgam fillings predominantly contain silver a known bactericidal agent and mercury which a known toxin and has bactericidal property. So how is it that the plaque bacteria survive near the filling margins and produce fresh caries?

Amalgam fillings are made from an alloy. The properties of the chemical elements bound into an alloy are different than the properties of those elements in different forms. The fillings do not release any biologically significant form or biologically significant amount of either silver or mercury. They are essentially inert.
Plus silver antibacterial effects are quite modest. The existence of fine cracks and gaps between amalgam and tooth provide wonderful hiding places for bacteria - and that shelter is probably more important to the bacteria than any negative effects of the silver.


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Can replication occur if DNA is methylated?
Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?

Don't have sources at the moment, but as far as I know: Yes. Methylated DNA cannot only be replicated, but it can also be passed on to subsequent generations as part of the Epigenetic info inherited by the offspring.

Absolutely.  It's a pretty cool process, actually.  Most (well...) DNA methylation occurs in the context of what are called CpG; that is, a C (Cytosine) followed by a G (Guanine).  Because C and G are the Watson-Crick pair for each other, the sequence on the opposite strand will also be CG.  Usually, both Cs are methylated, which turns out to be rather critical for maintenance of methylation.
DNA replication occurs through a semi-conservative mechanism, which means each old, original strand is copied and paired with a new strand.  The new strand has no methylation on it, however; it is at this point that the enzyme DNA methyltransferase (DNMT1, specifically) comes into play.  DNMT1 finds the CpGs methylated on one strand ("hemimethylated") and methylates the other strand, providing complete inheritance.  Here is a nice summary, and this is a review that (briefly) summarizes the evidence that CpGs may play a role in irigins of replication (the jury's still out).

Thanks for the answer !In PCR ,do we always use methyated dna ?

@biogirl I dunno, do you?  Theoretically your input sequence, if it's straight genomic DNA from an organism, could/should be methylated, but DNA polymerase does no methylation at all; that is done by DNMT1 and others, and is much slower than replication.  After PCR, none of your product will be methylated.

I have never done a PCR :) If I take DNA from an organism like human(whose DNA is naturally methylated) and then deliberately demethylate it, can it get replicated in PCR or in a cell ?

Sorry, that's what I was trying to say above, you can't.  PCR is pretty straightforward, it's basically just DNA polymerase.  Each strand of DNA is split and copied, over and over.  As I said above, DNMT1 adds methylation, not DNA polymerase, so none of your PCR product would be methylated.  Adding in DNMT1 after each cycle would be prohibitively time consuming.


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What Role Antagonists Play in the Study of Drugs?
I am pretty unfamiliar to pharmacology. I'm doing a research on drug abuse, particularly opioids' mechanism of action. I encountered several times evidences that come from studies using antagonists especially naloxone that are to prove something is 'a specific opioid effect':

Opioid-induced miosis in the human ... This action is a specific
  opioid effect as demonstrated by its antagonism by naloxone.

I wanted to know the rationale behind these kind of conclusions. Also an elaboration on the role antagonists play in drug research will be appreciated.

An antagonist is a substance that blocks a particular pathway (a receptor). You can therefore test whether a particular drug acts through the opioid system by using an opioid antagonist. If your substance still works despite the presence of the antagonist (which should block the opoiod receptors), you can conclude that it is not working thorough the opioid system.
Conversely, if your drug is blocked by an opioid antagonist, that is good evidence that your drug works through the opioid system.

What many drugs and compounds do is bind to cell receptors. These receptors then change shape and various things may happen in the cell as a result (including relaying a message to other cells).
Something that binds to a receptor and causes activity is called an agonist. Something that binds to a receptor and causes a partial response is called a partial agonist. Something that binds to a receptor but does not cause activity is called an antagonist as it takes up those receptor sites meaning that nothing else can bind to them and cause and effect.
An opioid effect is one of many effects caused by opioids. Naloxone is an opioid antagonist. It binds to the same receptors as opiates but without causing an effect. If a normal person has naloxone it won't actually cause an effect. If someone who has taken an opiate takes naloxone however, the naloxone will compete for receptor spots, knocking off the opiate and reversing the opiate effect. Also, if someone takes naloxone and then immediately has an opiate, that opiate will not work particularly well as some of those receptors are already taken up with naloxone.
Hope that helps.

