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What is the scientific name of this tree?

The tree flowers prior to the monsoon season and sheds it's leaves in Winter and regrow them in Spring and Summer.
I have seen three different colours of the flower (growing in my neighbourhood): pink, violet and white.
Place-India, Kolkata, West Bengal. Season - Monsoon.

It is Lagerstroemia, perhaps Lagerstroemia indica, the common crape myrtle.
https://en.wikipedia.org/wiki/Lagerstroemia
Myrtle in french means blueberry: "From Medieval Latin myrtillus, diminutive of Latin myrtus (“myrtle”), from Semitic: Arabic مُرّ (murr, “bitter”), Hebrew מֹר (mor, “bitterness") ." Myrtle is an unrelated family with tough spicy seed pods which are used as a condiment including eucalyptus.
Crape, refers to the frilly flowers, from Latin Crispus, Crispy: frilly, crèpe is often used to refer to frilly fabric and it also means pancake in french, which is a chapatti with butter and milk and an egg from the bible.
Because you said it is common, I checked google images for "india frilled pink flower tree", it was about 20 images in. There should be a Hindi/Indian script of the wiki page, with the Indian derived name.

I found two of them today in south france here, where temperatures reach -15 some years: https://goo.gl/maps/xM3sFJe5bpC2


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Living on pure glycogen?
I was recently fascinated when I learned about polysaccharides (I am a biology newbie) and was wondering about some of their properties. After doing some googling I was unable to find any information regarding this scenario.
This is purely theoretical, I am not insane enough to actually try this.

If my only source of carbohydrates was ingestion of pure glycogen,
could I live healthily? (assuming I obtain all other necessities for
life)
Approximately how many grams of glycogen would I need to live for a
week (assuming I weigh 150 lbs)? Is this even possible to calculate?
What does pure glycogen taste like?

See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802397/ yes if you take glycogen alongwith proteins, fats, etc. you can survive. As for taste, I don't know how it tastes, it should be tasteless but should become sweet after some time due to action of enzymes.

If you added that as an answer, I would upvote it. It doesn't address question #2, but it is vastly better than the current lack of answers.

You asked three questions here, so I'll answer them one by one.

Yes, you can survive with glycogen as the only source of carbohydrates, assuming that you also take other nutrients like proteins, fats, vitamins, etc. also because carbohydrates cannot supplement all of them. See this article:

There are three macronutrients: carbohydrates, protein and fats. Macronutrients are essential for proper body functioning, and the body requires large amounts of them. All macronutrients must be obtained through diet; the body cannot produce macronutrients on its own.

No, there's no way to calculate this. If we were talking about glucose, a definite range could be given. But since glycogen is a polymer with variable amount of glucose molecules linked together (at least I couldn't find an exact number),  its not possible to tell how many glycogen molecules are needed for the daily metabolism in the body.

Glycogen is an organic, non-polar polymer, insoluble in water just like starch. It does not have a specific taste, but once you eat it, an enzyme called salivary amylase will break it into glucose, maltose and limit dextrins, causing it to taste a bit sweet. See this article:

This enzyme acts on starch, glycogen and related polysaccharides and oligosaccharides producing beta-maltose by an inversion.

Source

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Is fructose really a poison like alcohol?
I came across this video claiming that fructose is like a poison with detailed explanation on how it is metabolized. With a search on internet I found an article which challenges the claim and sounds convincing. In the article I also learned that the original claim was made by Dr. Robert Lustig.
Dr Lustig is a scientist and the article is not a peer reviewed scientific article. I am not an expert in the field and I am not sure which side is right.
Could you tell me which side is right?

I'm voting to close this question as off-topic because this is definitely better of Skeptics.SE

Everything is a poison with the right dosage Here is a fun chart you can use to see what I mean. Even water is poisonous if you drink enough of it.
fructose in no more poisonous than glucose. No study has shown fructose to be dangerous when eaten in normal healthy diet. It is poisonous but only in the sense that water is poisonous if you drink to much of it.
And you should reread your own source the article concludes it is NOT more poisonous than glucose. It also concluded that the paper that claimed so was erroneous because it used animals with different metabolic pathways and the differences were not significant in any case. Nor is it possible to eat a diet high in fructose without it also being high in glucose (see above study) so it would not be an issue even IF Dr. Lustig was right about the lipid metabolism.
News media loves to focus on single isolated studies with odd conclusions which is basically the worst way to represent science, wrong or erroneous things get published all the time and get quickly found out but the media tend to latch on to the former and never report the latter.
Processed sugar is bad for you for completely different reasons, basically the same reasons donuts and bacon are bad for you, they are empty calories, it is just that Americans (and a few others) eat way way more refined sugar than the other two, absurd levels of it, for comparison it is as if you were eating large amounts of bacon for every meal levels of absurd. There is also the aspect of diabetes which has to do with how much and how often we eat sugar not an issue with the sugar itself. (if we instead ate half a pound of bacon grease every day that would be the thing causing problems.)

What makes processed sugar worse than the same sugar in a fruit? It is the dose what make the poison, as you say.

It is the fact you are getting a lot of sugar and nothing else, with fruit you are getting vitamins, fiber, even small amounts of nucleic acids, proteins, and lipids that both slow down how fast you absorb it(blood sugar rises slower) and help make you feel full so you eat less. for instance you would have to eat about 3 apples to get the same sugar as an average (~300cal)candy bar or one bottle of soda  but three apple would fill you up and take longer to digest. taking longer to digest gives our insulin levels a chance to compensate for the rise in sugar and helps us eat less.

But that doesn't maker sugar per se bad, but the way of nutrition.

sugar is an essential part of nutrition you need a certain amount of sugar, you need a certain amount of lipids as well,eating bacon is not inherently unhealthy, but eating a tub of bacon grease would be bad for you. It would be impossible to eat a tub worth of grease by eating bacon you would get full first, by separating the grease it becomes much much easier to eat to much. The same is happening with sugar by separating it from the fruit, we can easily eat to much of it. which is what american especially are doing, mostly by adding it to everything. It is even added to many meats.

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Correlation of non-coding DNA with coding DNA
I sequenced the first exon of the MC1R gene of 15 labradors (genomic DNA) to look for the loss-of-function mutation (C.916C>T) and as expected, it was where it should have been (916th base pair). As i compared the SNPs with the phenotype of the dogs i found a second mutation that also correlated 100% with the phenotype of the dogs. The mutation is located 45 base pairs before the start codon of the first exon. As far as i'm concerned the region that lies right before the first exon should not be part of the coding DNA. If so, why could this mutation have been evolutionary conserved? Or am i simply mistaken in that the mutation before the first exon could also be part of the gene for MC1R (meaning there would be an intron before the first exon which i'm not sure if that's possible)?

Is that in a regulatory region of the gene or within a splicing region?

I only sequenced the first exon of the gene

That is contradictory. How can you sequence protein-coding parts only and find a mutation in a non-coding part?

I sequenced a little more than just the first exon of course because the results towards the ends of the sequencing product are usually not so clear

@AlexDeLarge exon need not be protein coding. UTRs are part of exons.

Which leads to my first question again: is this a regulatory region of the gene (probably not) or within a splicing region (more probably so)?

@Lukeception what did you sequence? RNA or genomic DNA?

Shame on me, of course you are right. ;) Still, @Lukeception should clarify in what part this second mutation is located.

@Lukeception If you do not provide additional information, this question cannot be answered. Please add all necessary details.

Which region did you exactly sequence? And the SNP is located in the intron behind exon 1?

So i sequenced a little more than the first exon. since it is the first exon, the mutation which is before the first exon should be in a noncoding region of the DNA, right? and yes, I sequenced genomic DNA.

@Lukeception Add these details to the question. Replying in comments would not be useful as nobody would scroll through the comments to understand the question. Moreover, comments are not indexed and therefore cannot be web-searched. Finally, your question should be complete in itself.

Am I missing something? Isn't this simply a second SNP very closely linked to the mutation of interest, so unlikely to segregate? Linkage disequilibrium.

If you have 2 different mutations (irrespectively of where they sit in regards to the final gene-product), and both correlate perfectly with a given phenotype, (and you have dismissed any other potential cause), you can not formally say, if the first mutation, or the second, or both mutations are required for your phenotype. (Though you can make educated guesses or rely on external information...)
Loss-of-function mutations do not have to be in the protein-coding region (but simply in one part of the genome, which is required for the expression of a gene towards a phenotype).
Polymorphisms can also be neutral - especially in artificially bred / selected animals, such as the wolf-like animals we now call labradors. You could easily envision a scenario where some neutral mutations was present in an individual, which would have a desirable / selectable mutation. If that neutral mutation is within a few 100bp of the selected mutation, it unlikely will have been uncoupled from the selected trait / mutation.

Just to clarify is the mutation is 45bp upstream of the protein start site, and outside the first exon. (the first exon needed not contain the protein start site. There are mRNA where the protein start site is in the second exon)
1 - Your mRNA does not start where you think it does. Mammals proteins have multiple isoforms. And perhaps your protein of interest has functional isoform with an alternative start site further upstream.
2- Labradors are inbred line. Most dog breeds are inbred. Perhaps the mutation outside the exon is just there for the ride.
3- The mutation has damaged the promoter. Your gene is fine. But since the promoter has been mutation, gene expression is now below levels needed to main normal phenotype.
4- The start of the first exon has been miss annotated.  The mutation is in the exon, specifically the 5UTR. And this mutation has effected ribosome binding in some manner

The region in the mRNA upstream of the start site is 5' UTR; 5' untranslated region.  Sometimes, UTRs have regulatory functions.  Or, the UTR mutation might just be along for the ride, and have no effect at all.  You generally can't look at a non coding SNP and tell if it's functional with no other information unless it messes with one of the first few bases of a known splice site.
EDIT:  I still don't understand.  Is the mutation in the first exon, before the start codon, or is it upstream of the first exon?  There is no splice site upstream of the first exon.


