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The antiquity of man
What are the oldest fossils of modern man? What is the evidence until now? I do not ask to know the evolutionary
chain that led to H. sapiens, but I wouldn't mind to hear it, nevertheless.
What are the official sources, like peer reviewed journals, confirming it?
I wish for reference and rigorous scientific analysis.

Welcome the Biology.SE! First of all, this is not a chatroom. It is a Q&A website. Second of all, from a simple web search, I have found this so I am flagging as a homework question with no research effort. Sometimes you need to learn how to make the best search. This is an example of when that is necessary. I don't know what you searched but I simply searched "oldest fossils of homo sapiens" and got many results. If you want to find peer-reviewed articles, you can use Google Scholar (probably with the same search term).

Welcome to Biology.SE. It very much depend on what you call modern man. I think this  wiki article will answer your question. Does it? The wikipedia article also contain the references you might be looking for.

Can you guys try and do better than Wikipedia?

@AMR The term modern human is slightly unclear and the wikipedia article is very complete. You did not do a better job than wikipedia.

In addition to that, understanding why the OP did not get the answer he was looking for from the wikipedia article will inform us of what was unclear to him.

@AMR the wikipedia article contains a large number of citations from peer-reviewed literature, is clearly laid out, accessible (unlike the Science paper that was your only citation), and points to a great number of other sources for reading. I see nothing wrong with it at all.

@MattDMo by removing the OPs reference to "Homo sapiens sapiens or Homo sapiens in general" you removed the fact that they understood that there are distinctions to the classifications of modern man. If you look at the Wiki article you will see that a number of the references are to Chris Stringer, the author I reference. And if you look at the title "Genetic and fossil evidence for the origin of modern humans." pretty much sounds like the right starting point for the OP, as they were not interested in other Hominids. And the 918 articles that reference that article will likely have an answer

Try this article as a starting point;
Stringer, Chris B., and Peter Andrews. "Genetic and fossil evidence for the origin of modern humans." Science 239.4845 (1988): 1263-1268.
It is old, but it has been cited 918 times to date. That should be more than enough of a breadcrumb trail to find what you are looking for. Also if you click through to the Science Magazine page, it also has a list of relevant articles below the abstract. You may need a membership to AAAS or library access to get a copy of the actual article.
Also try a Google Scholar search for Modern Human Fossil Record. The above article is the second article referenced in this search.

I am well aware of the suggested sources of info.

Then it was pointless for you to ask your question and waste people's time.

amr I am only learning this site. I have not finished my comment

When I posted for the first time my question apparently to a wrong sector, I was just explaining my frustration that there really is scant info on the web on this subject.   I mean where are your anthropology journals? Where are their guidelines and key questions regarding their field of scientific inquiry. I am not doing any homework, though my field of interest is related(health sciences).   So I ask for recent info from an established authority on the field.  Thank you for your responses anyway.

When you press enter , zoop comment posted. Do you understand now AMR?

I mean if I want to know for heart failure, or valvular heart disease, I will find authoritative info in a straightforward and open manner , from European Heart Journal, Circulation and Journal of the American College of Cardiology. I don't have even to do any googling. If I try to find info on anthropology on such a key question in their field, I don't have such luck.

And I can't help but point to the fact that though a newbie to this place I was faced from the beginning with somewhat hostile intentions; I would not be truthful if I didn't  say this.  How is a question "what is the content of water in human blood" answered and considered acceptable? Isn't this supposed to be an old knowledge and not so vague and uncertain like mine? Isn't this readily available through search engines? Does it not look like a homework question? Has that person made efforts to find answers? Please! In that sense almost any question asked in this sector has these attributes

you accuse me of

Major anthropological discoveries rise to the level of General interested, so you will often find those article going to the highest impact Journals such as Nature, Science, Proceedings of the National Academy of Sciences, The Philosophical Transactions of The Royal Society, The Royal Anthropology Institute, and so on. If you search Anthropology + those journal names, you will find resources such as http://anthropology.pnas.org and https://www.therai.org.uk. You also have museums such as American Museum of Natural History or The British Museum.

And I actually took the time to answer your question, so if you were already aware of what I gave you then you already had an answer to your question. All you really needed to do was look at the Journals that the those articles were in or look at their reference lists and the articles citing them and you could have established a pretty extensive list of the journals that cover anthropology. If I wanted to find out about Coronary Artery Diseases I might start in JAMA or NEJM, find a review on the topic, then go down the list of references to find the more specialized material. That's research.

I appreciate your answer, as pna.org was not an evident source of such material.

But, being a cardiologist I might add that trying to find an expert opinion on the heart is far easier, and done quickly and  with a greater degree of confidence. On the other hand, such info I requested, is not readily available and you have to have a fore knowledge about where to search. Anyway, I don't see why I "should" research extensively about a difficult subject(I did search and found unsatisfactory sources) , while I regularly see naive questions being posted and answered without fuss or qualms.


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Does sweat contain DNA information?
I was reading this article : Perspiration
The first question which came to my mind after reading the composition of sweat was whether it contains any information about the DNA or not?
I haven't had much interaction with biology since 12th grade (2010), so kindly answer in layman's terms and detail as well.

The consensus of the answers as of March, 2023 seems to be that human sweat does not contain enough human DNA to identify the person producing that sweat. This contradicts fictional court testimony in s1 e1 of "All Rise", a crime drama on Hulu subscription video. DNA identification of human fluids apparently requires them to contain human cells.

The Wikipedia page you linked says that sweat is composed of a liquid similar to blood plasma. As all DNA in humans is stored in the nucleus of a cell, it seems unlikely that the sweat itself would contain any DNA.
However, when someone sweats significantly, I can't imagine that no skin cells end up in the sweat. In any case in which this occurs, then the DNA in the cell is in the sweat. Additionally, with small amounts of sweat, I can't imagine how it would be collected without getting any skin cells in it.
This source confirms that sweat contains DNA in some form. Additionally, I think the following quote from here shows that it is stored in cells:

In every case, what is being tested is the DNA contained in cells of human tissue

Yes exactly. it was due to a heated discussion with a friend. We were discussing about DNA, I was sayin about how bodily fluids like blood, semen, etc contain genetic information. She said that sweat doesn't  and I couldn't find enough evidence to prove otherwise.

@ABcDexter AFAIK, those fluids only contain DNA because they contain cells. I'm not an expert, by any means, though.

@Christiaan I've found and added some sources that seem reliable.

@john01dav - great +1

So sweat does contain DNA and the genetic information ;)

I believe the answer is no.
Sweat is the liquid secretion of body cells, not including the cells themselves. If the cells are secreted when sweating, then you may find some DNA in your sweat. You are right on that. Serum contains many different types of lymphocytes, the majority of them--mature red blood cells, don't have nucleus. So they don't contain DNA. And, live skin cells cannot be sweated. Dead skin cells are easily found on the mucosal tissues of your body, however mucosal tissues cannot sweat! In a word, it's basically impossible to see DNA in sweat.

@ABcDexter In respect to your comments, semen is for sure to contain genetic information because of the presence of germ cells(sperms) in it. However, it's not the same way of how you sweat. Semen is from sex organs only while you can't say sweat is from a specific organ.

Yes but not humans DNA
Sweat does not normally contain human DNA, it does not pick up many skin cells under normal conditions, excessive sweat can pick up some however. However sweat is colonized by bacteria fairly quickly once it reaches the surface of the skin so unless you are extracting it directly from the gland it will contain bacteria with their own DNA.

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Does osmosis occur when we have two different substances?
Assume that we have a semi-permeable membrane with water on both sides. First, straightforward, case: On the right side, we have a concentration of the substance A, and on the left side, we have pure water. Obvious effect: water flows from left to right.
Now, imagine we have a second case. We have the same membrane, and a water solution of A to the right. To the left, we have a water solution of a different substance, let's call it B. Now, what happens? I can imagine a few possibilities:

the system behaves exactly as in the first case, because the substances have no influence on each other
the system behaves as if it was a solution of A on both sides, with water flowing in the direction of higher concentration (because it only matters if there is something dispersed between the water molecules, but it does not matter what)
some interesting cross-influence effect happens
either one of the three things above can happen, depending on the particular combination of substances A and B

Which one is the true effect? What happens, and why?
If you need an example of the actual substances, let B be thiamine and A be plain sodium chloride, but I am interested in the general case.