Very precise and simple explanation. Thank you so much.

@EhsanAbd No worries!


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Plant a whole fruit or only seeds?
I'm trying to figure out whether it is better for the plant to reproduce by planting its whole fruits with seeds inside them, or picking the seeds out and planting them without the fruit. In my case it's chili pepper, but I'm also interested in other plants that reproduce through fruits.
I heard that the whole fruit concept is about providing the seeds with some energy in form of their shell (the fruit) to give them a head start in terms of initial growth into a seedling. Is that true? Do all seeds benefit from growing from inside its fruit, or is it not very significant?

If your question is purely practical (which fruits are better to plant as seeds or whole), you might have better luck on gardening.SE. If you are interested in the biology side, then this is the place.

@kmm What if I'm interested in both?

That's fine. I think this question could be edited to get at the biology. And then ask which seeds to plant how over at gardening.

@kmm if you know how to make the question more about the biological aspects, please go ahead and edit. I only have some basic info on that, so I'm not sure I can make the question better myself.

I'd guess that, evolutionary, it would vary greatly depending on the plant. There are many strategies for seed dispersal: some rely on mammals eating your fruiting body, others on birds, others on blowing away in the air or floating in water, usually aided by what we might call the "fruit".

I'd argue that this relates to species-specific strategies of seed dispersal, so the answer depends on which species you're asking about. Here's an answer for chili peppers, which I think illustrates how complex and idiosyncratic these strategies can be.
As I mentioned in this answer, the seedsavers' manual Seed to Seed has great info on most plants, including the genus Capsicum (chili peppers). They say to clean the seeds from the peppers, and then dry them thoroughly but not in direct sun.
The Tewksbury lab has done someone amazing work on Capsicum evolution and seed dispersal from a biological standpoint. As published in Tewksbury and Nabhan 2001 (behind paywall, but described well in this Science in the News article) Capsicum fruits have evolved specifically to be eaten by birds, who do not have the receptors that make the fruits taste spicy to us and other mammals.
Essentially then, what you're trying to do when you hand-germinate seeds is to mimic the process of the fruit being eaten and passing through a bird gut. Tewksbury and Nabhan found that seeds from fruits eaten by birds actually germinated at a slightly higher rate than their control group of hand-processed seeds. In contrast, seeds eaten by mammals (who in normal settings totally avoid these spicy chilis) were destroyed and did not germinate.
Seed dispersal mediated by birds and other animals is one way that plants can be motile.

 Tewksbury JJJ, Nabhan GPG. 2001. Seed dispersal. Directed deterrence by capsaicin in chilies. Nature 412: 403–404.

Whealy K. 2012. Seed to Seed. Chelsea Green Publishing (p. 152)

I realize that I've come down hard on the "dispersal" side of the issue and that OP also mentions the possibility that fruits help in seed development. I'd love to read/upvote an answer that explores that aspect of the question.

Thanks, this is the kind of info I was looking for. Let's see if somebody else can answer the "seeds in fruit" part.

I'm not aware of any plants where the fruit provisions energy to the developing embryo. Generally this type of energy and nutrient storage would be done within the seed. Think of an avocado: both the large pit and the flesh contain a lot of energy, but flesh only serves to attract animals for dispersal, while the developing embryo only gets energy from the pit.
Generally, if you have a big fleshy fruit, it's because there was an adaptation to attract an animal to eat the fruit and disperse the seeds (plus extra breeding by humans to make our common edible fruits). Rather than the flesh of the fruit serving as a fertilizer, the scat associated with that dispersal may serve that purpose.
However, there is an astonishing array of fruits and fruit strategies, and many species do have their seeds dispersed along with their fruits. For example, all grass "seeds" are essentially tiny fruits, where the fruit part is reduced to some protective layers. Sunflower seeds are another example, where the hard shell will protect the seed until it can germinate. Many fruits aid in dispersal by the environment, such as wind or water, or by animals without being eaten, as in burrs.