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flavivirus virus genome, methylated guanine
I'm looking at the sequence of a flavivirus virus genome (mRNA). Kindly see the link MH900227.1. How can I identify the Guanine nucleotide that is methylated in the capping process?
Thanks,

You might give us a link to the sequence you are looking at. If it is a GenBank file the annotation might help. You might also tell us what relevant papers you have retrieved from the literature that discuss the topic and why they don't help you. See the Help on Asking Good Questions.

I've added the like to the sequence. I think it's a general question for biologist/virologist so I did not ask the authors.

What else do you know about this sequence? How was it generated? A quick blast search suggests that it is not a complete sequence and that it is missing the 5' end — do you have some reason to believe that this is a complete genome sequence? ——— Also, are you familiar with how 5' capping occurs — if not looking into that may help you better formulate your question.

Hi tyersome, The cap (GpppA) should be at the 5' end. However, the mRNA deposited in database showed different nucleotides in the 5' end. I did Blast search for all mRNA sequences available but it shows no (GA) in the beginning of the sequence. Since there are serveral "GA" nucleotides in the sequence , I wrote my question about how to identify the guanine that is in the cap and will be methylated in the capping process. Here is the other sequences of mRNA LQ868304.1  LQ868303.1 LQ868302.1 LQ868301.1 LQ868300.1 LQ868299.1

Why do you think the methylated G is present in these sequences?

I have two reasons for thinking your question isn't answerable.

As I said in my comment, based on BLAST results I don't think your sequence is complete — it appears to be missing the 5' end.
If the 5' end is missing then the end that gets capped is missing.

The 5' cap gets added post-transcriptionally and has a linkage (5′–5′ triphosphate) that prevents it from being sequenced.
That means that sequencing reaction don't see the G that gets methylated in the 5' cap.
This is why I suggest that you make sure you understand the capping process.

Thank you tyersome for your reply. (1) for the first reason, you are right. I updated the link in the question to a sequence which should be a complete one . (2) for the second reason, I suppose that the 5' cap will appear in the sequence, even-though if it added post-transcriptionally, in case the mRNA was directly isolated from the bacteria and not from the DNA. Please correct me if I 'm wrong.

I encourage you to make sure you understand how sequencing reactions work.  If you review that and look at the structure of the 5' cap I think you will understand my second point. (You could also look at the sequences of a few eukaryotic mRNAs — you will find that they don't always start with a G.)

That's a bit extreme. Ask yourself, how did they ever identify and characterize mRNA caps? The review I cite in my answer indicates there is a capped mRNA (Figure 1).

Question

“How can I identify the Guanine nucleotide that is methylated in the capping process?”

Answer

Not from the genome sequence MH900227.1 mentioned in the question. It is the sequence of the genomic RNA (given as DNA), it starts with an A and even the full Genbank entry lacks any annotation of whether there is a separate capped mRNA and, if so, where it starts.

To answer your question you will have to search the literature. There is a 2018 review by Göertz et al. entitled Functional RNA during Zika virus infection which should have (or lead to) the answer. It does appear from Figure 1 of that review that Zika virus polyprotein mRNA is capped, although the position is not immediately apparent just skimming the paper. Some hours of work and access to a university library is probably required to track it down.

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Is there a law that defines an upper bound for the speed of growth of an organism?
I was wondering if there is some biological law (or chemical/physical law for that matter) that limits how fast an organism can grow.
I know that the growth of a plant is often restricted by the deficit of some nutrient (e.g. phosphorous). Phosphorous fertiliser over comes this. However, if one were to give a plant its optimal ratio of nutrient, sunlight, CO2, etc... we could probably not increase its growth speed by a factor of 1000, by increasing the dose.
Why is this?
Is it because of the speed at which cells can replicate? or the speed at which light can be converted into chemical energy? or the speed at which minerals can be absorbed by the plant? or is it just a habit rather than a law?
Is it possible to calculate the upper bound of growth for an organism (or specifically any given plant)?
Please excuse if my terminology is rudimentary.

yes there are growth models but growth process is incredibly complex and there is no single law/model that would universally apply to all organisms. Logistic growth models are used for modelling most populations but they are very simplistic.


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Which books give data on how humans grow physically from birth till death?
I am searching books on how humans grow physically from the birth till death. I am not a biology student, and don't know any technical terms. I searched amazon but didn't find any such books. I need book to be precise. Even if the book is a textbook, it would be helpful.
If it is not possible to get all the data in one book, is there any other alternative reading to be made via multiple source reading.

The 'Illustrated textbook of paediatrics' by Lissauer et al. (ISBN 9780723438717) contains a section about the average growth of children from birth up until puberty. After puberty humans don't grow anymore unless there is a medical condition. However it is important to understand that growth is influenced by many factor including ethnicity, sex, socioeconomic status and health and therefore precise numbers are hard to find.
For the most accurate information you should look for scientific publications for you specific population.

Thank you for the reply. I seem to have been not precise in question, I intended to ask on how humans grow from the beginning and age till death. I am searching book(s) having these data, for knowing on what is to be made for living longer.....

... These books might allow knowing on what chemicals (food) is to be had for increasing time of aging or to decrease the rate of growth, and to check on whether the ready-made exercise or food program are allowing to live longer or not. I have till now found Embryology (Developmental Biology) books, I still need to search adolescent developmental biology and might need to find books on how humans age physically. I will try reading journal articles, if I don't find books.


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Does the difference in the height of artificial lighting affects the height of the plants?
I have some plants living on artificial lighting. I've noticed the following in the following two plants of the same species:
This one was grown with lamps very close to it (~10cm).

This one was grown with lamps far away from it (~1m).

The first one got smaller while the second one is much taller. It seems that at least for some plants, the difference of height in lighting affects the height of the plants/speed of growth/etc. As soon as I changed the first plant to a place with higher light, it seemed to grow (vertically) much faster. If that is true, I guess someone already noticed it. I'd like to read more about it, could you point me to references on this?

Don't forget that you have a sample size of 1. You therefore can conclude much from this "experiment". The difference can be due to soil differences or aeration. Also, the two plants are of the same species but they are not clones. There might well be genetic predisposition.

@Remi.b Yes, I did not conclude anything. It wouldn't make sense to conclude by asking if it is true.

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Are there critical points in ecosystems?
Some days ago, I was thinking (partially) about the complex balance that is needed for an ecosystem to exist. I got curious about the existence of some sort of critical point, something - that when taken out of the system - makes life vanish.
Is there a single species that when took out of one ecosystem destroys the life in it? Perhaps there's not a single species, perhaps there could be a minimal set of species in which this could happen.
Excuse me for the poorly formulated question. I'm not a biology student, I just get random curiosities from time to time.

You will definitely be interested in reading on the concept of ecosystem resilience

Another (overlapping) interesting place to look: the concept of keystone species.


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How does evolution work at the level of a caterpillar mimicking a snake?
I am referencing this video, where a caterpillar turns into what looks like a snake when it gets frightened, presumably to ward off predators.
Now how can this evolve?
I majored in Molecular Neurobiology and studied evolution, and random molecular evolution makes sense to some degree. Every now and then there are random mutations, sometimes which affect gene / cell-signaling pathways, which could cause reproductive advantages, leading to evolutionary adaptations. But to go so far as to be able to mimic an external structure like a snake, how is that possible? I don't see how that can randomly evolve.
It is as if as a species we have a plan on what we want to become, and we slowly realize that plan by somehow tuning the genes to, say, look like a snake. But that is just me trying to fill in the gaps with imaginative thinking, how something like this can evolve. There are many other examples of incredible things evolving, but this one demonstrates the question perfectly.
Briefly, can you explain how this sort of thing could evolve?

Because vision is not perfect, a predator could confuse a caterpillar for a snake under different conditions at different distances. is it cloudy out, is the caterpillar in shadow, partially obscured. At every step of looking more like a snake the caterpillar is less likely to be eaten in more and more situations. this is fairly easy to see because there are a variety of caterpillars that resemble snakes to varying degrees. Many are just simple spots that look like eyes. Even if it only fools only a few predators under only a few conditions it is still an advantage.  This is why mimicry in general is so common.

Consider the certainty of a predator, if the predatory is just confused about whether something is or is not a snake, it can still be a big advantage. That might be a snake but that other thing is definitely a caterpillar. Which one is the predator going to investigate the possible threat or the easy meal? Then the caterpillar that does not resemble a snake gets eaten and the poor mimic gets spared. Prey selection is a risk assessment and a certainty assessment at the same time, thus is exploitable.

Mutations are random; natural selection is not.
Caterpillars are eaten by animals like birds. If you get eaten as a caterpillar you don't get to reproduce, so there's a strong selection for anything that makes you less likely to get eaten.
Even a very basic snake-like appearance (maybe just a color) might cause some survival benefit - maybe not every caterpillar with that gene survives, but over generations more snake-like caterpillars survive than non-snake-like, so the population looks more snake-like.
I don't see the snake-like behavior part as any different evolutionarily from the appearance part, or distinct from any other defensive behaviors that animals make, such as posturing to look larger, etc. It's just a behavior that's unlikely to be beneficial until after the other appearance changes. No planning is necessary at any stage, just selection on characteristics that appear.
Be wary, too, of selection bias when thinking about the evolutionary likelihood of any one thing: you observe the things that did evolve, not all the things that are possible.