If A and B are at the same concentration there will be no net movement of water.
Everything is down to diffusion. In your example of solution A/pure water, water molecules on both sides of the membrane are diffusing through the membrane to the other compartment. However the "concentration" of water is less in solution A, so the rate of movement is less from solution A to water than it is from water to solution A. Water will continue to move into the solution until another force, such as hydrostatic pressure, counteracts the "osmotic pressure".
If solution A and solution B have solute at the same concentration then the rate of movement of water will be the same in both directions, so no net movement will occur.
(In a typical experimental set up using dialysis membrane none of this would apply with the solutes that you mention since they would also be able to move through the pores and you would end up with perfect mixing. You would have to use macromolecular solutes.)

To make sure I understand your answer: you are saying that if we have a high concentration of B on the right, and low concentration of A on the left, water will flow from left to right?

Yes, that's correct.

If one solution can permeate and the other can't, would there be any net movement of particles?

It's not actually diffusion. From Wiki (with source), "The diffusion model of osmosis is rendered untenable by the fact that osmosis can drive water across a membrane toward a higher concentration of water."

Actually, the so-called osmolarity of a solution is only determined by the concentration and number of dissociating species in the solute, and is irrespective of the chemical composition of the solute. This is an example of what is known as a colligative property in chemistry.
The van't Hoff equation gives the osmotic pressure exhibited by a solution:
P = icRT
where P is the osmotic pressure, i is the coefficient associated with the number of dissociating units in the solute, c is the molar concentration of the solute, R is the universal gas constant, and T is the absolute temperature. A nonionic species, such as glucose, would have a value of 'i' close to one as the molecule does not dissociate in solution, while NaCl in relatively dilute concentrations should have an 'i' value close to 2, as it dissociates into sodium and chloride ions in solution.
Thus in the case of the two solutions on opposite sides of the semipermeable membrane as you described, water would flow from the region of lower osmolarity to the region of higher osmolarity, until the osmotic pressure on both sides of the membrane come to equilibrium (due to the changes in concentration of the solutes by the net water movement).

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How is the antigen against which autoantibodies are formed, identified?
Say we suspect some new autoimmune disorder in a patient, and we collect blood for serology.
How are self antibodies differentiated from normal ones in the collected sample?
Once they are identified, how is the antigen towards which it is directed known?
Are there assays for this? Or is it identified by the structure of the variable region? Can a simple IHC be done on all body tissues using the purified isolated antibody to localise the protein?
I mean, what is the root for suspicion of an antigen? Like, what caused ANCAs (anti-neutrophil cytoplasmic antibodies) to be suspected in systemic lupus erythematosis (SLE)?

All of the above, basically. If it's a protein antigen, you can perform an immunoprecipitation with the auto-antibody and use any one (or more) of several methods (Western blot, various methods of sequencing, etc.) to identify the binding partner(s). DNA and RNA can be identified easily by biochemical means. You can also use ELISAs or similar methods like electrochemiluminescence which allow a greater degree of multiplexing.
Sequencing the autoantibodies' variable regions may give some information about the structure of the antigen, but not enough to actually identify the binding partner. Also, one key fact to keep in mind is that the antibody response in many autoimmune diseases is polyclonal (just as the T cell response often is), meaning there could be dozens to hundreds of different complementarity-determining regions (CDRs) to sequence, a very laborious process that may not yield much information.
Immunohistochemistry (IHC) can be useful for seeing which cell types the antibodies bind to, but it doesn't give great resolution on the subcellular level, and doesn't tell you anything about what the actual target is. Additionally, due to the amount of chemical processing a formalin-fixed paraffin-embedded (FFPE) tissue goes through, the antibody's antigen may not be exposed properly for the antibody to bind.
From what I can find, people suspected an association between ANCA and lupus due to the similarities in both diseases' clinical presentation. Here is a paper from 1996 talking about it, there are many others.

Thanks! How do you identify the autoantibody from the antibody chunk that's out there roaming around?


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Is there a gold standard for syphilis?
When you say the Venereal Disease Research Laboratory test (VDRL) has a specificity of x% and sensitivity of y%, what are you comparing to? What is considered as the truth?
Because, Wikipedia says, even a gold standard needn't be perfect. It is just the best test available(?). It too has its specificity and sensitivity (<100%)
So, my question is, when we say that the VDRL has a 75% sensitivity, what are we comparing it to? Is it the clinical diagnosis of syphilis according it the case definition? Wouldn't it be much less accurate?

This is usually meant in a clinical setting: So I think this is about detecting 75% of the infections.

@Chris essentially. See my answer for a bit more (I tried to keep it short). Specificity is also related to how specific the reagents are for their intended targets, vs. binding to related proteins/hormones/chemicals/whatever the test is measuring. Some tests are yes/no readouts, but I focused more on quantitative tests, which tell you how many virus particles per ml, for example.

Specificity and sensitivity are terms used in the pharmaceutical and in vitro diagnostics (IVD) industries that have specific meanings relating to how the particular assay in question was validated. Generally the values are being compared to spiked standards in matrix using recombinant protein or purified virus or whatever the antigen is (depending on how the test operates) where the analyte concentrations are known. With a certain number of titrations and assay repeats, along with a bunch of statistical calculations, you can then compute your expected and actual recovery, as well as values like the LLOQ (lower limit of quantitation) which gives you your sensitivity (we can reliably detect 1e4 viral particles per ml, for example).
Specificity is calculated using related antigens, such as proteins from other types of bacteria that are of varying degrees of relation to syphilis, or perhaps of different serotypes that aren't claimed to be detected by the test, or whatever. Again, you spike known amounts of these materials into your testing matrix (blood, sputum, urine, semen, whatever) and see what your test returns. So, say I have a virus with 2 serotypes (A and B) that I claim recognizes A specifically. I spike in perhaps equal amounts (for example, 100 units) of A and B, then run the A-specific quantitation assay. The readout might then say the sample only had 75 units of A, meaning 75% specificity of the reagents.
For more reading, search for "clinical assay validation" or something similar. There are a ton of papers out there giving guidance for particular types of assays, as well as regulatory agencies' interpretations of the relevant laws covering the tests. There are also many books, reviews, etc. if you're just looking for an overview. It's a huge field, and I've just given a very basic description to avoid writing pages and pages.

Thanks! How would these then account for the biological variation in the population? The same amount of bacterial load in one person may test positive but not in another. Do these terms not talk of that? Because, in syphilis there is a special term called biologically false positives (BFP) for VDRL, are they just a subset of normal FPs or excluded from it?

@Polisetty I don't know the specifics of this test, other than what is on Wikipedia, so I can't answer directly. I do know that the VDRL does not test the levels of the spirochete directly, rather it looks for levels of anti-cardiolipin antibody that increase after syphilis infection, and apparently have been shown to have a good correlation with viral load in the absence of confounding conditions like lupus. There are other direct tests that identify the bacterium specifically - they are used for diagnosis. I'm not sure how the BFPs (such as lupus cases) are differentiated from other FPs.


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Atlas from human brain structures to 3D coordinates?
I would like to visualize specific human brain structures in the three dimensional space and compute specific geometric properties of these brain structures (size, centroid, etc).
Therefore, I am looking for an atlas that maps human brain structures to 3D coordinates (in Talairach or MNI coordinates).
I saw online a lot of websites allowing the inverse mapping, which is from coordinates to brain structures. So I know that this data should be somewhere but I was not able to find it.
Any lead would be greatly appreciated.


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Why is exocrinous pancreatic cancer so lethal when compared to others?
I know it seems far fetched, but I would really like to understand why an interference with the regulation of production of pancreatic exocrine products (and which are they) is so lethal. I know that people having it generally live for one year or less (top is circa 5 years).
Why?

Sure. Go to [https://en.wikipedia.org/wiki/Pancreatic_cancer] and in the vastness there's the info.

I added it in the question. +1

One of the (but not the only) reasons for the high mortality rate of pancreatic cancer is the fact that it is so difficult to screen for. The symptoms (if any) are most often dismissed as general back or gut pain, and it can take quite a bit of testing before the true cause is found, by which time the cancer has already become metastatic. Unlike the digestive system, there is no good non-invasive way to image the pancreas (such as with a colonoscopy for colon/rectal cancer) except using radiological methods such as X-rays, so there is no safe way to provide for standard screenings.


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Differences in structural target for LPS detection by LAL and MD-2/TLR4
I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte lysate (LAL) assay. However, I cannot seem to find a paper that indicated what structure on the LPS lipid A moiety is used for detection.
In humans, structure-and-function relationships exist between the phosphate groups of bisphosphorylated glucosamine disaccharide backbone as well as the six fatty acyl tails and the MD-2/TLR-4 co-receptor system.
Does anyone have a paper, or a general lead, as to where I can find what area LAL uses for detection? I haven't had much luck with Google Scholar.

