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What is the definition of a mutation?
There are two alleles that determine the sensitivity of a person to Coumadin (a medicine for blood thinners used to treat a stroke etc). Sometimes you encounter the terminology that one has a mutation on both alleles (father's and mother's side). But why is that called a mutation and not just a variation? Does a mutation mean that it changed during lifetime, or is the difference between mutation and variation arbitrarily defined? Or is there really a kind of standard taken where deviations are considered to be mutations?

Good question!
The term mutation can be used with two different meanings. Each definition can further be split into two different more detailed definitions. The reason for this slight mess is mainly historical. In short, a mutation can refer to

An event

narrow sense
broad sense

An allele

definition based on ancestral/derived states
definition based on frequency

Before going into the details of these definitions, it is important to first define a few other terms.
A few other definitions
The terms I want to define here are Locus, polymorphic locus, allele, nucleotide and phenotype.
In short (simplified version), a phenotype is the way an individual look. The variations of phenotypes of the individuals in a population depends upon the variation of genotypes and the variation of environments that they encounter. This concept is very much related to the concept of heritability. You may want to read more about it here.
The DNA sequence is made of four nucleotides. It is the sequence of these nucleotides that affect the phenotype of an individual
A locus is refers to the position of a DNA sequence of arbitrary length. At a given locus different types of sequence can exist, such a coding or non-coding sequence, a gene or just an intron, only a few codons, etc..
An allele is one variant of a sequence (often a gene) at a given locus. If, in the population, more than one allele exists at a given locus, than the locus is said to be polymorphic. Most polymorphic loci have only two alleles. In such case we can talk about bi-allelic loci.
Mutation as an event
A mutation can refer to an event.
Narrow definition
A mutation may refer to the event of a spontaneous change in the nucleotide sequence of an individual such as typically an indel (insertion or deletion of one or few nucleotides) or a substitution (substitution of a nucleotide by another one). In other words, a mutation can refer to the event of changing allele (eventually making up a new one) at a given locus.
Broad definition
The broad definition is similar to the narrow one expect that it encompass more types of genetic changes. In the broad sense, a mutation may refer more globally to any genetic spontaneous change. For example a whole chromosome deletion or a full genome duplication are examples of mutations.
In my experience, most often when the term "mutation" is used, it is to refer to the broad definition of mutation.
Mutation as an allele
A mutation can refer to an allele. Note however that very often we prefer using the terms "mutant allele", "mutant state" or just "mutant" as synonym to refer to this allele. Pretty much the only circumstance in which we would use the term mutation here is in sentences of the kind "Individual A carries the mutation.".
Definition based one ancestral/derived states
A mutation can refer to the allele that is derived from a more ancestral allele. Consider for example, a given locus was NOT polymorphic in the past. A mutation (in the sense of "event") occurs and the locus is now polymorphic. The allele that has been created by the mutation (in the sense of "event") is sometimes called "mutation".
Definition based on frequency
A mutation can refer to the allele that is at the lowest frequency in the population. For example, consider a bi-allelic locus with two alleles A and B. If the frequency of the allele B is lower than $\frac{1}{2}$ (that is lower than the frequency of the allele A), then the allele B can be referred to as the mutation. The reason for calling "mutation" the allele that is at low frequency is that most mutations are deleterious and as a consequence the mutant allele is often at low frequency. As a consequence, using the Definition based on frequency and Definition based one ancestral/derived states is often not important.
To address your question specifically
It is a little hard to directly address your question as it seems to have several misunderstanding on the concept of mutation. In the same time however, it feels like you are turning around the realization that there are several definitions in use.

Sometimes you encounter the terminology that one has a mutation on both alleles (father's and mother's side). But why is that called a mutation and not just a variation?

The term mutation (whichever definition you pick) is intrinsically related to the concept of variation in the population but not so much to variation within a single individual (homozygote vs heterozygote).
If an individual "has a mutation on both allele", refers to the term mutation as an allele (in the narrow sense probably) and not as an event. More specifically it refers to one allele at a polymorphic locus (probably a locus of only one nucleotide) within the allele considered at the larger polymorphic locus considered.

Does a mutation mean that it changed during lifetime

A mutation (in the sense of event) is a change that if often view at the moment of reproduction but the mutation may have occurred anytime in the lineage of the germ cells. Note, one may consider also mutation that occurred (during the lifetime of the individual) but in the soma cells. Such mutation will NOT be transmitted to the offspring.

Or is there really a kind of standard taken where deviations are considered to be mutations?

Well...yes! A deviation is a deviation to a reference. In other words, we can replace "deviation" by "one allele of a polymorphic locus" in your question. And yes, a mutation (in the sense of a given allele) can refers to one allele of a polymorphic locus.

Good comprehensive answer that I generally agree with. However, I think you should add a reference or two to make it more authoritative.

Also, can you comment on what should be the minimum frequency of a mutant allele to call it a polymorph or variant.

@fileunderwater I am not aware of anybody clearly defining these terms (except for broad vs narrow definition of mutation). One could only find examples of cases where "mutation" is used with one or another definition.

@WYSIWYG I do not think there is any minimum frequency in principle. The use of a threshold appears as a result of a methodological problem. Sequencing makes error and to avoid to consider polymorphic a locus that is not but where sequencing error occurred, we use a minimal frequency.

A couple of dictionary entries (containing both mutation as event and new allele vs parental type) and this page from Understanding evolution should be a start. My point is that the current, unsourced, answer might be read as your personal opinion, when most of it could be well-sourced.

Most polymorphic loci have only two alleles. Why? Isn't polymorphic more relate to the population level?

Both the terms allele and polymorphic are meaningful only when considering a group (or population) of individuals.A locus is polymorphic if, there are variants, at this locus, among individuals within your group. Those variants are called alleles.

What I was taught by people in genomics is that "variation" is preferred for an allele that was not private to just one individual or family, but was found in pretty much unrelated individuals, while "mutation" is preferred for a very recently changed allele that is private to one individual or their family.  Sometimes, it seems the "mutation" is preferred when you mean to imply a clinically relevant difference caused by that different allele (as opposed to a polymorphism, which is usually what we call a survival-neutral different allele) I would say that the term "mutation" is being used incorrectly in your case unless the variant just appeared de novo, but maybe they do mean it in the second sense, because this difference clearly has a clinical phenotype associated with it.

I have a hard time to think of any case where one could hesitate between using the term mutation or variation as one refer to either an event or an allele and the other refers to the existence of polymorphism.


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What is the term for "technical extinction" of yet alive animals?
What is the term for an event in which a species is still alive, but has no chance of future reproduction and the species will be considered extinct once the current generation dies out?
For example a species of a tiger that has the last 5 surviving members left and which are all related and all male. Hence, even though they are still alive, there is no chance that the species will be able continue their bloodline and hence are already "technically" extinct.

This is technically called Functional extinction. With no viable reproducing population the species will almost certainly become extinct. Note that humans could potentially mess with this through the use of reproductive technologies.

Are humans functionally extinct?  It is all but certain the species will become extinct.  Probably long before the sun dies.  But even if the humans figure out how to migrate to another solar system, that is just putting off the inevitable.

@emory All species were created at some point in time, and all become extinct eventually, whether that be hundreds, millions, billions of years into the future. Humans are not functionally extinct, at least not by any useful definition of the term.

Functional extinction is a bit more broadly defined. I don't know if it accurately describes the last living individuals of a species past the tipping point, but it's still a good answer (upvoted).

For this matter, I'll call it Ecological Extinction. That means you still have an extant population, but the individuals in which you are focusing on do not interact any longer with their surroundings and environment as they should. For ex., they're no longer preying or being predators, they no longer reproduce because effective population (Ne) isn't enough.
There's an example in which you can make some research on, and it's about the Ecological Extinction of Nomascus leucogenys (white cheeked gibbon) in Yunnan Province, China.
There are some papers about it, which you'll easily find if you go to Google Scholar.
Hope I helped.

David, fantastic example. Do yo have anymore of these?

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Can someone help me answer or explain how to answer questions about DNA coding capabilities?
How is it that a DNA coding system with only 4 bases can yield so many possibilities? Also, how many unique coding sequences can there be with a DNA code that is 8 base pairs long? Hint: 4^n combinations. I've gone through this in my textbook, but I don't understand how to get the answer for it.

The title should be an actual, specific question. Also, homework questions are discouraged if you do not include an attempt to solve them (or at least some initial ideas).

I agree, you should think about this, though I gave you an anwser which I hope will get you to the answer to your problem set.

4 bases (A T C G) leads to 4 possible value per bit of information, which then leads to the formula: 4^n (n being the number of base). For the first part of your question regarding how can you have so much information, it has to do with n, as you increase the number of bases the number of different combinations increases exponentially. For a comparison, your computer stores information in a 2 value bit system (1 or 0).
If you plot the number of possibilities, you will see that DNA outpace computers very quickly, as an exponential of base 4 will go faster (2*2 = 4, 4*4 = 16, already at 2 bits you have 4 times as many possibilities)

With that in mind, you can compute the number of possibilities for any given number of bits (or bases in your case).

