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Human perception of time depending on age
From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to "accelerate" as we age.
Digging a little, most explanations I found basically reduced this to two reasons:

As we age physically, a time frame of constant length becomes ever smaller in contrast to the time we spent living
As we age socially, we are burdened with an increasing amount of responsibility and thus an increasing influx of information which impairs our perception of the present

To be honest, neither sounds entirely convincing to me because:

In my perception "local time" (short time frames that I don't even bother to measure on the scale of my lifetime) is also accelerating. Just as an example: When I wait for the bus, time goes by reasonably fast as opposed to my childhood tortures of having to wait an eternity for those five minutes to pass.
Even after making a great effort to cut myself off from society and consciously trying to focus on the moment, the perceived speed of time didn't really change. (Although I did have a great time :))

Which leads me to a simple question (and a few corollaries):

Am I just in denial of two perfectly plausible and sufficient explanations, or are there actual biological effects (e.g. changes in brain chemistry) in place, that cause (or at least significantly influence) this?
Is there a mechanism, that "stretches out" time for the young brain so that weight of an immense boredom forces it to benefit from its learning ability, while it "shrinks" time as the brain "matures" and must now act based on what it has learned, which often involves a lot of patience?
If there is such a mechanism, are there any available means to counter it? (not sure I'd really want to, but I'd like to know whether I could)

If I remember correctly it is known that young kids (<4-5 years) cannot distinguish between long and short time frames... I'll look if I can find the proper references about that. I don't know about adult though.\

@back2dos: How far off am I if I paraphrase your question as: "What is a biological/mechanistic explanation of how people learn patience?"

@SteveLianoglou I think it's related, but definitely not the same.  Patience would be more of a meta-phenomenon of how we emotionally deal with the passage of time, but there are issues of perception that are are more fundamental.  See this Nova video(1:40) which touches on this area a little bit.  It's more about whether the brain actually slows down than differentiating between 1 second or 2 seconds, but its indicative that this is an active area of interest.

@jonsca: Thank you, this sounds interesting, however the video is not available in my region :(

@jonsca: However I googled the guy and saw an interesting talk about possibilianism :)

Oh, I wasn't aware it was blocked anywhere, so I'm sorry about that.  I'm sure you could download his references, too.

It's because "life goes on long after the thrill of living is gone."

This is not really a biological answer, but a psychological one:
One important fact to consider is that the perception of time is essentially a recollection of past experience, rather than perception of the present.
Researchers who study autobiographical memory have suggested that part of this effect may be explained by the number of recallable memories during a particular time period. During one's adolescence, one typically has a large number of salient memories, due to the distinctness of events. People often make new friends, move frequently, attend different schools, and have several jobs. As each of these memories is unique, recollection of these (many) memories gives the impression that the time span was large.
In contrast, older adults have fewer unique experiences. They tend to work a single job, and live in a single place, and have set routines which they may follow for years. For this reason, memories are less distinct, and are often blurred together or consolidated. Upon recollection, it seems like time went by quickly because we can't remember what actually happened.
In other words, it can be considered a special case of the availability heuristic: people judge a time span to be longer in which there are more salient/unique events.
Incidentally, (and to at least mention biology), episodic memory has been shown to be neurally distinct from semantic memory in the brain. In particular, a double dissociation has been shown for amnesics who suffer from semantic or episodic memory, but not both.
My apologies for the lack of citations, but a good bit about autobiographical memories can be found in:

Eysenck, M.W., & Keane, M.T. (2010). Cognitive Psychology: A
  Student's Handbook.

You may also be interested in some responses or references to a related question on the Cognitive Science StackExchange:
Perception of time as a function of age

One more thing to note is, when you are 10 years old, the past year represents 1/10th of your lifetime. When you are 80, the past year is only worth 1/80th of your lifetime.

There may be some clues in neurobiology.
A possibility may be that a person's general emotional state may affect their perception of the passage of time, as argued in this article and references within.
Studies of people with damage to their orbitofrontal cortex (prefrontal cortex region) can experience sustained altered emotional states when compared to control samples.
These altered emotional states seemed to affect how they perceived future scenarios (specifically in a simulated gambling context) and the general passage of time compared to controls.
In particular, emotions such as fear and anxiety tended to "speed up" the passage of time whereas positivity and excitement (particularly with regards to future events) lead to a subjective slowing down of time.
Si it may be just that, as kids, we are just more "excited" in general which made for all those seemingly infinite long summers.
Another possibility is that perhaps it is related to the aging process? As we live longer, I can imagine a scenario where our perception of time would alter (slow down?). It would be interesting to study the perception of the passage of time between long-lived and shorter lived populations in this context.

Maybe the passage of time is perceived as a function of heart rate.
Waiting 5 minutes for a turn on the swings is 300 seconds for a 2 year old and 300 seconds for a 40 year old.  But that same wait is 575 heart beats for the kid, but only 300 heart beats for the adult.

An intriguing thought, because this correlation exists also for adults, although typically when your heart rate rises, there's a lot of things happening in a short time span, so therefore you have a higher awareness of the individual moment.

OTOH this would mean that endurance athletes would perceive their lives as very short :D

Not necessarily. Although endurance athletes would have raised heartbeats during exercise, they would have, in general, lower than the mean resting heartrates.

Perception of time can change drastically during an emergency.
When we are younger, much like during an emergency, the brain hasn't activated very many filters for sensory data.  The young have much to learn about the world and more detail is needed for the brain to make appropriate decisions.  Sensory information is recorded in great detail, making time seem to relatively crawl.
As we age, the brain learns to filter out more and more of what it considers inconsequential data.
A good example of these filters at work is the morning commute.  If the same route is driven at roughly the same time every workday, the brain begins to leave out much of the repetitive events and scenery from it's historical record of time.  Given enough repetition, the record of the event will include so little detail in memory as to almost seem not to have occurred at all.  A 30 minute commute will be perceived to have taken very little time -- if it's remembered at all.
As Ferris Bueller so aptly put it, "Life moves pretty fast... You don't stop and look around once in a while, you could miss it."

interesting way of putting it - I think this is very similar to Jeff's answer actually; it is all about how familiar you are with a situation

First:
As a child, it could be that the brain is not encoded with a lot of experience. Thus, processing of new information is less complex, and conclusions are made much faster. These conclusions are then encoded into the brain, making future experiences more complex.
A child may have concluded everything it is able to conclude within the first few seconds of arriving at that bus stop.
Second:
A brain with a lot of previous experiences, is able to occupy itself with "trivialities", such as watching snow flakes fall from the sky or thinking about what to have for dinner. Visualizing different tastes and smells.
A grown individual might be slower to conclude, taking more factors into account. It may also have more to ponder on.
Third:
The brain is thinking all the time. It is unconsciously cross referencing every sound, smell and other sense with previous experiences and actually quite busy. If there is a limit to the amount of energy that goes into the brain for processing stuff, a larger and larger percentage of those electrons will be busy "retriggering" signals. Almost like a city road map. It will take a short time for a number of cars to travel every possible route in a small city, than in a big city. Possibly, this has to happen in the brain as well, to refresh old memories.


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Does bioluminescence occur in humans too?
I read that Japanese researchers have developed very sensitive camera that recorded bioluminescence in humans; is it possible and if so what is the mechanism behind it?

I assume blackbody radiation doesn't count?

We have more bacterial cells than eukaryotic cells in our bodies, so maybe some of them are bioluminescent?

From the article you linked:

virtually all living organisms emit extremely weak light, spontaneously without external photoexcitation. This biophoton emission is categorized in different phenomena of light emission from bioluminescence, and is believed to be a by-product of biochemical reactions in which excited molecules are produced from bioenergetic processes that involves active oxygen species

They reference these two works. The first is a 1988 review from Popp et al. (1988):
Biophoton emission - Experientia 44:543–600. (sorry, I cannot find the link to a full text...)
Fritz-Albert Popp is the biophysicist who first developed the biophoton theory.
The second work they reference is by the same first author:
In vivo imaging of spontaneous ultraweak photon emission from a rat's brain correlated with cerebral energy metabolism and oxidative stress. - Kobayashi M, et al.
Finally, a search in Pubmed reveals various other articles by different authors studying different species.

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Could an organism theoretically produce a metamaterial-like structure?
I'm curious to know if this is physically feasible because during my reading up on synthetic biology and just general research i realise that life is capable of producing some exquisitely complex materials and biological structures and wondered if they could potentially recreate artficial materials that aren't found in nature well not yet anyway. Could such a structure evolve naturally or would it have to be designed or directed via synthetic biology techniques?
Thank you for your time.

Could you clarify what you mean by 'artficial materials that aren't found in nature'?  Are you talking about chemical production bacteria such as biofuels, or some animal that builds an item such as bone replacements out of coral?

Hi, im talking about materials that have so far only been produced in labs or manufactured using technology and have not to our knowledge been produced or grown by any living thing. I only wanted to know if life could create such complex structured materials.

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Why doesn't a substance like loperamide promote analgesia?
Loperamide is frequently used to slow gastrointestinal motility.  It is available over the counter (in the US, I don't know about elsewhere) without any regulations whatsoever, yet it's derived from an opiate.  Knowing that the opiates slow the intestinal motility, it makes sense that it shares the same side effect.
What doesn't make sense to me is why it doesn't share the same primary effect of analgesia?  Clearly it binds to opiate receptors in the gut, but are they the same subtype as those in the CNS?  Or is it that the structure of the drug is such that hardly any crosses the blood brain barrier?