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Eating rarely but a lot, or often but little
I wonder if it matters if an average person eats the same amount of food distributed between a few (2-3) meals during the day, or constantly having small snacks.
I'm interested in several aspects of such food consumption:

How does it affect appetite?
How does it affect fat accumulation?
Are there any notable side effects caused by either way of eating?

1)Eating little with many breaks is healthy..
Eating rarely but many times increases your fat...
The logic is simple.
Before the Logic..let me shoot a fact.
In mammals: conversion from glucose to fatty acids has a direct pathway(I am speaking biochemistry), but there is no direct path for conversion of fats to glucose..(whereas in plants both paths are direct..)
So If you eat more food at one time, the glucose which body needs is used and the remaining glucose is converted to fat.
when the body again needs glucose, it needs to take a long pathway to convert fat into glucose(* only if you workout), by that time your Hypothalamus gets a signal and you feel hungry. So you again eat to satisfy your hypothalamus and the process continues, with more accumulation of fat in your body.
But in the little meals, there is no accumulation of fat.
2)In either case, the Appetite is affected in the normal and same way.
3)There are no side effects for either pathway, but you have other side effects from the fat accumulated. :P

Can you add some citations? I fear there is little scientific certainty about almost everything in this answer.

I suggest reading Biochemistry pathways. Cannot cite you at one pathway, because it's all interlinked. You learn a lot of facts and understand a lot of human metabolisms, right from why a diabetic guy breath is alcoholic to how proteins build muscle. Interesting stuff.

It isn't about not knowing biochemistry. Please don't be condescending - citations are especially important to prevent misinterpretation by non-experts on health-related topics. There is little to no logic to your answer: stating that it is "simple" doesn't make it correct. A "direct pathway" from fat to glucose is not necessary because animals can use energy sources besides glucose. Glucose is only a common energy source when carbohydrates are being used.

Eating many small meals or eating large meals is irrelevant. The only thing that matters is getting the right amount of calories needed for your body to function properly.
Fat accumulation does not happen if you do not go over your daily calorie limit.
After a big meal your food is not only stored as fat but as a polysaccharide form of glucose called glycogen that is stored in the liver and or muscles for later use.
Therefore, there is no better way to eat, it depends on what size you like your meals to be as long as you stay within your calorie range.
See http://www.choosemyplate.gov for more information.


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Why is mammal coloration so dull?
I have seen species of birds, insects and fishes with splendid colours. But when it comes to mammals (including us humans), they almost always appear in shades of brown, grey, orange, or in black and white. I don't recall seeing any pink, green and purple. Why is that so?

That mandrill face in the picture you uploaded is pretty brightly colored.

Great question. At least according to this BioScience article, it seems like most of the answers are still unknown. No time to fully review it now, but this paper in PTRSB by the same author looks very good, and basically takes as its starting point that black and white stripes / spots is as colorful as mammals get, and is already surprising in mammals, "a class of vertebrate generally thought to be drab and cryptic".

Most mammals have poor colour perception, which might be the reason for the lack of bright colours. Plenty of mammal species are very contrasty with deep blacks and bright whites on the same animal, which might be all that's required. Primates have much better colour perception than most mammals, and there are a few monkey species that have bright blues and oranges. Of course, I have no idea whether mammals were more colourful before colour vision was lost; this is pure speculation on my part.