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Cesium-137 From Fukushima Meltdown
I've been reading up on the Fukushima nuclear meltdown and its effects it had on the environment. The iodine-131 initially released from the incident decayed after 8 days, but other isotopes such as cesium-137 and strontium-90 have a half-life of 28.7 and 30.2 years (about 300 years to completely decay).
Apparently, large quanties of cesium-137 were found in neighbouring countries as well as in seafood near Japan.
Now, for something like nuclear isotopes, not having the required knowledge can lead someone to fear something that might be harmless (or confirm some doubts about the issue), hence why I am here.
From my research on scientific websites and different governmental regulations, I found out that food and water in Japan have a legal limit as to how much cesium-137 a food item can contain. Especially since cesium-137 ressembles potassium and therefore being easily taken up by the body, this is worrying.
To my understanding, the way a radioactive isotope creates havoc in the body of an individual is that:

It ressembles a normal element we usually consume, like iodine, potassium for cesium-137 and calcium for strontium-90.
The body digests it and it is stored in the body.
It emits radation for a certain period of time, anywhere from 8 days for Iodine-131 to years for cesium-137.
The prolonged radioactivity from these isotopes causes cancerous cells to occur.
A tumour or other form of cancer develops.

If this is what happens for isotopes like cesium-137, how can it be possible to eat food or drink water containing ANY cesium whatsoever? Sure, the radiation isn't so bad, but what is important to take into consideration is that this is internal and highly centralized radiation. This is a completely different thing to external radiation.
For my questions about the topic, I would like to know three things (which could really put many doubts to rest).
QUESTIONS
The first is, is my understanding described above correct?
The second is, how does this affect us healthwise? We are stuck with these debris of cesium-137 and strontium-90 for the next 30 or more years, but what effect do they have on us?
If someone ingests an atom (or a small amount) of cesium-137, what affect will this have on this person's body?
Finally, for someone living in North America, how much of these debris are there, either that got here from the wind, products, food, water, etc.?
EDIT: If someone knowledgeable on the subject could answer the questions directly (highlighted by means of italics), it would be very much appreciated.

On Bio we encourage single, specifically targeted questions. Hence, I vote to close because it's too broad. I encourage you to reduce the stack of questions and generate one, or more separate questions.

@Christiaan Hi Christiaan. The specific questions are clearly listed at the end of the text. The text before that is simply to give the necassary and preliminary information for the questions. On the contrary, I think it adds precision. The questions alone could make the subsequent discussion rather imprecise. I highlighted the questions to make sure they can't be missed. Please do not close the discussion. Thank you.

If someone knowledgeable on the subject could answer the questions directly (highlighted by means of italics), it would be very much appreciated.

@samseva your last question on effects in North America is quite different and I would suggest that you remove it from this post.

@WYSIWYG Hi Wysiwyg. I should create a new topic instead?

@samseva you can but you have to add more details. Moreover, the question is more about environmental science than biology. So I am not sure if that would be considered on-topic, here. You may try posting that question in [earthscience.se] with some relevant additions.

I’m voting to close this question because the OP never corrected the problems pointed out in other comments (multiple questions, some of which are seem to be off-topic as asking for medical advice).

Most of the question has been accurately answered by @davidblomstrom, however regarding the internal exposure to of cesium-137, through ingestion or inhalation, allows the radioactive material to be distributed in the soft tissues, especially muscle tissue, exposing these tissues to the beta particles and gamma radiation and increasing cancer risk.
Also due to the consistency of Cs-137, it comes as a crystalline powder (due to its property of binding with chlorides) which makes it "easier" to be distributed after a nuclear fallout.

If the lead containers of Cs-137 are opened, the substance inside looks like a white powder and may glow. Cs-137 from nuclear accidents or atomic bomb explosions cannot be seen and will be present in dust and debris from fallout. read more

Sources

"Cesium-137." Vermont Department of Health. Vermont Department of Health. Web. 31 Jan. 2016. http://healthvermont.gov/emerg/drill/dirtybomb/facts-about-cesium137.aspx.
Albertini, Dr. R. "Cesium." University of Vermont, 2002. Web. 31 Jan. 2016. http://www.atsdr.cdc.gov/toxprofiles/tp157-c3.pdf.

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What are the biological processes of ingesting radioactive particles?
As someone who has basic understanding/education in physics and how radiation works, there is something that is confusing me and which I would like to shed some light on (I posted about this previously, but the discussion diverted to the risk of radiation in North America from the Fukushima incident, rather than the biological processes of ingesting radioactive particles).
With background radiation, and even relatively high levels of surrounding radiation, I understand that the risk is non-existant to very minimal. However, it seems that lately, people and officials are saying that food near and even in Fukushima is completely safe to eat.
In the case of surrounding radiation, sitting next to something that reads 3000 μSv/h is completely different to eating food that also emits 3000 μSv/h of radiation. In the former situation, once you walk off, the exposure stops. In the latter, radiation is constantly emitted inside your body.
Even more, the amount of radiation is not absorbed by the body equally, but it is usually very concentrated in a particular area of the body, as the particles lodge somewhere and sometimes bioaccumulate. From my understanding, the exposure to the surrounding cells is therefore more intense and prolonged.
To what degree is ingesting radioactive particles in food considered safe (or if at all), such as those in food near Fukushima, when taking into consideration that a concentrated and continuous source of radiation is different from an external one?

You are asking too many questions at once. Please narrow it down to, preferably, single question.

@another'Homosapien' Edited it into one question.

Your question has a rather glaring assumption which is that the amount of radiation emitted by food sources is equivalent to the amount of radiation received while sitting on top of the Fukushima plant. Even if a fish was as radioactive as an equal mass of concrete at the site, the dose you are getting at the site is because of all of the other things surrounding you.
The answer is simply that the food sources near the plant have been deemed (by the officials you mention) to emit a dose of radiation that is less than the level deemed harmful (again, by the officials you mention). It is of course possible that either the estimate of the radiation dose from the food is low, or the level deemed harmful is too high; that discussion is too broad for an answer here.

"The answer is simply that the food sources near the plant have been deemed to emit a dose of radiation that is less than the level deemed harmful." Any reference to back up that claim? I would strongly doubt that ... as far as I know, there are still places in Europe you shouldn't collect mushrooms because of radiation poisoning caused by Chernobyl.

@AlexDeLarge I carefully used the word "deemed" in my answer: I'm referring to the comments made by officials that say the food is safe. Personally, I'd avoid eating food from that area. I only meant to answer the OP's edited question about continuous internal vs external radiation. I edited my post to clarify this.

@BryanKrause That was an example (and yes, slightly exagerated to make a point) and a very small part of the post. 3000 μSv/h isn't the equivalent of "sitting on top of the Fukushima plant."  It's possibly more than 1000 times less than that.


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Estimated protein size using CDs data
The number of amino acids in a protein is important to predict their size. I used coding DNA sequence (CDs) to predict the average of the protein size of E.coli k12 from a sample provided by the seqinr R package. The size of each sequence is stored in variable x.
I used two histograms to fit the distribution of this variable and their logarithm.

I suggest that the log linear distribution is more reasonable.The average E can be calculated then:
E1=mean(x)/3

E2=exp(mean(log(x)))/3

Which average do I have to use?
Is there a correlation between the base composition and the predicted average?

You seem to have two questions but I don't really understand them. Here is my try to rephrase your questions. 1) What standard theoretical distribution best fit the observed distribution? This is a question of statistics, not biology. 2) Is there a correlation between GC skew and protein length? This question has little to do with the rest of the post.

Which average do I have to use? They are both the same, since you're using the exact same data. It's only the presentation that's different, as you're comparing a linear plot to a log plot.

@MattDMo Not necessarily. OP might want average log weight which is not the same as log of average weight.

Can you elaborate your question? I am having a hard time understanding what you are exactly asking for.


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Except for protecting ears from cold air, does a woollen cap provide any other significant advantage in winters?
I have woollen earmuffs and they are really comfy. They do the job of protecting ears well enough and I don't really have to worry about hair statics as they only cover ears and not my hairs. But many times I do get advice against using those earmuffs and wear a woollen cap instead.
If protecting ears is the only reason of wearing caps than I don't think i should leave my earmuffs but most people, though unknown of any scientific proof, claim that caps have more of a advantage than just that. Is it really so?

I've never seen woolen headphones, and have a hard time imagining them, but there is a lot of practical iinformation about the value of insulating (not necessarily wool) head coverings, and their value in heat retention.  Of course it depends: for instance, if you have a thick head of long hair, a hat is going to be of less value than if you're bald.

Well I suppose that you are imagining some music type headphones with made out of wool. That's not it. They are just like a cap except that they don't cover your head, just your ears.

If you mean something like this https://www.amazon.com/Fleece-Ear-Muffs-Warmers-Earmuffs/dp/B01LZGPNAI they're called earmuffs, not headphones.  They keep your ears warm: a cap will keep the rest of your head warm, too.  And if it's really cold, you can wear both :-)

Oh, thanks for the correction. Never knew their actual name, even the shopkeepers in my region didn't!

This article is what you need: http://www.bbc.com/future/story/20130708-is-most-heat-lost-from-your-head . Citing an excerpt from it:

[H]aving your head immersed in cold water only adds 10% to your overall heat loss in a cold pool. And given that the head accounts for 7% to 9% of the body’s surface, that doesn’t seem excessive.
But before you throw your collection of woolly hats in the bin, there’s another finding to bear in mind: when the head is allowed to get cold and the body is effectively insulated, the body’s core temperature drops a lot more rapidly than most people would expect.

In the end, wearing a woollen cap prevents the body's core temperature to drop too low. So if the rest of your body is well covered, you can skip the cap and put just your comfy headphones on; if, on the other hand, your clothes don't protect you well, putting a woollen hat on may be the easiest way to not feel cold.


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what do I need to use for protein protein interaction network
I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with another protein and a relationship
YAL011W YBR231C 0.804967
YAL011W YDR190C 0.790977
YAL011W YDR334W 0.840367
YAL011W YDR485C 0.815874
YAL011W YJL081C 0.574536

or sometimes I only see this
YAL011W YBR231C
YAL011W YDR190C
YAL011W YDR334W
YAL011W YDR485C
YAL011W YJL081C

what do I need to make a network ? and which structures normally used for making these networks.