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Do our blood vessels exude chemicals?
I watched a youtube video explaining how mosquitoes detect our blood vessels through "chemicals that our blood vessels exude naturally"
I was wondering if it's true that our blood vessels exude any chemicals, and which chemicals are they.
[Link to the video in case anyone is interested https://youtu.be/rD8SmacBUcU]

If so, it's probably more accurate to say that mosquitoes have developed a way to sense chemicals our blood vessels exude, not that our blood vessels exude chemicals mosquitos can sense. It's a subtle difference, I'll agree, but kind of important.

@WillihamTotland Thanks, i edited out the mosquitoes part in the title, since my interest is really whether or not our blood vessels do exude any chemicals.


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What does "kcal/mol" mean when speaking of enzyme catalysis?
After thinking about it, I'm confused by what the reaction barrier of an enzyme actually means.
Imagine a reactor containing enzyme and substrate.
If the enzyme in the reactor has a reaction barrier of 15 kcal/mol,
a) then when 1 mole of product has formed, that means 15 kcal have been consumed, independent of how much enzyme is present in the reactor.
b) then when 1 mole of enzyme is present in the reactor and 1 mole of product is formed, 15 kcal have been consumed.
Is it option a), b) or otherwise?

Let us imagine two companies A and B.
Both companies use very similar technical equipment to carry out a biotechnological process where a chemical reaction is catalyzed by an enzyme.
Company A uses an enzyme with a reaction barrier of, say, 15 kcal/mol, while company B uses an enzyme to catalyze the same reaction but this enzyme has an activation energy of only, say 12 kcal/mol.
For every Mole of product, company B saves 3 kcal worth of energy needed to drive the factory.
Does that make sense?

While a lower activation energy is beneficial, I don't think a difference in activation energy of 3kcal/mol will translate into 3kcal/mol energy savings. It all depends on what requirements you have for the kinetics (reaction speed) and product yield. If you want faster kinetics you will have to make more energy available, but this may also change the equilibrium conditions. When optimizing reaction conditions, you will likely have to make tradeoffs involving reaction kinetics, catalyst amount, catalyst price and reactor temperature, depending on the specific reaction and the reactor design.

Let's think of a first order reaction  in terms of rates. Say enzyme 1 has a rate of 1000$s^{-1}$ and enzyme 2 has a rate of 2000$s^{-1}$, it's clear that enzyme 2 will only require half the time (at the same temperature) to produce 1 mole of product. Do you agree? So I only need to heat the reaction volume for half the time as I would when using enzyme 1.

Yes, I agree, an enzyme giving a lower activation energy will generally give a higher reaction rate, and that will definitely affect the economics of the operation.

I guess then the most reliable way to do this would be to calculate the time required to produce 1 Mole of product (given the rate constants) and then calculate back to the activation free energy differences. From this also I guess one can say that the unit "kcal/mol" indeed refers to 1 Mole of product.

I'm not sure I understand you correctly. Could you perhaps give a calculation example?

I mean just by using $k(T) = \gamma(T)\frac{k_\text{B}T}{h}e^{-\Delta G^{TS}(T)/RT}$ (see here http://www.sci.ccny.cuny.edu/~gunner/Pages-422/PDF/section.1/catalysis/cat.truhlar.pdf) and from this getting back $\Delta G$.

If you already know the rate constant at a given temperature and all the other factors then yes, you can calculate the activation energy. I don't see why you would need to do that though? If you already know the rate constant, you don't really need to know the activation energy to calculate your energy needs, unless you want to use it to calculate the rate constant under different conditions.

Sure, the rate constant already is very informative. Still if you can assist me in this initial question: If all is equal between reactors A and B, except the activation energies, then after having produced 1 Mole of product, one reactor required dE less energy to arrive at 1 Mole of product where dE is the difference in activation energy. Do you agree? I'm assuming both reactors require the same amount of energy to be heated up to the same temperature.

No, and that's what I've been getting at. As mentioned, the activation energy is only "borrowed". To find out how much energy you need to input or remove from the reactor to keep the temperature steady, you need to look at the heat of reaction. See the difference in height of the line at "reactants" and at "products" in the figure in the answer by Chris? That's what matters. If you have further questions on this, I think you may find people on the Chemistry StackExchange who can explain better.

The reaction barrier (also termed activation energy) is the energy that is needed for the reaction to take place. An enzyme is "only" a catalysator which lowers the necessary energy (and/or makes the reaction possible under the conditions) but some energy to start a chemical reaction is still needed. See this image (from here):

To your questions: A and B are essentially the same - but the reaction time necessary with small amounts of enzyme is much longer than when 1 mole of enzyme is present. The amount of energy needed to catalyze the production of 1 mole of product stays the same.

Shouldn't we say - energy barrier of the reaction rather than that of the enzyme (as TMOTTM has written in the question) ?

It would be more accurate. But it still makes sense, since it is the energy for the reaction with the enzyme.

@biogirl you're right.. mea culpa.

The activation energy for a reaction is given for a given extent of reaction, typically per mole of product formed. In general, the amount of enzyme present in the reactor is irrelevant with respect to the activation energy. So option a) is closest to correct. However, note that the activation energy does not tell you how much energy is consumed taken up during the reaction, only how much energy is needed for the activation energy to be exceeded and the reaction to proceed. The kinetics of a reaction, is a separate issue from the thermodynamics of the reaction, which determines the equilibrium concentrations of substrate and product. What the enzyme does is lowering the activation energy, thus speeding up the kinetics of the reaction and allowing equilibrium to be reached. In practice, the activation energy in the absence of the enzyme may be so high that the reaction would not proceed at all, and thus equilibrium would not be reached.

I agree, the activation energy would give me the amount of energy consumed during catalysis alone. Heating up the mass would be on top of that. But one can imagine that this component remains constant for different enzymes.

I think there might (still) be a misunderstanding here? The heat of reaction doesn't come on top of the activation energy - they are two separate things - and a catalyzed reaction does not consume or produce more energy than an uncatalyzed reaction. Think of it like this: The activation energy is the maximum energy that is "borrowed" when the reaction happens.

I might have been unclear. I know that $\Delta_f H$ is an indication of how spontaneous the reaction is.
With regard to the word "consume": I respectfully disagree, because to form 1 mole of product, an uncatalyzed reaction does require more energy input.

Indeed, you need to have more energy available, but the energy you spend on reaching the activation energy you also get back, so I feel "consume" is the wrong word to use. I don't see much point in arguing about that though - thanks for clarifying.

Let me put it differently, please see edit of original post.

To better understand the activation energy concept my teacher had given us an excellent example.  Suppose you are driving a car and want to cross a mountain. You could either go to the mountain summit and then come down or you could directly cross it through a tunnel. What enzyme does is to construct a tunnel for the reaction to proceed.

I dont think I have a problem with understanding the concept of a potential energy surface, in fact I would be a bit careful with that analogy. But it is a good starting point. Rather than a tunnel, I would say the enzyme finds a rout which doesn't reach that high up as the summit. Speaking of tunnels can be misleading when talking about enzymes, so one has to be careful about the terms one uses.

@TMOTTM yes I agree. Tunnel is a bit too much.


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Is there any evidence or example of "trade" or "money" in single cell organisms?
Single cells (like bacteria or eukaryotes) are extremely complex "machines" which can take input and produce output, and generally just live life. The question is, is there any example of "trade" (as in, "commerce") between cells, or within a cell at the molecular level (trading one protein for another, or a generalized "currency" where you could trade a general thing like money for anything else? I imagine there are, but not sure if people have put cells into this mental framework before.
Receptors on a cell seem to be somewhat a form of exchange/trade, "give me a molecule and I will start this chain reaction for you". There's probably many other forms of trade in this light. But what about money/currency?
This is, generally, an open-ended question. To make it closed. Provide one complete example of trade and money, and/or link to relevant research.

Another example might be Rhizobium in root nodules (see here). It takes about 16 ATP to 'fix' one molecule of N2 into (2 NH3). The bacteria supply the plant with 'fixed' nitrogen, and the plant supplies the bacteria with nutrients and energy (possibly being the direct source  ATP?). 'Free' Rhizobium cannot 'fix' N2.

Look into biofilms for bacterial mutualistic relationships.

Trade or currency implies a value placed on it - as in one cell could hold out for 2 ATP vs 1 for another, which requires thought ...so no. There is exchange, but it isn't trade or currency.

Cross-feeding is a common type of symbiotic interaction in which one organism can utilize a substance produced but not utilized by another organism. It's very common in bacterial communities, and often mutualistic (though not always). But there's no perfect analog for currency in this context. More like bartering goods and services.

Lichens might be such an example. Algae living with fungi in a mutualistic relationship.

These are multicellular organisms, right? I am looking for single celled organisms or within single celled organisms.

@Lance Plenty of unicellular fungi combine with unicellular photosynthetic green algae or cyanobacteria to form lichens. Check out the article in my link.


text:
Does the body have a mechanism for cleaning plaque buildup in arteries?
Is there a self synthesized substance in the body, or a mechanism that can break down plaque in arteries ?

Could you elaborate the question and make it more specific? There is a mechanism of thrombolysis and fibrinolysis if that i what you are asking for. https://en.wikipedia.org/wiki/Fibrinolysis and https://en.wikipedia.org/wiki/Thrombolysis

@Polisetty , I mean a mechanism to clean plaque buildup on arteries, i will edit the question.

@Polisetty The links were helpful too, but i understand that it only deals with blood clots.

Unlike the clots, plaques are a part of the pathological endothelium and actually cant be cleaned as such. Though, the cholesterol can be drained out by HDLs. By intervention, balloon angioplasty and the like can clean it up partially. So, again the answer differs based on what you're looking for.

@Polisetty  So in that case, i guess the answer could be an elaboration on the "cholesterol can be drained out by HDLs" part.

Yes, ldl can be removed once the level falls low enough I.e. Below 1.7 mmol/l.

Atherosclerosis can be reversed to some extent by certain diets and change in life style that result in decrease of excessive weight, blood pressure and cholesterol levels.
Studies
1) Dietary Intervention to Reverse Carotid Atherosclerosis (Circulation, 2010)
In a study in Israel, in 140 participants, who were mostly age 40-65 and overweight, they observed an average of 5% reduction of the the volume of the carotid artery wall, which reflects the reduction of the plaque.

Two-year weight loss diets can induce a significant regression of
  measurable carotid VWV [vessel wall volume]. The effect is similar
  in low-fat, Mediterranean, or low-carbohydrate strategies and appears
  to be mediated mainly by the weight loss–induced decline in blood
  pressure.

2) Intensive Lifestyle Changes for Reversal of Coronary Heart Disease (JAMA, 1998)
Forty-eight patients with moderate to severe coronary heart disease were randomized to an intensive lifestyle change group (10% fat whole foods vegetarian diet, aerobic exercise, stress management training, smoking cessation, group psychosocial support) or to a usual-care control group, and 35 completed the 5-year follow-up quantitative coronary arteriography.

Experimental group patients (20 [71%] of 28 patients completed 5-year
  follow-up) made and maintained comprehensive lifestyle changes for 5
  years, whereas control group patients (15 [75%] of 20 patients
  completed 5-year follow-up) made more moderate changes. In the
  experimental group, the average percent diameter stenosis at
  baseline decreased 1.75 absolute percentage points after 1 year (a
  4.5% relative improvement) and by 3.1 absolute percentage points after 5 years (a 7.9% relative improvement). In contrast, the
  average percent diameter stenosis in the control group increased by
  2.3 percentage points after 1 year (a 5.4% relative worsening) and by 11.8 percentage points after 5 years (a 27.7% relative worsening) (P=.001 between groups. Twenty-five cardiac events occurred in 28
  experimental group patients vs 45 events in 20 control group patients
  during the 5-year follow-up (risk ratio for any event for the control
  group, 2.47 [95% confidence interval, 1.48-4.20]).
The experimental group reduced LDL cholesterol levels by 40% at 1 year
  and by 20% after 5 years.
When we began this study, we believed that the younger patients with
  milder disease would be more likely to show regression, but we did not
  find this to be true. Instead, we found that the primary determinant
  of change in percent diameter stenosis in the experimental group was
  neither age nor disease severity but adherence to the recommended
  changes in diet and lifestyle.
those who gained weight were more likely to show progression of atherosclerosis.
Experimental group patients had a 91% reduction in reported frequency
  of angina after 1 year and a 72% reduction after 5 years (Table 5). In
  contrast, control group patients had a 186% increase in reported
  frequency of angina after 1 year and a 36% decrease in frequency after
  5 years.

Mechanisms
Reversal of atherosclerotic plaques can be achieved by removing the causes. According to Atherosclerosis: Process, Indicators, Risk Factors and New Hopes, (Int J Prev Med, 2014), decreasing excessive body weight + exercise + cholesterol-lowering diet + cessation of smoking can result in:

Less damage to the arterial intima
Higher HDL/LDL ratio, meaning adequate removal of LDL (by HDL) from the blood into the liver and thus less deposition of cholesterol into the arteries
Less inflammation in the arterial intima


text:
Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic?
I was curious to see whether 3% hydrogen peroxide can be used as antimicrobial and virucidal product for daily use in home. There are  several disinfecting products in the market claim that use of these wipes for some minutes can disinfect the hard surface. Also, there are quite a few ethyl alcohol based hand sanitizers. Can 3% hydrogen peroxide be used as effective disinfectant and antiseptic - similar efficacy with those of the commercial disinfecting products?
Website https://www.cdc.gov/hicpac/Disinfection_Sterilization/7_0formaldehyde.html discuss use of hydrogen peroxide against a wide range of pathogens. I found that the bottle of 3% hydrogen peroxide lists it as  antiseptic - to use for gargle etc. Can 3% hydrogen peroxide be used as a disinfectant for a broad spectrum of microbes?

Nope. Some microbes express high levels of catalase, in which case 3% HOOH does nothing to them.

If you need to disinfect regularly for medical reasons, it would be best to consult with your medical doctor. If there is no specific medical reason, and you are not particularly exposed to pathogens, the information of the "center of disease control and prevention", of the US government, which you refer to (and contains a detailed answer to your question) is more trustworthy than companies that have large budgets for advertisement to pull the money out of your pockets, with sub-perfect products, and with scaring people. If you are exposed to pathogens at work, consult your bio-safety officer.


text:
Can only fully matured sperm fertilize an egg?
Are only mature sperm able to fertilize an egg? If so, is there typically a reserve of mature sperm that are saved after an ejaculation or does a male need to wait for new sperm to mature before trying to fertilize an egg again? In humans it seems that the the shortest maturity period for sperm is around 42 days (New Findings on Sperm Life Cycle Could Impact Fertility Treatments). Do the new immature sperm serve any purpose after ejaculation?

Do you mean naturally?

@WYSIWYG, yes, not IVF.

There seems to be the misconception that sperm maturation period starts over after each ejaculation. It is a continuous process : at any given time, there will be populations of cells at various stage in the process; for instance, sperms that are at day 36 will be mature in 6 days, regardless of intervening ejaculations that could expend mature sperms.

As far as I know, sperm cells undergo maturation in the epididymis, where they become motile. As Eliane pointed out, this is a continuous process, so the male does not have to "wait", because there is continuously a batch of sperm cells that will shortly become mature. Furthermore, maternal factors are required for the process of capacitation in which the sperm cell becomes capable of fertilization and undergoes motility increase.

An immature sperm cell is simply non-motile and even if present in the ejaculate, it will not be able to travel towards the fallopian tube to fertilize the oocyte. A sperm cell which did not go capacitation will also have no ability to fertilize an egg (that's why prior to IVF it's important to capacitate sperm).
My sources:

https://kjcscientific.wordpress.com/project-excalibur/
Gilbert's Developmental Biology (2009)


text:
Real-world examples of Darwinian extinction
Darwinian extinction (also known as "evolutionary suicide") refers to processes of selection-driven self-extinction, i.e. the cases where natural selection causes the extinction of an evolving population.
In the literature, there are many models of life-history evolution and (to a lesser extent) experiments with bacteria in which Darwinian extinction has been demonstrated. However, I couldn't find anywhere real-world examples (i.e. not from models or experiments) of Darwinian extinction of complex organisms within more or less constant environment.
Do we know of such examples?
And if we do, could you please refer me to them?
Edit: A mechanism of the Darwinian extinction could be, for example, the emergence of ”selfish” strategies w.r.t frequency-dependent selection, which are beneficial to individuals when rare, but may result in a deteriorating environment and smaller population size once they become common.

I think the OP is looking for something like an example of mutational meltdown or an example of a selfish genetic element driving extinction. In short an example of extinction that is of particular interest to evolutionary and conservation geneticists. I think the current answers (despite one being generously upvoted) do not answer the question.

Although you don't mention it in your question, I guess you'd like examples of extinction in (more or less) constant environment? Then I guess you'd like cases of extinction due to the introduction of an overseas species out-competing the original one.
Red squirrel is not extinct yet, but its sharp population decrease is mostly linked with competition with newly introduced grey squirrel, although habitat loss and concurrent introduction of a virus are also part of the causes. Read at https://en.wikipedia.org/wiki/Red_squirrel

It could be worth noting that the most important component of the decline is actually squirrelpox virus, which causes subclinical infection in greys but kills reds.

Well, wouldn't resistance to pathogens be part of Darwinian fitness? Although it is true that the virus is reported to have been introduced along with grey squirrels, thus it's difficult to decouple the population reduction due to its introduction and the interspecies competition.

Yes, constant environment. And thank you for the example, looks promising. But I was more interested in ”selfish” strategies w.r.t frequency-dependent selection, if you know of any such examples. I'll edit my question.

@Joce Differential pathogen resistance is part off interspecies competition.

Yes, but what I meant is that if the pathogen is introduced (or exposition increased) at a given time, this is modifying the fitness of the species independently of interspecies competition. Thus part of the adjustment in population size may be a response of this new environment only (and would be obtained for same exposure to virus w/o the competing species presence)

@joce it would, yes. 'Competition' is a broad description of what is happening; I'm just suggesting this answer might be improved by a more specific description of the mechanism.

@Joce ''this is modifying the fitness of the species independently of interspecies competition'. No, the differential response to the same pathogen between species is not independent from interspecies competition but part of interspecies competition. -1

@AlexDeLarge: have you read my comment? If the introduction of the pathogen is concurrent to the introduction of the competing species, then you could have extinction of gray squirrel without any competition, simply by epidemics. If the pathogen was already present, then you are right that the population diminution can be read as the outcome of the interspecies competition.

@AlexDeLarge: As this is not appropriate for a comment, I have started a new question to discuss this. See http://biology.stackexchange.com/questions/49246/interspecies-competition-and-pathogen

The loss of self-incompatibility (gaining the ability to breed with oneself) in the Nightshade family has been demonstrated to result in both a higher diversification rate and an even higher extinction rate, overall leading to a lower diversification rate in self-compatible lineages.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.702.1437&rep=rep1&type=pdf

It hard to find example like that because evolutionary suicide does not mean it must end with extinction
I think this 2 words is not equal. Member of every specie would evolve into something disadvantage to specie as a whole, but then it would rapidly lead to equilibrium and/or evolution arm race before extinct
I could say most predator evolve to starve their specie, if they have many offspring then the prey would all gone and they will starve to death as a whole. But before all prey die the predator would gradually fall and the prey member will rise up again into equilibrium
There are also specie that develop infanticide or cannibalism. But before that specie gone extinct the group that develop those trait would have decrease, those group would gone extinct before the whole specie, or at least some group without those trait would have better chance to survive

This doesn't really answer the question. And by definition, Darwinian extinction results in extinction.

@101010111100 Darwinian extinction is extinction but evolutionary suicide is not the same word


text:
How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances
Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of.
I have to detect AA location within MAP (density) 3D matrix. And to verify with PDB format (which models same 3D structure). Each AA may have different rotamer (aka 3 angles usually used to describe AA exact position related to carbon C_alpha atom (the atom which AA side chain exits from). To justify inaccuracies - I need to show that (among other reasons) - inaccuracy is caused since not all possible rotamers existed in my training set (I use machine learning classification to decide what AA is it, and where it stands within cryo- EM scan).

sounds like a very specific question - you may want to give a little more detail to help others follow what you are asking - just my thougts

I clarified upon request, thanks for suggestion to improve chances for proper and and exact answers.

As far as I am aware, Python commands are instructions you write on the command line to run individual lines of Python code. I presume it is a Python program you are after, but why do you specify this one language?

I am student at Computer Science department, and this post is about bioinformatic workshop I must proceed through. Teaching stuff guidelines require to implement in Python. Python is interpreter language where you can write single command. And you can build as well huge projects with many files - which call each other.

Python has dozens of packages specified for various uses. And this versatility is as well a challenge to find "the niche" where programmer needs to spread his code. So I ask here what are commands or packages. Or other external programs of on-line web sites which provide conversion from PDB file format to list of all AA rotamers instances.

I'm voting to close this question as off-topic because this site only accepts bioinformatics questions relating to the underlying biology of the computations, not how to do the computations themselves. If you have tried some code and need help, you may visit [so], but they will not give package recommendations or write your code for you - you must show effort. You might also want to visit a bioinformatics forum such as Biostars for suggestions.

I don't know whether it was you who down-voted my answer, but let me try to clarify before this is closed. The rotamer is one of three conformations of the side-chain dihedral angle chi1. If you use a program such as dhedral it will give you a table of dihedral angles, including ch1 (except for gly). It would seem trivial to then check within defined ranges to determine whether chi1 corresponds to trans gauche+ or guache–. To repeat, Dunbrack is one of the people who has worked in this area (http://dunbrack.fccc.edu/bbdep2010/) and may be able to help you.

I’m not sure if it is what you are after, but I have used Roland Dunbrack's dihedral perl script to get dihedral angles, the header of which is:
 RL_Dunbrack@fccc.edu

 usage
 dihedral.pl filename [chain]

 dihedral.pl pdb2hla.ent
     will print out all dihedrals from file pdb2hla.ent
 dihedral.pl pdb2hla.ent A
     will print out dihedrals only from chain A

I don’t know if it’s on his website as I got it from him personally. If not, or even if it’s not what you need, email him — he is likely to be able to help you.

I downvoted this for several reasons. First, the question is off-topic. From How do I write a good answer? in the [help], Answer well-asked questions. Not all questions can or should be answered here. Next, the OP is specifically asking for a Python script, and you (sort of) gave them a Perl script. Python != Perl, most certainly. Finally, you didn't provide the actual script! You listed the header (which is useless), and basically said "Go find it yourself" even though you have it in your possession.

First @MattDMo, you've every right to vote down my answer (and suggest the closure of the question). I had thought the downvote might have been from the poster. In my defence, I couldn't make the script I had freely available as I had obtained it directly from Dunbrack when I needed a replacement or update for a previous program of his (for Silicon Graphics or something). It doesn't have a free distribution licence, so it would have been discourtious and illegal for me to distribute it to third parties. As for giving the header, that was a quick way to indicate what the program did.

The OP couldn't have downvoted, because they only have 1 rep. You need 125 rep to downvote. I understand why you can't distribute the program, perhaps my wording could have been a bit better. Overall, it just seems to me that you might have been better off just not answering, or leaving a comment suggesting the OP get in touch with Dr Dunbrack, since the answer itself isn't terribly helpful. Just my 2 cents, no hard feelings :)

@MattDMo — Fair enough. No hard feelings.


text:
Why do animals excrete organic nitrogen compounds instead of N2 gas?
Protein metabolism produces ammonia, which needs to be disposed of; but oxidation of ammonia into water and dinitrogen produces energy, while creating urea or uric acid consumes energy, and excreting it expands water. So, it seems like there would be some small advantage to animals exhaling N2 instead of excreting nitrogen in liquid or solid form. Nevertheless, no animal does so, and as far as I know, the only organisms that do are denitrifying bacteria and archaea.
So, is there a good reason why animals shouldn't produce nitrogen gas? bother with that, rather than just exhaling nitrogen gas? Or is it just a matter of "evolution isn't directed"--a random quirk that the ancestors of animals didn't happen to develop ammonia-oxidizing pathways?
There are a few reasons I can think of, or that have been suggested to me, that nitrogen production might actually be deleterious, but I can't find references to back up any of them:

Nitrogen has low solubility, and bubbles in blood or tissues are bad. Would this actually be a limiting factor?
The pathways that oxidize ammonia in microbes might interfere with other parts of animalian metabolism. I have absolutely no idea how plausible this is.
The energy gain from oxidizing ammonia may be too small to justify the cost of maintaining metabolic machinery for it.

So, is there any actual science on this?

Please everyone remember to answer in the answer box and not the comments.

If the answer is helpful and adequately explains why uric acid is the end product of the elimination of ammonia in animals, then it's customary (and the polite thing to do) to accept it.

for any evolution question a good rule of thumb is to ask yourself what benefit would this have? for instance exhaling N2 is not a benfit its one more gas you have to get rid of that is competeing for space with the oxygen you want to inhale.

In an answer to a previous evolutionary ”why“ question I devoted a paragraph to the general problem with questions of the type “Why has such and such not evolved, it would obviously be advantageous?”. Two points I made were:

“It would be too difficult, costly or would have disadvantageous consequences”

and/or

“The assumption that it would convey a selective advantage… is incorrect.”

In the present case both apply. A mechanism that evolved for elimination of ammonia in a particular species would be fixed if it did just that. Not if it also might do something else for which the organism already has highly evolved and sophisticated machinery†. And it is worth my repeating that the idea that energy costs are a limiting factory in the evolution of multicellular organisms is false. We are not bacteria competing for a limited supply of nutrients so we can procreate more rapidly. We have energy to “waste” (and long gestation periods).
Second, the fact that so few organisms can oxidize ammonia to nitrogen implies that this is a multistep conversion with chemical difficulties that can only be overcome in certain environmental niches. In contrast, the urea cycle is built up largely from pre-existing part reactions that had already evolved in a wide range of bacteria (see, e.g. this Bioessay review). The key reaction that produces carbamoyl phosphate from ammonia and bicarbonate has a counterpart in pyrimidine synthesis, and although there are separate enzymes for these processes in eukaryotes (pyrimidine synthesis uses glutamine, rather than ammonia) a single bifunctional enzyme is found in bacteria (see the Wikipedia entry for carbamoyl phosphate synthetase).
† I have not dealt with possible problems mentioned by the poster regarding the generation of nitrogen gas in the blood as these are only secondary to my main points, which would exclude the idea from the start.

Since animals get most of their nitrogen intake through protein / amino acids, breaking that down to molecular nitrogen is a multi-step process. Indeed that breakdown process can provide energy all the way down to the molecular components.
However, in a multi-step process, if you have limited resources, it is generally speaking an advantage to focus all your resources on the most efficient step. This way you can convert more energy than if say you'd put only half of your resources on the most efficient step and the other half in a less efficient step.
If we are just looking at one of the most basic amino acids, Glutamic acid, we have a Gibbs free energy of formation of -476 kJ/mol (chemeo.com). Glutamate can be broken down in a single biochemical reaction to ammonia and a carbohydrate. Ammonia has a Gibbs free energy of formation of -16 kJ/mol, which indicates that the first degradation step provides much more energy than the subsequent steps. Because of this, organisms that get nitrogen in the form of amino acids have an energy-efficiency advantage if they only do the breakdown until ammonia and not all the way to molecular nitrogen.
Of course that leaves an ecological niche for other organisms to make use of the wasted ammonia and convert the remaining energy there. Actually this is also a multi-step process, which is mostly done by different microbial species (ammonia oxidizer, nitrifyers, and denitrifyers). This has been studied from the perspective of microbial division of labor.


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Why does photosynthesis specifically produce glucose?
Why not a pentose? Or a tetrose? Or a deoxy sugar? Or just some other hexose, like fructose?
Is there some chemical reason life should have settled on glucose as the standard photosynthetic output, or is it just random? It seems very suspicious that this ubiquitous molecule nicely break down into exactly 3CO2 + 3CH4, or 6CO2 + 6H2O - 6O2, or 6H2CO, when such convenient formulas are not true of the actual immediate products of carbon fixation.

Or why a sugar at all?  CO(2) is the most oxidized form of a single carbon atom, and in photosynthesis carbon is reduced (where water is the source of electrons), but not fully reduced: the most reduced form of a C-6 compound is hexane, not glucose (and the most reduced form of a single carbon atom is methane)

@user338907 The plants use the glucose too. It's not (just) a waste product. It isn't particularly helpful to extract the most amount of energy out of photosynthesis just to then waste way more than that when trying to build e.g. cellulose. Evolution doesn't select the "best" process in isolation, it's always part of a specific environment. Mind, that's not knowing where glucose came from - it's very likely that was long before photosynthesis developed. And of course, photosynthesis doesn't actually produce glucose - it produces GAP/G3P. That's quickly turned into glucose, usually.

Glucose is such a ubiquitous energy storage molecule, that we show the simple photosynthetic chemical equation to include the capture of six CO2 molecules to create one glucose molecule. However, the steps specific to photosynthesis, the light-dependent and light-independent reactions, don't produce glucose directly. Instead, they produce an intermediary molecule, the 3-carbon D-glyceraldehyde 3-phosphate (G3P), which can directly enter the general metabolic cycle, which includes gluconeogenesis. Gluconeogenesis includes a pathway from G3P to glucose.
So, photosynthesis itself doesn't produce glucose, but can be considered to add to the production of glucose because it is integrated into ubiquitous metabolic cycles.
There are existing hypotheses as to why glucose is so ubiquitous. One hypothesis is that glucose is less likely to nonspecifically interact with proteins than other molecules of its kind (aldohexoses) because it is more stable in its cyclic form (instead of the open-chain form) compared to other aldohexoses. Another hypothesis is that β-D-glucose has all five of its hydroxy groups in the equatorial position, making them more accessible to chemical modification, such as esterification, acetal formation, and linkage into polysaccharides.

Excellent answer. I would just emphasize that cellular life existed on Earth existed for at least a billion years before the evolution of photosynthesis. That's a long time for organisms to have refined the storage and utilization of organic molecules for energy. It makes a lot of sense that photosynthesis would evolve in a way that most efficiently feeds into these existing metabolic cycles.

I'd always assumed that being a precursor for handy molecules like starch and cellulose would have made it quite an attractive choice for plants as well


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Does drinking alcohol having UTI may help to kill the bacteria?
It's well known that ethyl alcohol kills bacteria. And amount of alcohol in urine may be detected by EtG tests (as long as 3-4 days after intake).
Does drinking alcohol in reasonable amount by healthy individual (non alcoholic) having UTI helps to kill bacteria in the urinary tract (in order to get rid of them quicker)?

Nope, it does not. Alcohol is resorbed by the body and metablized. Additionally, to kill bacteria, you need 70% alcohol - which is a very bad idea to have this concentration in your body.

@Chris That looks like an answer disguised as a comment...

@RHA At the moment it's a comment. It doesn't have any references or whatever, maybe I find some time later to write a real answer. In this  case I will delete my comment.

Drinking alcohol does not seem to be effective treatment for urinary tract infections.
In this study, drinking 0.85 g ethanol/kg body weight (60 g ethanol or ~150 mL of 40% ABV spirit by a 70 kg person) resulted in 1 g of ethanol in the urine. 1 g of ethanol in 200 mL of urine = 0.5% alcohol.
According to CDC:

In the healthcare setting, “alcohol” refers to two water-soluble
  chemical compounds—ethyl alcohol and isopropyl alcohol...These
  alcohols are rapidly bactericidal rather than bacteriostatic against
  vegetative forms of bacteria; they also are tuberculocidal,
  fungicidal, and virucidal but do not destroy bacterial spores. Their
  cidal activity drops sharply when diluted below 50% concentration,
  and the optimum bactericidal concentration is 60%–90% solutions in
  water (volume/volume).

In this study, the minimal inhibitory concentrations (MIC) and antimicrobial effects of ethanol on Listeria monocytogenes in tryptic soy broth was determined. Ethanol at concentrations up to 1.25% did not inhibit growth, but growth was strongly inhibited in the presence of 5% ethanol.
According to BJPS, the minimal inhibitory concentration of ethanol is 4-9%.
A typical symptom of urinary tract infection is frequent and burning urination. Alcohol irritates the bladder, so it can make the symptoms worse (Mayo Clinic).

To begin answering your question,

Does drinking alcohol in reasonable amount by healthy individual (nonalcoholic) having UTI helps to kill bacteria in the urinary tract
  (in order to get rid of them quicker)?

We have to clarify that EtG detects ethyl glucuronide which is a byproduct of ethanol and remains in the urine for several day. The presence of ethyl alcohol in urine is significantly shorter somewhere between 8-12 hours (reference).
So what does this mean? Well, in order to "kill" the bacteria causing the UTI it must be exposed to a minimal inhibitory concentration of ethyl alcohol for a certain amount of time. Depending on the bacteria causing the infection this concentration and exposure time varies.
So if the concentration of ethyl alcohol was high enough and the flow of your urination and micturition long enough, maybe, but is unlikely to have much effect.

Good answer, but I would get rid of the last paragraph. The concentration of ethanol in urine is never going to be high enough to kill even a small percentage of bacteria present. In the United States, a person is legally drunk if their blood alcohol content (BAC) is between 0.08% and 0.1%, depending on the state. Even assuming that unmetabolized alcohol is concentrated 10-fold, and a person is very drunk with a BAC of 0.3%, 3% EtOH won't kill much of anything, especially if it's in a biofilm, as UTIs are.

@MattDMo i think this should be edited into the answer


text:
What is Colloidal biology and does it have any scientific background?
There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007:
“MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940*
written by PhD habilitation research professor Ute Deichmann at the Leo Baeck Institute (LBI) in London and leader of the History of the Biological and Chemical Sciences Research Group at the Instritute for Genetics, University of Cologne.
Therefore, the question is: What is Colloidal biology, what are the basic differences between molecular biology and does it have any background in modern scientific community?

The WP page on colloids http://en.wikipedia.org/wiki/Colloid#In_biology has a useful jumping off point (see subheading "In biology"). There is a discussion in the book "A History of Molecular Biology" my Michel Morange.

There are two antipodes: The molecular (or makromolecular) biology, which has the concept of large macromolecules which fulfill one task. This can for example be an enzyme which breaks down its subtrate. The properties and the structure of all molecules of the enzyme are the same and the factor determining the function of the enzyme.
The coloidal biology assumes that the function is granted by adding small amounts of an enzyme to water to form a colloid, which thenchanges the properties of the water in the way that it does break down the subtrate. Life was also explained as the sum of the functions of the colloids building the body.
This theory came up in a time when macromolecules and their functions where not very well understood. The better understanding of macromolecules rendered this theory irrelevant. This is also neatly sumarized in the conclusions section of the article you cite.


text:
Can diseases be transmitted wirelessly?
According to the recent research about Electromagnetic Signals from Bacterial DNA (A. Widom, J. Swain, Y. N. Srivastava, S. Sivasubramanian) it seems there is a possibility of a "wireless" version of intercellular communication which was found in bacterial communities.
The paper's abstract reports:

Chemical reactions can be induced at a distance due to the propagation
  of electromagnetic signals during intermediate chemical stages.
  Although is is well known at optical frequencies, e.g. photosynthetic
  reactions, electromagnetic signals hold true for muck lower
  frequencies. In E. coli bacteria such electromagnetic signals can be
  generated by electric transitions between energy levels describing
  electrons moving around DNA loops.

The authors further note:

There has been considerable interest in bacterial communities wherein
  a bacterium is connected to neighboring bacteria by means of narrow
  nanowires[5-7]. It is believed that the purpose of the nanowires is to
  allow for intercellular electronic communications. More advanced on
  the evolutionary scale are the more modern bacterial communities which
  are wireless. The electromagnetic signals sent from a bacterium to
  neighboring bacteria can be due to relatively low frequency electron
  level transitions within DNA.

Conclusions says:

Although biochemical reactions are often described in terms of
  molecular contacts, electromagnetic signals can often be employed to
  allow chemical reaction control at a distance.
...
The wireless broadcasts can in principle be of both the AM and FM
  variety due to the magnetic flux periodicity in electron energy
  spectra in bacterial DNA orbital motions. AM signals can arise from
  the Bohr transition frequencies between different electronic energy
  orbitals about the DNA loops.

Wired article Bacteria on the Radio: DNA Could Act as Antenna comments:

Theoretical physicists have proposed an explanation for how bacteria
  might transmit electromagnetic signals: Chromosomes could act like
  antennae, with electrons traveling gene circuits to produce
  species-specific wavelengths.
In Widom’s arXiv paper, he and other physicists calculate that as
  electrons flowed through loops of DNA in E. coli and Mycoplasma pirum,
  the species tested by Montagnier, they should generate wavelengths
  similar to what was recorded.
“Different species have different lengths of DNA” in their
  chromosomes, he said. “These lengths probably determine frequency.”
“This could be a wireless version,” said Widom. “Bacteria that set up
  nanowires are, on an evolutionary scale, fairly old. It’s occurred to
  me that more modern bacteria may use wireless.”

It seems that the concept of electromagnetic signal transmission in bacteria is not new and such an idea originates with Nobel Laureate virologist Luc Montagnier (2009), who detected electromagnetic signals after wrapping inductor coils around flasks of water, hooked up to an amplifier, which contained E. coli and Mycoplasma pirum. The frequency of the signals measured was about 1kHz.
That kind of communication could also explain the phenomenon of quorum sensing mechanism, where bacteria communicate with one another to establish the population density of micro-organisms of their own kind within their proximal environment.
Based on above, the question is, is there any possibility that the diseases can be transmitted wirelessly? Are there any further research around this topic?

While some of this concept indeed exists (bacterial nanowires), the rest is utter nonsense. Calling this publication paper is also an exaggeration, as this has been published on arxiv which does not provide peer review. Diseases are only transmitted by real microbes (bacteria, viruses etc.). The naming of Luc Montagnier makes this completely cheesy as this man hasn't made any real science for years and only done pseudoscience.

Even if DNA can create an electromagnetic signal around 1KHz that doesn't imply communication. Molecules can absorb or emit electromagnetic radiation at several frequencies, but no one claims this is communication. If the signal is real, it's probably just an intrinsic property of DNA, and putting a solution of pure DNA in water would probably produce the same signal. If someone comes back and demonstrates that bacteria grown while exposed to a strong 1KHz signal show different properties than a non exposed control, then I'd be more interested.


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How do animals decide what to eat and what not?
I want to know this in particular about animals that no longer eat what they used to eat. The best example in my opinion are chickens. Chickens are often held to eat all kinds of food we would otherwise throw away. Most of this, they would never find in nature.
Chickens almost eat everything, but there are things they don't. Also, they often have a clear preference for some food.
How can they differentiate this food? Do they use smell? Looks? How can they know smells of food they never had before?

To answer with a question: How do you decide what to eat (if you don't know whether something is edible)?
All animals have evolved taste and smell (and I'm sure even prior to eyesight). The purpose of taste and smell in terms of nutrition is to determine if something is edible. If something tastes bitter or extremely sour, this is mostly a warning sign for toxins or advanced microbial degradation. The same accounts for smell: If you let raw meat foul, the smell is unbearable. Why? Because our brain is telling us not to eat this.

Probably a lot of external and internal factors combined. But the most important would be the smell, eye sight and taste.
Smell can be, I would say 60-70%. When some particles arrive to the smell receptors, htne on the cellular level the receptor gives a "report" to other parts of the bady, especially brain etc. E.g. some seabirds, like storm petrels, recognize the odor of a compound emitted by krill, their main fare.
Almost all birds have great eyes, so this is a great long-distance food check.
But to be honest the taste is also a big issue and I think that all birds go through a phase when they eat everything and after learning what tastes good and bad (with combination of how it look like before they eat it and how it smelled, the infomrmation is stored in the brain.
Even though the birds have problems with complicated thought processes in their brain, I think that they are more than capable of storing and reusing this "good-bad-food" information from their brain.
There could be other factors like e.g. some birds are allergic to some food (yes, animals can be allergic too, even though their immune system is much stronger then ours) and the body will store in the brain to not eat that in the future.


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Insulin and monoclonal antibody production
When producing insulin, the gene for its production is inserted into the plasmid of a bacterium that is allowed to replicate freely.
Why can't the same thing be done with antibodies (as I understand it, currently cancer cells are fused with mammalian cells that produce these antibodies, and now the tumour is allowed to replicate, much like the bacterium, making more antibodies)?
What is different about these two proteins that means fairly distinct processes of production are required for each?

See http://en.wikipedia.org/wiki/Glycosylation

I recommend that you take a look at this:

Jeong KJ, Jang SH, Velmurugan N. (2011) Recombinant antibodies: engineering and production in yeast and bacterial hosts. Biotechnol J. 6:16-27.

This fairly recent view discusses the progress and prospects for producing functional antibodies in yeast and bacteria. As pointed out by @Nick in the comment to the OP, the main stumbling block in both cases is the engineering that would be necessary to ensure correct glycosylation in the heterologous expression systems. This quotation from the cited review sums up the situation:

The N-linked glycan structure in the Fc region of antibodies is indispensible for binding to receptors (FcγRs), but glycosylation has been one of the major limitations in choosing possible production hosts. Eukaryotic yeast as well as bacteria, including E. coli, have not been used as the main hosts for the production of recombinant antibodies (full-length IgG format) for use in humans because of glycosylation problems.

They do however go on to discuss some interesting developments such as the expression of a Campylobacter N-glycosylation pathway in E.coli, as well as strategies for the production of functional antibody fragments.


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What makes teeth feel sticky after drinking Coca-Cola?
I asked some of my friends and we all agree that teeth feel funny after drinking Coca-Cola. Other similar soft drinks also cause this effect, but this one most noticeably. It's like teeth become sticky and moving them against each other (by moving jaw) creates rubbery feeling.
What ingredient in this soft drink makes teeth like that?

I'm not sure where this question belongs, but as I'm interested in whatever ingredient causes this effect, I posted here. Not sure about tags, too.

we don't have zero in our region, so I can't compare

I see the question as wildly off topic. We are not a site for everything about food; we only focus on how to cook food, and all effects of the food on the body are off topic. The last rule mostly saves us from healthiness crackpots, but even if your question is not so likely to attract them, we still don't have the expertise to answer it.

I could imagine that happens due the calcium in the saliva. This reacts with the phosphoric acid from the coke to calcium phosphate, which is more or less insoluble. I am not sure though, if this thread fits here.

The sticky feeling comes from the sugars present in soft drinks. The sugar sticking to the surface of the teeth is then broken down into acids by bacteria and this affects the teeth. A list of the amount of sugars in different soft drinks can be found here. Also reading the dental decay section of Wikipedia gives the info that many carbohydrates are present including glucose, fructose and sucrose. On a dentistry forum (reference), it says that even artificial sugars can stick to teeth and get metabolized except xylitol.


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Molecular animations of, say, protein synthesis, are simplified, but how exactly?
In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein as if drawn by a magnet. As far as I know they move randomly. But still, translation occurs at a rate of about 15 amino acids/second and 75 ATP/second, so the rate of gobbling shown in the video clip is not off the mark.
I can think of two explanations:
1) The microscopic world is counter-intuitive. It is so frenetic that normal diffusion is enough to supply the hungry protein. The video simply doesn't show all the input molecules in order not to clutter the picture but essentially it is correct. However, amino acids are not small, and they are attached to the much larger tRNA, so they must be moving relatively slowly by Brownian motion.
2) There are additional helper proteins that concentrate or channel amino acids and ATPs in the vicinity of the ribosome or replicator. Never heard of these.
What is the real explanation?
Edit: To clarify, the question is not about the simulation side of things as such, such as how hard it is to actually make a true simulation. Most simulations, including weather prediction, involve a certain degree of approximations and simplifications. But in this case, there is something definitely untrue in the video clip, namely the molecules being attracted to the ribosome. As explained by a moderator, this means that it is not a true simulation but a "cartoon". So the question is: what would an ideal "non-cartoon" true simulation look like? Would the tRNA be diffusing in at a very fast rate, or are there helper proteins that, for example, tether tRNA in the vicinity of the ribosome? The moderators seem to indicate that diffusion is enough, but I would like to see a reasoned out answer with numbers that show this is the case.

tldr:

Making these things accurate representations is really hard
Accurate representations can be hard to look at anyway, so aren't always good to convey understanding

Molecular dynamics simulations that span long periods can be really expensive because of how computationally demanding they are, and they rely on accurate structural information about all of the molecules involved which isn't always available. The animation you linked might not be an actual simulation for that reason, but you'd have to check for yourself. Really fine grained accuracy probably isn't a priority for making a cool teaching tool like this one, you just want people to understand the just of it and the Brownian motion there might be a stylistic choice. Again, you'd have to chase it up for this specific example, I just want to give you something generalizable to other animations.
To make macromolecules like this actually interpretable by humans it's important to simplify them. One of these simplifications is normally called a 'cartoon', I don't think they guy in your comments was taking a dig at credibility of the video. It's also important to hide all the water molecules because they get in the way of you and seeing what's going on, so that's another way in which it's been simplified.
If you haven't already, have a look at some proteins in the PDB on the structure viewers and switch the mode from the cartoon/ribbons to other models like ball and stick. Ribbons are a useful way to simplify the structure representation so that you can see what the backbone is doing.
Here's one that I like:
https://www.rcsb.org/3d-view/4KEY/1
And you're right, at the systems level of something like protein synthesis, lots of stuff is involved and it's not practical to show all of it. For something like that it's easier to show these processes a a graph (term for connected nodes), check out the KEGG database for examples:
https://www.genome.jp/kegg/pathway.html#cellular
Hope this helps

What I don't understand is, why exactly is it so hard to simulate accurately? Is it because there are many more tRNA molecules than can be shown clearly (they would clutter the visual), or is it because the molecules are moving much faster than in the video clip (you would hardly see the tRNA fly by)?

It's more the number of time steps and the number of atoms in the simulation. So in that video we have a few different proteins, some DNA, tRNA etc and a lot of water molecules (which are hidden). That's a lot of atoms and for each one you need to calculate its new coordinates between each time point based on its local environment. So the demand on a computer is really huge. Also all the parameters are based on measurements taken from model systems like dialanine (maybe, out of my comfort zone a little bu here),  which might not be perfect. If this doesn't help, could you restate the question?

From David Goodsell's The Machinery of Life:

To get an idea of how fast this motion is, imagine a typical bacterial cell, and place an enzyme at one end and a sugar molecule at the other. They will bump around and wander through the whole cell, encountering many molecules along the way. On average, though, it will only take about a second for those two molecules to bump into each other at least once. This is truly remarkable: this means that any molecule in a typical bacterial cell, during its chaotic journey through the cell, will encounter almost every other molecule in a matter of seconds.

The Baffling Intelligence of a Single Cell by James Somers and Edwin Morris says if we scaled up a cell to a football field, basketball-sized proteins would fly at 1,800 km/h (1,100 mph).
Imagine how fast you smell burnt toast. And those molecules had to cross meters. The cell is tiny. Even with entirely random movement, every possible molecular alignment happens pretty quickly.
In a visualization, of course, we only see the one molecule that arrives at the correct place and angle. We don't see the millions of other collisions that didn't result in a reaction.

The good explanation is the second part of your question which you never heard of.
Actually for every movement in the cell, proteins play important role rather than nature of solvent (hydrophobicity, hydrophilicity or other forces) play any significant role. Brownian movement is also insignificant as you know AA (Amino Acids) can be more polar or less polar. Also they can't guide themselves to the desired location in the cell. Proteins which relocated them, cause their faster efficient and direction movement (may be due to formation of gradient or some sort of pulling pushing force due to interaction with other proteins.)
[UPDATE]
Exploring more into this, I came to know that the movement of anything is dependent on a gradient (May be concentration, electrochemical, pH etc...). So everything inside the cell is well planned and well documented inside the genome.

Please cite peer-reviewed papers or reviews that provide evidence for your assertion that there are proteins that relocate amino acids in a cell.

Better I move to researchgate or some other place or I try to publish my review paper than arriving here. You are continuously engaged with my interaction.

That is your decision, however it may be worth your while reminding yourself how SE works. It is a Q&A site in which answers are assessed, not only by the poster but also by other members of the site. If you make an assertion without providing evidence in support, the poster has no way of knowing whether or not you are right. Nor can other list members who may know something on the topic assess your answer properly. In this case I could have just said "this is wrong", but perhaps there is some recent work I have missed. So it was more appropriate to offer you the chance of providing evidence.

So there should be instruction to search on PubMed, Sciencedirect or Scopus should all those answers. Why to create redundant text?


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Are a bonsai tree and its normal version the same species?
I would like to know if bonsai type of a tree is a separate species from its normal version. Do they differ by genes, or is it just a matter of different physical care?
Can I grow a bonsai tree from seed of a normal outdoor tree (of course, I understand that not every species will endure being dwarfed)? Can I grow a normal outdoor tree from some seeds labeled "bonsai"?

I'm voting to close this question as off-topic because it should go to Gardening.SE

Yes. For any species that it is possible to grow as a bonsai tree, it is also possible to grow that species as a non-bonsai tree. The process of creating a bonsai tree involves growing a tree in a severely restricted pot with a minimal amount of soil, and trimming both the roots and branches to maintain a desired shape and size. It is the small growing space and regular pruning which keeps bonsai trees small, not the genetics of the tree.
You may wish to check the list of species used in bonsai on Wikipedia to get a sense of which species make good bonsai plants.

What if we grew bonsai trees for many generations, selecting the individuals "most suited" for the bonsai process? I don't know how long it would take, but eventually there should be genetic changes to help the plants adapt to the selection.

Sure, you could. That would be standard artificial selection. But given that bonsai as currently practiced doesn't require such selective breeding, why would you make the effort?


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Why does blood come from mouth when people are shot in the chest area?
In almost every movie scene when a character is shot in the chest area, some blood comes from his mouth or sometimes even coughs blood before he dies.
Are these kind of scenes realistic/possible? If yes, why does blood come from mouth in this situation?

Substances such as blood trigger the Cough reflex, so if for any reason blood accumulates in the airways, it will be ejected this way.
If you have a look at chest anatomy, you can see how this could be caused (look at Trachea down to the lungs, aorta and the carotid arteries above the heart). A shot through the chest can peforate many large blood vessels, along with the airways, and cause leakage inside.
I would consider it quite hard to hit the aiways like that though, the bullet would have to enter the chest quite near the centre as the cough reflex is not triggered by substances in the lung itself, only in the airways. There may be other ways of blood getting into the airways, but I would assume that a scene with a shot near the breast and then blood coughing would be unrealistic.

Image source: Micheau, A (2010) ANATOMY OF THE MEDIASTINUM: ILLUSTRATIONS AND CROSS-SECTIONS. From: http://www.imaios.com/en/e-Anatomy/Thorax-Abdomen-Pelvis/Mediastinum-Illustrations

Nice answer, +1. Could you include a link to where you got the image from please?

Here you go, there's many more nice pictures where that came from :)


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Which ionic channels of Pacemakers can work in very low frequencies in extrasystole?
At frequency 0-3 Hz.
Like computer processors which can work at low frequencies and controlling under- and overvoltage.
Normal most significant channels are Ca2+ and K+ that are changing.
However, I am not convinced that they can work with such a low frequencies.
There must be some other channels that are triggering the extrasystole on.
Which ionic channels of Pacemakers can work in 2-3 Hz triggering extrasystole?

I think none.
It is so specific frequency range that the possible sources are

autonomic nervous system and
some reflex arch.

Also, the frequency is logically low with autonomic triggering.
My conjecture is that sympaticus starts up extrasystoles.
I think it must go through some reflex arch to be so specific.


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Why HIV patients have greater virulence of M.tuberculosis?
I am reading Murray Microbiology book.
Some facts

M. tuberculosis is an intracellular pathogen.
At the time of exposure, M. tuberculosis enters the respiratory airways and infectious particles penetrate to the alveoli where they are phagocytised by alveolar macrophages.
In contrast with most phagocytised bacteria, M. tuberculosis prevents fusion of the phagosome with lysosomes (by blocking the specific bridging molecule, early endosomal autoantigen 1 [EEA1]). NB probably here something relevant
At the same time, the phagosome is able to fuse with other intracellular vesicles, permitting access to nutrients and facilitating intravacuole replication.
Phagocytised bacteria are also able to evade macrophage killing mediated by reactive nitrogen intermediates formed between nitric oxide and superoxide anions by catalytically catabolising the oxidants that are formed.
Dissemination to any body site occurs most commonly in immunocompromised patients, like HIV patient.

If you read this article, you will find that CD4+ and CD8+ T-cells are probably the major mediators of the immune response against M. tuberculosis. Since HIV severely depletes the number of CD4+ T-cells (and to a lesser extent other kinds of lymphocytes), it stands to reason that the frequency of infection and virulence will be substantially increased in such patients.

Thank you very much for your answer! I extended it by reading Murray and adding the result below.

I think one reason for greater virulence is the fact that M.tuberculosis prevents fusion of the phagosome with lysosomes.
I think this picture is little relevant here

I am thinking what is happening in these two parts here:

This answer does not provide enough support why there is greater virulance in HIV patients than in normal people.
And particularly why the preventation of the fusion of the phagosome with lysosomes leads to it.

Extension to Kanchi's answer by using Murray Microbiology textbook
Dissemination to any body site occurs most commonly in immunocompromised patients, like HIV patient.
CD4+ and CD8+ T-cells are the major mediators of the immune response against M.tuberculosis.
Since HIV severely depletes the number of CD4+ T-cells (and to a lesser extent other kinds of lymphocytes), it stands to reason that the frequency of infection and virulence will be substantially increased in such patients.
In patients with HIV infection and with a low CD4 T-cell count, the disease usually appears before the onset of other opportunistic infections, is twice as likely to spread to extrapulmonary sites, and can progress rapidly to death.


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Which animal species are known not to murder (a targeted attack leading to death) members of their own species?
Is there any evidence to suggest that some animal species do not murder  (a targeted attack leading to death) members of their own species? If so, which are the relevant species?

I think it might help to give a little bit more context - is this purely idle curiosity (in which case the answers will be all over the place) or do you have some particular goal ... ?

I asked this question from a general interest, as a view on murder (and the lack of it) from an ethological perspective.

Here are a few suggestions:

Any coral
Any sponge
Blue mussels
Sheep
Dugong
brown-headed cowbird
Blue whale
Common earwigs
Plasmodium falciparum (causing malaria)

If by the use of the term "evidence", you are expecting a peer-review paper that discuss the matter, I am afraid you wont find any as it is not really a question of interest to researchers. If you can prove wrong any of the above suggestions I will be happy to remove it (and eventually add some others).

Thank you very much for your answer. Would you think it would be possible to create some kind of a preliminary classification, as to categorize species into particular reasons which may cause the inability to, or non-occurence of, killing their own?

I suppose you would based the distinction based on whether a behavioural change might change the ability to kill an individual from the same species. You might quickly get into semantic issues esp. with species that have no brain. Also you would quickly run into the issue of guess work as you can't test the ability of a blue whale to kill another one because you cannot play out with blue whale behaviour as you want (and that would be way too expensive anyway).

As your follow-up question is a guesswork type of question, you might have better luck on WorldBuilding.SE but I am not quite sure what their rules are.

Did you mean the plasmodium parasite when you meant malaria?

Yes, that's what I meant. I edited to Plasmodium falciparum. I was looking for something deadly which does not kill members of its own species. There might be more obvious ("more true") examples.

@Remi.b Pandas do exhibit aggressively dangerous behaviour, therefore it's likely that some pandas have killed eachother. Cf. e.g. https://www.washingtonpost.com/opinions/five-myths-about-pandas/2015/08/28/d4a96b1c-4bfe-11e5-bfb9-9736d04fc8e4_story.html: Indeed, they do harm one another, particularly when males are establishing dominance or competing for females. Males in China’s Qinling Mountains are often observed with torn ears and bite wounds from tussling with other males. And in 2007, the first captive-born male reintroduced into the wild died after an apparent fight with other pandas.

@Remi.b I assume that the same counts for sheep? I am not inclined to think that, even regarding domesticated sheeps, the features which would normally account for dangerous damage during aggression have been bred out by domestication?

@Remi.b Regarding the questions surrounding "semantic issues" which you raise, I assume it's best to define killing as murdering due to a targeted attack. I have adapted my question accordingly.

@Remi.b The brown-headed cowbird is also known to be aggressive and kill other birds (cf. e.g. http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1188&context=usgsnpwrc). Why can we be sure that this doesn't sometimes happen to members of its own species?

It is a fundamental concept of the philosophy of knowledge, you can't ever be sure that something is not happening. I just know there are not territorial and I don't think they fight for access to mate.