I don't think, there is a precise answer about the evolutionary mechanisms, but "mechanically":

mammals have principally just two types of pigments: eumelanin and pheomelanin, both of which have their color variants, but within a known range. Bird pigments, besides melanins, include carotenoids and porphyrins. Arthropods generally have carotenoids, melanins and ommochromes [and other pigments?]. E.g. carotenoids and ommochromes alone can create rather "exotic" coloration from a mammal point of view (green, pink, violet).
both birds and insects actively utilize iridescence. With fur it seems to be technically much more difficult to achieve than with feather or scales.
many (most?) mammals do not differentiate colors. Birds have much better vision abilities in this respect. From a selectionist point of view this cuts out a considerable part of selection acting upon coloration, which could otherwise produce broader spectrum of phenotypes.

Nice answer. Come to think of it, no wonder our eyes are most colorful because it is made of carotenoids. Thanks!

In addition to the arguments presented in the accepted answer, I would like to add that most species of mammals are red/green colour-blind. This has to do with the fact that for much of their evolutionary history, mammals were nocturnal creatures and so the ability to see different colours wasn't necessary.
This dates back to the mesozoic period when mammals had nocturnal lifestyles in order to avoid predation from dinosaurs.
Here's an article that summarizes recent research on this topic: http://www.utexas.edu/news/2012/10/29/effects-prehistoric-nocturnal-life-mammalian-vision/

The Answer is simple..EVOLUTION..
The colour of an living organisms depends on 2 things 1) attracting other sex. 2) escape from the predators.
In birds and insects: They doesn't much depend on other sex for living(except for the process of reproduction)and there is no need t exhibit  physical work for attracting other sex... For example if you take a peacock the male needs to be colourful to attract female. but there is no physical work....Let The Other example be some Insect,then if it is colourful.. a predator may not eat for its bright colour..
this made insects and birds evolute into colourful..
But in mammals. the attracting and escape both depend on physical work... a lion being handsome cannot attract lioness..  :P It need to be physically healthy to escape from predators and give an enough competition to other lions in his territory...
this made evolution for mammals much depend on their capability of body.. rather than physical attractiveness.. for example in a forest a tigress will obviously pair with a Tiger which has more territory than a more attractive handsome tiger without territory(this is not a case with insects)..

This isn't really a good argument. Mate choice in mammals (as in other creatures) is complex. For example, I'm pretty sure the character of the mane (size?, colour?, fluffiness?) plays a role in mate choice, since it's the most obvious reason for the strong sexual dimorphism.

I think that the basic concepts here are right on – there's a balance between attracting the opposite sex and hiding from predators (crypsis); among other strategies, including putting off predators with bright coloration (aposematism). However, the answer is a bit unclear and it would be very nice to see some references.

sorry for the ambiguity.. i have just edited my answer adding some more examples.. I have a video on y insects and birds have more colourful than mammals.. Its a documentary by discovery "PlanetEarth"..

Unfortunately, your edits don't address the main problem. Your entire premise that mate choice in mammals doesn't depend on "physical attractiveness" isn't supported by evidence. Lionesses choose their mate partly by the attractiveness of the mane, several primates have rather conspicuous sexual displays (the inflated cheek pouches of orangutans, the silver fur on the back of the silverback gorilla, the bright facial patterns on mandrills, etc.).


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Is the resting state of the forearm in the pronated or supinated position?
It seems to me that my forearm is naturally in a more pronated position than the anatomic (supinated) position and that it actually takes work to make it hold the supinated position. Anyone an expert in human anatomy/physiology here or know of any sources that could point towards a more scientific answer?

The main reason why the anatomic position is supinated is because the radius and ulna are crossed when the arm is pronated and parallel when the arm is supinated. It doesn't have anything to do with the resting state of the arm, it's just the easiest way to arrange the bones neatly for description and analysis.

I agree with the above answer. Also, we all tend to use our forearm more in the pronated form (holding, hand shake, driving, etc) so I guess it becomes second nature to us.