What does PPI Stand for? Google UK suggests Payment Protection Insurance.  Please avoid abbreviations in titles and define them in questions.

@David sorry david , it stand for protein protein interaction

If you are asking solely about data structure, the two data formats that you have given are essentially the same. Each row represents a PPI, so in a network a line (edge) will link the proteins (nodes) given in columns one and two. Column three is an edge score, but it can indicate a few things,  confidence in the interaction or strength of the interaction. Your network will for a single central node with 5 nodes linked to it in a wheel shape.
PPI networks may also be represented in Proteomics Standards Initiative Molecular Interaction XML Format. This provides a controlled vocabulary for programmatic access to data.
The choice of data structure, there are many, is yours but simple formats (as above) are often sufficient. It is important to be mindful of the meaning of the network, are the PPIs directional? Do you have estimates of interaction (edge) confidence? Do you have estimates of interaction (edge) strength?
Cytoscape will allow you to visualise a protein-protein interaction network (PPI) such as the two that you have given. The Bioconductor project provides a number of options for the visualisation and analysis of PPI networks in R.
If you want to create or build a PPI network from a single protein or list of proteins then Cytoscape, and possibly plugins such as Genemania, can also do that.
String is also useful for building PPI networks. The developers have focussed on a wide-range of species and their data export options will allow you to see the same network in a variety of data formats.

your answer was great , I really appreciate it, Let me ask you a question, I have identified a list of proteins lets say 100, then if i go the String , it gives me a network, but I have no idea how it is built. Lets put it in this way, would you mind to give me a small example of if one has (as an example) 10 proteins ID, how he can reach to a network ? I already liked your answer , thanks

It's somewhat complicated but the creators of String have published a number of papers which describe how the  database was assembled. If you want to know about individual interactions clicking on an edge provides that information.

I have read many of them, I think it is like a black box, they normally work with physical interaction but not easy to understand :-) . can you give me an example using Cytoscape then ? do you know what I want to know? I want to know how to make the structure ready to be used for PPI network . this is all what I want to know .

If you are viewing a network on the string webpage clicking on the evidence pane below the network window provides a basic description of each evidence type. If you want a file of interactions to work with; Tables/Exports > "as simple tabular text." will provide a file that can be imported into Cytoscape, the first two columns are your interactions, import those first. Cytoscape provide good tutorials. Have a try and maybe ask another specific question if you get stuck? Goodluck.

ok thanks, I asked as a second question http://biology.stackexchange.com/questions/48624/how-to-make-many-cluster-in-one-figure


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map list of proteins into an already built network
I have a built reliable network which can be downloaded from here
http://www.filedropper.com/mynetwork
This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example
set1: Q9Y4Y9, P62310, Q9Y4Z0
set2: Q9Y333 ,P62312, O15116
set3: Q9Y4Y9, P62310
set4: Q9Y4Z0, Q9Y333, O95777, P62312
set5: O14497, P51532, Q8TAQ2, Q92922, P60709, O96019

I want to know if it is possible to map the above IDs to the built network? I don't mind using another algorithm, or software , only the result is important
Thanks

There are markup languages used for describing the network. They have the mapping and the network viewer loads the network file written in the markup language. You have to add more details; as it stands the exact question is a bit unclear.


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Finding out the best concentration for my plant extract to be used as drug for diabetes
I am using plant extract of Ajuga parviflora and found out that it possess anti-diabetic properties by using alpha-amylase inhibitory assay. I used various concentration 250 µg/ml(29% inhibiton of alpha-amylase), 500µg/ml(37%),750µg/ml(46%) and 1000µg/ml(63%). Basically, alpha-amylase results in increase in glucose level after eating food. So  i wanted to know that how could i find out that what is the best concentration of my plant extract to be used as drug.

This sounds like a homework question. Is it?

No, i am in my final year of my btech working on a plant and when a plant report some property then it is better if we can also give its best concentration.

You have to try to determine the best concentration.
Usually there are multiple clinical trials, first in animals, then in humans to

figure out the effective dose
look for side effects
compare the new drug's efficacy with existing drugs

I think this is better as a comment as it doesn't answer the question which in any case looks very like a homework question.

@David Actually I started writing a comment first and was expecting a "please don't answer in comments" response :) And it didn't occur to me this could be homework.

@David Owh, and the answer was: You have to try.

"humen"? spelling is human...

@SolarMike Yeah, was confused by the man/men and woman/women plural.

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Does meosis takes place in cell cycle?
Cell cycle is as follows- g1,s,g2,m( mitosis). Does this m stands for mitosis only or does this "m" stands for meosis also

Do you Know what the difference between mitosis and meiosis is?

The headline of your question seems to be incomplete. Is there a word missing?

Yes i know that

This is a question of convention really.
When people discuss the cell cycle, they usually refer to diploid cells (for diploid animals). So in your context, M stands for mitotic phase and does not directly apply to meiosis.
In meiosis, you could say that the cell also undergo a M-phase (actually two in a row, see footnote) but then the cell cycle becomes irrelevant as you get 4 haploid cells (gametes) that cannot duplicate by themselves anymore, effectively breaking the cycle.
Footnote
The M-phase in the cell cycle is a simplification of the process of cell division as this phase can be further sub-divided into a Prophase, Metaphase, Anaphase, Telophase (PMAT for the purists) followed by cytokinesis. In meiosis, you have a slightly different PMAT process during meiosis I (i.e. 1 cell -> 2 cells) followed by another PMAT (2 cells -> 4 cells). You can find additional information here.


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How can a mutator gene can cause a mutation when it is shut off?
defination of "Mutator" - a gene that increases the rate of mutation of one or more other genes.
However, in the book "Molecular Biology of the Cell" (bruce alberts) it states that when a mutator is shut down, then that shut down increases the rate of mutation. How does that process work? It seems to contradict its definition? If the mutator is shut down, then how can it create mutations?

Please give a reference of that textbook. In a general way, I can say that it works like Trp Operon https://en.wikipedia.org/wiki/Trp_operon


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The smaller the cell the greater its surface-to-volume ratio?
I read in a book that the smaller the cell the greater its surface-to-volume ratio (the surface area of a cell compared to its volume).
And larger cells have limited surface area compared to its volume.
How is this possible? I don't understand.

also consider the width of the surface and the number of atoms it contains as a lipid, it's not strictly geometry.

@comprehensible It is just geometry: http://www.brooklyn.cuny.edu/bc/ahp/LAD/C5/C5_ProbSize.html

This is more about understanding geometry than biology.

This is a very basic question that requires you to think in terms of geometry. Just think.

Did you try finding an answer yourself? Please share it and see our homework policy.

I am preparing for a entrance test.  I read this in a book for that test.  ...its not a home work

Homework policy should explain what questions are considered Homework, elementary topics which may appear trivial to biology professionals fall in it.

This is a basic property of geometry: for any given shape, area will be generally proportional to the square of the length, and volume will be proportional to its cube. (this isn't true for all shapes by any means; the "generally" refers to the principle that length, area and volume are 1, 2 and 3-dimensional properties respectively, not that all or even most shapes behave this way... although a lot of the shapes that happen to be common in the Universe do. See end of the answer).
For example, if a sphere has a radius of R, its surface will have an area of 4*Pi*R², and its interior will have a volume of 4/3*Pi*R³. This means its surface-to-volume ratio will be 3/R, which is inversely proportional to R, meaning when R increases it will decrease and vice-versa.
Like so:
\begin{array} {|l|l|}
\hline
R~(\sim length) & R^2~(\sim surface~area) & R^3~(\sim volume) &  1/R~(\sim surface~area / volume) \\
\hline
1 &   1 &   1 & 1~(= 1/1) \\
\hline
2 &   4 &   8 & 1/2~(= 4/8)\\
\hline
3 &   9 &  27 & 1/3~(=9/27)\\
\hline
4 &  16 &  64 & 1/4~(=16/64)\\
\hline
5 &  25 & 125 & 1/5~(=25/125) \\
\hline
\end{array}
Put another way, if your shape is growing in 3D then whenever you add a bit of length you'll tend to add much more area (because area is increasing along two directions of length) but you'll be adding even more volume (because volume is increasing along three directions of length), and more volume than area means the area-to-volume ratio becomes smaller.
It helps that cells are convex and can often be approximated as spheres, so the rule absolutely applies to them. It's different with squiggly shapes, or cases where you aren't growing along every axis (for example this principle is true if you increase a cylinder's radius and length, but not if you just increase its length; at that point length, surface area and volume are all increasing along a single dimension and thus all at the same rate; check the equations to see this). You often do find such squiggly, long or thin shapes in nature, and this is often an adaptation to get around the surface-to-volume decrease issue. Examples include your intestines, or the interface between the placenta and the uterus.

Its still not clear but thank you a lot for the answer

If the above answer is not clear to you, you might want to review your basics in geometry and algebra. You can as well comment specifically on what you don't understand from the current answer to let @Rozenn (and other users) what specific point needs to be clarified.

Got it now,.............

Let's approximate a cell by the simplest possible shape, a cube. Let's say the sides of the cube are 1mm (that'd be a large cell...). It's volume is obviously 1 mm3, and since it has 6 sides, a surface area of 6 mm2. That gives us a surface to volume ratio of 6. Now let's cut this cube in half. Now every part has a volume of 0.5 mm3. But what happens to the surface area? Four of the six sides are cut in half, and we keep one of the original side. But we also get a new side from where the cut took place. So our new area is 1+1+4*0.5 = 4 mm2. This gives us a surface to volume ratio of 4/0.5 = 8, which is greater than the original 6.