I guess the LRR of the TLR is responsible for LPS-PAMP identification (Lipid A). Not too sure.


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Can yeast in a primary fermentation of wine be used as a source of yeast for new fermentation?
So if I were to pitch bread yeast, and get to primary fermentation, which as I understand it, is the point at which regular cellular respiration can no longer continue due to a lack of oxygen , which is needed for the electron transport chain. Therefore the yeast switch to fermentation, which produces my desired product, ethanol.
But as I understand it, at this state the yeast are no longer reproducing and are in a survival mode.
Therefore if I were to cut a 2$L$ bottle of my primary ferment in half, and then add more sugar and water to the now separate 1$L$ bottles, and oxygen (if possible), up to 2$L$, would I be able to have the same amount of ethanol produced/would fermentation even occur?
I feel there would be diminishing returns even if it was possible, since yeast can only reproduce asexually so many times, which happens during stressful times, which this process might induce?

Yes, it is possible to reuse yeast in both beer and wine fermentation - commercial brewers do it all the time for cost savings and batch reproducibility, and although I'm not as familiar with making wine, many sites including this one say it's perfectly fine, as long as the viability of the cells is high enough.
The yeast aren't necessarily in stress-induced survival mode during fermentation, they're just living (and metabolizing) anaerobically. They may no longer be reproducing, or doing it very infrequently, but they'll remain perfectly happy little buggers (that's a technical term) for quite a while. Give them more food (sugar), and they'll keep fermenting. What eventually stops the process with wine is the level of ethanol rising too high for their comfort. If you were to dilute the ethanol out with water, they'd keep going.
Now, I wouldn't recommend doing this indefinitely (some strains may exhibit genomic instability, etc.), but new batches can certainly be produced with existing pitches.


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Do axonal conduction delays have a function?
I'm reading about mathematical models of biological neural networks, which can be grouped into two categories:

The model accounts for the fact that a signal takes time to travel from the excitatory to excited neuron
The signal is modeled as if it travels instantaneously between neurons

I'm trying to understand whether a signal delay is introduced for the purpose of realistically modelling a neural network, or whether it has other functional roles in the model. So by function I mean a role in the information-processing capacity of the network that extends mere physical limitations of axon signaling. I'm referring specifically to their function in biological neural networks
Here are three distinct cases that I expect the answer should fall under, to further illustrate what I mean by function:

They don't, signal delays are a mere physical necessity of biological neural networks, irrelevant for the information-processing aspect of their operation. The differences between delay durations are primarily due to the fact that low reaction times are metabolically expensive and spatially-inefficient and are thus reserved for specialized purposes such as reflexes, instead of having a wider functional role as a parameter.
They do, signal delays are fundamentally required for neural networks to process spatio-temporal patterns. However, the differences between the durations of delays are unnecessary to explain any fundamental internal property and are still due to external factors.
They do, and the differing durations themselves are operational parameters, i.e. the function of a sub-network can only be fully understood if the ratios of the delays in signal transfers are taken into account.

It's unclear from your question whether you are asking about the importance of timing delays in biological systems, or about the purpose of timing delays in artificial neural networks.

@BryanKrause I've edited in a clarification, this has to do with biological neural networks, and of course mathematical models of them, not the classical broader computer science concept but continuous-time numerical simulations

Your point #1 is correct, signal propagation is not instantaneous in real physical world. But for some models it is "good enough" to approximate action potential to go through axon in an instance.
There is also biological role of signal propagation timing. One example, is classic Hebbian learning model. Based on "fire together - wire together" idea, connected neurons that become active relatively close in time, will increase synaptic connectivity, illustrated here:

General temporal dynamics are present in both models, and Hebbian learning is achieved via a simple rule dz(i, j)/dt = x(i)*x(j), where z is connection strength and x is the activation. That rule perfectly approximates Hebbian learning through time for neurons i and j without there being a need for a signal delay between them. Axonal delay is far from the only source of temporal dynamics in networks

@jcora i though that delay is driving learning, but source of the delay is unspecified. It can be regulated on different levels, including axonal propagation speed.

See also this paper from Izhikevich in which he claims that the conduction delays can be instrumental in timing-based assembly formation, memory encoding and recall.

@aaaaaa that paper is likely exactly what I needed, will report back when I check it out:)

@jcora .paper was not my suggestion :)

ah right I see haha, well than ty @vkehayas


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Why are many unable to defecate and urinate simultaneously?
Many people (including myself) do not defecate and urinate simultaneously, but rather in succession.  Only after one is completed, the other commences.  I have noticed this in myself, but the internet suggests this is neither unique nor universal: for example, see quora, reddit, grasscity.  I don't seem to find any references explaining why people would be unable to do both at the same time.

Why the downvote?

Probably because we don't deal in personal health questions here. I usually just vote to close in those cases, and usually leave an explanatory comment, but people are free to downvote as well.

@BryanKrause I see.  I never intended to ask a personal health question but I can imagine why it may be perceived as such with the personal introduction.  I have reformulated it to be more generic.

After the edit, this does not appear like a personal medical question. I recommend reopening.

Something related to increasing pelvic/abdominal pressure during urination mandates external sphincter to contract simuntaneously.


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Why aren't plants and animals capable of assimilating $\ce{N2}$ directly from the atmosphere?
From a E-book  written by Hungary scientists, the reason is $\ce{N2}$ is inert.

Is this correct?
How does the chemical properties of gas species ($\ce{SO2}$, $\ce{O2}$, $\ce{NH3}$, etc) influence the assimilation process by organisms?

By the way I think this does not have a direct relation with geochemistry or atmospheric chemistry, e.g. asking about how these processes affect the atmosphere or Earth, or things like the whole nitrogen cycle. Rather you are focusing on the specific processes that occur in the organisms (and nothing about environmental interaction), that's biochemistry. That's all just IMHO tho, you can ignore me if you don't agree :-) .

As @Wolfgang Bangerth commented, inertness just means that nitrogen gas doesn't undergo reactions because the NN triple-bond has a very high bond energy and the activation energy for reactions that break the bond (even though thermodynamically favourable) is therefore high. So I suppose that you could say that a major chemical factor in the reactivity of gases is their bond energies.
The key reaction of biological interest for nitrogen is reduction to ammonia, as referenced by the comment of @aretxabaleta. Stryer makes a couple of points that seem chemically relevant (http://www.ncbi.nlm.nih.gov/books/NBK22522/). He says that the reaction pathway for the reduction of nitrogen involves unstable intermediates, and he also mentions that the nitrogenase enzyme in Rhizomium is extremely sensitive to inhibition by oxygen. I am no expert, but I presume that the instability of the intermediates is related to their ease of oxidation. Leguminous plants maintain a very low concentration of free oxygen in their root nodules by synthesising the protein, leghaemoglobin, which mops oxygen up.
So the answer to the question in the title — why animals (at least) don't fix nitrogen — could well be because as aerobic organisms they would find it very difficult to provide an oxygen-free environment to do this. And the fact that animals can get their metabolizable nitrogen second- or third-hand means that there is no evolutionary pressure to develop such a mechanism. (Most bacteria and plants manage without too.)


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Driving force for speciation for millions of species today
I would like to know if speciation really occurs (trans-speciation). Have we had enough time for millions of species? A creationist argument is that the slow changes in traits in organisms, taking tens of thousands of years to yield a visible change in variation as evolution suggests, does eventually trap yourself in to a problem of "Time Riddle". You just don't have enormous enough time at hand for all these species to come into being. A quick average time calculation suggests that you should have a new species come into being every 15-20 yrs [just rough average time estimation suggests that in about 1 billion yrs ~50 million distinct species evolved]. Though I believe in evolution, I cant understand this part.

A small note: You don't believe in science. You understand it.

???  this is not my answer

It is not an answer. It is a comment..

Have we had enough time for millions of species? - yes. How do I know? Because there are millions of species. Life has been present on earth for billions of years. Also you seem to have plucked your numbers out of thin air - where is the data to support them?

Also: 3.5 billion years of life, and 10 million species says that one evolves every 350 years. But remember that speciation can occur in parallel (not sequentially), so growth in numbers can be exponential (i.e. 1 becomes 2 species, both of these can then speciate).