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Mesophytic Climax community in succession?
My textbook says that in all cases of ecological succession (xerarch, hydrarch, etc.), the ultimate climax community, assuming constancy of environment, is a mesic community. Xeric or hydric pioneers are ultimately succeeded by mesic climax communities. Why is this so? In an environment under consideration, if for example water stress prevails (characteristic of xeric environments) shouldn't the final community be xeric and hence better adapted to the environment? Is my book wrong, or is there something I am missing in the understanding of the development of climax communities?
Moreover, I did find it written somewhere that mesic communities do depend on the climate of the place. But then doesn't the fact it is mesic contradict a few climatic conditions wherein ecological succession might occur?
Reference:-
Ecological Succession
Climax Community

What textbook are you referring to?

@fileunderwater I have read this in several independent sources and lengthy class-notes. Here are a few places(not the best at all) where the fact (common mesic climax) is taken as a fact in several discussions.  [1]:http://books.google.co.in/books?id=3iBRNAEACAAJ&dq=life+purves&hl=en&sa=X&ei=Q2pCUqThGofmrAewuoHABA&ved=0CEYQ6AEwBA   [2]:http://books.google.co.in/books?id=FEMOAAAAQAAJ&pg=PA45&dq=climax+mesic+conditions+succession&hl=en&sa=X&ei=EmpCUqi1NojXrQfMmIGoDA&ved=0CDwQ6AEwAzgK

I assume your question only applies to secondary succession. I would clarify this in your question.

The concept of a "climax community" has not been accepted as reality for more than 40-50 years. Frederic Clements was an early botanist examining succession in the first 20 years of the 20th century. It was Clements who developed the concept of the climax: he posited that the habitat and the populations acted upon one another in a reciprocal way until finally a stable state (the climax) was reached.
However, the work of Gleason (e.g, 1926), Tansley, Watt (1957), Whittaker (e.g., 1972), Davis (1969),  etc. have changed the field's understanding of succession and its acceptance of the existence of a stable "climax". Whittaker was first to propose the use of the term "stable state," as it carried less assumptions about the community' inability to be replaced.
It's now clear from work of countless studies and authors (along with my own research), that disturbances play a significant role in plant dynamics and that previously accepted 'stable states' are perhaps only remnants of historical characteristics of the system (see below). As a result, some accepted stable-state communities no longer appear to be the norm in some areas (likely due to both present and past disturbances and fluxes in the system). See Abram's papers for a discussion on hypotheses of this phenomenon in the Eastern deciduous forest of the U.S.
Regardless, even in a system without disturbance (which none exist), the stable-state community would be fully dependent on climate, substrate, community assembly limitations and geographic/environmental/biological filters.


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Why Only DNA can Contain Hereditary Material?
Well I'm well aware that it is proven that DNA contains  genetic material via transformation and Hershey-Chase Experiment of T2 bacteriophage. Still I was wondering what is the reason only DNA contains it and not protein or RNA.
What I've learned is that DNA is the most stable of all these molecules and it has the ability to replicate itself.
Other than this I can't find any solid answere.
Thanks!

RNA might contain material that you can classify as 'hereditary' (specific to that individual of the species, a subset of the species gene pool) but since the prevailing methods of meiotic gamete formation, sexual reproduction and the fact that all enzymes are formed due to transcription from DNA and not by the inherited RNA, DNA is the one that is inherited and hence acts as the heredity carrier and not RNA.

DNA/RNA also has a relatively obvious way by which it can be replicated- having a purine base pair with a pyrimidine.

RNA has the ability to replicate itself - it could be the genetic material, but it simply isn't.  its degraded in the cell quickly. its hard to be hereditary material when you are destroyed.

@shigeta, certainly there are RNA viruses that are excellent examples of RNA functioning as hereditary materials.

that's true, but trying to respond to the question as stated as i see it, not sure its what i wanted to point out.

DNA is unable to replicate itself, a complex of protein, RNA, and DNA are involved in DNA replication.