Tthnx bro.. your answer was also helpful

Others have mentioned cubes, and the principle is the same, but I prefer to think in terms of spheres.
The volume of a sphere is $\frac43 \pi r^3$
The surface area of a sphere is $4 \pi r^2$
The surface-volume ratio is thus $\frac3{r}$.
You can plot the function $\frac3{r}$ (see here), or just know that this is an inverse relationship -- as $r$ goes up, the ratio goes down; as $r$ goes down, the ratio goes up.
This is a different way of saying -- a smaller object (which has smaller $r$) has a greater surface-volume ratio.

The answer of Rozenn Keribin and Gerardo Furtado already explains the basic principle very well. I'd like to add another aspect, though. The effect of the increased surface to volume ratio also comes into play in the case off nanotechnology where small particles are compared to bulk material.
Consider the following example, where a cube with edge length 1 m is devided into smaller cubes with edge length s:
\begin{array} {c c c}
\hline
edge length ~s & number~of~particles & surface~area ~A (m²) & total~volume\\
\hline
1~m & 10^0 & 6*10^0 & 1~m^3 \\
1~cm & 10^6 & 6*10^3 & 1~m^3 \\
1~mm & 10^9 & 6*10^5 & 1~m^3 \\
1~µm & 10^{18} & 6*10^{11} & 1~m^3 \\
1~nm & 10^{27} & 6*10^{17} & 1~m^3 \\
\hline
\end{array}
As you can see, the total volume of all particles is always 1 m³ since you only cut the original cube of 1x1x1 m into smaller pieces. However, this example highlights that you have a much larger total surface area for all particles if they are smaller when compared to larger particles.
This means that the effective surface area of the obtained particles increases with the inverse of the square of the size while the total mass (and volume) stays constant. The surface of the particles is proportional to their (bio-)activity.

Anyway, you contributed ;-)

Still not clear but thank you a lot

@roxaite I modified my answer - please check, if it is more clear to you now.

Got it chris..thank you for simplifying your answer...


text:
Insect ID. Montreal, Qc (Canada)
I've found this bug in my appartment today and I was wondering what insect it is? Thank you.


text:
How are negligibly senescent animals dealing with senescent cell buildup?
Well known animals like the rougheye rockfish, which can be bought from the fish market, appear to be negligily senecent. Senecent cell buildup appears to play a key role in senecence, in mice at least (http://www.nature.com/nature/journal/v530/n7589/abs/nature16932.html). Is there no buildup of senecent cells in such negligible senescent animals over livetime?


text:
TRANSFAC Matrix.dat retrieve count matrix using BA or CC field
In the TRANSFAC Matrix.dat most of the motifs are given in the form of count matrix, but a few of them are given as some kind of frequency matrix. Those aren't ordinary PWMs because rows don't sum to 1, but these sums are more or less stable across rows.
I would like to have a raw count matrix in all cases, so I trying to retrieve the count matrix from those several "fractional" cases.
At first I thought that the field BA (Basis - statistical basis of the matrix) MANDATORILY starts with a number of sequences actually used in the matrix, so I would be able to simply multiply:
$$
\frac{\text{nucleotide value}}{\text{row sum}} \times
\text{number of sequences from BA}
$$
Moreover, sometimes in CC field there's information like: core from: 11
Unfortunately, the results are not very close to integer value, so this cannot be explained by rounding errors.
For example, in a certain row we have (btw, the row sum is $10.73$ from rounding errors):
3.99   4.07   0.87    1.8
BA  17 compiled ... sequences; total weight of sequences: 10.74
CC  core from: 11, length: 6
$$
\frac{4.07}{10.74} \times 17 = 6.4423
$$
$$
\frac{4.07}{10.74} \times 11 = 4.1685
$$
In my opinion these values $0.44$ or $0.16$ couldn't be explained by rounding errors. There's no description (link to article) enclosed to this motif. That aren't log-odds because all of them are non-negative values.
In this particular case, if I use the formula $count(x) = round( (\frac{x}{10.74}) \times 11 )$, the resulting counts will sum up to $11$, so it's fine.
This method with value $11$ replaced by $17$ doesn't result in set of values summing to $17$, but $16$.
The problem is that in another example I have
BA  17 compiled binding sequences; total weight of equences: 12.86
CC  core from: 1, length: 4
In this case I should rather multiply by $17$ not $1$ to get the sum of $17$.
As you see, I cannot stick to either BA or CC for all such motifs.
How would you retrieve the raw count matrix in a such case and what could be the problem in my approach? (jumping between BA and CC values)
Could anyone explain how those values in matrix have been derived, is it some kind of log-odds?

So databases like TRANSFAC are of somewhat... variable quality. Those matrices maybe have been derived from a program that just doesn't output a count matrix, but instead outputs a frequency matrix directly. What I would do, and what i have seen people do in published papers, is just multiply the matrix by 100 and round down. It's a kludge, but you'd better be quality checking the matrices somehow anyway, otherwise you're going to get 90% crap.

Franky speaking, I rejected the idea of matrix multiplication by 100 from the very beginning, because I would get tremendous number of sequences, which would destroy the regularization process. I'm using a full regularization method (with numerically computing E, not approximation 1.5) by Sven Rahman, Tobias Muller & Martin Vingron. The tremendous jump from 17 sequences to 1074 sequences would substantially affect the regularization.

Ah, sorry, my mistake. I didn't look at your numbers carefully enough. it looks like either those are already PWMs as opposed to count matrices (i.e. the values are log(count_freq/background_freq) ) or somebody has already done something strange to them. If it's the former you should have noticed some negative values. If it's latter you can try and do something like making the BA 100 and rounding them.
Also it's not clear what algorithm you're talking about regularizing in that comment. Link?

I edited the question  to shed some light on my example. In my problem a particular regularization method is completly unimportnant, I only need the raw count matrix and that's all. For your curiousity (that won't help with this question) I'm using method from an article "On the Powern of Profiles for Transcription Factor Binding Sites Detection", which is in my opinion second to none.

Yes, unfortunately you clearly don't have the raw count matrix. The only other process which could have generated matrices like that is the process of adding pseudo counts. People often add things like (sqrt(BA)) before conversion to a PWM to avoid taking the log of zero. You could see if you can work out the original BA from that. In general though I'd avoid trying to recover bad data like that. Count matrices should be integers.

I'll simply stick to my method and always test it with BA value and if in this approach I don't get sum of results equal to value in BA I world simply tryb with CC value. Maybe I won't be force to use such atypical matrices without RAW count.

That seems reasonable enough. The paper you cite is a little out of date, and I'd recommend reading some more recent ones as well. And be aware that if you use their threshold selection method you're going to get rather different results than the p-value based thresholds used in most papers.

So, which more recent method/paper do you recommend as the most powerful? (method that not only control Type 1 error, but also let you leverage the Type 2 error - false negatives rate?

The basic method you're using is as good as any other simple model, and you won't do much better unless you want to invest a LOT more effort and do deep learning. The problem is that you can't pick any single 'most powerful' method because the threshold you pick will depend on the biological question you want answered. Also, be aware of what an approximation the PWM models are - you either have ChIP training data,which is v. messy, or PBM data, which doesn't reflect cellular conditions.


text:
Headshot = instant kill?
While whatching a film, I've been thinking about how does a headshot kill someone, and how long does it take?
For example let's say you've beeing shot by a normal (police) handfired weapon - no shotgun or sniper weapon.
I know that the rhombencephalon regulate the most important vital functions like breathing and if the shoot goes throught it, that there will be no change.
Question:
But if the bullet passed the brain throught the telencephalon, which function is mainly thinking, and don't hurt any
brain regions who handles life keeping functions (like the rhombencephalon)  do you die instantly (like in movies) or have any change (fall into a coma)?

Depends on which part of the head is hit (and bullet ballistics). Headshot=instant death only happens in Counter Strike :P

Of course I know, that it depends on which way a bullet go, but in case of it passed the lobus frontalis and damage not the highly critical functions whould there be a change?

Heard of the famous case of Phineas Gage? He survived but apparently his entire personality changed.

Yes, that makes sense to me, because the lobus frontalis handles emotions, personality, humor, ... and when it gets damaged some variables can be changed.

IMO this question is less about biology than ballistics. The effect of destroying a particular structure in the brain is probably known, including the likelihood of instant death (whatever that means). The likelihood that a bullet causes such damage is a separate question.

On my first day of an ER rotation (Charity Hospital in New Orleans), a man walked into the ER with a chief complaint of "I was shot in the head." Sure enough, he had a bullet hole directly in the middle of his forehead. On his review of systems, his only complaint was "headache". The only physical findings were the hole in his forehead and blood in the back of his throat. Luckily it was a small caliber bullet, it went right down the middle missing everything important, and he had swallowed it after it exited the base of the skull. So... no. He didn't die.

@anongoodnurse this is really an interesting case !! Hope he's recovering well.

@anongoodnurse He ate the bullet after it had exited his skull? Or did it exit into his throat? Or am I misunderstanding you? Thanks for sharing either way - really interesting to hear.

@fileunderwater - It had exited the base of his skull at the back of his throat and he swallowed it (presumably in the gush of blood.) I found the bullet in his stomach when I did a pre-op chest xray along with xrays of his head. (This was a long, long time ago!) He stated he had never been shot before, so with the bone fragment locations and the history, that was the conclusion. I'm still amazed by the whole thing.

@anongoodnurse Ok, that makes more sense than eating it. Amazing story either way. Do you know if he recovered fully?