I'm voting to close this question as off-topic because its flawed, unclear, and poorly researched (seemingly random numbers in the calculations)

I think what the user is asking is how can millions of species have evolved within the earth's given timeline, ergo can you actually explain evolution from a linear model B derives from A, C derives from B. The clear answer is no, you cannot it is much more complicated than that. So maybe the correct question is What forces drive evolution such that we can observe over a million species today?

u have no logic to vote for closing the question & how come its off-topic. U forgot to see that I said- I DO BELIEVE in evolution. I just cant understand this part, WHICH a creationist put before while discussing. I also dont knw what the hell did he get this numbers from? Thats why I want some clarifications.

@KoustavPal thnk u , can u explain What forces drive evolution such that we can observe over a million species today? I ll be grateful, I cant understand this part.

Cool, I'll provide a suitable answer to this question. Maybe you can edit the question and change it to the same?

@rg255 Perhaps you can give a simple example using average mutation rates and timescales. This would basically answer the question of how many DNA changes are possible in a given time. Tanivr: You should understand that mutation and fixation are different phenomena and there are environmental factors that limit the number of "species"; so if some mutations were not selected against, then we would have had many more species.

@Tanivr I suggest to you that you just keep the question specific to the scientific point you are asking. You would agree that your debate with your creationist friend has nothing to do with the actual question. My first comment to you is for telling you that in the process of science we understand things and that is why we know they are true. Belief on the other hand implies that you don't understand something but accept it as true. Try editing your post by making it precise, adding references and removing irrelevant material. I am voting to keep the post open :)

@Shrunk I think it is a reasonable cross post. There is a difference between lay skepticism, which seems to have focused on mathematical possibilities, and a biological justification. I do agree though that the question seems fishy - it approaches the situation with the assumption that there has not been enough time. In reality, there has been enough time because it has happened. The question should be "how much time has it taken" and not "has there been enough time?".

This answer is towards the question, what forces primarily drive evolution such that we can observe a million species today? which is what the user wanted answered.
To answer this question, we can start off at many places. So I wanted to start off at Kimura's neutral theory of evolution which encompasses both Natural selection and genetic drift. I wanted to start here because although it is true, it also brings to light a fundamental trait of phenotype which has been highlighted in this paper which suggests that mutation rate in a species as a whole is not very divergent, but the same rate varies by several magnitudes when comparing genes having lower rates in highly expressed genes and higher in lowly expressed ones.
This brings to light another feature of gene mutation. A very simplistic view is that gene products are perfect for their function, that is not the case (I need to find a proper reference for this, maybe someone can help me with that?). Gene products are never the most thermodynamically stable nor the best at performing their intended function, but rather they are positively selected for once a mutation produces a product that provides increased fitness to the organism.
Till now this answers two things:

Mutation is the governing factor driving evolution.
Unless a new mutation increases fitness of the organism it is considered as a neutral one.
A species as a whole has nearly the same mutation rate.
Depending on their contribution to survival genes have different mutation rates.
A gene will choose to preserve function over improvement because it may result in a loss of function.

So now let us come to the part about millions of species. If you followed me till now, you understood that based on different mutations changes will arise. I would now like to bring in the theory of Punctuated equilibrium which basically states that a species once developed remains nearly the same for it's geological history. Below is an interesting image from the wiki page.

So according to this theory once a species has appeared, until it disappears it will remain largely the same. It will disappear does not mean the entire line will die off. Rather, it means a substantial part of will die off, allowing niche populations to colonise the now empty ecosystem. Or a change in climate may now allow a certain niche species to migrate out of their ecosystem to provide competition to the already existing species in the ecosystem and then to oust them from their place (look at yourself for example), the migratory pattern exhibited by homo sapiens during the end of the last ice age led to the removal of neanderthals from their ecosystem (this is very traditional and overly simplistic but mostly correct so I will not provide the complicated parts here).
This theory worked on the theory of geographical speciation which goes on to state that geographical changes may lead to population separation, which leads to the different species. This is because, in their own ecosystems they will be privy to very different environmental stresses such as climatic conditions, competition, predation, food availability and disease. So after a million years these two populations which were the same will now be very different.
So I think, I have provided a suitable answer to this question, because your view evolution as something very linear. Which it hardly is. There are many factors which guide it, and this is how today you can see millions of species. Another thing to note is that of the millions and millions of species identified on earth today, multicellular organisms represents a handful of crumbs from the pie. Most of it is actually micro-organisms (Anyone know the source for some exact numbers?)

Your math is wrong.  Assume for simplicity that speciation is binary: that is, a speciation event divides one species into two.  50 million species is between 2^25 and 2^26.  So producing that number of species in 3 billion years would require any lineage to speciate on the order of once per 120 million years.
Remember, as per comments above, that evolution works in parallel!
Another point to remember is that most of the species existing today are insects or microorganisms.  Would we even notice the development of say a new species of beetle, if it happened in the Amazon Basin or New Guinea highlands?


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Can we infect with "bad" genes other organisms?
We know that some organism's DNA stay with human for life (Herpes) and we also can, i think, design such "gene" that can interact with human's DNA-polymerase very intensive.
If we attached this gene to herpes virus and after that it infected human, would our "artificial gene" be produced and replicated by human DNA-polymerase and how it can affect infected human? Is it possible? What are difficulties we can face?

Perhaps you may want to rephrase your question as "can virus mediated lateral gene transfer happen in higher eukaryotes/animals". That would be a good question. Avoid asking open ended questions like "what difficulties can we face".

It is common in biology to use a virus to deliver new genetic information to a cell. Such a virus is called a viral vector. Retroviruses can be used to enable the viral DNA to be incorporated into the cell's genome. Usually viral genes are removed, making the virus unable to replicate once the cell is infected 1. Using viral vectors in vivo to "correct" disease-causing genetic mutations is a commonly studied aspect to gene therapy 2.
For obvious reasons, people for years have been considering how genetic engineering and gene therapy may be used as a bioterrorism weapon, and ways to ensure our safety if it is used as a bioweapon 3.
1 - http://www.ncbi.nlm.nih.gov/books/NBK19423/
2 - https://ghr.nlm.nih.gov/primer/therapy/procedures
3 - http://dujs.dartmouth.edu/2013/03/genetically-engineered-bioweapons-a-new-breed-of-weapons-for-modern-warfare/#.V1hdeJMrKN8


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Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide
I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason.

Think carefully about how a gene's sequence is turned into protein - the gene is transcribed, mRNA is created, it runs through the ribosome where tRNAs match the codons and bring in the appropriate amino acids, then the polypeptide chain is spit out. Is there anywhere in that series of steps where the sequence of bases written in DNA could somehow change? Are there any spots where bases might be "clipped off" for some reason?

@MattDMo You should convert that into an answer.

@MarchHo well, I didn't exactly give an answer, though, just pointed the OP in the right direction. Vaguely.

This sounds a bit too much like a homework question

I can think of at least 3 reasons in addition to the one you gave:
1: As mentioned in the comments, RNA splicing takes place on most messenger RNA encoding proteins in eukaryotes. Sections of the mRNA may be spliced out, therefore multiple mRNAs with different codon sequence can encode the same gene.
2: Translation is a stateful process, since it depends on the frame of the codon. Therefore, a gene with the sequence GGATGATGATGTAA will encode the same protein as a gene with the sequence ATGATGATGTAA, due to the start codon shifting the frame of translation downwards.
3: Genes contain untranslated regions in regions before the start and after the stop codon. These nucleotides cannot be predicted from protein sequence, but are generally important in regulating protein expression.

Introns are not included in the polypeptide sequence.

This is rather a comment than an answer.

Now its an answer....


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Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?
I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering if one method is better to use than the other.

Did both assays agree though?

Hi Sara I Have a nice guide method for you. In this time I cant send it to you because...' I will send it to you soon

Is the Bradford result much higher than the one for the A280?

Bradford is better and better than that is BCA. A280 relies on the presence of tryptophan which is not necessarily present in all proteins in same numbers.

@WYSIWYG For A280, shouldn't the tryptophan (and tyrosine and cystine) be accounted for in the extinction coefficient? Bradford/BCA is also dependent on amino acid content and is relative to a standard. If the unknown and standard proteins have a wildly different Arg/hydrophobic content, the results won't be very accurate.

I suppose the AA content will be important for A280 if it's being done relative to a standard as opposed to using the extinction coefficient.

Make sure the buffer your sample is in is compatible with the assay you're using, and that is is free of detergents, etc., as they can skew both assays. There are detergent-compatible assays available, check Pierce. I agree with @WYSIWYG that BCA is superior to the two you're currently using, just make sure you're using an appropriate standard. For example, if you're measuring IgG, don't use BSA as the standard.

I suppose SDS-PAGE could be another approach to estimate a concentration, but mostly to make sure you protein solution has protein.