I think any discussion of this question can benefit from a historical perspective. For a long time, it was in fact believed that proteins was the hereditary material. The Nature Scitable page on the discovery of DNA (1) starts with the following passage:

In the first half of the twentieth century, Gregor Mendel's principles
  of genetic inheritance became widely accepted, but the chemical nature
  of the hereditary material remained unknown. Scientists did know that
  genes were located on chromosomes and that chromosomes consisted of
  DNA and proteins. At the time, however, proteins seemed to be a better
  choice for the genetic material, because chemical analyses had shown
  that proteins are more varied than DNA in their chemical composition,
  as well as in their physical properties.

While perhaps easy to dismiss in hindsight, it is possible to understand the reasoning of the day. The "central dogma" of molecular biology, that genetic information flows from DNA to RNA to proteins was only described later, and explained how the production of complex proteins consisting of 20-odd amino acids can be directed by a polymer consisting of only four nucleotides. This allows great complexity and variety in phenotypes while maintaining simplicity of the genetic material. The central dogma also facilitates the seperation of the use (through protein expression) and storage (as DNA) of genetic material.
As Watson and Crick noted in their famous paper, the double helix of DNA, when discovered, immediately suggested how the genetic material could be elegantly copied. While the more complex structure of proteins would likely require a more complex copying mechanism, the specification of amino acids through three-nucleotide codons in DNA allows the regularity of the DNA material to be retained for easy replication while allowing complex proteins to be produced.
However, even though DNA is the primary genetic material today, the situation may have been different at the time life first appeared. According to the RNA world hypothesis, RNA may have been the original genetic material and that DNA is a variation of RNA, not the other way around as it is commonly seen.
For a fuller historical perspective, I recommend the book "What is Life?" by Erwin Schrödinger, which was written before the discovery of DNA as the genetic material.

In contrast to some of the accepted points in this thread. DNA is not the only hereditary material. The RNA world hypothesis remains hypothetical, but  its primary point is that RNA may have been the original hereditary material as it is slightly simpler than DNA. However, there are extant organisms that use RNA as their genomic basis.
There are many viruses which use RNA based genomes (either single stranded or double stranded, (Class IV/V and Class III viruses as described by the Baltimore Classification). There are also class VI viruses which use an RNA genome that passed through a 'DNA intermediate' phase during the infection/replication process. The latter class are "Retroviruses" as they need their genomes to be converted back to DNA. The most famous example of such is the HIV virus.
Crucially, the progeny viral particles re-package RNA, which is carried with them until the next infection cycle, making it their hereditary material.
(I realise this is an old thread at the time of my answer, but this is important for completeness)

Further, piRNAs can serve as hereditary material in animals: e.g.: Houwing, S., et al., A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish. Cell, 2007

The simplest answer one could offer to this question is hidden in the structure of the DNA itself. DNA is double helix structure with the presence of 3'->5' end and 5'-3'  coiled helically in the double strand ( it is the direction in which DNA is synthesised as per formation of replication fork via the enzyme DNA dependent DNA polymerase.

The inability of the Proteins, amino acids etc to replicate themselves makes no sense to have them as genetic material ( as also concluded by Martha and chase experiment).
Now, here is the point which leads the most logical question?
Why not RNA ?
In fact it is much better in the Job that DNA does, it is very fast in replication almost have the same structure,  but the fact that the presence of OH group makes RNA very reactive and Unstable does not make it idle for transfer of hereditary material in nature, we should know that thousands of nucleotides are synthesized by DNA polymerase during the replication of DNA from the template DNA which is highly accurate and precise even slightest of error can lead to very big mutation and the presence of the Deoxyribose and complementarity principle makes the DNA best suited for Genetic material.
Although a whole of a different class of the organism exists that have RNA as genetic material, they are called retroviruses eg. HIV virus so the question that DNA is the only genetic material in all living organism is not true, although yes it is the genetic material in Humans and majority of the organism due to the above reasons.
EDIT : AS @WYSIWYG mentioned there are also many viruses which have RNA as genetic material but are not called Retroviruses, nonetheless DNA is not the only genetic material that exists.
Kapeesh !