@MauroM - Charity was the busiest ER in the country when I was there. He didn't die while I was there, but he was kind of "lost to follow-up" (hard to keep track of.) I think he was fine, though.

@fileunderwater - As fully as we could tell. He was discharged to home without complications by neurosurgery/neurology. Can you imagine how easily it could have hit his spinal cord? Just amazing.

According to this article appearing on the website of the American Association of Neurological Surgeons, gunshot injuries to the head are fatal in 90 per cent of cases. Many victims die before reaching the ER, and the 50 per cent who survive the initial trauma die in the ER.

The comments on this question have pretty much covered everything I had to say. Generally, you're more likely to cause brain damage than an instant kill by shooting someone in the head, though it does depend on what part of the brain is hit and the kind of projectile being used.
Normal small-caliber weapons pierce bone and tissue and that's about it. Small arms marksman training teaches you to focus on center of mass because you're more likely to get a kill by bleed-out or organ trauma than the considerably-more-difficult headshot.
WYSIWYG mentioned Phineas Gage in the comments, who survived having an iron bar driven through his skull thusly. He suffered a severe change of personality but was otherwise fairly functional. (Full wikipedia article contains sections on various studies about brain damage).
The idea of a headshot being an instant kill most likely comes from use of hollow-point bullets and/or high caliber weapons like sniper rifles. Hollow-points expand on contact with or shatter inside the target, causing much more damage than a normal bullet. The larger impact area of a hollow-point or the higher velocity of a powerful rifle are what cause the familiar "exploding skull" visual.
(An additional personal theory: since headshots are much more difficult to achieve due to the small target, I believe they are used as an instant-kill reward in a lot of video games, adding to the myth. Realistically the victim is severely disabled, making it equivalent to a kill in game-terms, but would likely recover given proper medical attention.)
The extent of the damage, however, depends on what part of the brain is hit. I'm not an expert on neurology so unfortunately I can't answer that aspect of the question. Blood and/or fluid entering the brain through the wound, however, could very likely be fatal.
In summary: small arms like a police handgun wouldn't likely cause an instant kill with a head-shot. For practical purposes, the probable instant debilitation of the target may count as a "kill" without technically being immediately lethal.

Small arms are perfectly capable of killing via headshot. You have to take the caliber, velocity, type of bullet, location of impact, distance from gun to target, and path of travel of the bullet into consideration. A shot just above the bridge of the nose will kill with anything from a 9mm on up, and would likely kill with a hollow-point .22 with sufficient velocity to pierce the frontal bone. Most police sidearms these days are relatively high-velocity 9mm, larger but slightly slower .40S&W, and the even larger .45, which while relatively the slowest can still easily penetrate and kill.


text:
Empty room, Room full with stuffs & Auditory adaptation to reflection of sounds
Background
When a room is full with stuffs like furniture, electronic utilities, books etc. it's hard to hear reflections of sounds made by us (talking, playing an instrument, sound from falling objects).
But, when the room is empty we quite easily hear the reflections of sound which is according to physics perfectly legit.
However, what seems interesting to me that when we suddenly empty a room with stuffs, the change in hearing reflection of sounds has a great impact on our ear. I personally experienced  this phenomenon several times while emptying a room for cleaning and other purposes.
Question

Is it because of the sudden nature of the phenomenon described above, the phenomenon seems to have a greater impact on our ears?
What would happen if we try to get used to the empty room environment? Would sensory adaptation slowly diminishes our sensibility towards reflection?

Just to be clear, what do you mean when you say "great impact on our ear" ?

I am wondering if maybe this type of question could be answerable on Physics.SE? I have a feeling that there may not be a biological explanation, but maybe it could be explained by the soundwaves themselves. I'm sure someone there knows how sound-waves interact with different surfaces and themselves, and I'm sure someone there knows how noise-detection works.

@Bob I think it's more psychological than physical!

Well, bring it to Psychology.SE then. I was just trying to let you know that there might be more options =D

@Bob There is no Psychology.SE

Riight.. CognitiveScience.SE

@Dexter Greater impact than what it used to have!

@Bob But there is a psychology tag in this site


text:
Do some colors trigger more neural activity in human brain?
On this webpage I found this:

The study found that “globs” in the brains of monkeys reacted differently to colored
  stimuli, and reacted based on color. The brain was most triggered by specific colors
  (red, then green, then blue) and colors with the most saturation. What this tells us is
  that these colors immediately impact a user and draw attention.

Question: Do humans show similar increased neural activity to some colors?
Then I found a perception curve in this webpage

While this curve tells that yellow and green are seen before other hues while red and violet are difficult to perceive; I am not sure if yellow and green elicit more neural activity in the brain.
Anything to say on this matter?

The paper from Stoughton & Conways (2008), where the linked Design Shack webpage refers to, explains that in the visual nucleus in the brainstem (LGN) as well as in the primary visual cortex, most of the color-selective neurons are selectively responsive to colors in the red-cyan axis (Fig. 1).

Fig. 1. RGB color space. source: Commodore 128 forum
This indeed means that these colors evoke more brain activity in these regions of the brain.
Note that a perception curve mentioned on the linked D'Source webpage is nonsense terminology

Why do you think it's nonsense?

D Would you elaborate on why do you think its nonsense?


text:
Why do birds sing?
Some birds sing. But why do they do it?
Does singing gives them any biological advancement? Like in mating, communication etc. Or they do it for enjoyment like humans? ( Might be possible!)
Edit: I have seen most birds which live close to human habitation sing; I really don't know if wild birds sing like these birds. And another good thing is that they do it usually at dawn and dusk. So, it can be a kind of signalling. I think when dawn arrives, they do it for signalling others to go for searching food, materials to make nest with etc. At dusk, they do it for signalling everyone for returning home. Maybe it's kind of an hour-bell.
It's my guess. I don't know for sure!

@canadianer What did you edit?  I don't understand.

I was trying to improve the grammar. It's still a little off.

Maybe you'd be interested in why humans sing...

According to this paper:

Song Function and the Evolution of Female Preferences: Why Birds Sing, Why Brains Matter
by Stephen Nowicki and W. A. Searcy

A birds song can have two main functions.

Male bird's song is used as a mating call to attract Females. Females in turn prefer birds who can sing longer and have complex songs. The quality of a birds song is an indicator of their good genes. A bird infected with parasites is considered to have a considerably low quality song.

It is also used by Male birds to mark their territory. If a male bird hears another birds song it would start singing or increase the rate of its singing. Also in another study linked in that paper refers to a study where birds with punctured lungs who were unable to sing and had a hard time maintaining their territory.

And also a bird's song should not be confused with it's call. A bird's call is mostly used to alarm other birds of the flock of danger, communication and locating members of the flock. A call is less complex and more noisy.

But I also hear birds 'singing' (honestly, it sounds like shouting) at dusk. And if you have read the other answer, I think you know you're only talking about the dawn songs. But what about the dusk 'songs'?

@Mockingbird added another paragraph to address this

Some birds do sing at dusk (European example: Blackbird, every evening). Why should singing at dusk have a different reason?

There's actually info for that on the web:
https://www.google.fr/search?q=Why+do+birds+sing%3F&oq=Why+do+birds+sing%3F&aqs=chrome..69i57j69i60&sourceid=chrome&ie=UTF-8
quotes from easy to find web pages:
songbirds make up almost half of the world’s 10,000 bird species including warblers, thrushes, and sparrows.
Bird song is a very specialised form of bird call that, unlike all the quacks, honks and tweets we hear throughout the year, serves one function only – to ensure the breeding success of the singer, to indicate clearly that the singer is healthy and fit and ready to breed.
It's largely a boy thing, designed so that other females of the same species are attracted and males of the same species are repelled.
Bird song is most highly developed in a group of birds called passeriformes. Don't worry, we are surrounded by them, wrens, robins, blackbirds, song thrushes are all passeriformes. Some tropical birds are know to duet, with the female singing too.
Females need to know this if they are to choose the right partner. Then, the song has to say something about the health of the singer. A long, loud song for instance indicates a certain amount of stamina, a bird in good condition.
Similarly with repertoire. It appears that in some species, a wide variety of sounds in a song is especially attractive to the ladies. Many species even mimic other birds' songs just to increase their repertoire, and it's not unknown for other sounds, such as cats' calls, to be included as well.
As bird song is part of the breeding cycle, most birds sing in the breeding season. This means that birds will start singing in late January and stop singing in July.
They are prompted to start singing, it appears, by increasing daylight (more light sets their little hormones racing and in response, they sing).
They stop singing when they start moulting, usually July time, as the last thing you want to do when your feathers start falling out and you are not quite as quick off your perch is to advertise your presence to predators.
Some birds, of course, sing in winter, robin being the best known, but this is linked to defending feeding territories rather than breeding. Interestingly, in winter, female robins sing as well as males.
Just as there is a seasonal cycle to bird song there is also a daily cycle, with the most intense period being at first light, the so called 'dawn chorus'. Why sing so intensely at dawn though?
First of all, male birds may die overnight if they have not been able to feed well during the previous day.
So, first light is a time when when birds can announce their survival, and this advertises something of their feeding abilities to potential mates - and of course, it's important that females know if males can find food or not, especially when they will be relying on this after their chicks have hatched.
Also, a side product is that birds looking for territories can hear where the spaces are and move in.
Secondly, many females lay eggs at first light and immediately after this are at their most fertile. This is a time when males need to fend off other potential suitors, and as we now know, song is a key way they do this.
Hence the dawn chorus.

Are these all quotes? You should make that clearer and add citations.