This is more of a chemical question I think, but the gist of it is that, unlike its predecessors difenoxin (Motofen) and diphenoxylate (Lomotil), it was specifically designed by Dr. Paul Janssen and other researchers at Janssen Pharmaceutica to have limited bioavailability from the gut (it is easily first-pass metabolized through cytochromes), as well as being too lipophilic to be dissolved in water and thus administered intravenously (and thus, junkies hoping to get a "hit" from loperamide through injections will be sorely disappointed), while still retaining its ability as a μ-opioid receptor agonist to the receptors in the myenteric plexus (resulting in the slowing of peristalsis). (Difenoxin/diphenoxylate in fact is administered with small doses of atropine to discourage abuse.)
In addition, efflux mediated by P-glycoprotein in the blood-brain barrier helps retard the entry of loperamide into the CNS. The concomitant administration of a P-gp inhibitor like quinidine (a stereoisomer of quinine used as an antiarrythmic) with loperamide, however, will cause respiratory depression and other CNS effects that are characteristic of μ-opioid receptor agonists.


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Can a color-deficient person be made to visualize the missing colors?
Hope this is within the scope of this site.
Color-deficient persons lack the cells in their retina needed for differentiating some (or all) colors.
However, the part of the brain that actually processes images is not deficient.
Is it possible to somehow make a color-deficient person "see" the missing colors by directly activating that part of the brain responsible for processing colors?

@RoryM I would use "vision" instead of "sight" here? Do you agree?

@AlexanderGalkin Yes that would be more accurate.  As that tag also fits the other question I'll re-tag that too so that the tag persists after a month =)

It is a very interesting question and I did some efforts to investigate the literature on this topic, but yet I don't have a definitive answer for you. But let's start from the beginning.
First of all, the reason for color deficiency can be not only lack (rare) or impairment (more often) of certain types of color-perceiving cells (cones) in retina, but also brain injures: the central color blindness can develop after head trauma or as a result of some neurodegenerative deceases, like Parkinson's decease. In case of brain origin of the color blindness it is usually the complete color blindness (no color is percieved), whereas congenical primary color blindness (receptor-based) is usually just the unability to distinguish one or two colors, whereas the rest can be more or less separated.
I searched Pubmed for the literature on the topic and found a recent PNAS paper about the simulation of primary and secondary visual cortex on humans using intracranial electrodes. As they describe their results (bold font by me):

When percepts were elicited from late areas, subjects reported that
  they were simple shapes and colors....

But the paper investigated only healthy humans, no color impaired subjects were used for the tests, so cannot conclude from here whether we can elicit the perception of the color the person is incapable to see with the eyes using these stimulations.
I took this paper as the starting point and did some reference research, looking for the paper referenced there and for newer publications referencing this one: PNAS is one of the top journals in this area with very high impact factor and if there were a publication about brain stimulation and color blindness I would have definitely identified it.
During my investigations I came accross a series of interesting articles devoted to "cortical visual neuroprosthesis for the blind" (read this paper<1> from 2005 for review on this topic), but this is the treatment of conventional blindness, not the color blindness. There was no intersection in keywords or titles for color blindness and brain stimulation, both in the referenced articles and in the complete article database.
So, I would suggest that you address some talented experimentalist with your question and maybe one day, who knows, we will read your name under the Nature article dedicated to the novel way to cure color blindness.

<1> -- unfortunately not available publicly for free, I am sorry.

"no color is percieved" This is achromatopsia.

Yes!  And no.  But first, some background.
Your central nervous system has (or is believed to have, as do other primates) a number of different organizational structures.  Cells within a column (the cortex is composed of about 7 layers, and a column would be a vertical group of neurons from these layers) respond to stimuli with similar features.  There are also higher order structures of collections of columns, such as orientation pinwheels(1)
Note that in the above picture, color is used to indicate orientation and not what color the column responds to.  Color sensitivity itself is (as far as I'm up to date on things) simply known to occur in color opponency columns, see this paper by T'So(2) where for instance red and green color opponent columns would be found together more often than not.
The key point to take away from that is that your cortex has to develop these columns.  Without them you wouldn't have normal color vision, even if you circumvented the retina and LGN entirely.
That brings us to the "Yes!" part of my answer.  If you've got a person that lost their color vision late in life, they should have relatively developed color columns in their visual cortex and assuming that we could wire to those areas in a meaningful way, in sufficient resolution, and could manipulate their voltages in a directed manner (we can't) then they certainly should be able to see in color with direct cortical stimulation.
However if someone was born without color vision, I do not believe this would be possible.  Not without more work than simply sending a signal in, since there is strong evidence(3) that development of the columnar organization of V1 requires visual input during later stages of development.  I have read some cases where they took people with very simple retinal diseases (photoreceptor loss) and attempted to restore their vision.  There was an extremely strong positive correlation between how old the patient was when they lost vision and the degree to which any sight could be restored.
References:

 Ohki K, Chung S, Kara P, Hübener M, Bonhoeffer T, Reid RC. 2006. Highly ordered arrangement of single neurons in orientation pinwheels. Nature 442: 925–8.
 Ts’o DY, Gilbert CD. 1988. The organization of chromatic and spatial interactions in the primate striate cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 8: 1712–27. [pdf]
 Swindale NV. 1981. Absence of ocular dominance patches in dark-reared cats. Nature 290: 332–333.


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What is the smallest number of amino acids required for life?
Is there any hypothesis on the minimum number of amino acids required for life?

One could argue that the answer is zero as long as you define a virus as a living thing, even if it uses (living) amino acids to reproduce it's not needed for survival. If you even talk about survival in viruses... This is however more of a philosophical sidenote...

You can divide the 22 (including selenocysteine and pyrrolysine)  proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique features like cysteine which can form disulfide bonds.
Some amino acids are very similar, for example isoleucine and leucine, it is plausible that one of those would suffice to create most protein folds.
There are several examples of proteins designed with a smaller alphabet of amino acids, one example is the E. coli orotate phosphoribosyltransferase (Akanuma et al., 2002). The simplified enzyme consists of only 13 different amino acids and 88% of it are composed of only nine different amino acids. Even after those drastic changes the enzyme still folds correctly and has enzymatic activity.
There is one study (Fan and Wang, 2003) that tried to answer exactly the question you asked. They came to the conclusion that around 10 amino acids are necessary to create properly folding proteins:

First, we study the minimum sequence complexity that can reserve the
  necessary structural information for detection of distantly related
  homologues. Second, we compare the ability of designing foldable model
  sequences over a wide range of reduced amino acid alphabets, which ﬁnd
  the minimum number of letters that have the similar design ability as
  20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different
  approaches give a remarkably consistent view, that the minimum number
  of letters required to fold a protein is around ten.

Akanuma, S., Kigawa, T. & Yokoyama, S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proceedings of the National Academy of Sciences 99, 13549 -13553 (2002).
Fan, K. & Wang, W. What is the minimum number of letters required to fold a protein? J. Mol. Biol. 328, 921-926 (2003).

Thanks for pointing this study out, though don't you think it would be suprising if every codon for isoleucine in a bacterium were substituted for leucine that the bacteria lived?  Not sure it would make it as there are often single cases where an otherwise innocuous particular amino acid was important.

If you allow for the "RNA world" hypothesis, then the minimum number of amino acids needed for life would be zero, because RNA in that context would be self-replicating and would not need proteins (or their amino acids).
Since this question was asked in 2012, with respect to modern life on Earth circa 2019, Craig Venter's lab put out a 2016 paper in Science about their engineered organism called JCVI-syn3.0.
This organism is engineered to contain the simplest, smallest set of genes required to sustain life, i.e., metabolism, reproduction, etc.
The latest version of its genome is 531 kb long and is made up of 432 protein-coding genes. In the Supplementary Materials of that paper, there is a file called Database S1, an Excel spreadsheet. The authors state that this spreadsheet contains the amino acid sequence of proteins coded for by genes in JCVI-syn3.0.
When we take this column and filter out non-protein-coding or untranslated genes, we get a listing of sequences, like so:
MSFNKLNQTYLDWINHPNLDQELKELLNKADDNELNAAFNLELKFGTAGIRGILGAGPGRFNVYTIKKVTIAYAKLLQTKYSNDLNKGVVIGHDNRHNSKKFAKLVADILTSFNIKAYLFKNNDLQPTPVVSFATKALNCIGGIVITASHNPAEYNGYKIYDPYGCQLMPHDTDVIANYMNEITNILDWTFISNNNLLEIVDQTVIDKYFEMIKNLEFYKDQDKSNLKIIYSAVNGTGSLYTPIVLKQSGYEVIEVKEHAFEDETFKNVINPNPEFDPAWKIPLEYAKKYDADIIILNDPDADRFGMAIKHNNEFIRLNGNQTGAILIDWKLSNLKRLNKLPKNPALYSSFVTSDLGDRIASETYNANVVKTLTGFKWMGQEMLKEPLNGLNFVFAYEESYGYVIDDSTRDKDGIQASIIAAEACWYYKNQNMTLVDYLNQLYEKYGYYYTTTYNLNFKPEEKDSKIAPIMKLLRTTGIKQINNLKVVKIEDYINGLYNMPSEDLLKIYLEDKSWIAIRPSGTEPKLKIYFVIVDSSLQKAENKAEKIYTELKTILNI
MFKVKFADIGEGLTEGTVAEVLVKVGDVVKEGQSLYFVETDKVNSEIPAPVAGKIAVINIKAGQEIKVGDVVMEIDEGSGASVASEPKAEAKQEAKVEVVEENASVVGATPVSNDLIVRKQASTVTKSSTIKATPLARKVAADLNIDLSLVTPTGPNQRILVADIKNYHSSSAQPASQPAPTPTLVASQPAPAPTPAITPAIKVVEPSAPLSWDEVPMNGVRKATVKAMTKSHTEIAAFTGMKNTDITETHKMRTELKDHAAASGIKLTYLAFIIKAVAKSLRDMPNINVRGDFANNKIQFMHNINIGIAVDTPNGLMVPVIKGADHLSVFEIAIKISELANKAKDGKLTRAEMTEATFTVSNFGSVGLDYATPIINSPESAILGVGTMSQTPLYINGELQKRFIMPLSMTCDHRIIDGADAGRFLIKVQDYLSKPVLLFM
MQIPIIKPKKAPPLTIEEINEIKQHSSYEKSYLKTFNKYKKKVEHRIYFKTSFWWDIFIIALAALANTITTDYFILATGDTGLFPGGTATIARFLSIVLNKHITSISTSSSFFIFLFIVNLPFFVFGFIKVGIKFTLTSLLYILLSIGWNQIITRLPIINPNEWSLIINYKLISSLPTEWSSKLWLFVFSIFGGFFLGITYSLTYRVGSSTAGTDFISAYVSKKYNKQIGSINMKINFTLLLIFVVLNTVIMPIYKIDSTAKLSVLNTLTDEQFTEIYNKAKDSGKFILDFNSHHHFYLPSNWSVSDQQIWTRQQIAQIIASNTNFTNYDNLTTIIKLKFVFGPSLFASFICFVIQGVVIDRIYPKNKLFTVLISTTKPREVKNYLFESGYRNNIHFLENQTAKKENGYIAQSVIMIHIGLMNWKPLQAGANNIDPDMMISFIRTKQVKGPWSYSLDTQKRELSLYKKVITDRRLMARIEKESILLTKQKITNDKKLKSKSKTF
...