Viruses with RNA as genetic material are simply called RNA viruses. There are many RNA viruses that are not retroviruses (for e.g. poliovirus, influenza virus).

@WYSIWYG something interesting you made me learn today. Thank you so much.


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How to calculate or know by experiment the entropy of enzymes or protein?
How do you calculate or experimentally determine the entropy of enzymes or protein?  In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy.  Any references are welcome.

What do you mean by "entropy"? Are you referring to conformational entropy or to Gibbs free energy (ΔG) for folding etc?

both.And I'd like to know the Boltzmann's entropy

See this page: http://equilibrator.weizmann.ac.il/  and references therein.

In practice, like Energy calculations, Entropy is a relative numbers and difficult to get.  Computational chem and bio have been working on this problem with mixed success.  The summary of what I'm going to say here is that when you try to calculate the differences in entropy (or energy for that matter), the Gibbs Free Energy differences in most biological processes such as enzyme/substrate binding, protein/protein or protein/DNA interactions or protein folding etc is so small compared to the errors in these calculations that the computations are hard to believe.
Entropy is ultimately a term one would use in calculating the Gibb's free energy which will tell whether a given chemical or molecular process will occur.  So it's a valuable number to have.  Gibbs Free Energy (G) equals Enthalpy (heat) minus the temperature (T) times the change in entropy.
G = H - T$\Delta$S
The Entropic term, $\Delta$S is described in chemical systems often as a change in the combinatorial change of the system and the change in the heat capacity of the system. The first of these could broadly described as a 'mixing' term.  When more than one solvents or a solvent and a solute diffuse into each other mix completely, the number of possible states is maximized.
The heat capacity of the system is a more often the focus of entropy calculations for proteins and biological molecules.  This is because the conformations of the biological molecules, especially how free they are to move around are thought to contribute to the entropic part of G.
So attempts have been made to estimate from NMR and crystallography as well as molecular dynamics how much domains and side chains are free to move.  Unfortunately this is only an insufficient proxy for biological entropy.  A substantial if not dominant contribution to the T$\Delta$S term comes from solvent.
How is this so?  Water molecules form structures around proteins which are not static, but do involve many water molecules residing there on the average to see them in crystal structures and NMR experiments.  While the individual waters are exchanging rapidly, they are not in the same entropic state in water solution as they are when they form a hydration shell around an aromatic or charged side chain.
Attempts have been made to parametrize the solvent entropy by looking at the buried nonpolar surface in a folded protein, looking at the mobility of sidechains before and after folding/binding, but these metrics appear to be configuration dependent to the point that they can't calculate the protein entropy via these efforts, at least heretofore.
Conventionally, molecular dynamics tries to calculate this by surrounding the proteins or other molecules with water molecules and some approximation of the overall entropy is calculated on the entire system.  It turns out that small differences between the water molecular models and the simplifications in ball and stick/Hooke potential water models we make are also problematic approximations when there are hundreds or thousands of water molecules in the simulation.

Good，please continue


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Which fish will have more developed gills?
A fish lives at the depth of 1000-2000m and another at the depth of 200-700m. Which of them would have a more developed gill system ?

Can you expand on what you consider "better"? As long as both can live fine at their respective depths, then I would call both sets of gills "good enough", which is really all that matters.

Moles living in dark don't have well developed eyes. Similarly,which of these fishes would have more developed gills ?

200m is still pretty deep...
However, I'd give my money for the surfacers. Oxygen concentration decreases with the depth, and so abyssal fishes have very low metabolism, mainly focused on anaerobic muscles. This is also true for fishes that live in the bottom (benthic), which probably also applies for those living in a few hundred meters. If not, they will probably be active swimmers and then they will probably need bigger gills in order to maintain aerobic movement. Even if we're talking about abyssal and non-abyssal benthic species, I think the abyssal ones would probably be even more anaerobic.