They are excerpts yes, i read through 1-2 pages and chose the best information to edit from the BBC page and a couple of other pages titled "why do birds sing" ... i would love to spend more time on it, but considering that typing "why do birds sing" brings up 15 ornithologist zoologist pages titled "why do birds sing", i figured it was best to not take time over it beyond answering briefly and in great depth using resources that are 2 seconds of search away. searching google for 2 seconds is the minimum research necessary for a Stack question. wouldn t you say so?

I doubt that the original authors you plagiarized would care about any of that.

Are you having a problem? you should make that clearer and add adult behavioural credentials. Because i doubt that the comments you insinuated would make anyone care...  It's the BBC, a wildlife conservation and information broadcasting governement organization that i pay and that have never cared about anything like that, just like NYC museum archives. it's the BBC.

I thought I was quite clear: give proper attribution to your sources.

i thought i told you i don't like stentorians... i was tired last night my reply is from 12ocklock. the attribution got erased when i edited the question, as you may recall the original reply had attribution. i dont know where it went. erase the answer i don't have time for stentors.


text:
Why pain caused by blunt objects vanish after some time and return at the event of touching?
Background
When any bone/muscle of body is hit badly by a blunt object, it hurts pretty bad of course for some time. But, after some time the pain goes off completely or to some extent.
Then, if we touch the wounded spot, the terrible pain returns.
Why?
If the pain goes off as the healing process of severed tissues, blood capillaries, then why does it return at the event of touching?
My reasoning: I think there is a sophisticated pain mechanism responsible for this phenomenon.Firstly, pain warns our nervous system to be cautious against any new injury. As time goes on, sensory adaptation diminishes the pain. But the event of touching is a new pressure for the blunt wound.So, the pain comes back again. But, I need well-referenced answer to support my view.
Papers: The most relevant paper I've found till now: 1 which is behind paywall

Invisible? The pain is in the same place?

Well, then if the pain is gone, the damaged tissue is repaired, no? Then where did the new damage come from?

I am not even sure why the pain goes in the first place if it's not completely healed. Maybe our brain has this weird pain mechanism which after sometime reduces pain and then triggers pain when touched to give a signal that something is wrong. Maybe it's evolution.

Let us continue this discussion in chat.

BASIC REASON WHY THE PAIN DISAPPEARS FOR SOMETIME:
There are gating mechanisms involving pain both in the spinal cord and in the brain.
Although the pain gating pathways in the brain are multifold complex,the spinal pathway can be simplified.
The latter may be understood in a simplified manner in 2 ways:

When there is a nociceptive stimulus,the epicritic receptors are stimulated.Sensory fibres from them synapse with internuncial neurons which inturn transmits impulses via the ascending tract to the periaquiductal grey. This region is capable of inhibiting pain impulse transmission to the spinal cord or thalamus by modulating impulses via the descending tracts.
This type is called supraspinal control
Another spinal reflex-type gate control operates in which stimulus like rubbing over the pained area ,application of warmth or cold causes inhibition of pain.
This is due to the impulses by large type (myelinated)A-fibres which arises from the  rubbed areas synapse with the internuncial neurons which are already synapsed with the epicritic sensory neurons of the dorsal root.The ends of such type of fibres release neurotransmitters that inhibits transmission of pain impulses through the internuncial neurons .
This is termed as segmental suppression

WHY DOES THE PAIN RETURN AGAIN:
This is because the pain receptors are the slowest to adapt.It's exactly as you said because it keeps the body apprised of tissue damaging stimulus.
So when there is the return of the noxious stimulus we can understand the tremendous summation effect which takes precedence over the gate control.
This occurs by a greater output of neurotransmitters from the synapse of the pain sensory fibres which outdoes the inhibitory effect of the neurotransmitters favouring gate control of pain.


text:
Confusion about the role of capping and polyadenylation in nuclear transport
Before termination stage of transcription a GMP cap is added to the 5' end and poly-A tail to 3' end of mRNA.
The link(http://sciencing.com/role-rna-polyadenylation-5434666.html) says:

The poly(A) chain is important for transport of the mRNA from the nucleus where it is synthesized to the ribosomes where protein is translated.

I don't get this point. How does polyadenylation affcts the transportation of mRNA?
Wikipedia says abour capping's functions:

Regulation of nuclear export;
  Prevention of degradation by exonucleases;
  Promotion of translation (see ribosome and translation);
  Promotion of 5′ proximal intron excision.

I don't get how it plays a role in nuclear export.

What research have you done before asking it here?

Actually I read the importance of this activity but didn't understand some keypoints. I will edit it now.

@Mockingbird I really like this as a resource, I think you can start at the subheading Key steps in mRNA processing: http://jcs.biologists.org/content/joces/122/12/1933.full.pdf


text:
Was Myxomatosis Man Made?
I can't seem to find any conclusive information about the origin of Myxomatosis. According to Wikipedia

It was first observed in Uruguay in laboratory rabbits in the late 19th century. It was introduced into Australia in 1950 in an attempt to control the rabbit population.

However I find this passage unclear.
Was this a naturally occurring disease that we then used as a means of population control, or did we have a hand in its creation?

It was identified as a disease in 1896.  How do you think people were able to "create" viruses in 1896?

@layork That would depend what you mean by "create". As far as I'm aware, a virus present in rats doesn't mean that it is necessarily transferable to rabbits without modification.

Do you suggest that myxoma virus was first found in rats? @Pedr

Myxomatosis has natural origins in the wild rabbits of South America. In 1942 Aragao showed that wild Brazilian rabbits has acquired (not innate) immunity to the myxoma virus from a previous infection.


text:
Which species of Agave are known to have inedible flowers?
It is well documented that many species of Agave have edible flowers, however I keep coming across statements to the effect that "most species" of Agave have edible flowers. This implies that it is known that some do not, but I have been unable to find any specific references to species known to be inedible. I'm particularly curious about Octopus Agave (agave vilmoriniana), which I could find no confirmation either way, but would like to know any information & sources regarding the inedibility of any Agave species.

According to Wikipedia each agave plant produces several pounds of edible flowers during its final season.


text:
Enzyme Inhibition in relation to Aspirin
I see that aspirin (in part) works by inhibiting cycloxygenase isoenzymes and that this inhibiting is irreversible. I've had a few classes mentioning this topic in passing, but never with depth.
I guess my question regards the permanence of the word "irreversible." I assume enzymes have a life span, so to speak, and that the same isoenzymes both die and are being replenished at some given rate.
Am I correct in thinking that the cycloxygenase enzyme is permanently inhibited until its death (catabolism)?

As far as I know, aspirin is an acetylating agent,. meaning that it attaches an acetyl to a serine (via a covalent bond) inside the active site  of the cycloxygenase enzyme. With the active site now being unable to used, the enzyme will die by degrading (its structure will define this time) or denaturing (due to external changes in environment), whichever occurs first.
I have no sources, this is all from what I learnt a while back through textbooks and teachers, so I'm not prepared to write an answer just yet, but I hope this helps!

Yup. Inhibited until degradation since as @butallati mentions, they acetylated - chemically modified. In fact this irreversibility has a significance - that the enzyme can be replenished in the endothelium but not in the platelets.

I had an interesting insight from a lecture: "If someone takes irreversible blockers, will you ever recover the function of the tissue? Yes. Old receptors will be catabolized and eventually new receptors will be synthesized by the tissue." So its death is from catabolism

@adNauseam ""If someone takes irreversible blockers, will you ever recover the function of the tissue? Yes". Up to a point. If you take enough of an irreversible acetylcholine esterase inhibitor (like sarin), you won't recover the tissue function… since you'd be dead.

‘Reversible’ and ‘Irreversible’ are standard designations in enzyme kinetics. It may be that your instructor was using the word in this sense.
As already commented, irreversible inhibitors bind the enzyme in such a way that they don't dissociate from it. Either they form a covalent bond or their affinity for the binding site is extremely high. Reversible inhibition is generally found with competitive inhibitors — those that resemble substrate enough to bind to the active site and compete with the substrate for it. Unless they have an extremely high affinity there will be an equilibrium between bound and unbound inhibitor, and the inhibitor can be competed out by substrate — i.e. the binding is reversible.
You can read about this in more detail, but still at an introductory level, in the Wikipedia article on Enzyme Inhibitors  or this section in the online version of Berg et al.


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Selectivity of anti-bacterial affect of oxygen
As far as I know, oxidizing agents (AKA reactive oxygen species or ROS) are potent antimicrobial agents that act on a broad range of bacteria and viruses, as well as inactivating certain toxins. Is this correct? How do ROS exert their effect on microbes? Do they inactivate certain toxins, and how?
Few quotes from this article:

Oxygen destroys pathogen.

Oxygen disrupts the integrity of the bacterial cell envelope through oxidation of the phospholipids and lipoproteins.

Aerobic organisms possess enzymes that deactivate oxygen so that reactive toxic molecules containing oxygen do not damage the cells.

Do ROS selectively kill pathogens but not non-pathogenic microbes or the multi-cellular organism's cells? If so, what causes ROS to only damage pathogens or damage them significantly more than it damages the organism's cells and non-pathogenic microbes?

The source you quote is a semi-literate advertising puff. What gives it away is the sort of anthropomorphic nonsense "But there are unicellular microorganisms that fear oxygen" which you used in your original title. This will not do on a scientific site. Microorganisms are unable to "fear", just as oxygen is unable to "know". I have modified your title and suggest you read about anaerobic bacteria.

First and foremost, the comments may be right that this question is being asked with the ulterior motive of promoting a product, but it is nevertheless true that hydrogen peroxide and other oxidants (AKA reactive oxygen species, or simply ROS) are potent antimicrobial agents, so I'm going to attempt to answer this question concisely.
I only study immunology tangentially, but my studies on aging usually overlap with immunology due to the role of reactive oxygen species (ROS) in diverse cellular pathways, including DNA damage, protein folding, and immunology.
The ROS produced by organisms (particularly hydrogen peroxide, peroxide radicals, and superoxide) aren't "selective" antimicrobial agents any more than bleach is. Both endogenous ROS and exogenous oxidants like bleach will attack (oxidize) any sufficiently strong electron donor:
https://en.wikipedia.org/wiki/Bleach#Antimicrobial_efficacy
ROS act both directly and indirectly to promote immunity, ROS are produced in many epithelial tissues constitutively (i.e. independent of infection) as well as in response to infection by pathogenic organisms. The detection of pathogenic organisms is cell-dependent, and immunological signaling pathways determine whether or not ROS production is appropriate; this is one mechanism by which ROS can be used "selectively" against microbes. On the other hand, innoculation with non-pathogenic microbes can be sensed through immunological signaling pathways at the cell/tissue level and can result in a reduction of extracellular ROS production below constitutive levels to allow colonization by symbiotic microbes:
Yang, H., Yang, M., Sun, J., Guo, F., Lan, J., Wang, X., & ... Wang, J. (2015). Full length article: Catalase eliminates reactive oxygen species and influences the intestinal microbiota of shrimp. Fish And Shellfish Immunology, 4763-73. doi:10.1016/j.fsi.2015.08.021
This article describes this phenomenon in detail, while giving a brief introduction to the other relationships between ROS and immunology that I mentioned. I should stress that this phenomenon is probably not the primary determinant of the effectiveness of ROS as an antimicrobial agent; your comment about microbes with negative reduction potentials is more relevant, although not precisely correct.
The net oxidation/reduction potential of an organism has less to do with the effects of ROS and more to do with their resistance to it. Even if there are plenty of reducing agents (AKA antioxidants) around (NADH-dependent enzymes, reduced glutathione, thioredoxin, etc.), proteins and lipids can be temporarily or permanently damaged by oxidation. Even if antioxidants are available, this damage can overload the cell's capacity to quickly reverse the damage, or even temporary damage can send pro-death signals by disrupting proteins/lipids involved in cellular signaling (see wiki article on bleach). See the following section of the wikipedia article on antioxidants (and its references) for a more thorough understanding of the interplay between a cell's antioxidant capabilities, it's production of ROS, the accumulation of oxidative damage, and the effects of oxidative damage:
https://en.wikipedia.org/wiki/Antioxidant#Oxidative_challenge_in_biology
Ultimately, a microbe's ability to tolerate temporary oxidative damage (a complex phenotype to explain) combined with its ability to rapidly reverse oxidative damage (based on expression of antioxidant enzymes, accumulation of glutathione, and cellular oxidative metabolism) are the primary determinants of a microbe's resistance to ROS - which is the more accurate way to describe the concept that ROS are (weakly) "selective" for certain kinds of microbes.


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Are there well studied examples of ERAD-mediated membrane insertion, especially from viruses?
Membrane insertion of transmembrane proteins typically requires highly hydrophobic alpha helixes at the N-terminus, N-terminal signal peptides, tail anchors, or a combination of the three.
Byun, H., Gou, Y., Zook, A., Lozano, M., & Dudley, J. (n.d). ERAD and how viruses exploit it. Frontiers In Microbiology, 5
These processes occur co-translationally and are mediated by the SEC translocon and associated factors (especially GPI anchor transferases for tail-anchored proteins). However, my undergraduate research is focused on a viral protein which appears to be translated in association with SRP and co-translationally translocated to the ER by the translocon, but is not anchored to the membrane during translocation. This was shown (by others) by purification of the ER-associated fraction of the protein and centrifugation showing the majority pelleted with the dense, soluble fraction. A small fraction pelleted with the low density membrane-associated fraction, and my research further suggests that this membrane-associated fraction is important for its escape from the ER.
The protein I am studying functions in the cytoplasm, not in the ER or in the secretory pathway, and therefore its escape from the ER is essential for its function. The typical ERAD pathway for soluble proteins involves retrotranslocation through the Sec61 translocon channel (the same channel involved in co-translational translocation, but with different associated factors during ERAD), but this would result in unfolding of the protein prior to its retrotranslocation to the cytosol. On the other hand, the ERAD pathway for membrane proteins (the "dislocation pathway") appears to dislocate folded membrane proteins while retaining most or all of their tertiary/quaternary structure (previous citation and below).
Avci, D., & Lemberg, M. K. (2015). Clipping or Extracting: Two Ways to Membrane Protein Degradation. Trends In Cell Biology, (10), 611. doi:10.1016/j.tcb.2015.07.003
Knowing that the protein is not co-translationally inserted into the membrane because only a small fraction is membrane associated, and suspecting that the small membrane-associated fraction is important for its escape from the ER because the dislocation pathway allows folded protein to exit the ER, my question is:
How could the retrotranslocation pathway for soluble proteins be disrupted such that it would (infrequently) result in membrane insertion of this protein at an early step in retrotranslocation-coupled unfolding, such that the folded protein could follow the dislocation pathway into the cytoplasm?
I would appreciate any examples of similar processes in viruses or in eukaryotes, but any speculation on possible mechanisms - based on understanding of ERAD but lacking supporting examples - would also be greatly appreciated.
As this is unpublished research, I can't be too specific about what virus or even what model system I'm working in, but if there is additional information that would help, I'll be happy to provide it - if I can.
One final piece of information that is also relevant is that I suspect the protein's transmembrane or membrane-anchored domain is very close to its C-terminus. Another important question that this raises is whether retrotranslocation exclusively proceeds by feeding the N-terminus of a protein into the Sec61 channel, or if the C-terminus can be fed directly into the channel? If only the N-terminus could be fed into the channel, this would suggest most of the protein would have to be unfolded before the C-terminal domain became associated with the channel and was able to become membrane-associated, which voids the main benefit of the dislocation pathway; maintaining the folded state of the protein.
If somebody can answer only this question regarding the translocon (and provide some relevant reading), I would be incredibly grateful because it would suggest further literature search to help support the mechanism I am proposing.
Thank you!

This question is very dense and difficult to answer due to it missing key information. I've left a longer comment as an answer, but this is likely to get removed. If you could address the issues raised then a more constructive answer could be given.

The observed events are as follows:

co-translational translocation into the ER (may or may not lead to membrane insertion). This is abolished by deleting SRP and translocon components in a cellular model, and the protein is destabilized in these gene deletion mutants.

Low amounts of steady-state protein (but some) is membrane-bound

The protein may become associated with (not dissociated from) the lumenal face of the ER membrane during a failed ERAD process.

The very C-terminal end of the protein probably doesn't have a transmembrane helix, the N-terminus has a 10-residue helix


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If x amount of a chemical starts to become harmful for a mice, then will 3000x amount of it start to get harmful for a human (3000 times heavier)?
My reasoning is simply that since human beings are 3000 times heavier than mice, the safety threshold for exposure to a chemical should be approximately 3000 times higher for human beings as compared to mice, assuming similar biology for both the organism.
Is there reason to believe this to be true? Or is this too naïve an assumption? If so, why?
As a concrete example, I am trying to understand what a study involving the harmful effect of 100 micrograms of TLR 7 agonist exposure to mice, can qualitatively say about its effect on a human being. Can we roughly assume that 300 milligram of the same TLR 7 agonist will have similar effect on human being?
Edit: Some people have shown concern that this question of mine is duplicate of another question that I asked - How much of TLR 7 agonist is safe for human beings, as it is both linked to development of autoimmune diseases but is also used as Vaccine adjuvant?
I think this is not the case. The earlier question is about a puzzle- TLR7 agonist is both helpful as an adjuvant and also triggers autoimmune disease in the same organism when the organism is exposed to different amount of the agonist. The question is, what amount of TLR7 exposure in human beings is hence safe?
On the other hand, this question is about how the toxic effect of any toxin scales with the body size of the victim? An answer to this question can partially answer the earlier question if there are murine models that have studied safe exposure levels to TLR7 on mice. But a proper answer to my previous question will involve how TLR7 agonist acts on human body, and why it is helpful at some concentration and why it backfires at some other concentration. The question, on the scaling of effect of a toxin, on the other hand, asks for a general scaling law.

This is seems to be a duplicate of your previous question How much of TLR 7 agonist is safe for human beings, as it is both linked to development of autoimmune diseases but is also used as Vaccine adjuvant?.  Posting multiple similar questions comes across as spamming the site and is not going to be well received. Please delete this post and focus on improving the previous version.

There is a scaling factor, which used to be (body_weight)^0.67 (see here), but I have no idea what the currently accepted value is, or even if body_weight (rather than, say, surface area) is the currently accepted criterion.

@tyersome I think the two questions are totally different. The TLR 7 question is about a puzzle- TLR7 has been shown both as harmful and useful at different concentration. The question is- when does this phase transition happen? The question in this post, on the other hand, is about how the effect of a toxin scale with the size of the victim? The first question is about transition point from helpful to harmful in the same organism. The second is about effect of the same amount of chemical in organisms of different size. Totally different questions. Just inspired from the same thing- TLR7.

I think you need to learn some terms - look up things like LD50, MIC (minimum inhibitory concentration) to start with. Compare those between different species.

It need not necessarily scale with body weight. Body weight (volume) does have an effect on the pharmacokinetics but drug/xenobiotic/toxin metabolism can also differ between different species.

This isn't exactly comparing apples to oranges, but it is like comparing peaches to nectarines. Humans and mice are not exactly the same except for size. As an example of metabolic differences between animals, adults can ingest 50 g of xylitol without problems (maybe diarrhea). Fifty percent of dogs weighing 50 pounds will die given 2 grams.

@anongoodnurse Does this kind of scaling effect of toxicity with body weight exist for two organisms of the same specie, between a newborn and a 5 times heavier adult, or perhaps two healthy adults with same BMI who naturally have different weights?

This isn't a "scaling event of toxicity". It's a physiological difference in metabolism. The comments are quite clear.

@anongoodnurse I am not sure if I understand you. This is not my field, so maybe I am missing something. I asked you a different question altogether in my last comment. Intuitively, it feels to me that an x amount of toxin will do more harm to an healthy average child than a healthy average adult (larger in size). Can this assumption be scientifically justified? Both are same species. Can we use something like (body weight)^0.67 scaling factor to judge the effect of the toxin, as suggested in the comment by user338907 ?

@TLR78agonist - Intuition isn't science. Scientists don't give human beings of differing weights toxins to test their ability to metabolize/survive. Also, not all toxins are created equally. If toxins must be administered (e.g. some chemotherapeutic agents are quite toxic), they are given in the lowest dosage shown to be effective. That's based on trials, not intuition.

@anongoodnurse My point was, whether such a scaling effect exists within the same specie, human or non-human. Scientists test effect of stuff on animals all the time, so I thought someone may have tested this. Agreed that intuition is not science, but is often the guiding principle in science. Surely a scientific method will determine whether this thing that appears intuitive to me is actually true or not. I just wanted to know if it is scientifically known to be true.


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What natural defence mechanism does the human body have against lead poisoning?
It is known that lead ion takes place of necessary ions, like calcium, in the body, but does not perform their task, hence wrecking the system. So how does the body eventually recognise this threat and get rid of the lead deposit in the body? And if such a natural defence mechanism exists, why is it not effective enough?
For example, is the process in which lead gets stored in the bones one of the safety mechanism of the body, so that it stays away from other delicate organs?

INB4 mods put question on hold as too broad I would suggest you to break the question into multiple questions and post them separately.

@ronisaiba Thanks. I have tried to make the question more specific by removing some sub questions.

Lead-binding proteins are a common defense in many organisms (https://www.hindawi.com/journals/jt/2011/686050/).


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Does contracting Rubella give one some kind of immunity to Measles and vice versa?
Both these diseases- Measles and Rubella, have very similar symptoms, have similar complications and are often confused for one another. And both the diseases have a common MMR vaccine. So, are the culprit viruses also related, so that contracting one can give one at least partial immunity to the other as well?
The similarity in symptoms is striking. Both the diseases may start with cold and fever. Both give one rashes, that start from face, and spread to rest of the body. Both have similar complications associated with them like brain infection. In the end, both can cause miscarriage, preterm birth, or stillbirth, as well as a variety of birth defects in pregnant women.
I know from this source that lab tests exist which can tell whether a person has immunity to one of the MMR diseases (Measles, mumps and rubella) and not the other, implying that there is a possibility of immunity to one and not the other. But since the vaccines like MMR only ensure immunity for 99% people who get the shot, my question is- does there exist partial immunity (in some people and not others, or in less severe attack and not otherwise) to Rubella if one has contracted Measles before and vice versa?

Short answer: No, there is no cross immunity between these two diseases. Having the same symptoms doesn't mean that diseases are related.
Both have in common that they are caused by viruses, but similarities end here. Rubella is caused by the rubella virus, which is the only member of the genus Rubivirus and belongs to the family of Togaviridae and are encapsulated positive strand RNA viruses.
Measles on the other hand are caused by the measles virus, which belong to the genus Morbillivirus within the family Paramyxoviridae and are negative stranded enveloped RNA viruses.
Historically speaking, the measles vaccine was available first in 1963, with mumps following in 1967 and rubella in 1969. All three are attenuated live vaccines which have been combined into a single vaccine in 1971. The sequence of this developments also shows that there is no cross immunity. You wouldn't develop another vaccine, when the disease is already covered by another. Drug development is a very expensive business.


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How much of TLR 7 agonist is safe for human beings, as it is both linked to development of autoimmune diseases but is also used as Vaccine adjuvant?
This question is motivated by the fact that TLR 7 agonists have been linked to development and acceleration of Lupus-like disease both in animals and human beings. But at the same time, TLR 7 agonist at lower doses is also being used as vaccine adjuvant (in covid vaccine- Covaxin, for example).
I will quantify the what I know. The study on murine model shows that a dose of 100 microgram of TLR 7 agonist, 3 times a week, for 8 week, is lethal for mice and triggers Lupus-like disease. On the other hand, a single dose of covaxin has 15 microgram of TLR 7 agonist. That is, for two doses 4-8 weeks apart will give total 30 microgram dose to human beings.
Now human beings are about 3000 times heavier than mice. So, the lethal equivalent to human beings should be frequent doses of 300 milligram. What Covaxin gives is a total of 30 micrograms.
My question is, does this imply that Covaxin is safe for human beings? How do we interpret these numbers? Is there better understanding available in the field that can throw some light on what level of dosage of TLR 7 agonist is safe and when does it backfire?


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What does the acronym ‘PIN’ stand for referring to PIN proteins in plants?
There are so called PIN proteins, or PIN-formed proteins, in plants. What does this acronym mean?
Wikipedia briefly explains the function of the protein but not the origin of the name.  It's not explained even in the link-linked review paper, if I'm not missing something.

Like many genes and gene products, PIN proteins were named for a mutant phenotype and PIN is not actually an acronym; the source in your link does actually explain this (emphasis mine):

The significance and function of AtPIN1 was discovered through the phenotype generated by the loss-of-function mutation in the gene: mutant plants fail to develop floral organs properly and generate naked, pin-like inflorescences, which gave the name PIN-FORMED (PIN) to the family

Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., & Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters. Genome biology, 10(12), 249.

Thanks. So it is explained there… (I was lazy to read more than the summary, then I've did just /\<[Pp][a-z]+(\s|-)[Ii][a-z]+(\s|-)[Nn][a-z]+/ regexp search).

It begs the question: why was “PIN” all-caps at all? When something is all-caps, it makes people think it’s an acronym. I’m not a geneticist, or even a biologist, by training. So please enlighten me if there’s some rule in the field that justifies all-caps.

Explaining what actually is a “pin-like inflorescence” would be very helpful.

It is not an acronym; it is an abbreviation of pinnulate (or pinnulated), which means having the pinnulae of a pinnate leaf properly developed.
Gene symbols written in all caps indicate the wild-type condition of the organism: If a gene is referred to as PIN1, it means its product (an auxin transporter) permits normal branching (or at lest does not contribute to malformations); when it is written in lower case, pin1, it indicates the gene has a variant associated with a mutant (non-pinnate) phenotype.
PIN1: nothing is broken
pin1: a single stalk without pinnulae (in the case of Arabidopsis)
If the mutant looks like a pin, it is a co-incidence (probably a mnemonic suggested by a English-speaking teacher). The original meaning derives from pinna, which refers to the normal appearance of leaves and flowers.

Welcome and thanks for your answer. Can you add sources to support your claims and allow folks to background read on your answer?

Hearsay. That's the explanation I heard from folks in my orbit. Here's one example:
https://youtu.be/jFiqj9NKQfc?t=1452
Apparently, while functionally accurate, it is incorrect as a matter of origin. The discovereres of PIN genes named them pin-forming.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC160035/pdf/030677.pdf
They do write gene names in lower case, so that's not where the confusion originated.
There are pictures in the paper illustrating the mutant phenotypes.


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Books about human evolution
I want to read some books about human evolution and about other extincted types of humans.
The book "Sapiens: A Brief History of Humankind" writes about history of agricultural and scientific revolution too, which is the part that is not interesting to me as it sounds more like history. However, I want a book about humans living millions years ago up to and before agriculture. I want to know how modern human evolved and what there were besides homo sapiens.

https://www.amazon.com/Humans-Evolved-Seventh-Robert-Boyd/dp/0393614867

It sounds like you are more interested in archaeology and even history than in evolution. This sounds particularly clear as you talk about the scientific revolution. Maybe History.SE would be a good place to ask this question. Note that evolution, in biology, is usually defined as a change in allele frequency over time (a definition that you may or may not understand) and it does not seem to be what you are interested in. I'm voting to close.

@Remi.b By mentioning the scientific revolution in "Sapiens: .... " I meant that I am not interested in this part.

I'm voting to close this question as off-topic because it is about history and archeology and not biology

The Journey of Man is a great book that really dives into the archaeology but also the genetic history of evolution.

I haven't read this, but I see it's published in 2003. If so, it's completely obsolete, missing enormous technical advances since then, completely unaware of the entire Neandertal interbreeding story, preceding the discovery of at least one branch of Homo (denisovans at the least). Would not recommend.

It is good to know that a field could change that much dramatically within 15 years. In Physics it is not so much like that! (of course that depends on the sub field)

I came across 'The Last Ape Standing' by Chip Walter that sounds like it might be something you would be interested in.


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Can you suggest me some books/articles about how female birds indicate receptivity to copulation?
Where can I find informations about the topic? I need to find some examples.
I also really need this particular information: I know that many female mammals display lordosis behavior that indicate receptivity to copulation, but can birds do that or it is a peculiarity of mammals only?

Yes, I'm afraid the answer will depend entirely on the species. Please [edit] your question and narrow it down. It is too broad for the site at the moment. You might want to have a look at our [help] to understand what's on topic here.

Thank you for the suggestion. I edited the question and I asked for reference if the topic is still too broad. Is it ok now?

Edited again because the question was put on hold