This text can be processed with a simple Python script to count the number of unique residues, e.g.:
#!/usr/bin/env python

import sys
import re

with open(sys.argv[1], 'r') as f: a = f.read()
b = re.sub('[\n-]', '', a) # strip out newlines and indels
len(list(set(b))) # count the number of unique codes

This answer suggests a minimally-viable organism codes for proteins that, altogether, use 20 amino acids.
I did not create a frequency table to see what is most commonly used, or what is least used, and what might be hypothetical targets for substitution with other amino acids. But that might be an avenue for further exploration.
In the future, Venter or other labs may find that there are ways to engineer an organism to use fewer genes, or protein-coding genes that use fewer amino acids or which use synthetic amino acids that have redundant chemical features that could allow it to substitute multiple residues, while preserving the protein's function.

The RNA world hypothesis does not preclude a peptide world preceeding it — only that DNA came later and that RNA had catalytic properties. Ventner's experiments do not relate to evolution, where it is difficult to envisage all amino acids emerging at once. It is more likely that certain simple amino acids were generated in the primaeval soup and formed peptides before the more sophisticated RNA bases emerged. The peptide backbone has the ability to bind certain metal ions, especially the Fe-S complexes involved in ancient redox reactions.

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Why 20 amino acids instead of 64?
This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 20 amino acids (or 22 if you include selenocysteine and pyrrolysine), so many of the amino acids are coded by multiple codons.
Is there any hypothesis as to why there are only 22 amino acids and not 64? Is it possible that there were 64 (or at least more than 22) at an earlier time?

It seems more likely that once there were fewer than 16 amino acids and codons were 2 nucleotides.  In earliest form, codons may have been 1-to-1 with nucleotides, with three or four amino acids used.  The redundancy in the present code may simply have remained in place after the extension of 2-nucleotide codons into 3-nucleotide codons.

@mgkrebbs Do you have any reference for that idea? It seems exceedingly unlikely to me. From tRNA to the ribosome, every part of protein translation seems to be adapted to triple nucleotide codons.

@MadScientist, No, this was pure speculation on my part.  Indeed present mechanisms are highly oriented to triple nucleotide codons.   Smaller codons would only have occurred back in the RNA world, before DNA was used.  The pattern of redundancy in the code is compatible with the 2-nucleotide idea, but could also be explained in other ways, such as selective pressure for synonymous translations of single-base mutations.

A quick look for literature doesn't show much, but this review paper shows that the idea of two-nucleotide codons is not unknown: "It is usually assumed that the primitive genetic code was simpler (for instance with a two-nucleotide codon and less amino acids) and expanded in the course of evolution."

Well, a few microbes can do selenocysteine and pyrrolysine apart from the twenty usual amino acids, and they respectively use what are usually the "opal" and "amber" stop codons for these...

I think the first question you should ask is: "Why 20? Why not 2?". From my point of view nature evolves from a very simple solution to more special solutions. So 20 is just a snapshot of evolution and we are about to see even more (if we just life long enough).

@J.M. selenocysteine is in no way restricted to microbes. In fact, all animals except a few insects encode selenocysteine.

Remember also that there are plenty of non-proteinogenic amino acids, such as hydroxyproline, which are nevertheless found in proteins despite not being encoded in the genetic code.

@MadScientist: Certain functions require every single one of these 20 amino acids. However, in isolated cases a selected subset of amino acids might very well lead to an active protein.

well you need at least one STOP codon so at max you could have 63.

Brian Hayes wrote a very interesting article from a mathematical point of view:
http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code
especially the "Reality intrudes" section. Basically people had created fancy mathematical reasons why it has to be exactly 20. Nature, being nature, does not follow the reasoning, but has its own ideas. In other words there was nothing especially special about 20. In fact there seems to be a slow grafting of a 21st amino acid, selenocysteine using the codon UGA. Also pyrrolysine is considered the 22nd. The last section suggests that the code was originally doublet, so coded for <16 amino acids. This can partly explain why the third base in each codon is not as discriminating.
So perhaps in the year 2002012 someone will be asking on biology.stackexchange why there are only 40 amino acids.

There is no evidence of selenocysteine being "grafted" in. Much the opposite actually, it has even been suggested that "UGA was originally a codon for Sec in the
anaerobic world, perhaps two to three billion years ago, and after introduction of oxygen
into biosphere this highly oxidizable amino acid could be maintained only in anaerobic
organisms or in aerobic systems which evolved special protective mechanisms". If anything it is cysteine that has been taking over.

@John Smith The link is down. I have found another link: http://bit-player.org/wp-content/extras/bph-publications/AmSci-1998-01-Hayes-genetic-code.pdf.

The first position of the anti-codon, the "Wobble" position, forms hydrogen bonds less well than do the second two.  This means that the last position of the codon has less coding potential than the first two.  The reason is that the anticodon is at the bottom of the anticodon loop of the tRNA, and so there backbone of the tRNA is bending back to pair with itself.  The nucleotides do not hold their bases flat and regular in relation to each other.
Here is a picture of the anticodon loop.  In this case 5'-CAU-3' is the anticodon for 5'-AUG-3', so it would be the C, right at the sharpest part of the bend in the anticodon loop, that would pair poorest.
Here is an interactive model where you can spin the tRNA/mRNA around and see that not all the hydrogen bonds are equal length, nor are all the bases coplanar.

I am not convinced that is a cause, as much as a consequence of the redundancy. It could be that cells used to have a lower number of aa (<16), that could then be coded with only 2 nucleotides. As new aa entered the game, a triplet system developed, but this introduced (unharmful) redundancy in the code, which did not put any selective pressure towards having a strong bond in the 3rd position.

The first link is dead.

There are two other ideas to throw in here.
1) just to add to KAM's thoughtful answer.  There was also a thought that the last base also gives a lot of flexibility for GC content which responds to some
2) lets not forget that redundancy in the genetic code helps give some resistance to mutations which might be disruptive.  the amino acids less disruptive to a typical protein fold are more common in the code. (we have some idea of this from studying mutations of protein structures.)
3) some biochemists have proposed that there is a sense that the 20 amino acids we have are a fairly stable set - that adding other amino acids don't help create better proteins.  Peter Schultz learned some of this as his group really wanted to add extra, human synthesized amino acids into native proteins.
 I was at a talk where he noted that attempts to make cysteine with a longer side chain caused the amino acid to cyclize to form a thioolactone.
Thinking along these lines adding another CH2 group to proline might not make packing better.  There is probably some value, but just not enough to disrupt all the sensitive machinery for making and realizing the genetic code.

Maybe you mean "thiolactone", not "sulfolactone" (which is a different sort of chemical group that one can't really form with cysteine homologs). There's a mercapto group in cysteine and (possible) homologs that the carboxyl group could react with, if the amino acid isn't in zwitterionic form. With cysteine, kinetic and thermodynamic factors heavily disfavor the cyclization to a four-membered ring. The four-carbon and five-carbon analogs can respectively cyclize to five- and six-membered rings, and those are kinetically easy to make.

thanks, fixed -its been a while since i did any organic chemistry.


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Which plants live for more than one year and less than two years?
What kinds of plants live for more than one year and less than two years? Are there any categorical or taxonomical names for such plants?

Are these homework questions? If so you should be tagging it as homework.  But please keep in mind that stackexchange sites aren't here to do your homework for you.

A biennial, then?

Hi @Problemaniac - welcome to the community.  As mentioned above please use the homework tag where possible.  Also, from a formatting standpoint the Q1/2/3 isn't necessary =)  Regarding the close motion on this question, I do agree that this is perhaps too localised.

@Rory: I suggested an edit to make the question less localised and more fit for this site.

@TimN I'm limited as to how many characters I can place in the edit approve reason box - I think that it should be up to the OP to remove the examples part of the question when and if the community closes it as too localised.  Without the removal of the middle point then the edit would meet the too minor category so unfortunately I couldn't approve it - please do keep submitting edits to other questions however =)

This is not from homework actually. I've found answers (see edit).

@Problemaniac finding answers yourself is absolutely fine =D  It might be a better idea to post them as answers rather than editing them into your question though, as this may be clearer to future people who may find this question by google for example.

The plants are called Biennial plants.
Examples would be carrots or dandelions.


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What is the largest perennial herbaceous plant?
What is the largest perennial herbaceous plant? My guess would be some kind of banana or bamboo.

That would be the banana. That being said, I seem to have a hard time finding a record of where the largest banana plant was found (but lots of records for largest fruits)...

This sounds like another homework question.

Is the [tag:taxonomy] tag appropriate here?

It is not homework. Question about facts aren't necessarily homework. Please don't be biased.