Does Oxygen concentration decrease with depth? The opposite is true for the first few meters.

Yes, but that is because there's a biotic oxygen consumption (and production) that is higher in the most illuminated area. Once you have descend a bit beyond, the oxygen source is both photsynthesis and diffusion from air, both of wich may be hundreds of meters above. In this dark area, oxygen diffusion is limited, and carbon dioxyde accumulates too.

You make a good point but the solubility of Oxygen increases with depth since it depends on the pressure. I have no idea if this increase will continue or if it reaches a plateau after a few meters. I agree that at great depths, the lack of photosynthesis should mean that the oxygen content is lower, but I wonder how much that is balanced out by the greater solubility. I haven't been able to find a reliable reference citing oxygen levels at greater depths. I would guess the concentration goes up for the first ~10-15 meters and then falls from there.

Solubility may increase due to pressure, but it will remain pretty low no matter what. Without an internal production, and with so many organisms consuming it (below a certain point there is no photosynthesis, but there is still sediments to metabolize and there are animals and bacteria feeding by the leftovers that falls from the surface), the oxygen levels in the bottom of the ocean is minimal.


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What exactly happens if during translation, an amino acid is not present?
Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a "normal" way.
What exactly would happen if an amino acid required in the protein is absent ? I know that the protein would not be manufactured properly but I want to exactly know what would happen to the ribosome and the mRNA. Are they destroyed? Are they simply separated? Who regulates this?

It is not true that the anticodon of an uncharged tRNA can't bind to the mRNA.
Bacteria have a mechanism called stringent response. This response is complicated, here is a shorter and simplified explanation. Further informations can be found at the wikipedia pages linked in the text.
If during translation a certain amino acid is absent, an uncharged tRNA binds in the ribosome, causing the synthesis of the alarmone (p)ppGpp by activation of the RelA enzyme (in E. coli), associated with the 50S subunity of the ribosome. The translation blocks and (p)ppGpp interacts with β subunit of RNApol causing:

the reduction of its affinity for the σ70 transcription factor and therefore reducing the transcription of rRNA genes;
the increase of its affinity for σS and σN, transcription factors needed, rispectively, for the adaptation at the stationary phase and the lack of N. Also biosynthesis of amino acids is enhanced.

Once the situation is restored, the enzyme SpoT (coli) hydrolizes (p)ppGpp.

Point to know : aminoacyl-tRNA binds to mRNA its not just t-RNA..
So if there is no Amino-acid there is no aminoacyl-tRNA of that aminoacid.. so if there is no aminoacyl-tRNA, the anticodon of tRNA doesn't form a bond with mRNA, so the protein production halts (until the Amino acid produced).
If the protein is not formed within a certain long time, the premature protein folds itself and breaks. Then a molecule (example: ubiquitin for certain type of bacteria) attaches to this premature protein and marks it for degradation.
But there are still chances of protein production with slight mutations.
Mutation: tRNA with the same anticodon and different aminoacid can easily bind to the A site of the ribosome in the absence of the correct aminoacyl-tRNA, so the protein production doesn't stop in this case but the protein has a mutation with different aminoacid.

Could you give a source for your answer?

How can a tRNA with the same anticodon bind to another amino acid ?


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Are simple esters like those used as flavouring agents metabolised into their constituent carboxylic acids and alcohols in the human body?
By this I mean to ask whether say ethyl butanoate is hydrolysed in humans into ethanol and butyric (butanoic) acid. This is of interest to me as a pharmacology researcher because butyric acid, for instance, serves as a potent histone deacetylase (HDAC) inhibitor and hence increases gene expression but it has very poor oral bioavailability and I am curious as to whether there's any theoretical basis for suspecting that using butyric acid esters as prodrugs would be a more efficient way of delivering butyric acid.
Here is the molecular structure of ethyl butanoate: