text:
Why does alcohol cause the hemolysis of RBC in a large proportion?
I had today an experiment that we put 95% alcohol to the blood which made it completely transparent so hemolysis must have occurred.
I started to think about the reasons.
I think that this is because alcohol dissolved the lipid membrane of cells outside of the cell.
Alcohol molecule is also very small.
I think that I can go through the bilayer too.
So I started to think that the other possible reason was that alcohol went inside the cell so caused

dissolution of the membrane from the inner side
increase in the volume of the cell so bursting

What are the main reasons why Alcohol cause hemolysis to the red blood cell?

Off hand I'd say your guess was a good one.  Most cells will fall apart when put into that much alcohol.  Note that biological standpoint, even 1% is too much alcohol for a human being to survive.

Well, it turns out the situation is more complex. I had assumed the answer was what rwst suggests or something to do with osmotic pressure. It seems that we don't really know that well.
In a paper from 1991, Chi and Wu suggest the following possible mechanisms :

Membrane fusion during the shedding of exovesicles might produce a transient decrease of the permeability barrier.
Increase of lipid dynamics by the alcohol could decrease the packing of the
bilayer. The membrane barrier behaves like a soft polymer, which can sieve solutes. The meshes in the polymer might become larger if its packing density is
reduced.
Lateral phase separation of lipids could induce packing defects in the lipid domain. This has been observed for long chain alcohols and postulated to be responsible for the increase of membrane permeability by amphiphiles.
Increase of the dielectric constant of the membrane by the alcohol would also increase the partition of hydrophilic solutes into the membranes. Such an increase has been postulated to be responsible for the increase of the permeability by aliphatic alcohols.
Modification of the intrinsic membrane domain might follow modification of the membrane skeleton by the alcohol. Accordingly, aggregation of intrinsic proteins might cause membrane modification mentioned under point 2 to 4.

The authors state that it is not possible to decide between the
various possibilities, but they seem to prefer point 5:

Although it is not possible to decide between the various
  possibilities from the present data, we showed that the
  release of membrane fragments from ethanol-treated RBC was not a
  requirement for the creation of membrane pores since it occurred at a
  time much later than the detection of K ÷ leakage. In addition, we
  found that changes of membane rheological properties preceded the
  permeability increase. These properties have been related to
  the membrane skeletal protein spectrin. Moreover, ethanol has
  been shown to affect the skeleton. The processes leading to
  the formation of pores in ethanol-treated RBC may thus relate to a
  deranged cytoskeletal network, followed by the aforementioned
  alteration of membrane properties.

The plot thickens, apparently, low concentrations of alcohol protect erythrocytes from hemolysis while higher concentrations can cause it. The following are extracts from Tyulina et al:

The seeming paradox between the direct haemolytic effect of ethanol on
  erythrocytes (Fig. 1) and the stabilizing effect of ethanol on
  erythrocytes undergoing NaOCl-induced haemolysis (Fig. 2) could be
  explained by the relatively small destabilizing effect of ethanol
  which is observed (<1% haemolysis) over 16 h. This effect would be
  negligible in the short time period (generally <10 min) assay for
  NaOCl-induced haemolysis where 100% of the cells are haemolysed. An
  alternative explanation for this paradox is that the mechanisms of
  haemolysis induced by ethanol and NaOCl are different.

It therefore appears that ethanol does not induce significant
  oxidative stress in the human erythrocyte, and these data are in
  agreement with previous studies (Seeman et al., 1971), in which it was
  found that low ethanol concentrations could protect erythrocytes
  against haemolysis. Although the mechanism for this protective effect
  is unknown, it has previously been suggested (Halliwell and
  Gutteridge, 1999) that ethanol can serve as a hydrogen donor in the
  elimination of the hydroxyl radical with formation of water and the
  2-hydroxyethyl radical.

The authors then state (emphasis mine):

In summary, we conclude that the damage to erythrocytes which occurs
  on in vitro exposure to ethanol may be caused, at least in part, by
  unmetabolized ethanol directly, rather than by the oxidation of
  ethanol to acetaldehyde or its conversion to FAEE.

I would guess this "direct effect" is something very much like what rwst suggested but the fact that the authors, who clearly work in this field, do not say so makes me think that the situation is more complex.
So, in conclusion, the exact details of alcohol's hemolytic properties don't seem to be understood in great detail. Admittedly, neither of these articles is very recent, if anyone can find a more up to date account I would love to read it.

REFERENCES:
Chi LM, Wu WG. Mechanism of hemolysis of red blood cell mediated by ethanol.
Biochim Biophys Acta. 1991 Feb 11;1062(1):46-50.
Tyulina OV, Prokopieva VD, Dodd RD, Hawkins JR, Clay SW, Wilson DO, Boldyrev
AA, Johnson P. In vitro effects of ethanol, acetaldehyde and fatty acid ethyl
esters on human erythrocytes. Alcohol Alcohol. 2002 Mar-Apr;37(2):179-86.
Trandum C, Westh P, Jørgensen K, Mouritsen OG. Association of ethanol with
lipid membranes containing cholesterol, sphingomyelin and ganglioside: a
titration calorimetry study. Biochim Biophys Acta. 1999 Aug 20;1420(1-2):179-88.

So the point 5 is about the proteins in the membrane that alcohol will modify.

Yes @Masi that is my understanding. But also a resulting perturbation of the cytoskeleton.

Ethanol, in less than 50% concentration, emulgates lipids and, through interference with hydrogen bonds, leads to conformational changes in proteins. Higher concentrations lead to denaturation of proteins and osmolysis of cells through small defects, so they finally burst, as ethanol forces a concentration equilibrium. This is why it's a good desinfection substance. But you could use any other small molecule polar solvent.
http://en.wikipedia.org/wiki/Ethanol#Antiseptic


text:
Does the Heart Require Gold?
I distinctly remember an episode of NOVA from the early 1980’s that concerned itself with gold. One of the points that was made was that there are trace amounts of gold in the human body, specifically in the heart, and without this gold our hearts wouldn't beat. I've never been able to find another citation of this. Is this true?

According to this source, gold is not a necessary trace element for living organisms.
Would have been cool, though...

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Can Naegleria fowleri enter through the eyes ( example rinsing/splashing eyes with water)
I understand that it primarily enters the body through the nose by by "feeding on the olfactory neurons in the nose" as answered here in a different question. Would the nerve cells in the eyes present a similar entryway?

@Gabriel could you perhaps opine on this?

In a 1987 article "Nonenteric Infections Acquired through Contact with Water", the author mentioned that "Infection of the ears, throat, respiratory tract, and cornea are also encountered" by virulent strains of Acanthamoeba and Naegleria fowleri. The only reference that implicates Naegleria fowleri is this one, but it doesn't mention modes of infection.
The long and the short of it is that Acanthamoeba infections can be acquired through contact with the cornea, but it's not clear whether Naegleria infections can also be acquired in this way.
n.b. The first link takes you to the JSTOR page.  In the event you do not have access, here is the PubMed page.

Is the extract you quoted specific to Naegleria fowleri or just water borne pathogens in general? Thanks for your input.

@Jarnal: I edited the post to answer your comment-question, but I am aware that this doesn't answer the original question. I cannot provide that answer; I only delved into the article posted by ohcanada.

@dd3, thanks, your input provided helpful clarification.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Scoring sequence against position weight matrix
I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability
If I have a sequence say "AAPGTGASMHSGLLW" how would I score it against the matrix? I tried taking the product of probabilities corresponding to the matrix, but I end up with a really small number
Any ideas?
Edit:
Consider the simple matrix:
    1    2   3     4
A 0.3 0.90 0.5 0.0001
B 0.2 0.05 0.4 0.2
C 0.5 0.05 0.1 0.8

The best match is, with a score of:
CAAC = 0.5 * 0.9 * 0.5 * 0.8 = 0.18

If you change the first letter to an B instead of C
you get a match, with a score of:
BAAC = 0.2 * 0.9 * 0.5 * 0.8 = 0.072

Which is a huge difference for such a small change...
This is even worse with my larger matrix since the score is easily affected by small probabilities

Maybe your sequence is a bad match?

I edited my question with an example. See above ^

The probabilities are correct. You must take the product (in log space this is equivalent to sum). The reason the probability looks small is just that you are perhaps thinking the score should be close to 1. However, this is not the case. To get a score of 1, you need the PWM to have 1/0/0/0 at all positions and get a perfect match.
So what should you compare to? What people usually do is compare this to a background distribution, the easiest being uniform, so the PWM is 0.25 everywhere. For your example, the score in this case will be 0.25^4 = ~0.004 and this is what you should expect by random.
This is why people usually look at the ratio between the score of the PWM relative to the score for the background model (and usually take the log2 of that), which in your case will be 0.18/0.004 = ~46 so the sequence you got is 46 times more than you would expect by random! And for your second example, 0.072/0.004 = ~18 times more than expected, so that is still high.
More conceptually, what you are doing is comparing two probabilistic models, your PWM and a background PWM, and comparing the probability to get your observed sequence according to each one of them. This is a common approach in general for comparing probabilistic models, even if they are more complicated.

Thank you for that detailed answer! I am trying to get scored between 0 and 1 (i.e. a probability).
I thought about taking the ratio of the score to the best match to the PWM.
I'm guessing from what you just explained, I would have to divide by 0.004 for the sequence score and the best score. So using the score from BAAC : (0.072/0.004)/(0.18/0.004)? Would this work?

Also, if I have real life background probabilities (i.e. determined from a large database) would I just take the product of everything?

@Omar regarding normalizing the score between 0 and 1, you can normalize the score in the way you suggested (note that the background model probability cancels out so you don't need it). The interpretation then will be different, as it will not tell you anything about how likely it is to find your sequence by random. So I guess it depends what you want to use the scores for. Note that as long as you divide all your sequences by a constant score, be it background or the highest probability, the ratios between the scores of different sequences will be maintained.

@Omar regarding background models, if you are not using uniform background and you are making predictions on a given organism, it would make sense to calculate the A/C/G/T percent of the whole genome, and use that as the background model, i.e. PWM with the same length as your PWM of interest, just that all positions have the same genomic probabilities.

Thanks. I am using amino acid sequences so I guess the background model would be (1/20)^15 then. I run into the problem when dividing the product of my score by the product of the best score since they are both very small numbers: for example 10^-19 / 10^-12 = 10^-7, which is indeed between 0 and 1 but it does not give me a sense of how similar it is to the best. What I am looking to score is how well some peptide matches a PWM (ranging from 0 to 1). Does this make sense? Appreciate the help

@Omar since the numbers are very small, you can work with their logs (of course then you need to change division to subtraction). Apart from that, I still don't see why you think the numbers are "don't make sense". As I explained, 10^-19 can be either high or low, depending on what you are comparing to.

Well I see how the numbers make sense now. But my problem is rather getting my numbers to a 0-1 scale so that I can apply a cutoff in mind (maybe 0.8?) to filter peptides by the ones that bind better compared to the best match. I see how 10^-19 / 10^-12 would give me a number between 0 and 1. If I log2(10^-19 / 10^-12) I would get -23. Which essentially means there is 23 times less chance of my sequence occurring compared to the best. But my problem is mapping that value back to a probability 0-1

let us continue this discussion in chat

According to [this page][1], you should take the sum and not the product:

Once a Profile has been derived from a set of functionally related
  sites, the Profile can be used to scan a query sequence for the
  presence of potential sites. Usually you run a window the length of
  the matrix along the sequence, and sum the coefficients from the
  matrix corresponding to each nucleotide in each position on the window
  sequence. Formally, the score of a matrix M for a site s of length l
  (s = s1, ... , sl, and sk being one of {A, C, G, T}) is computed as

$m_s=\sum\limits_{j=1}^lM_{s_{lj}}$
I highly recommend you read the rest of the page, the author, Roderic Guigó, is an authority on the subject.

He is assuming by Msij he means the log(frequency/background.frequency). I dont have the frequency matrix. Just the probabilities.

It shouldn't make a difference, the score for the sequence should still be the sum of the scores at each position.

@terdon actually it does make a difference, in probabilities it is a product but in log space it is mathematically equivalent to the sum...

@Bitwise, all I am saying is that the summ is still sufficient to score the match. Said sum will not, of course, be a probability but it will be maximized at the region of the highest sequence similarity. In any case, your answer is much better and you are clearly more knowledgeable on the subject than I so I won't argue the point.

@terdon not arguing, it is just important to correct so the information will be clear. Consider a PWM that in first position has A with probability 1 and second position C with probability 1. The sequence AA has a probability of zero for binding this sequence (1*0), but the sum will give you 1, which is half the maximal score and thus clearly wrong. PWM is a probabilistic model of the binding affinity so it has to be manipulated as probabilities.


text:
How to seek information on the duration of biological entrainment processes in mammals?
This is a question that is a little bit hard to define for me. I'm interested in learning more about times of "attractor/entrainment" processes that may take place in the body/brain of mammals, and particularly humans. I want to get a general idea of how long it takes for a mammal to switch into a new mode of operation, be it behavior or physiological change? Is it days, weeks or more?
For example, a polar circle animals may change the color of their fur in response to photoperiod changes. How quickly does the change get registered and take place? Is it days, weeks or months?
Another example might be a mating season of siberian hamster, where their testes weight changes in response to photoperiod duration. How long does it take for a behavior change like that to fully manifest?
I've read that it takes ~21 days for a human to create a habit or break one. Is there any biological basis for this observation?
I'm not sure how to search for information like that, as it seems to me such things might only be incidentally mentioned in scientific articles. Are there some keywords that may help me improve the search results?
Thank you for any input.

This is still somewhat ambiguous. I think you need to restrict your question to a specific process you are interested in. Learning and switching to a new state can happen on a much shorter time scale (milliseconds to minutes) in the brain.

You can narrow down your question. Just one precise question.. (You are asking 5 questions here )


text:
Does the light color spectrum and frequency matter for photosynthesis?
Do plants grow differently when given sun light, wolfram lamp, fluorescent light, LED light, infrared, ultraviolet, x-ray, unfocused laser and stroboscope?

absolutely - plants are green because they prefer light that is shorter in wavelength than green.  but like the rest of us they would die in quick order in an X-ray!  See: http://biology.stackexchange.com/questions/450/why-do-plants-have-green-leaves-and-not-red?rq=1

It matters a lot.
Take a look at this graph:

This graph is for the "normal" plants containing chlorophyll.
There're also "abnormal" :-) ones, simple water plants and cyanobacteria, that contain various phycobilins for photosynthesis instead of the chlorophyll.
If your question is practical, I'd recommend using specialy-designed fluorescent lamps called grow light.

Color of light matters. As the Answer with the graph shows, chlorophyll absorbs certain colors of light best. It is strange that it does not seem to absorb yellow light well, considering that the sun has the highest emission level there, but perhaps it was to keep the plants from roasting in excessive sun conditions.
I did an experiment in High School where I placed colored transparent gel material over otherwise identical plants. One was the control with no box over it, then there was Red, Yellow, Green and Blue. The Yellow and Green did very poorly and the plants appeared to be whitish, perhaps due to inadequate chlorophyll production? The plant under the Blue appeared normal, and the one under Red grew 'leggy' and very fast. This is a known result that plants growing under foliage tend to receive excess red relative to blue light, and it triggers rapid growth, presumably so that the part of the plant can get out from under other foliage.
In my apartment and workplace, I have north-facing windows, sometimes the shades are closed during the day, both factors simulating red-light effect, and the Wandering Jew plants that I have grow like crazy.


text:
Do antisense transcripts have different names than their sense strand transcripts?
I want to find which genes in the human genome can potentially be complementary to a transcript that could act as antisense transcript inhibtion? Are cis-NATs (naturally occuring anti-sense transcripts) considered different transcripts and named differently or do they have the same name as the sense transcript?

If the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession NR_027920 while the sense transcript of the same gene is NM_010835.
In general, each transcript that is transcribed from a given locus has a different accession. The same is true for alternatively spliced transcripts. If a given gene has 4 AS transcripts, each of these transcripts will have a different, unique accession. The human insulin receptor gene, for example, has two protein coding transcripts, each with its own accession: NM_000208 and NM_001079817.
You may be interested in a recent analysis of cis-NATs in 10 species[1] and also in NATsDB: Natural Antisense Transcripts DataBase[2].

Osato N, Suzuki Y, Ikeo K, Gojobori T. 2007. Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics, 176(2): 1299-1306, doi:10.1534/genetics.106.069484.
Li JT, Zhang Y, Kong L, Liu QR, Wei L. 2008. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, 36(15):4833-44, doi:10.1093/nar/gkn470.


text:
Why can't humans drink sea water?
Why can't humans drink sea water?
It would seem to be a huge evolutionary advantage for an animal to be able to drink sea water rather than have to rely on fresh water, and it's provably not impossible due to the existence of sea mammals that must filter the sea water somehow.
Could someone explain to me any likely reasons that this is the case?

Are you looking for the physiological reasons as to why we can't drink sea water, or are you asking why humans haven't evolved to be able to drink sea water?

For humans, our blood and other tissues have a salinity which is less than that of sea water. The osmolarity of blood is 275-299mOsm/L, while the osmolarity of seawater is ~1000 mOsm/L.
The major reason we need to drink and excrete (sweat, breath and urine) water is to rid the system of waste- i.e. water soluble chemicals or heat we do not need.  The kidneys do a lot of this work and they need a reasonable osmotic potential to help them.
The osmotic potential is the tendency of molecules, for instance salts, to diffuse from one reservoir of liquid to another.  The kidneys burn metabolic energy (food) to create a slightly higher concentration of waste chemicals into the bladder/urine.  Other organs will fail or also work to maintain a local salt concentration (e.g. any nerve cell which depends on Na+/K+ concentrations to transmit their signals.  But the kidneys are the gatekeepers of salinity in the body.  They work hardest (and can get injured) when there is more salt in the water we drink. If you drink sea water you will quickly find your kidneys overworked and not really functioning.
That's why salt water will tend to make you thirsty (if you can drink any at all). Most people will gag when they drink even a little sea water, much less a glassful.
Sea mammals actually eat their fresh water. They rely on the fluid they get from fish to keep their salt balance.  Its true that some animals like fish and molluscs etc have adapted other means of keeping their salt balance in check.  Its just also true that its a lot of work to keep this ability and when animals move away from the oceans, they quickly lose that ability.

A small addition, as I found that many people do not know this: for the same reasons, consuming too much drinking water can also be lethal for humans. This is called water intoxication or water poisoning and it is also caused by disruption of the osmotic balance (in the opposite direction).

Answers in Genesis? An odd choice of source.

I couldn't actually find a textbook that says this any more... feel free to post a different link.  I couldn't find one in a reasonable amount of time...

Edited to remove the AiG quote and replaced with more authoritative sources.

Note that eating fresh water implies that all the vast volumes of creatures living on lower levels of the food chain, those who can't just eat others, ought to have developed their own osmosis management techniques, and so they did, which means it actually is a quite generally employed approach, but, it seems, only "for the masses", not for the classy inhabitants like us, or fish... (BTW, sea cucumbers, for example, even "build" their (-> isosmotic) body of salty water, so, hey, fish, don't eat that as some beverage!)

@Sz. its true - most salt water organisms have osmotic control I think - even mammals eating salt water fish probably have adaptations for all that salt.  I don't doubt that human beings could also have those adaptations, but they just dont at this point.


text:
Has the age at which menopause occurs changed throughout history?
I was reading recently that the age of menarche has decreased in the last 150 years, and was wondering if the age of menopause in humans has also changed recently?
Would there be selective pressure for it to increase currently, given that the average age of women having their first child is increasing in the West anyway?

Quick answer: Yes, but not in the last 150 years.
There seems to be no clear link between age at menarche and age at menopause (taken from [1]):

While earlier studies were able to establish an association between
  early age of menarche and later menopause (Frisch 1978; 1987), more
  modern studies have not been able to confirm this effect (Whelan et
  al., 1990; van Noord et al., 1997).
Aristotle's assessment was similar to those of Hippocrates and also
  Roman authors, so it seems that 2000 years ago most women entered the
  menopause in their early 40s. Mediaeval authors, however, gave the 50s
  as the age when menses ceased-much closer to the timing for twentieth
  century women.

Jean Ginsburg in [2] states (emphasis mine):

In the past 100 years data from schoolchildren have shown a steady
  fall in the age at menarche in industrialised communities. Has
  there been a corresponding change in the age at the menopause?
  Unfortunately, reported surveys of the menopause have suffered from
  methodological defects. [...]
Nevertheless, those studies least subject to bias show a striking
  agreement that the median age at the menopause is currently around 50
  in Western industrialised societies. In Britain it is 50.78, in the
  United States 49.8 and in white South Africans 48.7 with little
  apparent change over the past century. In non-European women, however,
  the menopause seems to occur earlier-in South Africa and the United
  States black women have an earlier menopause than white women.

So, while early menarche is, apparently, irrelevant, age of onset of menopause has increased since antiquity but has remained relatively stable since the middle ages. Therefore, there have been no significant changes in the age of onset of menopause in the time frame you defined (150 years).
Finally, Bengtsson et al [3] state that:

Our study has, thus, not supported the view that the menopausal age is
  rapidly changing.

C. Keck, Predictive Factors to Determine Age of Onset of Menopause, PAMJ
, 3, 2005
Ginsberg J. What determines the age at the menopause? BMJ. 1991 Jun
1;302:1288-9.
Calle Bengtsson, Olof Lindquist, Lasse Redvall, Is the menopausal age rapidly changing?, Maturitas, 1(3), February 1979, Pages 159-164


text:
Has the human 7-day week had any impact on the evolution of species?
Most (if not all) industrialized countries follow a 7-day work week now, such that we are bound to follow a certain weekly trend in matters such as pollution generation, where to go (e.g. stay in town during weekdays, more likely to go to parks during weekends), what to do (mow the lawn on weekends).
Is there any evidence of any species evolving to adapt to the pace of the human 7-day week lifestyle?

I think I could sketch out some of the premises for how it could happen, but unfortunately I'm unaware of any specific research (which is how you phrased the question) so I don't dare give that answer since it's not in your question

I have no clear evidence of a specific species, but two pieces of the puzzle:

species can adapt to living in cities: birds living in cities are bolder (i.e. allow humans to come closer before flying away), and apparently even some genetic changes can be detected.
it may be possible for species to evolve a circaseptan rhythm: beach beetles may have a seven-day rhythm to accommodate for different heights of the tides (spring/neap tide). (PubMed / PDF)

Two comments: (1) The question asks about adaptation in an evolutionary perspective (which should be said is but a fraction of what is evolution (genetic drift etc. should not be forgotten!)). This implies that the there must have been a shift in the gene pool of the species that adapted.

(2) Experiments on bacteria and yeast show that you can have a clonal population adapt to a severe selection in less than 200 generations. In fact some do in as little as 30. Taken with that the 7-day work week should only have been a relevant strong selection criteria (if it at all is) for about 100 years. That means that the species most probably has to have a short generation time with a maximum less than 3 years. But that said, I agree with you that there could be either a cognitive entity that adapts or a circadian. But to prove that it is the work week and not urban society at large!

And a suggestion: The bacteria "flora" in the stomach could in some humans have adapted to the tides of carbon-source/toxin shifts with the host behaving on the work-days and getting drunk etc on the weekends.

@deinonychusaur: I would also expect epigenetics to possibly play a role there...

@nico: I agree that epigenetics could lead to quick adaptation. But rather than causing the species to evolve, I'd say it's a way for the genotype to resist environmental change so that the genotype doesn't need to change (hence no evolution). Further, I find it hard to see how epigenetics could cause rewiring of the signaling network of a cell so that a new 7-day circadian rhythm would appear. It could, maybe, silence cautiousness or so in the first scenario (but once again, this would not be explicitly a 7-day week adaptation, nor an evolutionary process).

@deinonychusaur: actually my previous comment was referring to the first point in the answer, and frankly I am not sure why I addressed it to you (it was early this morning... :P)!

@deinonychusaur: good point about the gut flora. Would be interesting to see how some of the flora adapts to a 7-day cycle of alcohol ingestion. Don't we all drink ourselves silly on Friday nights? (Half joking)


text:
What does "delineate" mean in this context?
I was reading a Scientific American story, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello), when I came across this sentence:

“The problem for scientists is that oceanic waters tend to mix, which
  makes monitoring and delineating an experiment in the ocean
  challenging.”

I'm wondering what “delineate” means in this context. I think I grasp the general idea of this sentence, but it is the exact meaning of the word that has been troubling me.
Could someone kindly enlighten me on this?
Thanks!

I think this would me more on topic at English.SE, but (from Merriam-Webster):

Delineate:
1 a : to indicate or represent by drawn or painted lines
                b : to mark the outline of
2 : to describe, portray, or set forth with accuracy or in detail   — de·lin·ea·tor  noun

In this case, it could be either meaning that is used. Either 2, as Richard Smith said in his answer, to define the experiment's parameters in general, or 1b, to mark, limit a specific area of the ocean in which the experiment will be done. Obviously, delimiting an area in a body of liquid is not very easy.

Didn't think of that!

Thanks for your help, terdon. Your explanation has given me a clearer understanding about the implication. I like 1b myself.

To delineate an experiment is to describe precisely the conditions and the states of all the parameters.
So in your sentence it probably means a scientist might struggle to keep track of all the confounding factors (changing salinity, composition, dissolved gases, particulates, pH, temp, etc.) which might affect an experiment in such a dynamic system as the ocean.


text:
What does "cellular" mean in this context?
I came across a confusing word when I was reading a Scientific American story, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello). It goes like this:

“One key to the whole experiment’s success turns out to be the
  specific diatoms involved, which use silicon to make their shells and
  tend to form long strands of cellular slime after their demise that
  falls quickly to the seafloor.”

I'm wondering what “cellular” means in this context. Does it mean “of (diatom) cells” or “porous”?
Could someone kindly enlighten me on this?

My understanding is that the slime in question is formed of the bodies (the cells) of the dead diatoms. Where does porous come into it? Is it mentioned in a previous sentence?

Diatoms are generally porous, so perhaps that's why they thought it might mean that. But I've never known 'cellular' to mean porous.

Thank you so much for your answer, terdon. My original intepretation was that too. But since diatomite is renowed for its porosity (which was not discussed in the article), I am wondering if it could mean "porous" too?

Thanks for your comment too, Richard Smith. My Collins dictionary does include "porous" as a meaning for "cellular".

@Shummy, this is getting way off topic but I imagine your dictionary had "porous" as a possible synonym of "cellular". When talking about fabrics or clothes, cellular can mean something "knitted so as to form holes" (from NOAD). Porous could be taken a synonym of cellular in that, very specific, context but is not relevant here.

Thank you all for your answers and comments. You have helped me to get a much clearer understanding.

'Cellular' in this context simply refers to slime of (diatom) cellular origin. The word 'cellular' is not referring to porosity. It appears the author wanted to be clear that the slime is from the cell, and not of some other origin. Perhaps the distinction is necessary, because the author mentions that the cells are dead, and dead cells rarely produce metabolic products, like slime.


text:
Flow cytometry issues
I'm having problems with data analysis here.
I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.

What is your fluorescent output?

The answer I have come to is the difference between FCS2.0 and FCS3.0 files. The binning pattern is different, and as such FCS2.0 files arbitrarily lowered my flow cytometry values compared to what I saw on the FACS DiVa software.
In the end, exporting with FCS3.0 was the way to go. If your software supports this, I'd highly recommend doing so!

I have this issue too with data from a Partec PAS III. I don't consider it a problem, as it's really just the x-axis which is one order of magnitude higher. At the end, all values coming from the machine are arbitrary values, so as long as the change is systematic, there's no problem.


text:
Can the RNA in the HIV virus make viral enzymes without entering the nucleus?
If the provirus was not formed yet, can the virus make viral enzymes?
(I know that it already has some, but supposing it doesn't)

"...but supposing it doesn't.."
What you mean is: it would be feasible for the virus only  to translate (in cytosol) the reverse transkriptase, then transcribe "all" from the DNA ("provirus").  And if so, would "making (any other) enzymes" from RNA, not DNA,  be contradictory to such rule? This seems a "hidden" no win question...

I am afraid your question is really not clear. You are asking one thing in the title of your question, another in the question body and a third in your comments. If you are asking (as you did in your comment above) what would happen if a virus with no enzymes were to infect a cell, see below.
In the case of HIV (and other retroviruses) some of the most important enzymes contained in a normal viral particle are:

A reverse transcriptase (RT): this enzyme reverse-transcribes the viral RNA genome to cDNA,
An integrase: incorporates the cDNA produced by the RT into the host cell's DNA.
A ribonuclease : an enzyme that can degrade (cut up) RNA. In the case of HIV this is the same protein as the RT.
A protease: an enzyme that can degrade other proteins.

Viruses work by copying their genetic material (their DNA or RNA) into the host cell's genome and then hijacking the cell's replication machinery to make more copies of the virus. So, what would happen if these enzymes were absent?

Without an integrase, the virus would not be able to insert its reverse transcribed DNA into the cell's genome.
Without an RT, the virus would not be able to copy its RNA into DNA.
The ribonuclease activity is also needed for successful reverse transcription to double stranded DNA (see [1] for a review and explanation of why.)
The protease is necessary for the formation of new viral particles. Mutations in this enzyme result in aberrantly assembled virus particles with low infectivity [2].

What you really must remember is that viruses are extremely streamlined. Everything they contain is essential. In some ways, you could say that viruses are the most highly evolved species (assuming they are living species), they are the most highly specialized "life forms" we know of and they have managed to get rid of all non-essential functions. The flip side of this is that everything that is left is essential, the virus cannot function without it.
So, to answer your question, a virus without any enzymes is, essentially, not a virus. It would not work, would not successfully infect cells.

References:

Greg L. Beilhartz and Matthias Götte, HIV-1 Ribonuclease H: Structure, Catalytic Mechanism and Inhibitors, Viruses 2010, 2:900-926
Bukrinskaya A. HIV-1 matrix protein: a mysterious regulator of the viral life cycle. Virus Res. 2007 124(1-2):1-11.


text:
Can children restore brain cells?
By "children" I mean young people at the age of 10 or lower.
I know that the adult brain cannot restore brain cells, but what about children? I mean, the brain must develop from a few cells to a 90 billion cells somehow, when do we lose this ability?
I'm also interested in cases when a child gets hit into the head (concussion). Can the damage  be fixed over time?

There is a misconception in your question about the absence of neurogenesis in adults. It is definitely present in adults as has been shown by a host of recent studies. If you want some technical details on neurogenesis or a question about what exactly changes in children at the end of critical period.

@Artem Kaznatcheev: true, however neurogenesis and regeneration are not necessarily the same thing (i.e.: neurogenesis does not imply regeneration, although the opposite is obviously true).

@nico I didn't mean to suggest that they were, otherwise I'd submit my comment as an answer. I was just going off a vibe I got from the question. I don't know anything about regeneration and so did not got beyond a comment.

@Artem Kaznatcheev: surely I was merely pointing that out in case it was not completely clear especially for the OP :)

Just a note, the definition of the word 'children' is 'pre-pubescent'. It is frequently misused to refer to adolescents and even post-adolescent young adults colloquially, but in scientific settings you should be safe using it properly.

I am not an expert in neurobiology, but this is what I have been able to find:
In general, the PNS (peripheral nervous system) does have remarkable neuroregeneration capabilities. However, the CNS (central nervous system), which includes the brain, has extremely limited neuroregeneration abilities. However, there are some interesting examples of CNS recovery:

Children under six who undergo, unfortunately, a hemiectomy, whereby one half of their brain is taken out, are able to regain almost normal function because of the brain’s ability to rewire and literally take over the functions of the missing other half of the brain.

I am guessing one thing that can explain this is that in children, the CNS is still developing, and so if there is damage, the CNS can just entirely replace damaged parts (this might be different than "fixing" which is required in adults).
Again, I am not an expert on this and would be glad to hear a neurobiologist's opinion.

Would be nice to find a proper source for the hemiectomy quote

@nico here is one relevant reference I found: http://brain.oxfordjournals.org/content/126/3/556.long

Hemispherectomy is prognosed with good outcome results in kids, but not because they re-generate all the lost neurons. The example is an interesting one, but not so relevant in the light of the question.

Speaking to Artem Kaznatcheev's comment, it is not true that the adult brain is post-mitotic.
Dr Bernard Rabin has shown is his scientific research, often in collaboration with and funded by NASA, that the adult brain is not post-mitotic, meaning that cell growth and division does occur. The primary focus of his work is to examine the relationship between high-energy irradiation of the brain (such as on a long-term space mission, say to Mars) and normal aging, and how diet can affect that age-mimicking decline. A list of papers he has published in the field of the aging brain is here.

As to your first question: Also adults can regenerate brain cells, albeit in a few restricted, specific regions of the brain. A continuous level of neural regeneration occurs throughout adult life in at least two locations. The first is the subgranular zone of the dentate gyrus of the hippocampus, the region of the brain involved in learning and memory. The other is located in and near the anterior lateral ventricular wall of the cerebral cortex. While neurogenesis in the adult hippocampus is relatively limited, the subventricular zone is thought to continuously replace interneurons in the olfactory bulb (Clarke, 2003).
As to your second question: a single blow to the head is generally considered not much of an issue. It is repeated injuries to the brain that kills neurons. For example, a knockout in boxing seems impressive and damaging to the brain, but it is in fact the repeated hits to the head, e.g. during the course of numerous bouts of boxing (or American football), that irreversibly injure the brain. A single blow will likely be dealt with by healing processes of the neural damage. Multiple blows will eventually kill neurons. As to whether those killed cells are regenerated; perhaps a few, as it is known that brain damage can result in the attraction of new cells, but it is the plasticity of the brain that will play the biggest role in the healing process, i.e., lost functions are redirected to other parts of the brain, but not regenerated.
Reference
- Clarke, Bone Marrow Transplantation (2003); 32: S13–S17

This isn't quite the same; however, children can have parts of their brains removed and then the remaining parts of the brain can take over for that removed part. There are not also lasting effects of this even.

There is a neurosurgeon by the name of Benjamin Carson who has done a procedure called a hemispherectomy. A hemispherectomy is the act of removing one side of the person's brain. This procedure can only be done in children under the age of either 10 or 12 (I am so sorry, I can't remember right now).

The reason this can only be done in children is because the side of the brain not removed is able to take over for the removed side, this cannot occur in adults.

As far as I recall, the age cut off for the procedure you're describing is closer to 1-2 than 10-12

@RoryM sorry about that. I guess I definitely didn't remember the age:)

This answer can be ascribed to neuroplasticity alone (existing cells take over other functions).


text:
Amount of neurons in the heart
Finding numbers for the amount of neurons in the brain is quite easy. Finding them for other human organs is harder. How many neurons are there in the human heart?

In terms of cell bodies? Zero.  There are autonomic projections from the spinal cord (sympathetic) and vagus nerve (parasympathetic) to the sinoatrial node, the atrioventricular node, and at discrete points in the atria and ventricles.

How can the sinoatrial node fulfill it's function if it doesn't have neurons inside itself? It creates action potentials. Isn't that what being a neuron is about?

@Christian Apologies if my answer was a bit terse.  While the tissue of the SA node is excitable (has channels, etc.) I believe it is still considered to be part of the cardiac musculature.  Some refer to the activity in heart as action potentials, but really it is the effect of passing the electrical excitation along the membrane (in the case of the heart, the musculature) rather than along an axon.


text:
What were the mammal ancestors like 65 million years ago?
What we know about our mammal ancestors that were alive (and survived) at the extinction event 65 million years ago?

Many of them looked like little rodents. However, several distinct mammalian lineages were already present, including Monotremes, marsupials and placental mammals. Throughout the whole Mesozoic era, mammals were already quite diversified! Also, even though most of the mammals that survived the K/T boundary were rather small, there were already some larger mammals around in the Cretaceous.
Here is a nice picture of a symmetrodont:

See a nice page on early mammals.

A recent genetic analysis suggests that they were probably bigger that we thought before :
http://www.newscientist.com/article/dn22343-mammals-ancestor-was-not-as-puny-as-we-thought.html

In a 2013 study, that combined genetic data and morphological data, the last common ancestor of placental mammals was estimated to be a four-legged creature likely ate insects, weighed from 6 grams (about the weight of some shrews) up to 245 grams — and was more adapted for general scampering.  Also, its cerebral cortex — the part of the brain linked to higher mental processes — was probably convoluted, folds linked with greater brain activity, http://www.livescience.com/26929-mama-first-ancestor-placental-mammals.html
The same study estimates that this ancestral creature arose some 200,000 to 400,000 years after the end of the age of dinosaurs. This is in line with what paleontology suggest... but is in contrast with other studies based purely on genetic data, which puts the last common ancestor of placental mammals 36 million year before the dinosaur extinction. (which depends on how accurate you can estimate the speed of the genetic clock which is dependent on number of generations and thus the lifespan of the animal...faster in fast breeding, short lived animal. Slower in long lived, slow breeding animals)

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


text:
Should we be looking for extra-terrestrial life on comets?
I have just read What elements are a possible basis for life? and I find myself wondering whether instead of seeking advanced life-forms at remote locales a La SETI, and perhaps fundamentally differently, we ought to be looking for similar microscopic life forms on comets that pass off-and-on.
Granted, a comet may be near absolute 0 for a lot of the time, but microscopic life-forms are known to be capable of surviving lean periods by using a cyst, for instance. As far as the rest is concerned, comets probably contain some amount of ice, and hence water, too. Similarly a comet's sprint around the sun could provide some limited amount of gravity/mass too.
So, should we be looking for life on comets?

Yes we should be and we are! Scientists have been analysing cometary material - but its a challenging task. The problem with looking at meteoritic material from comets on Earth is that it is generally contaminated with material from Earth. In addition, meteorites get physically altered during their passage through the Earth's atmosphere due to the high temperatures of re-entry.
So, the trick is to send missions to the comet. However, then the difficulty is in designing a mission that can analyse samples in situ. NASA's Stardust mission got around this by sample return to Earth. The probe visited comet Wild-2 and found the amino acid glycine among other interesting organic compounds. However, no evidence of life was found (metabolic products, organisms etc.) Further missions to comets (and asteroids) are planned, but they are not going to explicitly look for life.
Elsila, J.E., Glavin, D.P., & Dworkin, J.P. 2009, Meteoritics and Planetary Science, 44, 1323

Changed inorganic to organic, i assume that is what you meant. I apologise if it wasn't.

thanks @terdon that is what I meant! mind you, they found some very interesting inorganic compounds too ...

I imagined so, that's why I asked about the edit :).

This is a cool idea and definitely we have found a lot of the chemicals important to life are associated with comets which have a lot of water too.
Another issue besides the v. low temperatures on comets, when they warm up to the sun are not long lived so I wonder if the a shorter lifespan would be an issue when they are seen in the temperate zones of the solar system.
Still any cometary mission should try to do a biological survey when such things are more economical.  Right now even high profile missions like the current Mars missions are not spending any time looking for bacteria as we know it, but rather for other indications that life unlike our own might be there.  Its been very cautious going for xenobiologists so far.


text:
Conversion rate of topical Retinol to Retinoic Acid (Tretinoin)?
I'm wondering if someone out there has more information than me. Retinoids have well known metabolic pathways in vivo, and it's usually something like: Retinyl Palmitate --> Retinol --> Retinaldehyde (Retinal) --> Retinoic Acid (Tretinoin) which is the biologically active form of the Retinoids.
Retinoids are used in cosmetics all the time, and while Retinol is available OTC, Retinoic Acid (Tretinoin - a.k.a. "Retin-A" by brand) is available by prescription only since it is a 'stronger' version of Retinol. It's not difficult to find 1% Retinol creams or higher, but Retinoic Acid treatments top out at 0.1%.
However, I can't help but wonder 'why'? One study I was able to dig up was here: Retinoic Acid Biosynthesis and Metabolism PDF. The table on page 5 shows Physiological Concentrations - starting at 50 microM for Retinol and ending at "<50nM?" suggesting an ultimate conversion rate of a little less than 10% which would make the 1% Retinol treatments roughly equivalent to a 0.1% Retinoic Acid treatment (and a 2% Retinol treatment to a 0.2% Retinoic Acid treatment - double what's available by prescription).
Do other studies/other evidence support the rate of conversion of Retinol to Retinoic Acid to be roughly 10% or suggest than a 1% Retinol topical treatment is equivalent to a 0.1% Retinoic Acid topical treatment? Or are there some other interfering factors that reduce the utilization of Retinol to Retinoic Acid that I'm missing?

My guess is that the effect you describe is due to compartmentalisation: both retinol and retinoate are practically lipophils and so will localize in membranes and other lipid "pools", while both human retinal dehydrogenase enzymes are cytosolic. Probably the only occasion they have to get at their substrate is when it's bound to RBP. This however introduces another factor complicating the simple model.


text:
Why must the alcohol decolorizer be used for 30 seconds or less for Gram staining?
I had today a class in microbiology and my teacher said that the Decolorizer component is the critical one and cannot be more than 30 seconds.
The decolorizer has alcohol in high concentration, my lecturer says 95%.
I know that alcohol dissolves the lipid membrane, more exactly here for RBC which should be a similar situation here, not completely sure however.
What component is the critical one that you cannot keep alcohol on your bacteria samples more than 30 seconds?

My guess is that this is because of its toxicity to the bacteria.

@Bitwise: if you're doing a Gram staining you most probably don't care about killing the bacteria.

@nico I was referring to the cells losing their structural integrity (the cells obviously need to be visible).

The crystal violet stain will be removed if the decolorizer is left on too long.  I'm assuming that the crystal violet complexes that are retained in the gram positive bacteria's peptidoglycan layers end up being washed away (perhaps from overdehydrtation).


text:
Genetic engineering for insulin production
In order to put human DNA inside a bacteria in order to have it create Insulin, from what type of cell would you need to take the gene for insulin?
I thought it should be from any somatic cell, since the DNA is identical, but I'm told it should be only from the pancreas, why is that?

You may like to read this link. It provides a lay explanation for your exact question. http://www.littletree.com.au/dna.htm

You may want to take a look at the Open Insulin Project.

In short, because the easiest way to get the protein coding sequence of the gene is to create cDNA based on the mRNA, and insulin mRNA is only expressed in pancreatic cells.
Insulin gene consists of two exons. That means, amplifying the genome will not give us a coding sequence -- two pieces of that sequence will be interrupted by a large, non-coding intron.

On the figure above, you see the translated (i.e., coding a protein) sequences represented as opaque boxes. They are linked by a slightly curving thin line -- this is a fragment of sequence that will get excised during mRNA maturation.
To get the coding sequence in a straightforward manner, one can create cDNA from mRNA using a reverse transcriptase. Processed mRNA does not contain the intron. And clearly, pancreas cells express the insulin gene mRNA at very high levels, enabling such a procedure, whereas it is practically not expressed by other tissues.
EDIT: Since I see these comments upvoted, I need to debunk them here:

There are introns and splicing in both, bacteria and archea. Both type I and type II introns are present in bacteria. See this review on bacterial type II introns.
Bacteria also have post-translational modifications, including glycosylation. Once thought to be rare, there is an increasing body of evidence that it plays a much more important role than previously thought. See a paper from a decade ago here.

Just to write it explicitly: Bacteria have no splicing mechanism, so inserting the human genomic DNA into the bacteria will not result in a correct mRNA transcript.

Also, insulin is an uncommon protein in that it does not get post-translationally modified by glycosylations, phosphorylations, etc. These modification mechanisms do not exist in bacteria. This is why bacteria are used for biotech protein production.

@Bitwise: that is not true -- there are bacterial introns and bacteria have splicing -- but yes, the mechanism is different, so it would not work in a straightforward manner.

@leonardo: again, strictly speaking bacteria do have posttranslational modifications of proteins including glycosylation.

@January I stand corrected, thanks. I thought bacteria only have self-splicing introns without any splicing machinery.

@Bitwise: but you are right -- they don't have a spliceosome, but self-splicing is also a splicing mechanism.

@Bitwise, January - I stand corrected. I meant to say the modifications from eukaryotic cells is different. :)


text:
Are there any websites offering graphs for the light absorption of different enzymes?
I have found graphs for the light absorption of water, haemoglobin, lipids, melanin, etc., but I am having a hard time finding graphs about enzymes.
Are there any websites or other reference sources for this type of information?

It is not typical to investigate spectral absorption of compounds that are not useful for light absorption qualities, such as the compounds you've listed. Enzymes in particular will have less information because of the changes in binding partners our physical conformation to be enzymatically active. If you think there should be known info then I would try Google Scholar, Pubmed and a google search, in that order.
Edit:
The intended meaning of the question is related to spectroscopy and quantification of protein concentration. There are two common ways to determine protein concentration using optical methods (spectroscopy). The methods use colorimetric assays (colour intensity is proportional to protein concentration) or light absorbance at a reference wavelength. Both methods rely on light absorbance at a specific wavelength, but the former relies on an reagent that changes colour in response to protein quantity, and the latter depends on direct UV light absorbance. Here's a quick breakdown of each.
For both of these assays, to determine the quantity of a specific protein, they require a source of purified protein.
Colorimetric Assays:
These are traditional biochemical assays, of which the most widely used are the: Bradford, BCA and Lowry protein assays. These assays rely on reduction-oxidation reactions between the key assay reagent (Bradford's reagent, bicinchonic acid, or Lowry's reagent) and protein. For example, the BCA reagent is reduced in the presence of protein, causing a chelated copper ion, Cu(II), to be reduced to Cu(I), and effecting a purple colour. This purple colour intensity, which read at a specific wavelength (~520 nm) will indicate the amount of protein.
Near-UV Absorbance:
This method relies on 280 nm (near-UV) absorbance. Usually absorbance at 260 nm is also used for a correction factor. Specifically, amino acids with aromatic rings (eg, tryptophan) cause absorption at 280 nm. Peptide bonds absorb at 200 nm, and various other bonds, pH, ionic conditions, all influence and absorb at various wavelengths.
These methods cannot be used with a protein sample alone, because there are a number of conditions that can affect readings. To correct for this, a protein standard is also used. A protein standard uses a series of known concentrations of a known protein. The common protein concentrations can range from 20-2000 µg/mL; the common protein standards are bovine serum albumin, chicken ovalbumin or purified IgG. The protein standard acts as a reference for protein concentrations that are valid for that experiment, under those specific conditions. A curve is fit to the readings of the protein standard, and the sample concentrations can be read off the standard curve by using the absorbance readings.

I read that they usually use specterscopy to determine the concentration of the enzyme.
They cant do it without knowing its absorbance,right?

I think the usual lab method is measuring the enzymes' activity by supplying the substrate and measuring how much product is created in what time.

@AbdelrahmanEsmat - they don't need to know specific information about the enzyme (or any protein's) absorbance because it is inferred based on knowledge of how amino acids absorb light at specific wavelengths.

@rwst - This is true, and is only possible if an in vitro assay for enzyme activity exists. It also relies on the purified enzyme being active, which is not always the case. The question asked was more broadly stated.


text:
Are there any solitary species of ant or termite?
The social insects consist of the ants, the bees, and the termites, which live in colonies rather than living solitary.
But I've heard that there are some species of bee which are solitary and don't live in colonies.
Are there also any species anywhere of either ants or termites which are solitary?

Actually, most bees are solitary and don't live in colonies. In the UK 90% according to https://www.growwilduk.com/content/everything-you-need-know-about-solitary-bees

i.e. bumblebees and burrowing sand bees, bees that build small nests, and vespids that have gall nests.

I do not know of any solitary ants, but there are species that form very small colonies.
One such species is Jerdon's Jumping Ant (Harpegnathos saltator). They usually live in colonies smaller than 100 individuals and workers may reproduce, so the colony can survive after the queen's death.

No solitary ants have been described by scientific journals. If they had, they would be a famous exception, their ecology and survival strategy would be very interesting, to know how they rear their broods. It is mostly nectar and parasitism that makes Hymenoptera broods easy to manage alone.
velvet ants are solitary and resemble ants but they are actually wingless wasps.
Meranoplus primitive old world ants are the most likely to have solitary species, and have simpler clades, i.e. no queen, all workers may lay eggs.
Pristomyrmex punctatus also has no queen.

Carpenter ants are solitary you will see one queen in a house full of termites and other ants that live in colonies
I have spent 35 years remodeling homes infested with termites and ants the carpenter ants which are huge are never seen tohether
The queen finds termites and other smaller types of ants
She will stuff these other ants and termits into a tunnel made by the wood chewers and lay an egg and seal the tunnel
The larva hatches and eats the food left
Pupates and digs its way out of the tunnel it then either gets pregnant or looks for a mate if male
Eating the infesting ants and termites
In 35 years of remodeling and construction with many many homes torn apart i have never seen more then 1 carpenter ants at a time
There are smaller black ants people mistake for the larger cousins but ants that actually tunnel in wood are not carpenter ants
Carpenter ants invade their food's tunnels and feed them to the eggs which they abandon after sealing them into thier egg tunnels which were made by the termites or other ants
Ants are canibals by nature and eat other type of ants
Carpenter are no exception to this rule

There are no solitary termites. All the termitoides are social. You can found some clades that have small colonies like Kalotermitidae, but that is it.


text:
Reattaching body parts
Is there any living organism that has the ability to remove and reattach body parts at will?
I'm not talking about regeneration (like in starfish). Say I'm chasing prey, and I decide that my tail will be a hindrance. So I leave it behind, and reattach it after the hunt.

I've never heard of reattachment... that would be a very exotic trait :)

I dont think this would be possible from the simple idea that all cells need energy, and if there's no nutrient flow, then how would the cells inside the detached body part stay "alive".  Doctors can currently reattach body parts right now if it's within a certain amount of time, but no animal yet can just reattach at will.


text:
Why does high-voltage mostly shock a person, and even small current kill?
This may be the wrong forum to ask.
For instance several people are known to have survived a direct lightning strike; albeit the number of fatalities are probably far larger. Anyway, I found myself wondering why high-voltage may shock a person and throw them off whereas high-current even small current is, purportedly, a killer.

Related questions on Skeptics and on Physics: http://skeptics.stackexchange.com/questions/1664/it-is-not-the-voltage-that-kills-you-it-is-the-current http://physics.stackexchange.com/questions/7911/why-can-different-batteries-with-the-same-voltage-send-different-currents-throu

@nico: Thanks! An answer on the linked skeptics post links an article that answers the question

These statements are not true, simply speaking. Currents as little as few microampers can kill a person if, for example, applied directly next to the heart. A few seconds of 220V can kill a person even if the current is in miliamper range (Biksom, cited below, mentions 4s at 120mA). However, it is true that it is not the voltage alone that kills, that there are other factors (most importantly, the effective current, which, however, normally increases with voltage).
Look, Ohms law states that R = V / I (resistance equals to voltage divided by current). Given a constant resistance, a higher voltage produces also a higher current, full stop. Given a voltage of, say, 24 V, and the resistance of our bodies being 1000 - 4000 Ohm, the current will not exceed 6 - 24 mA. Note that in case of 220V this largest current would be less than ten times these values, so well below 1A! Yet, this is sufficient to kill an adult.
What's more, extremely high voltage can actually break the skin and effectively lower the skin resistance, which results in an even higher current (see formula above).
So where does this popular knowledge come from? Well, we know that things like electric sparks can have very high voltage, but are harmless. They are harmless not because the current is low, but because the duration and the total energy is low, since the total energy is given by power (in watts) times seconds, and power P = V * I (voltage times current).
Also, it comes from anecdotical evidence, since being shocked by thousands of Volts and survive can make you famous... precisely because it is extremely rare to get into contact with a high voltage line which can supply a steady flow of the current and survive.
Another reason became apparent in the comments: confusion between the factual current of the jolt one is getting and the nominal amps on the fuse. The former is given by the resistance and voltage; the higher the voltage, the higher the current. However, an 1A fuse is likely to blow quicker than a 10A fuse, thus cutting the line before the current penetrates our body to reach the heart and bring it into fibrillation.
It is a similar story with lightnings: duration is extremely short, but more importantly, in most of the cases the lightning did not run through the person who survived -- because if it did, they would be dead (also, see this fascinating bit). It either run over the skin, seeking the path of the lowest resistance, or through a material nearby.
Also, high frequency currents are less likely to penetrate the skin.
Literature links:
Biksom, "A review of hazards associated with exposure to low voltages"

Sorry I'm not sure abou this.... can you provide references? I think 220V with milliamps is not usually, or even commonly fatal.  Most of us have gotten shocks from home outlets (110V 10+ amps) and not had to go to the hospital or anything.  Do europeans die when they get home electrical shocks - their standard voltage is 220-230V?   Anecdotes aside, if i had to choose, I think there's reason to prefer a high voltage jolt with low current vs lower voltage with lots of amperes.

110V 10+ amps would have killed you on the spot. However, the point is that these 10 amps are nominal, the most current that can be provided without blowing a fuse. The real current is given by the resistance and voltage. Also, the physics is such: given that your resistance remains constant, you do not have the alternative "high volts, low amps vs low volts, high amps".

My mistake. I did indeed mean even little current fatal rather than large current fatal. Whereas several kV may even be survivable. I'll just make the correction

I come in touch with several kV every day (static electricity).

@January you said 'milliamps'.

It depends entirely where the current passes through. If the circuit is completed through your hand, you are unlikely to die no matter what the current. But it it completes across your chest, you run a much higher risk of fibrillation and heart attack.

I think the real answer here is not simply current or voltage, but rather the power and duration (energy) deposited through the body. Neither high-current nor high-voltage are necessarily fatal by themselves, just like low-voltage or low-current can be fatal. The greather the voltage and/or current, and the longer it is applied to the body, applied to sensitive areas (eg, brain, heart), the more likely it is to be fatal.


text:
What is the difference between orthologs, paralogs and homologs?
These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?

Another pet peeve: homology is qualitative, not quantitative. So saying "significant homology" or "weak homology" is just wrong.

I hope you are getting the point here - the definitions are clear, but determining whether two genes are paralogs or orthologs is in the grey area.  Adaptation can give a gene new functions and phenotypes even without duplication, so two paralogs can be as different as orthologs.

@shigeta, I'm not sure what you mean. Usually, orthologs are more similar than paralogs, exactly because functional divergence often follows duplication. Paralogous genes often have different functions and, therefore, less sequence similarity than orthologs. As for acquiring novel functions without duplication, believe me I know, I have spent the last couple of years working on moonlighting proteins :).

I'm saying that orthologs might resemble each other relatively little - their sequence can diverge to the point that they don't align or they may acquire secondary functions i addition to the original function.  Think about e coli - fly orthologs.  In the bacterial genome space this is a common issue.

Regarding the function of paralogs, it should also be mentioned that in some cases they do not diverge in function but instead retain their function but work in different conditions or as genetic backups.

In biology, definitions are only 'suggested guidelines'.  Often the organisms don't cooperate though.

Yes, biology, that wonderful land of shades of grey... @shigeta, i agree completely, its just that in your original comment, you said "two paralogs can be as different as orthologs", I guess you meant it the other way around.

First, a note on spelling. Both "ortholog" and "orthologue" are correct, one is the American and the other the British spelling. The same is true for homolog and paralog.
On to the biology. Homology is the blanket term, both ortho- and paralogs are homologs. So, when in doubt use "homologs". However:

Orthologs are homologous genes that are the result of a speciation event.
Paralogs are homologous genes that are the result of a duplication event.

The following image, adapted (slightly) from [1], illustrates the differences:

Part (a) of the diagram above shows a hypothetical evolutionary history of a gene. The ancestral genome had two copies of this gene (A and B) which were paralogs. At some point, the ancestral species split into two daughter species, each of whose genome contains two copies of the ancestral duplicated gene (A1,A2 and B1,B2).
These genes are all homologous to one another but are they paralogs or orthologs? Since the duplication event that created genes A and B occurred before the speciation event that created species 1 and 2, A genes will be paralogs of B genes and 1 genes will be orthologs of 2 genes:

A1 and B1 are paralogs
A1 and B2 are paralogs.
A2 and B1 are paralogs.
A2 and B2 are paralogs.
A1 and A2 are orthologs.
B1 and B2 are orthologs

This however, is a very simple case. What happens when a duplication occurs after a speciation event? In part (b) of the above diagram, the ancestral gene was duplicated only in species 2's lineage. Therefore, in (b):

A2 and B2 are orthologs of A1.
A2 and B2 are paralogs of each other.

A common misconception is that paralogous genes are those homologous genes that are in the same genome while orthologous genes are those that are in different genomes. As you can see in the example above, this is absolutely not true. While it can happen that way, ortho- vs paralogy depends exclusively on the evolutionary history of the genes involved. If you do not know whether a particular homology relationship is the result of a gene duplication or a speciation event, then you cannot know if it is a case of paralogy or orthology.
References

R.A. Jensen, Orthologs and paralogs - we need to get it right, Genome Biology, 2(8), 2001

Suggested reading:
I highly recommend the Jensen article referenced above. I read it when I was first starting to work on comparative  genomics and evolution and it is a wonderfully clear and succinct explanation of the terms. Some of the articles referenced therein are also worth a read:

Koonin EV: An apology for orthologs - or brave new memes. Genome Biol, 2001, 2:comment1005.1-1005.2.
Petsko GA: Homologuephobia. Genome Biol 2001, 2:comment1002.1-1002.2.
Fitch WM: Distinguishing homologous from analogous proteins. Syst Zool 1970, 19:99-113. (of historical interest, the terms were first used here)
Fitch WM: Homology a personal view on some of the problems. Trends Genet
2000, 16:227-31.

Very nice article, +1

@January, isn't it? I've been sending it to everyone who asks me the ortho vs para question for years. Thought I'd share it with y'all here :).

So given a pair of genes that have diverged by both speciation and duplication, they are orthologs or paralogs depending on which divergence event occurred first. Is that right?

now I am completely confused :)

@liyuan in that case, just use homolog and leave it at that.  Or come into [chat] and we can try and explain :)

Both orthologs and paralogs are types of homologs, that is, they denote genes that derive from the same ancestral sequence.
Orthologs are corresponding genes in different lineages and are a result of speciation, whereas paralogs result from a gene duplication. This often has important implications: while orthologs often fulfill the same role, paralogs tend to diverge in their function, so paralogy is a worse indicator of functional analogy than orthology.
This, however, is only the tip of the iceberg, since the situation can be much more complex (see, for example, the hidden paralogy problem).
There is a great article by Fitch on that subject.

Are there new ideations to address the issues Fitch had raised 20 years ago?

First, the definition: two genes are homologs if they derive from a common ancestor. Generally speaking, if two nucleotide sequences have at least 30% (or greater than 10% amino acid sequence) identity, they are likely to be from a common ancestry, however, they may not be homologous. Note the reverse does not apply: two genes can also be homologs if there is no similarity; this happens every time the drift was long enough (many genes are no longer similar---beyond random identity---after 1 billion years; only highly conserved genes keep some similarity).
In addition to the other answers another diagram and further terms:

(after W. M. Fitch, Trends in Genetics, 16, 5, May 2000, p.228)

B1 and C1 are (1:1) orthologs
B1, C2 and C3 are (1:n) orthologs
A1 and AB1 are xenologs (horiz. gene transfer)

I think (1:n) ortholog is a synonym for outparalog.
Klaus D. Grasser: Annual Plant Reviews, Regulation of Transcription in Plants (Volume 29). Wiley-Blackwell, ISBN 1-4051-4528-5, p. 37.

I am sorry but this is simply not true. >=30% nt and >=10% aa are not sufficient to demonstrate homology. For example, 2 long proteins can share a domain. They can easily have >10% aa identity and not be homologous at all. In any case, >=30% nt does not mean there is "no other possible explanation" but homology, you are forgetting convergent evolution. For a well known example, AFGP proteins from D. mawsoni and B. saida show 69% sequence identity but are not homologous.

I'm aware of convergent evolution, as well as repeating sequence parts. There is also the conservation of domains with respect to non-functional parts. That's why I wrote "in general".

Given the quality of your many other answers, I imagine you must be aware of it :). I am just saying that there is no magic sequence similarity threshold that signifies homology. I was reacting to this phrase: "there can be no other explanation than common ancestry for this fact".

I modified your answer to be less forceful in its statement that terdon took issue with. If you don't agree with it, you can reject the change.


text:
What determines the colors and patterns of a clam shell?
Earlier this week I was looking at some bivalve shells that had ornate patterns which ranged in color from a light orange-pink to a deep orange-red. Here is an image I found online that seems to be of the same type of shell:

The friend who was with me said, "I wonder where the color comes from." We were trying to look for two shells with similar colors, patterns, and approximately equal sizes, and it was hard, even though we were looking through a large collection of similar shells.
What determines this ornate pigmentation? Is it influenced by environmental factors such as the minerals in the water? Does it have anything to do with the age or health of the organism? Or is it purely genetic? Is this determined by the same basic biological principle that determines the color of human hair, or is there something different at work in shells?

http://www.conchologistsofamerica.org/articles/1997/why-do-shells-have-their-colors.html

This post is pretty well written and seems to say that the evolutionary forces that produce shell color like this is not known.  There are suggestions that the color is camoflage or the result of metabolic byproducts or that the pigments serve to strengthen the shell.  Its hard to believe some of these theories given that some shells do fine without coloring (at least that humans can see).
Structurally, shells are living things.  [They consist of many layers of thin irregular calcium carbonate hexagonal plates that make the mineral portion of the shell. The plates are held together by a protein glue and renewed by cellular action][3].  Whatever their evolutionary motivations, the colors are biomolecules which are in the biomatrix binding the plates together. This is a reason that shells that are left out to dry in the sun can become bleached and brittle.
I wish I had some better references about the shell structure, but I'm remembering a lot of this from a one afternoon book report given in a class, not from any intensive study on my part.
This has influenced some ideas about things like tank armor, by the way.  At least there is funding for biomaterials research by agencies interested in tank armor.  Lamellar armor made of segmented plates can withstand tremendous impacts at a single point like a shell being dropped from a great height by a seabird or a shell hitting a tank. Plates just a few microns wide and a fraction of a micron deep shaped like irregular hexagons are hard to make if you aren't a mollusc so far though.

We were wondering the same thing after a day at the seaside.  It's apparently pretty complicated.  Here are a couple of articles I found about it.
https://academic.oup.com/mollus/article/72/2/157/1256402
"Mollusc shells have vivid colours and intricate patterns, but the pigments are practically unknown."
"The same colour in different taxa may be due to different pigments; different colours in the same taxon are due to different pigments; different colour saturation is due to different concentration of the same pigment."
"All the... coloured parts of the shells can be satisfactorily explained as due to polyenes and aragonite. Polyenes can be pigments, coloured compounds, as found in parrots' feathers..."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930200/
"... the extraction and identification of pigments is extremely difficult. For example, in one recent study, more than 30 kg of shells of Haliotis discus hannai were required to obtain only 2.7 mg of purified pigment"
"Pheomelanins are macromolecules that contribute to the colour of human red hair, and although most commonly known in mammals and birds they have recently been identified as the screening pigment in the shell-eyes of chitons [77]. Pheomelanins may be brown, yellow or red in colour."
"There was no resolvable pattern of association between trace elements and pigmentation due to either porphyrins or eumelanin."

I would think that the minerals that are in the immediate environment have quite a bit to do with the color that is manifested in each shell.

This an opinion rather than an answer. If you want to invest time to write a proper answer (it can be rewarding!!!) please read this page https://biology.stackexchange.com/help/how-to-answer


text:
Why do drugs which are hormones have long half-life?
Hormones normally have short half-life.
How is it possible that they have long-life in drugs?

Can you give a specific example? Water soluble hormones differ from non-soluble in their half life. Also, many drugs contain modified hormones (e.g. insuline analogs).

Peptide hormones have short half-lives because there are enzymes in blood plasma to degrade them. Half-life of any substance depends on, among other things, their route of metabolism and delivery.

All I can say with the limited question is that steroid hormones can be very long lived - most others will degrade relatively quickly.

The question is a bit vague, but in general a drug formulation is made of the active principle plus a series of other non-active compounds call excipients.
Excipients have multiple roles such as:

They act as fillers to add volume to the drug. Often only very small amounts of the active compound are present in each pill/capsule/etc. and it would be complicated for the patient to handle these very small amounts.
They act as binders to keep everything together and avoid the pill to crumble.
They can modify the pharmacokinetics of the active principle by speeding up or slowing down its release.

(there are many more resons to add excipients, see the relevant Wikipedia page for a longer list)
This last point is what you are looking for. If the hormone (or any other molecule, it doesn't really matter) is complexed with excipients it will be released in the blood or metabolized slower/faster depending on the specific molecules/formulations/mode of administration.

This is a good, broad answer to the OP's question. I would add, for protein hormones at least, they tend to be secreted as autocrine/paracrine/endocrine hormones, and by definition need only carry a signal for a brief period of time before the hormone is degraded (otherwise signalling would go on for longer than is necessary). For example, insulin has a half-life of on the order of minutes.

@leonardo: that is a good point. The example of insulin is interesting as insulin has an half-life of ~5 minutes, but the commercial insulin formulations have a whole range of duration, even up to 24h. http://www.diabetesguidelines.com/health/dwk/pro/guidelines/ispad/09_02.asp

That's also true. These formulations are often modified fpo that they still activate the receptor but resist enzymatic degradation so diabetics can use less insulin, less frequently.


text:
Are there genes in humans from the common ancestor of all organisms?
How long ago can human genes be traced? Are there any genes that go back unchanged to the beginning of life on Earth? And if so, how many?

Glycolysis seems to be a core pathway of all domains of life: http://biology.stackexchange.com/questions/2934/why-is-glucose-our-primary-source-of-energy

The term to look for is 'ubiquitous' (genes/proteins). Apart from glycolysis and ribosome there is nucleotide synthesis and some (but not all) amino acid synthesis. This list is still not complete.

I very much agree with bitwise's answer. I just want to point out that even in terms of nucleotide sequence there are some extremely conserved genes.
The most highly conserved are ribosomal RNA genes. The image below shows the conservation of 16S rRNAs from archaea, bacteria, and eukaryotes (eukaryotes do not have 16S in their cellular genome but the gene is present in the DNA of mitochondria and chloroplasts). Residues in red are conserved across all domains of life (image source):

A very nice study from 2008 [1] identified tRNA genes as the next most conserved and ABC transporter nucleotide binding domains (NBDs) after that. The alignment below (taken from the paper) shows the conservation of NBDs from various species. Note that they include eukaryotes, archaea and bacteria:
[2]

If you look at orthologous genes in general, without specifying a specific level of sequence identity, then you can find various genes (notably those coding for the enzymes of the glycolysis pathway as mentioned in the comments) that are conserved across most, if not all, cellular life.
So, to answer your question probably yes. At least, there are genes in humans today that can be found in all or almost all other life forms. Whether there were present in LUCA we cannot know for sure, it does seem likely however given how widespread they are today.
Reference

Isenbarger T.A. et al, The most conserved genome segments for life detection on Earth and other planets, Orig Life Evol Biosph. 2008 Dec;38(6):517-33.

Depends on what you mean by unchanged. If you mean a gene that maintained the same nucleotide sequence, then the answer is no.
If you meant a gene that descends from a very ancient gene, i.e. one can find orthologs in very distant species, then the answer is yes. Many of the basic molecular systems are relatively conserved, including several metabolic paths and information processing machinery. This homology is one of the strongest molecular supports for evolution and also one of the reasons that genetic engineering works so nicely.

One thing still missing from the other answers: How many genes? One answer: about 6400, i.e. ~30% of all human genes can be traced back to LUCA.
To come up with this number, I used the eggNOG database of orthologous groups. This database contains clusters of proteins that are probably homologous. So I checked how many human genes are in clusters that also contain bacterial genes. These are 6416 human genes, belonging to 1320 clusters.
Caveats: In some cases, the genes are too diverged and so their homology is missed. It is also possible that a protein evolved in bacteria after LUCA and then got transferred to eukaryotes, and vice versa.


text:
What is the known maximum ranging distance of a bat's sonar?
Bats are known to navigate by using echo-location.
How far away can a bat detect an object by its sonar?

This paper finds some species can detect as far as 67 meters, but the range varies between species.
Note that the bats can actively change their range of detection and trade off range for resolution (low range with high speed resolution for hunting in closed, cluttered spaces or high range with low speed resolution for hunting in open spaces), as explained in Wikipedia's article on Animal echolocation.
Cool stuff.

Are you sure they can switch between CF and FM calls? It was my understanding that CM bats are different species than FM bats.

@terdon the wikipedia article link which I gave says so. In fact it says that both can be combined in a call.

Sorry but I'm intrigued :). I cannot find any reference to a bat switching between CF and FM in the wikipedia article, in fact it refers to either CF or FM bats. There do seem to be some bats that use both but they don't  switch from one to the other either, rather their call has a CF and an FM portion. See here.

@terdon you are probably regarding changing between CF/FM, I am not expert on the terminology. However, in my answer I was referring to what they mention in the article as the "Pulse interval". The article says that bats can change the pulse interval and thus determine the maximum range they can detect objects.

Ah OK, I see now, thanks. Cool stuff indeed :).


text:
Were there lifeforms before LUCA?
This question got me thinking about something. LUCA is the last universal common ancestor of all current living organisms, which is a very different definition from the first-ever living organism. Is there any evidence that LUCA had evolved and diverged from a now-extinct, more primitive lifeform?
To rephrase, is there any evidence to suggest that at some point, the first-ever living organism(s) had diverged into two phylogenetic groups, one being now-extinct and the other describing all current life?

It is logically possible, however there is no hard evidence for it, and parsimony suggests against it.

@Galen I disagree that parsimony suggests against it. "Parsimony" isn't about having fewer things, it's about having fewer independent assumptions about how the world works. And life through evolution shows constant branching and extinction. Assuming this happened after but not before the LUCA isn't parsimonious. (though it would depend on where the LUCA is in the history of life and evolution to be fair)

@RozennKeribin I think you may be using a different usage of "parsimony" than I was. In evaluating trees via parsimony (in the context of evo-biol), we count the number of evolutionary steps required for each tree, and select the set of trees (ideally there is only one) requiring the minimum count of such steps. Adding branches at the root of the tree (before LUCA) will mean more evolutionary steps, ergo its smaller counterpart will be selected preferentially in this process. I like your usage of 'parsimony', but it may require demarcation when discussing the topic of evolution.

@RozennKeribin ... and it would have been helpful for me to demarcate the usage I was using. It is a recommendable practice in general. Although not the exact same type of example as what we're considering above, here is a pedagogical example of parsimony (in evol-biol) being used. http://evolution.berkeley.edu/evolibrary/article/phylogenetics_08

@Galen that's fair, I know phylogenetics has its own use of the concept of parsimony. That said I think it's used in cases where you're building a phylogenetic tree based on actual data, traits or entities we're trying to order. I don't think this is really what the [original] question was about; the question seemed to be about whether pre-LUCA side branches could/would have existed. I think one can give an answer without satisfying the much stricter standard of building a phylogenetic tree with such branches (which requires knowing what the side branches were like)

@RozennKeribin Agreed, it requires data to build trees with parsimony, and I find data to be an agreeable requirement for assessing evolutionary relationships. The original question is asking for if evidence exists for pre-LUCA branches, and to my knowledge there is no substantial evidence of this. Our models of descent with modification expect there to be such branches, but I think it is arguable whether to call that 'evidence'.

@Galen Absolutely, as far as the post's main question goes on whether there's evidence I think your original comment was 100% correct. I was just reacting to the last clause, which I felt made an additional claim and that's the one I disagreed with. (I'm mostly making this comment so the record shows I do agree we have no evidence of LUCA cousins, in case this long conversation made it look like we disagreed more than we do)

Well, what you seem to be suggesting is "Did life evolve twice on Earth?"
Your original question has an answer: Probably yes. It's not unlikely to think that the original cell evolved into two different paths and then one went extinct. However, that doesn't address LUCA. If we found fossil evidence of what we thought was LUCA, and then fossil evidence that LUCA had a genetic cousin - all that would do is push the application of the term "LUCA" on more evolutionary step backwards until both shared a common ancestor which would then be called LUCA. You can do this indefinitely until all life originates from a single cell, with countless offshoots which have gone extinct.
If you mean was there a whole other type of life - one that did not originate from LUCA and existed - then the best answer we have right now is "No." All life we know of, no matter how different and old, is still based on RNA/DNA and proteins. Fossil evidence supports this premise until about 3.5 BYA.
If there was an 'alternate' construction of life, we have not found the fossil evidence for it, and might not know what it was if we did. If the alternate form didn't utilize cells, we might not be aware we had it. If it did, but utilized different metabolisms or structures for proteins and storage - that evidence would be long gone by now.
Our best bet for answering if life can evolve differently than what we have today is out among the stars.

I actually wasn't referring to "a whole other type of life" as you describe, or if abiogenesis had happened twice on earth, but the first paragraph (not counting the first sentence) is exactly what I was looking for, and now seems all-too-obvious in retrospect. As you suggest, if we knew of evidence which described this early now-extinct lifeform, we would have to revise our definition of LUCA. Thanks for the epiphany!

I'd like a reference to rna world 3.5 years ago.  what is the evidence like?

@shigeta - RNA acts as both storage of genetic information, and can fold into proteins/enzymes (Ribosomes utilize rRNA, for instance). DNA has never been observed to naturally act as an enzyme, indicating a specialized role (and it is orders of magnitude more stable than RNA). So RNA is thought to occupy the area between Proteins and DNA, and since proteins have not been observed storing genetic information, RNA is hypothesized to be the first form of genetic storage, enabling Evolution via Natural Selection.

I'm aware of the RNAWorld hypothesis and so forth - but what is the "Fossil Evidence" you refer to in your answer?

@shigeta - www.paleosoc.org/Oldest_Fossil.pdf
Cyanobacteria, which are an extant species, have been traced to about 3.5 BYA.
Recently (http://www.sciencedaily.com/releases/2011/08/110821205241.htm) some fossils were found of sulfur using bacteria with a very confident date of 3.4 BYA. The latest one is probably the most sophisticated, as it utilizes chemical analysis to look for organic components that wouldn't be found in natural mineral formations.

LUCA was the LAST universal ancestor not the first.  Naturally it competed with other extinct species.   My reseach suggests that LUCA was resulted from the fusion of 2 genomes.  The evidence for this is that on reconstructing the amino acid sequences for LUCA enzymes we find some contain no cystine but do contain tryptophan or the opposite.

Some references to support your response would be great!

Can you please add some references? Actually it is more a comment.

No. LUCA is a construct based on comparative analysis. Because LUCA is defined as the last universal common ancestor, no genetic evidence can be use to determine what's LUCA's ancestor looked like. The only way such a question can be answered is if by some luck, you found a fossil..or a time machine.
Given that horizontal gene transfer is all but certain in the time frames we are looking at, LUCA is unlikely to be a single organism. But more like a community of organisms, sharing a pool of genes. And a subset of these shared genes became the core of all descendants of that community. These shared genes is LUCA


text:
What makes an animal/species suitable for domestication/training?
Humans have domesticated all manner of creatures during the course of their civilization - dogs, horses, several types of cattle, varieties of birds, and perhaps others too.
A prerequisite for an animal to be domesticated, obviously, is that there be some return from the animal voluntarily, or otherwise. For instance, milk from cows/buffalos.
What I'm looking for is an answer to the question what ... characteristics must an animal fulfil to be domesticated/trained. Docile is, perhaps, one characterstic. Amenable to training may be another. What other characteristics must be fulfilled before one would venture to consider training/domestication of another species?

The ability of an animal to be trained or domesticated appears to be genetic. A quick Google search revealed this Review: http://rspb.royalsocietypublishing.org/content/278/1722/3161.full.pdf

In the specific case of horses:
An excellent source for research into equine domestication is "The Horse, the Wheel, and Language" by David W. Anthony.
His thesis is that horse domestication began in the Russian and Asian steppes, where they were first hunted as food, then held in herds for meat and milk, but that it was also here that they were first used for riding.
He has conducted numerous digs in the Russian and Asian steppes and also done modern day tests with various materials to determine, from teeth wear patterns, when and with what sort of bit horses were first ridden and/or harnessed.
DNA analysis has shown that it was quite possibly a single mutation in a stallion that would allow the animal to be ridden and that this gene was passed on to mares.
In addition, Anthony did tests with various materials available to people then and used them as bits on modern day horses. He would then compare the wear patterns with those found in grave sites or buried refuse piles that contained horse skulls. His findings show that these skulls indicate wear on the teeth that would match what had been caused by using leather, bone or wood bits. Some of the findings are disputed, but he's spent years adding to this research and it seems to be becoming accepted.
This may have happened around 4-5,000 BCE - moving original estimates of horse domestication back another 2,000 years from the original 4-4,500 year estimates.
The title of the book refers to the massive effect this increased mobility had on the spread of the Indo-European steppe people and hence the resulting dominance of Indo-European languages from Ireland to India.


text:
How are Genetic Circuits Modelled?
I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure 4a. How is this circuit computationally modelled? Can you refer me to any graduate level texts on the subject?

The following papers are a good starting point:

René Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, Volume 42, Issue 3, December 1973, Pages 563-585 <= A classic paper in the field.

D. Thieffry, Dynamical roles of biological regulatory circuits. Brief
Bioinform. 2007 Jul;8(4):220-5.

E. Remy, P. Ruet, From minimal signed circuits to the dynamics of Boolean
regulatory networks. Bioinformatics. 2008 Aug 15;24(16):i220-6

You can also have a look at Computational Methods in Systems Biology, International Conference CMSB 2007, Edinburgh, Scotland, September 20-21, 2007. Proceedings, specifically the chapter "Decision diagrams for the representation and analysis of logical models of genetic networks" by A. Naldi, D. Thieffry and C. Chaouiya.

Thank you for the comprehensive list of starting references.

I would also suggest Uri Alon's An Introduction to Systems Biology.
Personally, I learned using JJ Tyson's body of work and I would particullary recommend Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

Thank you for the recommendation of Tyson's papers. I find his writing style to be quite clear and descriptive.