The tallest banana species is Musa Ingens (15m) which grows in the forest of Papua New Guinea and Indonesia. It also claimed as the the world's largest herbaceous plant. http://www.thestatworld.com/2015/12/musa-ingens-the-tallest-banana-plant-in-world.html

As mentioned above, the largest perennial herbaceous plant is indeed the banana.  Whilst the main reference to this ("Yes, we have more bananas" - an article in the Royal Horticultural Society Journal from May 2002) has been removed from their website it would be I'm sure possible to order should you need to.
This summary of the banana mentions that the pseudo-stem of the banana plant grows to 6-7.6m in height - I haven't found anything taller when looking around so it doesn't generate any reason to doubt the removed article.
Regarding the comments on Bamboo, there are 7 genera containing bamboo species.  All of these (Arthrostylidium Rupr, Bambusa Schreb, Chusquea Kunth, Dendrocalamus Nees, Phyllostachys Siebold & Zucc., Pseudosasa Makino and Sasa Makino & Shibata) are described as having persistent woody stems so don't meet your herbaceous requirement.

So what happens with bamboo? Doesn't it grow a lot taller than 6 meters sometimes? It's also perennial and herbaceous, right?

Not all bamboo species are herbaceous, some are woody. I'll dig into the relative sizes of the two variants some more tomorrow =)

@Problemaniac I've done the research and it seems I was mistaken last night.  All genera with common name bamboo in ITIS are woody as shown in my now revised answer =)

So was it a common misunderstanding that "a bamboo forest is/can be just one big tall grass of a kind"?

It would seem to be - I would imagine that confusion stems (no pun intended) from all bamboo species being contained within the Family  Poaceae, which has a common name of 'grasses'.  However the distinction between herbaceous and woody happens lower down at Genus.

It's not a misunderstanding or confusion - all bamboos are grasses.  Grasses are defined as the graminoids, which includes Poaceae (the true grasses, including bamboo), plus the Cyperaceae (sedges) and Juncaceae (rushes). So it is perfectly accurate to call a bamboo forest a forest of tall grass.

@RoryM: the link to 'summary of the banana' is dead now.


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First discovery of long-term depression?
LTP was first described by Tim Bliss and Terje Lømo in their paper Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path.
When was LTD first described? By whom?

The process of long-term depression (LTD) was first discovered in the cerebellum by Ito et al. in 1982:
Ito M, Kano M. Long-lasting depression of parallel fiber-Purkinje cell transmission induced by conjunctive stimulation of parallel fibers and climbing fibers in the cerebellar cortex. Neurosci Lett. 1982;33(3):253-8
Ito M, Sakurai M and Tongroach P. Climbing fibre induced depression of both mossy fibre responsiveness and glutamate sensitivity of cerebellar Purkinje cells. Journal of Physiology 1982; 324: 113–134.
Check this source.


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Can elements of one's environment act directly as hormones?
Can pollution and things in an organism's environment serve as hormones?

I'll leave this as a comment, and let somebody more knowledgeable flesh this out: it's a bad idea to put ripe fruit near fresh flowers, as the ethylene emitted by the fruit can trigger the eventual wilting of the flowers.

Still another one: a number of conifers produce the substance juvabione to prevent caterpillars that are feeding on them from molting.

A hormone is defined as "a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism" (I'm just taking Wikipedia definition).
Hormones work by binding to specific receptors present on their target cells so, if there is something in the environment that mimics the hormone, by binding to the same receptor they can act as hormones: these substances are called xenohormones and can often act as endocrine disruptors compounds (EDC), by acting on various organs in the body.
Probably the most known xenohormones are xenoestrogens that are been studied as possibly harmful for human health (e.g. linked to breast cancer), and as an environmental hazards, as they can, for instance, cause reproductive problems in fish.
Xenohormones are not necessarily bad, though. Some analogs of human hormones are used in therapy, having being synthesised specifically, for instance, to have higher potency then their natural counterparts.

Sure. Here are two anecdotes on xenohormones from unlikely sources.

In the 1940s, Merino ewes imported to Australia were found to be infertile, as well as sometimes having stillbirths. A bit of detective work showed that the reproductive disorders observed were due to isoflavones like formononetin found in the clovers (Trifolium spp.) that the Merino were grazing on. Due to the insufficient amounts of needed minerals in the soil, the clover plants were producing the phytoestrogens to defend themselves (sterilize your predators, and there will be less of them eating your kind). (1)
In the late 1950s, it was observed that Indiana sows feeding on moldy corn were exhibiting symptoms including engorgement of the vulva and stimulation of the mammaries. Researchers at Purdue University found that Fusarium (Gibberella) molds in the corn were producing a mycoestrogen, zearalenone, that were triggering those symptoms in swine.
(2)

N.B. I gave natural examples simply because everybody and his dog already knows (or should already know) about phthalates and other fine industrial chemicals having endocrine-disrupting effects...

Great examples I haven't heard yet!

Yes, they can.
An example of a man-made chemical byproduct affecting hormone signaling is Bisphenol A (BPA).
There is a vast body of evidence linking BPA to all manners of hormonal misregulation.
It would be impossible to try and enumerate all of the studies, and specific mechanisms or the extent of the signaling pathways impacted by BPA have yet to be clarified, however you can have a look to the huge amount of papers on the matter that you can find on Pubmed.

Now that's concise. :)

Perhaps too concise. Can you elaborate?

answers should contain enough information to stand on their own w/o links.  Links should only be used to support the info in the answer

@KAM I think it may be time to either expand on or remove your answer :)

@KAM: there is no need to take it personally... I suggested an edit to your answer that says pretty much the same thing, but in a more self sufficient way...


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How can a monocot get so massive?
Some monocots (such as palms) are impressively thick and massive, yet botanists maintain that they don't have secondary growth. Why do botanists say this?  How can it get so big without secondary growth?

The vascular system is different in monocots and dicots. In dicots the vascular tissues are arranged in concentric circles; one of these rings is meristematic cells (undifferentiated cells that can differentiate into any cell type). This ring of meristem tissue is called the vascular cambium and is where secondary growth occurs - xylem grows inwards and phloem grows outwards.
Whereas:

Monocots have a distinctive arrangement of vascular tissue known as an
  atactostele in which the vascular tissue is scattered rather than
  arranged in concentric rings. Many monocots are herbaceous and do not
  have the ability to increase the width of a stem (secondary growth)
  via the same kind of vascular cambium found in non-monocot woody
  plants. However, some monocots do have secondary growth, and because
  it does not arise from a single vascular cambium producing xylem
  inwards and phloem outwards, it is termed "anomalous secondary
  growth". (Wikipedia)

For palms specifically:

Palm trees increase their trunk diameter due to division and
  enlargement of parenchyma cells, which is termed diffuse secondary
  growth. (Wikipedia)

Parenchyma cells are type of cells found in plant ground tissue, which makes up the bulk of plant mass.

We tend to call dicots eudicots these days.

@poshpaws who is "we"? I work in the Ag industry and I hear "dicot" thrown around more often in conversation. Maybe it matters less when you're not trying to write academic papers. :)

Sorry, yes I should have said "the preferred academic term". In the real world people still call them dicots!

@poshpaws thanks for the comment though - it gave me reason to read up on all the plant taxonomy I'd forgotten and renewed my fondness for magnolias!


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Could someone recommend a book for surveying species?
I'm trying to get/renew basic knowledge of species. Could someone recommend a book for surveying "important"/"representational" species? I am looking for a book with good illustrations and that covers most "important"/"representational" species.
I am currently reading The Tree of Life: A Phylogenetic Classification, and it is thicker than I want to read as a first book in this kind.

The book you are using is the one I was going to recommend. With perhaps 8.7 million species (http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001127), there is no short route.

If you are OK with a web solution, this answer (http://biology.stackexchange.com/a/395/107) might be useful.

Most general surveys of species I've seen (in school, for instance) tend to go through the phyla (for animals) and the divisions (for plants) and looks at the general characteristics of each group. Would that be sufficient for your needs?

Yes.  That will be sufficient for my needs.

Judging from your response to Gurav in the comments, it sounds like introductory zoology and plant biology texts would fit the bill.
For zoology, we teach from Hickman et al's Integrated Principles of Zoology. It outlines the major phyla, their defining characteristics, with plenty of specific examples scattered throughout. There are nice little problem sets throughout, and it goes into a solid amount of detail for a first or second year zoology course.
For plants, I've used Graham et al's Plant Biology, which takes a similar general approach. Though it's perhaps a bit broader, and less species-focused.
Both of these books outline the major relevant groups, and use 'representative' species to illustrate various biological points throughout. They might be a good place to start!


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What is the prehistory of amino acids in cells?
As a followup to Why 20 amino acids instead of 64? and What is the smallest number of amino acids required for life?, I am trying to understand the prehistory of amino acids in cells.
All living cells now use 20 (or 22 if you include selenocysteine and pyrrolysine) amino acids. Perhaps in the past there were fewer amino acids used in cells, especially if the theory of a 2-nucleotide codon is to be believed.
Is there any theory as to the order in which these amino acids were incorporated into cells?
This paper (by Akanuma, Kigawi, Yokoyama, "Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set", http://www.pnas.org/content/99/21/13549.full) suggest that the full complement of 20 amino acids are not strictly necessary by reducing the number of amino acids in a certain enzyme to 13, yet still retain functionality.

the quippiest answer might be ZERO since its been shown that RNA can reproduce itself, at least in theory and probably at some point in biological history as well.

If there ever was a 2 bp code - i think it would have not produced proteins as we know them - there simply isn't enough variety to make a structure as we know it.  Proteins would have done something else at that point.  Not sure what to make of the question at that point. Maybe it was all keratin...