Chris- Both methods were equally far apart from the literature value. And thank you everyone else for your input.

@canadianer tryptophan quenches the fluorescence of tyrosine and phenylalanine afaik. Moreover 280 is the absorption maxima for trp; others absorb shorter wavelengths.


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What for a Kinase Assay?
I am wondering why to use a kinase assay, since we can extract the proteins from cells and then do a Western with the specific antibodies we want to use.

Welcome to SE Biology. However you need to provide much more background to your question before anyone can help you. What is the context of your question? What experiment are you doing? What are you trying to discover? Is this a teaching experiment or real research?

There's a very simple answer: scale. If a drug company wants to screen a million-compound library to find which ones inhibit the kinase activity of a certain target, they're not about to do a million IPs and a million Western blots. Instead, they'll use recombinant kinase and substrate peptides, with a variety of readout systems to choose from.
Other reasons include not having a good phospho-specific antibody to the substrate, very low expression of the kinase and/or substrate, complicated protocols necessary to activate the kinase in vitro, lack of a good model system, and more.


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Interpreting ChIP-qPCR or ChIP-seq
I have a really basic question. Studying ChIP coupled with q-PCR or sequencing, I see different levels of a certain protein among a genomic region. I cannot really understand how can we have different protein levels. I thought that the binding of a protein in a region is bivalent-it occurs or not. But, as I can understand, we can have different concentration/quantity of protein bound to a region? And if this is the case, how in ChIP-qPCR we get finally DNA fragments, so how can we measure this binding from the quantity of fragments?

Could you explain more what "I see different levels of a certain protein among a genomic region" means, and how you determined that? Also, your last sentence is not very clear.

Protein binding to DNA is not bivalent. ChIP is enriching for DNA to which your protein of interest is bound, but that protein may bind certain sites throughout the genome more strongly and frequently than others. Stochiometric effects play a role, as do the strength of the binding motifs.
Some proteins bind very specifically to a given sequence, but most allow for some degeneracy in their binding sites. A strong site will be bound more frequently (and thus more highly enriched during ChIP) than a weaker site. Not just the presence, but the frequency of binding is what ChIP really measures.


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Is hunting animals, crafting and attacking/defending from enemies intellectually equivalent to learning quantum physics?
Our brains were shaped after natural selection. Which means that, as long as we were being affected by it, our brains were changing, evolving.
Once we stepped out of nature and stopped being targets of natural selection, our brains (structurally speaking) stopped changing.
Civilizations rose, humanities and science developed, and you know the rest of the story.
But the brains that we used to create all that is the same brain that was shaped by natural selection. A brain that was concerned with animal hunting, food gathering, fighting with enemies, relating socially and so forth. It is curious to notice that we used that same brain to develop algebra, geometry, physics, astronomy, arts, and so on.
So, would it be correct to say that all those activities from our ancestors living in nature (gathering, hunting, fighting) are INTELLECTUALLY equivalent to quantum physics, i.e.? Because our brain capacity is limited to what happened to it during natural selection (while we were living in nature), so would it be safe to assume that whatever complex thing we can think of (such as quantum physics) is actually as hard as those activities our ancestors performed in nature?
This may be a very stupid question, but I couldn't find fallacies or wrong assumptions in my thought, but my conclusion seems to be a bit... unexpected? Please, correct me if I'm wrong, I'd really like to know the answer to this.

"Human brains enjoy ongoing evolution"

"Once we stepped out of nature and stopped being targets of natural selection, our brains (structurally speaking) stopped changing." Why do so many people think evolution is "done" and that we're the perfect organism that cannot be improved upon?

Every time a couple reproduces, evolution continues.

On what basis or scale do you intend to compare survivalist strategies and quantum mechanics quantitatively? As a side note, I am reminded of a book I once read about the early expeditions to map the Amazon. Despite having the tools of 19th century science, the explorers quickly changed their attitudes about the "savages" when they realized that the natives' intelligence and knowledge of the jungle far outstripped their own. I think your answer might be more along the lines of "complex tasks are complicated until you know how to do them". It's just hard to compare the two ideas meaningfully.

Huh, we stopped out of nature? I didn’t get that memo. Maybe I need to be online more. // Another comment: the question implies that our brain evolved to do quantum physics well. But in fact our brains struggle mightily with similar enterprises. In short, we are badly adapted to solving abstract problems, and need to impose a rigorous regime on our thought to stop us from fooling ourselves.

It's not that evolution stopped. The 5,000 years or so that humans have been civilized is a blink of an eye in the evolutionary timeline. Give society another 100,000 years or so, we'll see some remarkable adaptations begin to emerge.

Addressing some assumptions/presumptions apparently present in the question (this might be too long for a comment):
First, natural selection has not stopped. The sexual selection might be more active than ever, so there is ongoing "pro-fertility" selection and some segregation "pro-smarts". Not every member of contemporary potplation is capable, even with unlimited attempts at education, of doing something useful with quantum physics.
Second, surviving in the wild and fighting enemies are competitive enterprises. Which means that the task is of potentially unlimited difficulty: the better you are at survival, the more you procreate, the more pressure you put on limited resources of the environment, to harsher climates you spread. With enemies, especially those evolving along with yourself, this unlimited competitiveness is even more obvious.
So, the question could possibly be framed differently: how hard our ancestors, living in nature, made the intellectual part of the task of competing with each other? Apparently, about that hard.

Re the competitiveness and therefore unlimited difficulty: it’s theoretically conceivable for there to be an upper limit imposed by physical constraints. For instance, trees have an evolutionary arms race for height in forests, yet there are various physical limits on how high trees can evolve to grow. For brains, a conceivable limit may be due to the considerable amount of energy we need to expend for our smarts (this is pure speculation of course, but it’s plausible).

You seem to think that living in the natural environment is "easy". But, even when the climate helps, even when you have no war to fight or defend against, even so you have to know the habits of the animals which you will hunt, the fishes you fish, the proper season of the plants (fruits, fibers, roots...), which of them could be toxic, which could be medicine; when planting you have to know the season for planting, the season for harvesting, not to mention which plants grow well near which others, and which grow sick close to which others, what are the proper soils and proper irrigation for each species, how to deal with pests, etc.
As you can see, if you try to do those things, you will probably acknowledge that they're not necessarily easier than modern science. After all, nobody created the whole of "quantum physics" out of thin air. There were many different discoveries developed by independent researchers over a long time, with many trial and error in between, etc. And all this, of course, was only made possible after the extreme specialization that - in the end - probably turned us "modern civilized people" into the least healthy and more emotionally tormented version of our species.
So yes, to be human is enough challenge for anyone. To be a single mother is probably more difficult than any dry and tedious mathematical equations.

It may not be easy but it can obviously be done without any symbolic reasoning at all, for example by a worm or a fly. And even with symbolic reasoning one could argue that memorizing plants is not the same as contemplating curved space time or Riemann's conjecture. What you say may be right; but the argument is not rigorous.

@PeterA.Schneider Worms and flies only eat what their instincts have prepared them for. Even ants that tend aphids are not able to learn what "genetical enhancement" might be. Our brains have the biggest ability to learn, and we did this to domesticate dogs, horses, plants... The first man who thought he could mount a wild horse and fall, and mount again and fall again, until he finally tamed it, has surely had some "symbolic reasoning", didn't he? My point is, if we have room for symbols, this must have arised in the old past of our species.

I don't think this is really a biology question; philosophy, maybe. Or for the history and philosophy of science.
The main problem is: what does "INTELLECTUALLY equivalent to" actually mean? What sort of equivalence is it? There isn't a convenient Mohs scale we can use to measure the hardness of problems.
We don't actually have a good biological model of what it means to think about something. We know it involves neuron activation, and you've probably seen the use of fMRI to map exposure to various thoughts to rough activation patterns in the brain, but it's not a model we can replicate yet nor describe in truly precise detail.
We don't have a clear enough description of what it means to think about something to say which animals think and which don't. We know that crows understand object permanence. Some chimps can understand symbolic reasoning. Does that imply some equivalence with human cognition?
"stepped out of nature and stopped being targets of natural selection" is also an assumption which I'd like to question. When do you think this happened? The earliest I think you could possibly justify would be the invention of antibiotics in the 20th century.
It's possible that something like Turing equivalence applies to thought; once a particular level of symbolic reasoning is reached, from there the entirety of mathematics is reachable given enough time and effort.

"stopped being targets of natural selection" happens gradually, of course, and is not finished (one can still die from cancer before procreating). But physical resilience was less and less needed with the growing degree to which we shape our environment (build shelter, heating, grow food) and help each other (support the weak, heal the ill, technically fix issues like myopia).

I think you are underestimating the intellectual capacity needed by prehistoric humans to perform all their activities; in short, to survive. It is true, prehistoric humans did the same things animals did. But they did it in a fundamentally different fashion.
Animals are largely driven by instinct. By contrast, we humans have very few instincts — perhaps none! — we cannot overcome. We can choose not to follow even the most basic survival instincts: We can voluntarily hunger to death, refuse to procreate, go out in the cold and freeze to death, with a warm home in sight. We can even actively end our lives.
But this freedom from pre-cast behavior has enormous benefits: It enables us to adapt to environments to which we are physically not well suited. Too light-colored people inhabit the Sahara; fur-less humans dwell in the arctic. We grow food in arid places, by means of irrigation. What makes this possible is a system of knowledge and customs commonly referred to as culture. This puts humans in a unique position among animals. Our survival depends on our mental capacity, not any longer on our instincts or our physical shape.2 This shift is what characterizes us. This shift was made possible by a change in our brains.
Some time in the evolution of homo sapiens something astonishing happened. It is the ability for symbolic reasoning and reflection. We see things not only as what they are; we imbue meaning in them which isn't obvious at face value. We tell stories about ourselves, about our ancestors, and about everything else we see. We keep memories of the past, and tell them to our children. We have rites which reinforce these memories and our sense of belonging, belonging to the place and to each other. The stories we told (like heavens full of scheming gods) were often much more complicated than the reality they tried to explain (like rotating balls on elliptic trajectories). We could create an adaptive symbolic working model of ourselves and our environment; one which was elaborate and complicated, and often poetic and beautiful.3
This ability proved an evolutionary advantage in times of rapid environmental changes and allowed us to survive where other species went extinct. We developed a brain that's "almost entirely plastic" (Feynman)1.
This unique ability to create internal models of the ever-changing world around us allowed us to make Gedanken-Experimente, predict the consequences of our actions. We could be strategic. Ockham hadn't been around yet, and the Ptolemaic way of making sense of it all was blossoming.
This ability to create and manipulate mental models with a high degree of freedom (not hard-wired to specific inputs or instincts) is key to our humanity. The result of our evolution was a brain which is almost completely unshackled. It is aggressively designed to invent stories and see patterns. We are the zoon politikon as much as we are a zoon poetikon, a story teller and singer.
Our mind is not modeled for a specific environment. We can live everywhere we can physically go — and beyond! This enables us to do things that seem very removed from what we did when we evolved. We are physical explorers as much as we are mental explorers. The very advantage of this particular line of evolution, its very essence is that it is not only ready for the unknown, but actively seeking it.
Stay tuned.

1 The lady whose leg he pulled responded: "No, really!?"
2 In fact, our instincts, for example our aggression, appear to become a danger to our survival rather than a requirement.
3 As an example for sophistication and information content consider Australian Aboriginal mythology with stories possibly describing events thousands of years ago.

I won't address all the assumptions/propositions you offer in your answer, just the basic question:

would it be correct to say that all those activities from our ancestors living in nature (gathering, hunting, fighting) are INTELLECTUALLY equivalent to quantum physics, i.e.?

Yes
What do you need to live in prehistoric times?

Observe your environment
Understand what is happening (beyond basic animal instincts)
Form plans of how to survive better
Enact those plans (possibly as a community)

What do you need to do quantum physics?

Observe your environment (=read books, go to university)
Understand what is happening (=understand the mathematical formulas etc.)
Form plans of how to make it better (=have intiuitions about where to go for new developments in QT)
Enact those plans (=actually work out full-fledged new theories and successfully run them past the QT community)

(You can think of more points, for example "storing/accessing knowledge" and probably more).
Analogy: computers
There is an excellent analogy with computers. Since we developed the "Von Neumann architecture" for computers, computers basically did not develop much further. Yes, there were vast, unbelievable improvements in capacity and speed, but that's about it. Fundamentally, every computer you have today, including laptops, smartphones etc., are conceptionally exactly the same as the first computers around the middle of the 20'th century.
The achievement was to build a general computing device that can be applied to any problem whatsoever, without even knowing what the problem is. Once you are at that point, you're basically "done".
The same goes for the brain: once you reach the point where you have all the basics (understanding, reasoning, communication etc.), you're all set. You "only" have to increase capacity/speed to achieve almost anything. Obviously we cannot really scale capacity/speed of a single human brain; I would say we achieve this today by making fields like physics, mathematics, electronics etc. ever more compartmentalized. The time where a single human could know everything humanity has learned about a topic is long, long gone. But basically, it is the same.

Could you provide some references?

@Ebbinghaus, for which part of the answer do you need references? I believe it's pretty self-explanatory and general enough to not need any? The "Von Neumann architecture" is the only term requiring explanation, but it is quite ubiquitous, and any Google hit for it will suffice.

Unlike the other answers, I'd like to focus on the issue of intellectual performance. If you're trying to ask whether the hunters and gatherers used to use their brain capacities as much as we do, assuming we haven't evolved much since then, the answer is yes. Though, it hadn't been the same type of brain performance. Most of the knowledge needed for hunting is procedural (implicit) information, something you can learn by watching and repeating your parents' techniques. In nature you have to be careful not miss any predator's noise and you have to be always prepared to run. This characteristics fits the brain condition today known as adhd. And, indeed, this hypothesis of the origin of ADHD as an regiment from the times of hunter-gatherers is currently being confirmed by the genetic research.
So if I got you right, I think your hypothesis is right, we use our brain capacity as much as the hunter-gatherers did. But, as can be seen on adhd, non-adhd people are better equipped for the conditions of the today's world (therefore it's called a deficit, they usually score worst in IQ tests) but people with ADHD might have better chance of survival in the wild (because they use more of their brain capacity focusing on potential danger).


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Skin extra sensitive to heat after burn
I just got my finger burnt (first degree burn $\Rightarrow$ I didn't even bother to bear the wound). It didn't hurt much, even when I pressed the wound.
However, when exposed to heat (hot water, but not so hot to hurt undamaged skin), the pain became at least nasty.
Is it an evolutionary adaptation to avoid hot objects not to get burnt again?

All traits that you observe have accumulated because of evolution. Is your question on enhanced sensitivity of burn area about its "how" or "why" ? Your reasoning on "why" is plausible and there is nothing much to say about that. Most "why" questions tend to have a philosophical aspect to it because we can at best, only make sensible guesses.

The burnt skin is extra sensitive because it is injured, just like a broken bone or a cut - it is the body's way of saying be gentle. The general evolution of pain, and sensitivity, acts to teach us to not repeat dangerous/harmful things, but this does not explain particularly why a burnt bit of flesh is extra sensitive.

Local inflammation (nerve receives inflammatory signaling molecules from its local environment) and direct injury can both increase the sensitivity of nociceptive (pain/noxious stimuli sensing) nerves. This sensitivity can drive animals to guard the injured area. This may be beneficial to survival. Persons unable to sense pain often accidentally self-injure, perhaps further sensitization helps protect the weak/injured area). So it's plausible, but as WYSIWYG said, we cannot prove why this behavior arose. We can only make reasonable conjectures.


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What is the biochemical explanation for tingling and burning sensation in brain due to certain food?
Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour goes through the nasal cavity.
I read somewhere, the checmical which gives the burning sensation is isothyocyanates. And some of the posts roughly mention about sinuses being agitated due to this chemical vapour.
How to explain this from biochemical and biology aspect? e.g. What sort of a cell reaction, if any receptors involved etc. (Appreciate an answer that is similar to the type of explanation here.)

You are right the compounds provoking this burning/tingling sensation is called allyl isothiocyanate.
We (human) perceive these compounds in two different ways when ingested, namely via the gustatory and olfactory systems. The molecular receptor sensing isothiocyanates is called the transient receptor channel A1 (TRPA1) [ref].
Here a simplistic view of how ingredients are perceived:

Gustatory sensation
First we get a burning sensation in the buccal cavity due to TRPA1 receptors present on the surface of the sensory neurons of the trigeminal nerve. In essence isothiocyanates dissolved in the saliva will activate those neurons via TRPA1 provoking electrical impulses in the trigeminal nerve which leads to a burning sensation.
Retronasal olfactory sensation
For several food ingredients we also perceived an aroma (taste = gustation, aroma = olfaction, taste + aroma = flavor). The aroma of an ingredient is perceived by olfactory sensory neurons in the nasal cavity and because some of the ingested ingredient will be vaporized inside the buccal cavity and travel through the nasal cavity where they are perceived (retronasal perception).
Not so surprisingly, isothiocyanates will again be perceived by sensory cells of the olfaction system via TRPA1 hence a burning sensation in the nostrils.
How receptor activation leads to a neuronal stimuli
This is a very broad subject and I will only give an overview of what is happening. We first start with the activation of a receptor by an agonist (in your question, isothiocyanates binding and activating TRPA1). Upon binding of the agonist the conformation of the receptor will change from an inactive to an active state. The way the signal is transduced varies according to the type of receptor but for the TRPA1 channel what happens is that the channel opens leading to an influx of calcium ions ($Ca^{2+}$) in the cells which changes its electrical state (as calcium ions are positively charged), a phenomena called depolarization. Depolarization of specific sensory cells (here the one expressing TRPA1) start an electrical signal in the nerve which travels to the brain where it is then decoded. The exact way the brain decodes sensory signals is still under debate but a likely explanation is that only some neurons within the nerve are activated which allows the brain to decode the sensory signal based on the nerve activation pattern. As an analogy, it would be the same as having only specific wires (neurons) turned on within a bundle of wires (nerve).
Further reading
If you want to further extend your knowledge on taste perception at the molecular level read this excellent review Chandrashekar, 2006. For a in-depth review on olfaction refer to this book. For a book on signal transduction refer to this while for TRP channels activation this is a good reading.
The field is quite broad and there are many good references. Sensory perception includes two distinct and broad fields namely neurosciences and cell signalling.

I just saw the answer and you just blew my mind with that awesome image and the well referred explanation. I had no idea it is infact related to taste perception. This is the part I was hunting for: How receptor activation leads to a neuronal stimuli. With the opening of Ca2+ from TRPA1, are there any specific neurotransmitters released by  trigeminal nerve to send the signal? And now I have gotten a good direction to read further.

@bonCodigo Glad you found my answer useful! Technically it is due to the aroma perception (taste perception is exclusive to the buccal cavity).  Concerning your question yes upon activation (or more precisely depolarization) sensory neurons will release glutamate (a neurotransmitter) and start a neuronal signal which likely propagate in the nerve as any standard neuronal signals (i.e. via neurotransmitters release in synapses). I don't know enough about the subsequent events to give you a very detailed answer but I am sure you can find that quite easily if you look for olfaction signaling.

cagliari2005 I was just going through some stereochemistry revision (R/S system). The picture in this answer came to my mind. (after 2 years I still remember, hey)! Our olfactory system and everything inside the body is so fascinating, that the receptors in smell sensory system can recognise each distinct smell which comes from same molecule with a slight difference in sinical/rectus difference. It is just magnificent. I feel so naive that I am not able to understand even a 1% of it through my visible consciousness :)


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Given an amino acid sequence, how to determine the structure (helix, beta sheet etc)?
Assume there's a short sequence of an amino acids.
MAKMGSKKKAGHGGKEKLENMGE

I am using molecular structuring softwares to look at secondary structure. But it's blackbox method. In plain theory, how to determine what structure the above peptide will fold into? There must be a basic set of rules, prior to all the complex maths, and modelling?
Based on basic rules I also want to know what and how a different amino acid contributes to the formation specificity.  Will add more details.

@BryanKrause that's helpful. But what I really want to know why? Like what bonds, interactions of these amino acids contributes to the specificity of forming helix or beta etc. How it is so. I will update my answer. Cheers.

@benCodigo A lot of that would just be on the wiki pages for those types of structures. eg: https://en.wikipedia.org/wiki/Alpha_helix#Structure

Afaik there are no excat rules for this. The methods are based on (known) statistics of the presence / absence of certain amino acids in helices and beta-sheets (e.g. proline and glycine almost never occur in helices)


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How does pressure measured by sphygmomanometer translate directly to blood pressure?
As per my understanding a sphygmomanometer when wrapped around the arm and inflated only measures the pressure of the air inside the cuff, doesn't it? How does that translate directly to the pressure value of blood flowing across the artery?

Korotkoff sounds!
The blood pressure measurement process is fairly cool, and goes like this.

Inflate the cuff to well over plausible blood pressures (250mmHg or so).
Slowly deflate the cuff while listening to the artery.
When you start to hear sounds, that's when the systolic blood pressure is higher than the cuff pressure and the heart can squeeze a little blood through the cuff, which makes a little squirty noise.
As cuff pressure continues to drop it stays between the systolic and diastolic blood pressures and therefore bloodflow stops and starts and creates audible turbulence.
When the artery stops making noise, the cuff pressure is below the diastolic blood pressure and the cuff has no effect on the artery, so it goes back to laminar flow that doesn't make noise.

Measuring the pressure of the cuff is just part of controlling the pressure of the cuff. You could conceivably measure blood pressure by submerging their arm in water(mercury would not require a conversion, but vats of mercury are unpopular in doctor's offices) and listening for Korotkoff sounds and measuring the depths where they start and stop.
Edit: The actual question here is how does cuff pressure physically change the arterial surroundings, not how do we link the two clinically.
The body is mostly water, and water is incompressible. For small strains(amount of deformation) flesh isn't that springy and mostly "flows" like water. When you pressurize the cuff around the arm, the flesh of the arm equilibrates to the cuff pressure the way balloons equilibrate to the air pressure, only less dramatically because water is mostly incompressible. For small pressures and large cuffs, therefore, the cuff pressure is the pressure on the artery wall, and by listening for Korotkoff sounds while varying the cuff pressure the blood pressure can be roughly established.
The reason why you don't lose all blood flow to your extremities while diving underwater is because the systemic pressure on all of your body raises your internal blood pressure, making the net external pressure on any part of your body zero. (The cuff works by exerting a relative pressure difference on part of your body.) At high altitude the sphygmanometer is still accurate-ish because the cuff pressure relative to the atmosphere is still the same as the blood pressure, relative to the atmosphere. If you had air for blood(or any compressible fluid) your veins would collapse underwater. This is why your ears hurt while diving deeply if you don't equalize them: your ear is full of compressible air, and at depth the air attempts to shrink more than the flesh around it, pulling things out of place painfully.

Thanks for the answer, but please bear with me as I might be missing something very obvious here because even though I did understand how Korotkoff sounds help in the measurement, yet I'm still having trouble understanding how exactly do these readings on the sphygmomanometer (like 120mmHg for systolic pressure) actually relate to the pressure that's exerted by the blood on the walls of the artery? Doesn't the sphygmomanometer only measure the pressure exerted by the (compressed) air on the walls of the cuff? How does this pressure directly equate to the blood pressure?

When it comes to pressure differentials, the body is essentially incompressible(it's mostly water and water is mostly incompressible). The cuff is long enough and the arm fluid enough so that as long as nothing moves very far, the pressure on a long enough part of the arm is the pressure inside the arm. Your arm is too viscous to "flow" out of the cuff but otherwise it's not unreasonable to treat flesh as a surprisingly stationary liquid.

okay I understand that, the arm can be treated as stationary liquid, but I'm afraid I still don't see how that answers my question? Actually I'm slightly more confused as to how the arm comes into discussion at all? weren't we just talking about the artery and the cuff? I'm definitely missing something very obvious and I very much appreciate your responses.

The artery is embedded in the arm, isn't it? When the arm is under pressure, the artery is under pressure. The cuff doesn't pressurize the artery directly (it'd have to be surgically implanted) it just pressurizes your arm and relies on the arm to transmit pressure to the artery. Come to the chat, this is getting too lengthy for comments.

I see. Even earlier I imaged the cuff is directly choking on the artery but what I still don't get is how the pressure on the walls of the cuff measure pressure on the walls of the artery (or the hand, if the pressure is transmitted). I guess it's more of a physics question then, I'll have to spend some more time thinking about it. Thanks for your replies, really appreciate it.

One last thing, I was wondering about something you brought up >"You could conceivably measure blood pressure by submerging their arm in water" That's very intriguing point. 200mmHg = 0.26atm and 1atm is 10m deep in water so 200mmHg = 2.6m deep in water? Now if a sphygmomanometer applying 200mmHg on the arm basically stops the blood flow, does that mean that in 2.6m deep inside the water the blood flow would also be stopped? This is clearly not the case. Have I mistaken somewhere in my logic?

(Oh we should totally go to chat these are fascinating questions but they're drifting off-topic.) If you managed to get your arm 2.6m away from your body, that's exactly what would happen(maybe you have very long arms). If you brought your body with you, the body-wide pressure increase would increase your blood pressure systemically and cancel out the increased outside pressure. The closing is a relative pressure effect where the pressure on the arm under the cuff is higher than the pressure on the rest of the body. That's why it still works at altitude.