@shigeta: check the paper I've added as a reference

Edward N. Trifonov is a professor at the Institute of evolution at University of Haifa, Israel. One of the main research topics in his group is the reconstruction of the origins of life. In one of his papers, The triplet Code From First Principles, he proposes the the chronological appearance of the 20 amino acids. There are a lot of hypothesis and testable predictions, among which is the theory of S. Miller that some biological compounds have been abiotically produced in the atmosphere. This prediction has been confirmed by imitation experiments, yielding ten different amino acids, as glycine and alanine being the prevalent ones.
The author tries to predict the chronological order in which the 20 amino acids appeared by taking into account various criteria (studies, hypothesis and viewpoints) that propose some order, as each one of them contributes to the consensus order to a certain extent. This contribution is described in the form of rank. He compiles a list of 60 rankings of 60 different criteria to derive the consensus order. Some of the criteria are:

N1’. Criteria based on various evaluations of complexity of amino-acids. N1, N34, N35,
  N37 – as in (5), and N44 (6). G, A, S, P, V, C, D, T, N, L, K, I, E, (MQ), H, R, F, Y, W
N2’. Criteria based on evolution of amino-acyl-tRNA synthetases. N2, N7 (5).
  (AG), (DFHKNPST), (CEILMQRV), (WY)
N4’. Criteria based on amino-acid compositions of various sets of presumably ancient
  proteins. N4, N26 (5), N41 (7), N45 (8), N47 (9), N48 (10), and N58 (11).

The first ten (earliest) consensus amino acids are the same as in Millers’s experiments. The amino acids appeared last have their respective codons borrowed from already existing ones. The derived consensus order is G, A, D, V, P, S, E, (L, T), R, (I, Q, N), H, K, C, F, Y, M, W.
The author also proposes a reconstruction of the chronological order in which the 64 codons had appeared.

This is an interesting paper. I've not picked through it in detail, but it seems to assume we started with the triplet code immediately and did not pass through a doublet code as other people have proposed ( http://www.imb-jena.de/~sweta/genetic_code_and_evolution/evolution.html )

Yeah, the assumption is that the earliest amino acids (ala ang gly) were encoded by triplet codons. Perhaps you can look at Trifonof's eariler literature to see whether he discusses this.


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Which patterns do I have to avoid when modifying the 3'-UTR?
I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed.
After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded

I don't understand what you're doing.  It seems like you're altering 10 pre-miRNA genes in the 3'UTR of a protein-encoding gene.  What do you mean by "which kind of newly appeared pattern I've to be careful about"?  Are you wanting to assure that regulation of the protein-encoding gene is unaffected?  Why?  Are you going to knock out the genomic locus and rescue with your viral copy?

Yes I want to assur that regulation of the protein-encoding gene is un affected. I m gonna pertub the secondary structure of all pre mirna to delete the drosha processing. After that i m gonna put the region into a lentivirus and infect cells, and then check if the mirna are no more expressed.

If your goal is to avoid regulatory elements, I would not believe any prediction program, since new regulatory elements are found every day.  The best way would be empirical and just clone and infect with a mutated 3'UTR and see if your gene's regulation is perturbed.  You could at least swap the entire 3'UTR with that from another gene to see if there are even any gene regulatory elements in the 3'UTR.


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How will rising carbon dioxide levels in the troposphere affect photosynthetic producers?
Much discussion has been had about the affects of climate change on plantlife, but how will rising carbon dioxide concentrations affect the photosynthetic process itself? Since CO₂ is a reagent in photosynthesis, would we expect higher CO₂ to mean an increased rate of photosynthesis in a real-world context? Has there been any research on this?
I am thinking more of large-scale field tests rather than lab plants.

I presume you've already seen this and this, and need a bit more?

Its a good starter, although adding co2 to a plant in a box may not be particularly illuminating. Horticulturalists have added co2 to tomatoes in greenhouses for a long time. I was thinking of something more sophisticated. I will edit my question.

There are several key ways in which rising atmospheric CO₂ concentrations will affect photosynthesis, and these are related to the different types of photosynthesis. In order to properly answer your question, I'll provide some background about photosynthesis itself.
Photosynthesis evolved in a high-CO₂ atmosphere, before the oxygen-enrichment of the atmosphere (which actually happened as a result of photosynthesis). Most plant species operate C3 photosynthesis. In these plants, carbon dioxide diffuses into the cell where it is fixed by Ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) into a 3-carbon molecule (hence C3), which is then polymerised to make sugars. A crucial fact about RuBisCO is that it has both carboxylase (carbon-fixing) activity and oxygenase (oxygen-fixing) activity. This means that oxygen and carbon dioxide compete for the active site on the enzyme complex, leading to RuBisCO being quite inefficient and slow at fixing carbon in higher oxygen concentrations. That didn't matter in the high-CO₂ atmosphere of the early Earth, but in todays atmosphere O₂ concentrations are high enough that they severely limit the productivity of C3 plants.
However, plants haven't just been growing slowly all that time - several mechanisms for increasing photosynthetic efficiency have evolved. The most influential systems involve concentrating carbon dioxide in a particular area, excluding oxygen, and concentrating RuBisCO in that same area. This avoids the oxygen competition for the active site and allows RuBisCO to operate more efficiently. The key adaptation here is C4 photosynthesis - the system which is present in most grasses and many of the most productive plants on Earth (e.g. maize, sugarcane, Miscanthus). It has evolved at least 62 times independently. It works by having RuBisCO concentrated within 'bundle sheath' cells which are surrounded by a layer of suberin wax. This layer prevents CO₂ escaping and O₂ from getting in. CO₂ from the atmosphere is then fixed in different cells - 'mesophyll cells' - by another enzyme - Phosphoenolpyruvate carboxylase (PEPC), resulting in a four-carbon molecule (hence C4). This 4-carbon acid, (malate or oxaloacetate depending on the system) is then shuttled into the bundle sheath cells. There, the CO₂ is released again by a variety of enzymes depending on the system, creating a high CO₂ concentration in the cell where RuBisCO can then work efficiently.
In general, C4 plants are much (about 50%) more efficient than their C3 counterparts, and they are particularly well adapted to high temperatures and moist environments. So, to answer your first question: as atmospheric CO2 levels continue to rise, C3 plants will gradually be able to photosynthesise more efficiently. Interestingly though, C4 plants are predicted to also benefit from increased atmospheric CO₂. If global temperatures rise as predicted, both C3 and C4 plants will be able to operate more efficiently than they currently do, up to a maximum temperature beyond which enzymes will begin to denature faster and efficiency will drop. One consideration is that the difference in efficiency between C3 and C4 systems will decrease, which may significantly alter the makeup of plant communities around the world.
This is a vast oversimplification, but it is accurate for the predicted overall effects. Localised effects (i.e. productivity changes in a particular region or for a particular crop) will depend on habitat, physiology, etc.
Some key papers to launch you into the literature:

Leakey, A.D.B., Bernacchi, C.J., Dohleman, F.G., Ort, D.R. & Long, S.P. (2004) Will photosynthesis of maize (Zea mays) in the US Corn Belt increase in future [CO2] rich atmospheres? An analysis of diurnal courses of CO2 uptake under free‐air concentration enrichment (FACE). Global Change Biology. [Online] 10 (6), 951–962. Available from: doi:10.1111/j.1529-8817.2003.00767.x [Accessed: 31 January 2012].
Morgan, J.A., LeCain, D.R., Pendall, E., Blumenthal, D.M., Kimball, B.A., Carrillo, Y., Williams, D.G., Heisler-White, J., Dijkstra, F.A. & West, M. (2011) C4 grasses prosper as carbon dioxide eliminates desiccation in warmed semi-arid grassland. Nature. [Online] 476 (7359), 202–205. Available from: doi:10.1038/nature10274 [Accessed: 31 January 2012].

Thanks for your answer @Richard Smith. Very interesting. I was also wondering whether many plants are nutrient limited or not - i.e., even though CO2 increases, their growth may be deteremined by the availability of N, P, K etc...?

@Poshpaws Good question. It's quite a fundamental one, and important, so it deserves to be posted as a separate question - I'll ask and answer it and post the link back here.

In temperate and cold climate C3 plants do better than C4, becouse they do not have to invest in additional enzymes when photorespiration effect is neglible. So temperature increase would promote C4 plants.

@MartaCz-C yes that's true, good point.

Could you also accout for cell breath in your answer? That is how oxygen deficit affects plants? Also I wonder why researches into plant survival in Martian-type atmosphere show that photosynthesis is more efficient at low pressure CO2-only atmosphere rather than at normal pressure.

@Anixx that is a separate, but related question. If you ask it as a new question I will answer to the best of my ability.

I wanted to add a little more to the excellent answer above, especially since the OP asks about research into this question in a "real-world context".
There is a substantial body of evidence on exactly this question that comes from experiments at "Free Air CO2 Enrichment" (FACE) sites. FACE is an experimental method/technology in which standing ecosystems undergo CO2 enrichment without (much) disturbance to the ecosystem. It has been known that higher CO2 increases plant growth since the 1960s or so, but the motivation for FACE was to understand what the long-term and ecosystem scale effects of rising CO2 in the atmosphere would be. Many different ecosystem types (forests, crops, shrublands, etc) have been studied with this technique to date, some for fairly long periods of time. I think that  many of these sites are now being shut down.
Some key findings:

Net primary production (Plant C assimilation - Respiration) generally increased for plant species, but increases in productivity varied a lot between ecosystem types.
This increase in productivity diminished over time, an effect that was largely mediated by changes in plant N availability.
Different plant functional types show different responses. For example, herbaceous species saw less enhancement of assimilation (due to a decrease in leaf N) compared to woody plants at some sites.
At the ecosystem level, primary production is often limited by factors other than available CO2 - nitrogen or water for example.

There are a couple of excellent reviews available:

Nowak, R. S., Ellsworth, D. S. and Smith, S. D. (2004), Functional responses of plants to elevated atmospheric CO2– do photosynthetic and productivity data from FACE experiments support early predictions?. New Phytologist, 162: 253–280. doi: 10.1111/j.1469-8137.2004.01033.x pdf
Norby, R. J. and Zak, D. R. (2011), Ecological Lessons from Free-Air CO2 Enrichment (FACE) Experiments. Annual Review of Ecology, Evolution, and Systematics, 42: 181-203. doi: 10.1146/annurev-ecolsys-102209-144647 link.

This article discusses the importance of nitrogen in limiting forest productivity under high CO2:

Norby, R.J., Warren, J. M., Iversen, C. M., Medlyn, B. E., and McMurtrie, R. E. (2010), CO2 enhancement of forest productivity constrained by limited nitrogen availability. PNAS, 107 (45) 19368-19373. doi:10.1073/pnas.1006463107 link

+1 the network of FACE sites answers this exact question comprehensively. Still, providing referenced in std format rather than links would make the answer more useful.


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Overlapping genetic information in eukaryotes
In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do remember seeing quite a bit of variation in the direction of the overlapping genes (same vs different directions), the amount of overlap, and even the number of overlapping genes.
I know enough about gene prediction to take any computational predictions with a grain of salt--even those supported by transcript and peptide alignments. However, these cases have me thinking--does overlap of genetic information really occur in eukaryotes? I seem to remember learning (or hearing anecdotally) that it can happen in prokaryotes, and that seems to be understandable given the compactness of prokaryotic genomes. But can this happen in eukaryotes? Has this been studied, and are there cases that have been confirmed experimentally?

You might be interested in the INK4A locus (chromosome 9p), encoding both p19 and p16 genes, very close to p15. You can read a description here. All three proteins are known experimentally to exist.
Now, whether these are two different genes or the same gene with alternative splicing and start sites leading to different reading frames it's up to discussion. The point is that p19 and p16 share DNA coding sequence but not protein sequence nor function.

In general, the compactnes of genomes is a characteristic of prokaryotes, but there are several eykaryotes that have overlapping genes: many parasites and endosymbionts. The best studied of these are the fungal parasites of the phylum microsporidia and the nucleomorphs (remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes).
cDNA library was constructed from the microsporidian Antonospora locustae and 1,146 cDNA clones were sequenced. Here is part of the expression profile (1):

Of the 871 clones found to encode recognizable genes, 97 transcripts (11%) from 70 distinct loci encoded sequence from more than one gene (Fig. 1 A ; see also Table 1, which is published as supporting information on the PNAS web site). The polyA sites of these clones do not correspond to polyA tracts in the genome, so they are unlikely to derive from DNA contamination (see also below), but instead come from polyA RNA. In prokaryotes, polycistronic mRNAs commonly code for multiple proteins (11), but with few exceptions (12) eukaryotic mRNAs encode a single gene. A. locustae multigene transcripts encode two or three genes or gene fragments in various orientations (Fig. 1 B–I ), but they cannot all be polycistronic messages because there is no bias for genes being on the same strand.

Here is part of a review paper on the nucleomorphs genome (2):

As in other reduced genomes, the G. theta nucleomorph genome possesses a very high A+T content (75%) and gene density is extremely high: 1 gene per 977 bp and 44 genes overlap by as many as 76 nucleotides. Williams et al. (84) showed that transcription of the G. theta nucleomorph genome is affected by this compaction, with nucleomorph-derived messenger RNAs often possessing coding sequence for more than one gene, albeit with no strand bias. It appears that during the process of genome compaction, transcription regulatory elements (e.g., promoters, terminators) have moved from the intergenic spacers into the coding regions themselves (84).

I also have to point out that there are a few examples of overlapping genes in yeast: CCT6 overlaps with YDR187C and CCT8 overlaps with YJL009W (3).

A high frequency of overlapping gene expression in compacted eukaryotic genomes
Nucleomorph Genomes, Annual Review of Genetics
The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes


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Are there any plants that fix their own nitrogen?
I know that most nitrogen is fixed through industrial processes and bacterial symbiotic relationships. However, are there any plants that can fix their own atmospheric nitrogen?

Fun Fact: 80% of the nitrogen in human tissues was fixed synthetically via the Haber-Bosch process

There soon may be: http://www.cbgp.upm.es/en/noticias/NFIX_LRubio_BMGF.html

There are no known plants that fix their own nitrogen. However, there soon may be!
Because N is the major limiting factor in agricultural productivity, there is huge interest in plant systems which can fix their own. It's important enough that the Bill & Melinda Gates foundation have started a project aimed at reducing dependence on fertilisers by giving plants the ability to fix their own nitrogen. There are several potential strategies, the most obvious being encouraging more species to form symbioses with nitrogen fixing bacteria.
However, there's another proposal which builds on recent discoveries about the mechanism of nitrogen fixing in bacteria: we now know how the crucial enzyme complex is made (Rubio & Ludden, 2008). As a result, there are many people calling for efforts to engineer the system directly into a plant organelle (e.g. Beatty & Good, 2011; Godfray et al., 2010).
So, in 10-15 years time you can check back and the answer to this question might have changed! The most likely answer then will be "just the usual suspects: rice, maize, wheat".
References:

Beatty, P.H. & Good, A.G. (2011) Future Prospects for Cereals That Fix Nitrogen. Science. [Online] 333 (6041), 416 –417. Available from: doi:10.1126/science.1209467 [Accessed: 2 February 2012].
Godfray, H.C.J., Beddington, J.R., Crute, I.R., Haddad, L., Lawrence, D., Muir, J.F., Pretty, J., Robinson, S., Thomas, S.M. & Toulmin, C. (2010) Food Security: The Challenge of Feeding 9 Billion People. Science. [Online] 327 (5967), 812 –818. Available from: doi:10.1126/science.1185383 [Accessed: 2 February 2012].
Rubio, L.M. & Ludden, P.W. (2008) Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase. Annual Review of Microbiology. [Online] 62 (1), 93–111. Available from: doi:10.1146/annurev.micro.62.081307.162737 [Accessed: 2 February 2012].

Allowing plats to fix their own N2 sounds like the most dangerous form of genetic engineering possible. There are already so many noxious weeds - once a "food" can fix its own nitrogen, it will quickly become an uncontrollable weed. Innovation is not always good.

I would be more comfortable with giving phytoplankton the ability to fix nitrogen: they might not be able to transfer their new N fixing organelles to land plants as easily, while they would increase the global fish supply- probably more than giving traditional plants N2 fixing capabilities would increase food production. Even then there would be the possibility of creating "dead" zones.

Well, by definition a food plant can't be a noxious weed, because they aren't noxious. But you raise a valid concern - mostly engineered traits such as vitamin A synthesis or herbicide tolerance are maladaptive and so they pose little risk of surviving outside deliberate cultivation for long. N fixation would be an adaptive trait in many habitats. Still, I don't think that's a reason not to do it, it's a reason to address the problem with a solution.

Right @JoeHobbit, dead zones was the first concern in my mind. The ocean would look green from space. Don't other species need the ability to fix nitrogen too?

@RichardSmith What type of solution? Nothing is 100% foolproof. Even if the nitrogen fixing plants could not reproduce, there is no way of being certain that the genes couldn't be transferred to another plant that could reproduce.

@JoeHobbit Well, it doesn't have to be 100% foolproof - that's an unrealistic goal. What matters is, do the benefits outweigh the risks, and are the risks manageable? In both cases, the answer is yes. There are various methods of preventing transgene introgression, but too much to write in a comment. Feel free to ask a new question about it and I'll answer to the best of my ability.

As far as I know, all biotic nitrogen fixation is performed by prokaryotic organisms such as Rhizobium. I don't know of any plants which can carry out this function on their own.
Plants can't use atmospheric N2 because it is held essentially inert by the nitrogen triple bond. The process of reducing N2 to NH3 which is usable by plants can be summarized:
N2 + 8e- + 8 H+ + 16 ATP -> 2 NH3 + H2 + 16 ADP + 16 Pi
(where Pi is a phosphate group)
Nitrogenase catalyses the reaction reducing N2 to NH3 by adding H+ and electrons. The whole process requires 8 ATP and is therefore energy intense.
In order to perform this coversion, bacteria require sufficent carbohydrates from decaying matter or plant vascular tissues (this is how Rhizobium derives energy from the host plant).
However, I should add that  bacteria often have a mutualistic relation with the plant to perform this function, so in this sense you could say that plants can fix their own nitrogen.
There are also "free living" ammonifying bacteria in soils.
Ref
Science and the Garden, eds. Ingram, D.S., Gregory, P.J., Blackwell,  2008

thanks biocs. I couldn't work out how to do subscripts on the ipad


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If a human takes antibiotics are all bacteria in the body killed?
From my basic understanding, antibiotics kill living things, bacteria for example.
Do the antibiotics consumed by a human-being distinguish between what they kill? Or do they just kill every bacteria they find? And if that's the case, which bacteria do antibiotics find or do they find all bacteria in a human's body? Again, if that is the case, does that mean that after taking antibiotics for a certain time that the human body is free of all bacteria?

Depends on the antibiotic and whatever's in the subject's microflora. Not even "broad-spectrum" antibiotics can kill all species of bacteria. Even in "sensitive" species, there may be a few strains that have adapted a way to resist the onslaught of an administered antibiotic. Additionally, spores of some bacteria are not exactly the kind that can be killed with antibiotics...

No
There are several reasons why this might not be true, as Alexander has discussed. An antibiotic often has a molecular target that isn't present in all bacteria, it's extremely hard to get antibiotics to certain parts of your body, and some bacteria will be defended against a antibiotic attack by biofilms, resistance mechanisms, and sheer statistical probability.
That is not to say that many don't die. Indeed, one of the major causes of Clostridium difficile infection is that antibiotics kill most of your gut bacteria, allowing the somewhat better protected C. diff to proliferate, start producing toxins, and send you to the hospital with symptoms ranging from diarrhea to perforated colon and worse. That disease is a direct consequence of "Antibiotics kill some but not all bacteria in you".

The species epiphet is difficile. :) As I alluded to in the comments, spores aren't the sort of things that are affected by antibiotics. Even if you manage to kill off vegetatives, the spores will remain, and can start turning to vegetatives again once the antibiotics wear off.

Bloody autocorrect on the new OS grumble

Just a quick answer: No, there is no way to kill all bacteria in your body once they are there. The only way to keep a person sterile is to prevent any bacteria entering the guts during and all time after the birth. Look for gnotobiology and gnotobionts to learn more about these organisms (including humans).
Here are some reasons why:

Most antibiotics have selective action on certain type of bacteria. This is due to the mechanisms involved in their action, permeability through the bacterial wall, their effective concentrations etc. Even broad-spectrum antibiotics have selective action. None is universal (and it is hardly possible to create those).
Antibiotics can't reach all the places in your body. Many bacteria either create some barrier against the immune response or the body eventually builds one. In the worst cases the whole bacterial infection is isolated and petrified (calcifications), as it is the case for tuberculosis and so-called Gohn's complex in lungs.
As long as you are not isolated from the society and secluded into a sterile box you will have a steady contact with millions of bacteria which re-invade your skin and guts. There is no way you can stop it and your gut flora will beging to restore spontaneously.

"Many bacteria ... create some barrier against the immune response..." - indeed, colonies of bacteria can form biofilms that are impervious to antibiotics.

A follow up point: bacteria actually seems to transfer from mother to baby in the womb, so even birth by cesarian in a sterile environment wouldn't produce sterile babies.  Which is a good thing, since they'd probably die without a healthy established colony.  http://www.ncbi.nlm.nih.gov/pubmed/18281199

I'd also like to add that gnotobionts are not per se germ-free. Gnotobiontic  (from the greek gignoskein, γιγνώσκω, to know) animals have a known flora. Although one could also argue that germ-free animals also have a know flora, namely none.


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What is the origin of "melting" in molecular genetics?
I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that they're referring to the separation of DNA from the double stranded form to single strands.
Maybe it's just because chemistry isn't my thing, but when I think of melting I think of a solid gaining enough energy to become a liquid. How did the term melting come to apply to DNA in this way? Does the term melting have a more general definition in terms of thermal chemistry?

What if you just consider melting where the intermolecular forces (here, base pairing) give way?

There is also the term annealing, which refers to the reverse process. Makes for a pretty good analogy with how metals are processed...

Nick T But intermolecular forces "giving way" is not melting. Melting (in physics) refers to the phase change undergone by a substance from solid to liquid.

From a statistical thermodynamics standpoint, DNA denaturation and renaturation is certainly a phase transition. The question is going from which phase to which? I would argue that the description of a rigid polymer going to a freed fluid polymer sounds like a solid to liquid transition to me.

The melting temperature (Tm) of a double stranded DNA tract is defined as the temperature at which 50% of the DNA molecules are dissociated into single strands (and 50% form duplexes). Sure, it has a different meaning than in physics... but it is a really common term in molecular biology and I doubt people will stop to use it anytime soon!
There is a vast amount of literature about the calculation of Tm, which is very important also for practical applications, such as designing PCR primers. This page has some explanations and references about the maths behind it.
I am not sure when the term first appeared, but it has clearly be used since the dawn of molecular biology.
DNA denaturation/renaturation dynamics were first studied in the '60s.
See for instance:
STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: BIOLOGICAL STUDIES - J. Marmur and D. Lane - PNAS, 1960
Although Marmur and Lane do not talk about melting temperature, we can find the term already two years later in this 1962 paper:
Effect of Concentration on the Formation of Molecular Hybrids from T4 DNA - Andrzej W. Kozinski and Michael Beer - Biophys J., 1962
Evidently the term was already common there, as they don't care to define it (it's even in the abstract).
Who first used it? I'm not sure, if anyone knows feel free to add a comment or edit the answer.

Don't get me wrong. I'm not critical of the terminology, nor do I think it's inconsistent. I'm simply interested in the origins of the terminology, and whether it's at all related to other uses of the term, such as in thermodynamics.

The original researchers working on DNA knew nothing about its structure, but I assume they noticed when you got it above a certain temperature it got much runnier, and named the process accordingly?


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Are there neurons that can sense light shining in your ears?
I know someone who bought earphones that shine light in you ears. According to what he was told, there are neurons that sense light and then make you feel wide awake when activated, which seemed like snake oil to me. Apparently the pineal gland may be able to sense light and it does secrete melatonin - a sleep regulating hormone. I'm still sceptical though as its stuck in the middle of your brain. Would shining lights in your ears be able to have any effect on how awake you feel?

This would be a great question over at Skeptics too.

Related question here but not specifially about neurons rather "extraretinal photoreception in mammals".

There is no known mechanism for light detection through the ears in humans, as far as I know. It is certainly true that the pineal gland is part of the system that regulates the circadian rhythm (briefly, the daily sleep-wake cycle). However, while the pineal gland in birds and other non-mammalian vertebrates is directly sensitive to light, the mammalian pineal gland is not (see, for review, Doyle and Menaker, 2007 and Csernus, 2006).
In all animals, the circadian rhythm is regulated by a photoperiod cue and therefore requires light detection. In mammals, the light sensors are found exclusively in the retina, the sensory portion of the eye. There are two classes of light detecting cells in the retina. First, rod and cone photoreceptors mediate vision in the usual sense of the word. These cells contain proteins called opsins that absorb photons of light and thereby excite the photoreceptors that contain them, informing the brain that light was detected.
A second class of photosenstive cells in the retina are called intrinsically photosensitive retinal ganglion cells (ipRGCs) (see Do and Yau, 2010 for review). These cells mediate "non-image-forming" vision and are an important part of the circadian rhythm pathway. They also contain an opsin called melanopsin which is a photosensitive pigment. This is not to be confused with melatonin, which is the sleep hormone released by the pineal gland. The ipRGCs in the retina send the photoperiod cue to a brain area called the suprachiasmatic nucleus (SCN). The SCN then signals to the pineal gland.
If we are generous and assume that these light-emitting headphones are the result of misunderstandings, we can guess that the confusion arises from (1) the fact that some animals have a directly photosensitive pineal gland, but not mammals and (2) that the pineal gland secretes melatonin but not the photosensitive pigment melanopsin.

Update: From a bit of research, it turns out that the company selling the headphones is not "confused" as I politely offered. I don't think this site is the appropriate forum to refute their research or claims. Suffice to say that the retina is the only part of the human brain shown to be photosensitive.

I believe there are light sensors (TRPV3) in the skin for infrared light (heat), that convey that information back to the brain from the skin.  This is kind of light detection, but it is not direct detection like the rhodopsins in the eye.
By the way, without passing information onto neurons, cells probably have a lot of sensors they may use to respond to their local environment.  This recent article talks about how olfactory receptors can be found in lung and gut cells.  so its quite possible that the conventional light detecting genes (rhodopsins) would be found in skin cells, but they may not convey information to neurons.

Can you provide a reference for a case in which a TRP channel, commonly thought of as a temperature detector, is plausibly used as a light sensor?

There has been one small study that seems to show that human skin is photosensitive.

The study I think you are referring to appeared to find that shining light on the back of the knee could entrain a human's circadian clock (Campbell and Murphy, 1998). That study has been refuted by a later study (Wright and Czeisler, 2002, see comment by Baringa, 2002). Wright and Czeisler show no response to light behind the knees. Current consensus is that mammalian photosensitivity resides only in the eyes.


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Did researchers evolve multicellular yeast or did they just turn on multicellularity?
In this new paper "Experimental evolution of multicellularity" found via Ars Technica the researchers describe having developed multicellularity and apoptosis within 60 days from a unicellular yeast species.
Is it possible that what they have done is merely turn on an ability of that species that evolved previously and just lay dormant?  Do we know that that yeast species and all its ancestors were never multicellular?  The paper doesn't even mention the possiblity of this.

Well, they put the cells in particular conditions that determined the multicellularity, so they have not specifically given the cells this ability per se. And I do not think they are claiming to have done so.

The conditions they put them under favored multicellularity, and the cells ended up being multicellular, and their abstract claims "These results show that key aspects of multicellular complexity, a subject of central importance to biology, can readily evolve from unicellular eukaryotes."

exactly my point. I don't read "we gave an unicellular organism the ability to become multicellular" in that sentence. I read "we put an unicellular organism in a situation in which it became multicellular". It's like people reprogramming stem cells to become this or that type of cell, they don't give them any ability, they just put them in the good conditions.

You're right:

Within the Fungi, simple linear multicellularity of hyphae occurs in all major clades (see below), but only Ascomycota and Basidomycota display more complex two- and three- dimensional multicellularity in the form of sexual spore- producing fruiting bodies. In both of these groups, reversals to unicellular lifeforms have occurred, for example, Saccharomyces and many other related yeasts in the Saccharomycotina (Ascomycota) or Cryptococcus albidus and related species in the hymenomycete clade of Basidiomycota (de Hoog et al. 2000, p. 130).

Medina, M., A. G. Collins, J. W. Taylor, J. W. Valentine, J. H. Lipps, L. A. Amaral Zettler and M. L. Sogin (2003). "Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa." International Journal of Astrobiology 2(3): 203-211. doi:10.1017/S1473550403001551
(PDF)
Update: The authors responded to criticism like this on The Loom, here's an excerpt:

Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it.

Just to reiterate (I am not a biologist): this means that we know of Fungi that reverted from multicellularity to unicellularity, so the same could be true of this particular yeast they used?

The fungus they used, Saccharomyces cerevisiae, is part of the fungi described above. So the part I quote actually refers to this particular yeast (Brewer's yeast).

What are the original multicellular species from which S. cerevisiae evolved? Or are you are talking about organisms which have multicellular components of their lifecycle?


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Transcription and translation of prokaryotic operons
I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control of transcription, and the focus was always on determining whether the operon was transcribed under certain conditions (mutations, nutrients, etc). I don't remember much discussion about what happens after transcription. Today, however, I noticed something I had never seen before: three of the genes in the lacZ operon are transcribed simultaneously on the same transcript--I don't know how I missed this before!
My question is what happens post-transcription. Obviously there are 3 protein products. How are these products derived from the transcript? Is the transcript broken into 3 pieces, or does a single ribosome translate all 3 proteins from a single transcript substrate, or do ribosomes translate a single protein from a single transcript substrate at a time? Where could I find the relevant literature that elucidated the translation process?

As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.
The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), giving rise to three individual proteins.

How from one mRNA three protein products are translated? The polycistronic DNA consists of a promotor (Plac), which ensures that transcription will be initiated, and three open reading frames (ORFs) for for lacZ, lacY, and lacA. Upstream of each of the ORFs, ribosome binding sites (RBSs) are located. Translation is initiated by the binding of the ribosome with both the RBS and the start codon. Thus, multiple ribosomes can bind upstream of the three ORFs and thus resulting into three proteins.
There is not very thorough literature on the translation of polycistronic RNA in prokaryotes, mainly because the condition which is necessary for translation is the RBS and there is nothing specific for polycistronic translation. A brief overview on the subject can be found in several places, as I recommend the following:

Ralston, A. (2008) Operons and prokaryotic gene regulation. Nature Education
From Genes to Genomes: Concepts and Applications of DNA Technology
Molecular cell biology
Analysis of Genes and Genomes


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Is there any advantage to one blood type over another?
All humans can be grouped into ABO and Rh+/- blood groups (at a minimum).  Is there any advantage at all to one group or the other?  This article hints that there are some pathogens that display a preference to a blood type (for example Schistosomiasis apparently being more common in people with blood group A, although it could be that more people have type A in the areas that the parasite inhabits).  Is there any literature out there to support or refute this claim or provide similar examples?
Beyond ABO-Rh, is there any advantage or disadvantage (excluding the obvious difficulties in finding a donor after accident/trauma) in the 30 other blood type suffixes recognised by the International Society of Blood Transfusions (ISBT)?
I'd imagine not (or at least very minimal) but it would be interesting to find out if anyone knows more.

Do you mean advantage in an evolutionary context?

That reminds me about the sickle-cell disease where the malformed red blood cells show much higher resistance against the malaria plasmodium.

Sickle cell is considered autosomal regressive in classical genetics, but this malarial resistance only applies to the heterozygous case (in which blood cells are also normal). The altered cell morphology occurs only in the homozygous recessive genotype.

I've been doing a little more digging myself and have found a couple of other advantages:
Risk of Venous-thromboembolism (deep vein thrombosis/pulmonary embolism (1)).  Blood group O individuals are at lower risk of the above conditions due to reduced levels of von Willebrand factor(2) and factor VIII clotting factors.
Cholera Infection Susceptibility & Severity.  Individuals with blood group O are less susceptible to some strains of cholera (O1) but are more likely to suffer severe effects from the disease if infected (3).
E. coli Infection Susceptibility & Severity. A study in Scotland indicated that those with the O blood group showed higher than expected infection rates with E. coli O157 and significantly higher fatality rates (78.5% of fatalities had blood group O).(4)
Peptic Ulcers caused by Heliobacter pylori which can also lead to gastric cancer.  Group O are again more susceptible to strains of H. pylori (5).
Whether blood group antigens are displayed on other body cells or not has been linked to increased or decreased susceptibility to many diseases, notably norrovirus and HIV.  This is fully explained in the article that I was above summarising - "The relationship between blood group and disease" in addition to extended descriptions of the other two answers.

The less antigens a woman (or in fact a female of any species close enough to humans for this phenomenon) has, the higher are the risks of triggering an immune reaction during her pregnancy, if the child has those antigens.
The Rhesus incompatibility is probably the most common case of this problem.
One could thus assume that in populations that are genetically diverse in respect to blood groups, absence of antigens has negative effects on reproduction (unless countered by medicine).

For searching purposes: the general condition in neonates (whether brought about by ABO, Rhesus, or other factors) is termed hemolytic disease of the newborn or erythroblastosis fetalis.

These two papers study whether there is a relationship between the ABO blood type of a person and his/her attractiveness to mosquitoes. It was found that people with type O blood are more likely to be bitten than people with other blood types. Additionally, the relationship between blood type and the secretion of oligosaccharides from the skin had any effect on attractiveness to mosquitoes. It was found that type O secretors are very attractive to mosquitoes compared to type O nonsecretors and type A nonsecretors.
On the flip side, type A individuals are more susceptible to infection by plasmodia (i.e., malaria).

People with blood type O are more resistant to malaria and syphilis
  than those with the A and/or B proteins.

From the Encyclopedia of Evolution, Stanley A. Rice, page 40.

Can you provide references to the original research showing that? I cannot really find any on Pubmed. What I found is that individuals of Duffy- blood group are resistent to Plasmodium vivax invasion (Langhi and Bordin, Hematology 2006), but I cannot find anything on AB0. Also see: http://www.ncbi.nlm.nih.gov/books/NBK2271/


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How do members of cryptic species know who to mate with?
According to Wikipedia:

In biology, a cryptic species complex is a group of species which
  satisfy the biological definition of species—that is, they are
  reproductively isolated from each other—but whose morphology is very
  similar (in some cases virtually identical).

How do members of these species know who to mate with?  Or would they unknowingly mate with incompatible partners?

Do cryptic species not perform courtship rituals as other species do?

Olfaction (especially pheromones) has been very important for mating partner selection for millenia of evolution: this is often the mechanism that doesn't fail and disregards the morphology, size and other secondary properties of the partner :)

This is actually quite common in plants and is known as "pollen interference": essentially, the stigma is jammed up with pollen from incompatible partners, for instance other species. I suppose this could also be a factor in animals with broadcast spawning.

As both @Rory M and @Alexander Galkin suggest, there are various non-visual mating behaviors to allow these species to select mates and also allow taxonomists and researchers to identify these species. And they hit on the two major ones, courtship rituals (mating calls, throat bulging, dancing) and pheromones.
Let's have a look at some two examples:

The widespread amazonian frog Allobates femoralis is now being approached as a species complex, with mating differences between the biologically distinct species varying from mating call note differences to cephalic amplexus (head grabbing during mate selection) and other various behavioral differences.[1]
Some crickets mate preferentially based on their species-specific song. Though, there is probably some genetic mixing with those crickets.

I think it's important to note that the species are cryptic because we as humans have decided they're hard to tell apart. Now, that similar morphology is also potentially difficult for predators to tell apart, or may be used by one or both species to parasitize on the other, it may be kept similar by sexual selection, or it may just not have great selective pressures to change. But the important part is that "cryptic species" is a box that we've created to describe traits we see.
Cryptic species as a window on diversity and conservation is a decent overview paper. (it's avaliable here if you don't have journal access)

Thanks for that; I'm happy with that.  That survey paper, in particular, is quite interesting.


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When does oxidation destroy prions?
It seems like a no-brainer than oxidation, playing the, er, role it does in the universe, would destroy prions just like it destroys everything else.
But when does it do that? I assume this has been studied, since people handle them in laboratories and may need to sterilize their instruments.

Are you asking how strong of an oxidizing agent you would need to eliminate any infectious prions?

Rust is not destroyed by oxydation :P

Just to add to my previous comment: what I meant is that "oxydation destroys everything" is a gross misunderstanding. Oxydation, just like reduction, transforms one molecule into another. Oxydising an alcohol you can get a carboxylic acid. Have you "destroyed" the alcohol? Sure, but you have also formed a carboxylic acid!

Prions are fairly resistant to traditional method of sterilization.
Citing from: Guideline for Disinfection and Sterilization of Prion-Contaminated Medical Instruments

The prions that cause CJD and other TSEs exhibit an unusual resistance to conventional chemical and physical decontamination methods. Because the CJD agent is not readily inactivated by means of conventional disinfection and sterilization procedures and because of the invariably fatal outcome of CJD, the procedures for disinfection and sterilization of the CJD prion have been both cautious and controversial for many years.

The same paper also lists several effective and ineffective methods for sterilization (efficient method have > 3log10 reduction in prion content within 1 hour)
I am not going to list them all here but you can see Table 2 in the paper.
Just to answer your specific question about oxydation, certain oxydising agents are effective, others are not. Similarly certain autoclaving (=sterilising with heat) procedures are fine and others are not.
Another interesting paper Methods to Minimize the Risks of Creutzfeldt-Jakob Disease Transmission by Surgical Procedures: Where to Set the Standard?

If you google "prion oxidation" you'll see that there has been some research into this over the last 10 years, though it seems to be a minor focus of the overall field. There seems to be some interest currently in using ozone to inactivate prions. One company that offers a ozone-based sterilizer claims to be testing for effectiveness against prions, but that is an extremely long-term process (you have to isolate prions, subject them to your sterilization process, then inject them into the brains of mice or hamsters and wait to see if disease develops).
If you're curious as to how researchers sterilize material in the lab, I may be able to shed some light on that (I worked in a prion lab in 2006-07). Generally, disposable instruments and materials are used whenever possible and incinerated after use. Glassware is submerged in acidic detergent and autoclaved for 4 hours at (I believe) 132C. As far as I know, there is still no known way to completely sterilize stainless steel instruments - this was being studied at the time in the lab where I worked. Any piece of equipment that came in contact with human or bovine prions was kept in Biosafety Level 3 facilities permanently. I'm not sure what the decontamination process was for retired equipment. Separate equipment was maintained for "non-human pathogen" prions - hamster, mouse, etc.