Ah, makes perfect sense. That was pretty much the only question(s) I had right now. Thanks very much once again!


text:
What is an effective method for putting on blue rubber butyl stoppers?
They look like this.

We have to do a lot of gas sampling and these are really difficult to assemble. I've been scouring the internet for advice but there are none. Do you have experience with these? Have you found a good way to put them on that doesn't destroy hands, hearts, and dreams?

To clarify, the hard part is putting the blue stoppers in the tubes in the first place. Once they go thoroughly in, we can crimp them with our hand crimping tool. Since the time I posted this, I find a (little) better luck using a piece of cloth / putting the cap and the glass vial between a vice. With too much pressure, I actually broke a vial and glass shattered everywhere. The best way to put them in is with a twist, but that usually comes with an expense of bruised hands after extensive use.
Wish I had a camera on me, but they look somewhat like this:

does application of some lubricating agent to the tops help or would that interfere with/contaminate with your gas mixture in the bottles?

Alternatively you can try heating the blue top perhaps in warm/hot water and see if that helps!

Well these will be gas samples, so I'm not sure, but we are trying to stay away from too much contaminates. Thanks for the idea though! It should make more sense to heat up the bottles first, and we may give that a shot.

From what I can tell from this machine (https://www.youtube.com/watch?v=TwRtsAG5Oy4), the blue caps are put on the bottles first, then a loose version of the aluminium neck seals are put around the top of the capsule, which is then pressed in the machine to seal the lid hence if you use many gas sampling techniques, it might worth investing in purchasing a similar machine/technology to seal your samples, which would be the most efficient in the long run.
EDIT: as pointed by @user137 there are also hand crimping tools, which you can use, which are considerably cheaper, which as @user137 pointed out, can be found here

That looks expensive, you might be able to get away with a hand crimping tool. This site has a wide variety : http://vialcrimpers.com/


text:
Basic Local Alignment Search Tool (BLAST)
Why would BLASTP (Basic Local Alignment Search Tool) be a poor tool to search for motifs in protein sequences?

This question needs more research shown. As it stands, it looks more like a homework question that should be closed.

BlastP carries out a search for sequence similarity to infer function by comparing an unknown sequence with a sequence that has already been annotated with a function, but structurally similar proteins with different sequences can have the same function because function can be mimicked if the replacing amino acid falls into a similar category as the substituted amino acid. The four major categories of amino acids are: negative charged, positively charged, polar and hydrophobic.
Proteins have many shapes, while the double helix in DNA is the form in which DNA is most often found. Therefore, the structure of DNA is not as important for function as the structure of proteins are for protein function. So you need a tool that can compare the three dimensional shape of one protein to another (in addition to sequence comparison) to make an estimate of how likely there is going to be a similarity in function. The Research Collaboratory for Structural Bioinformatics offers a tool that can compare proteins by sequence as well as by structure. The following screenshot shows the options for comparison under each of these two categories:

This doesn't really answer the question at all.

Because it has a poor statistical model. It's basically a local alignment tool aided by a fixed-length k-mer index. It estimates homology in terms of sequence identity and while this is often enough to find homology in relatively conservative sequences, the heuristic scoring model doesn't really allow to search motifs. A motif in terms of bioinformatics can be seen as a series of state-switch events, hence you need a model that estimates similarity in terms of likelihood of observing such a sequence of state switches under  your prior state-switch matrix (inferred from a training sample). These models are known as Markov models and people usually utilize Hidden Markov Models to find motifs. There are good popular tools, such as HMMER
EDIT as per OP's comment

As motifs are locally conserved regions & BLAST also performs local
  alignment then why it should not be able to search for motifs?

A motif is not just a "locally conserved region", it's a specific sequence profile. BLAST doesn't extract any sequence profiles, it wasn't created for that. Given a pair of sequences it simply shows you similar patches. Hence BLAST is simply not the right tool for the task. They made PSI-BLAST for that very sake.
Moreover, many motifs comprise amino acids or nucleotides that can be quite separated in a primary sequence and only get close in a folded (secondary or tertiary) structure. Here your definition of "locally conserved region" fails as does BLAST.
As I've already mentioned, BLAST performs a heuristic local alignment, that is it assumes that two related sequences must contain at least one common k-mer (word) of specific length. This, given a precomputed word index, significantly increases performance in terms of speed and RAM consumption. But similar motifs can be present in non-homologous sequences or in highly divergent sequences that hardly evince any homology, and BLAST won't find anything at all.

As motifs are locally conserved regions & BLAST also performs local alignment then why it should not be able to search for motifs?

@katherinebridges I've edited my post.


text:
introduction to Chip Seq
I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've been looking at Chip Seq data. But to make sense of the Chip Seq data I wish to understand how the experiment is first performed.
Basically my question relates to step 1 of the following diagram:

Now my main question is how come the reads are overlapped? Where did we get so many of the (almost the) same reads?
My "understanding" is that:
1) They take a DNA sequence and crosslink the protien of interest. Then they get rid of the DNA sequence surrounding this area of interest so now we have a "small" sequence of DNA and in this small DNA is somewhere where our TF binds. Now we make copies of this small DNA seq and run it through a sequencing machine. Is this correct?
2) They take a bunch of cells = bunch of DNA sequences. Then they do the same procedure above (by crosslinking and getting a "smaller" DNA sequence of interest). Since they had many cells to begin with, this means they had many DNA seq to begin with. Now they shear the DNA seq and we have fragments. Then we align these up with the reference genome.

The basic steps of ChIP-Seq are:

Crosslinking proteins to DNA - this fixes the proteins in their natural positions
Nuclease digestion - this removes regions that are unbound to protein; nucleases are sterically hindered from digesting protein-bound DNA
Immunoprecipitation - this allows isolation of the target protein by binding it to a selective antibody
Sequencing to determine the bound DNA sequence
Mapping the reads to the reference genome

Why so many reads? They are taking many reads from different cells. Why are the reads so short? Many modern next-gen sequencing methods are limited to ~30 bp reads. Thus, the reads you see are not actually the entire protected sequence but rather just a shorter fragment from the 5' end (where sequencing starts from). The why behind this is explained by Jiang and Pugh, 2009 (Nucleosome positioning and gene regulation: advances through genomics):

Three DNA sequencing technologies have been used to map nucleosomes. Pyrosequencing using the Roche 454 GS20/FLX
  sequences nucleosomel DNA end-to-end, allowing both nucleosome
  borders to be linked in a single sequence. This method provides the
  greatest mapping accuracy, particularly in genomic regions of low
  complexity. By contrast, other platforms, such as those provided by
  the Illumina-Solexa Genome Analyzer and Applied Biosystems SOLiD,
  generate only 25-35 by sequence tags, requiring both nucleosome
  borders to be inferred. Nonetheless, these short-read technologies
  produce >100 times the number of sequence tags at a similar cost as
  the long-read technologies, and so the short-read technology is
  currently the only practical technology for mapping nucleosomes in
  large genomes. The higher tag count of the short-read technology
  enhances mapping accuracy and thus provides a practical way of
  mapping nucleosomes.

Why are the reads overlapped? I can think of a few explanation for that. For starters, Protein-DNA binding is variable in its specificity. In other words, a given protein might bind at the exact same site every time or it may bind 'around' a site or it may bind randomly. A protein that binds an exact sequence would be expected to produce reads that are more in phase that one that binds more variably. Next, the nuclease digestion process is random (or at least expected to be). Thus the DNA cleavage point relative to the protein is variable and your reads start from different points. Again, from Jiang and Pugh:

At any given genomic locus, the preferential positioning of nucleosomes--called phasing--can be described. At most loci, there is an approximately Gaussian (normal) distribution of nucleosome positions around particular genomic coordinates, ranging from ~30 by for highly phased nucleosomes to a random continuous distribution throughout an array. How much of this variation is due to genuine positional heterogeneity and how much is an artefact that is caused by overtrimming or undertrimming of the DNA at nucleosome borders by micrococcal nuclease during sample preparation remains to be determined.

Does that answer your question? Basically the reads are overlapped because there are many of them and they may differ either because of actual variance in the DNA binding site (which is biologically significant) or because of variance in the DNA digestion site (which is a methodological flaw). As with any biological experiment, you must perform many replicates to statistically determine the source of the variance and this is done by taking many reads. I recommend you read the article I quoted from, it is a good overview of histone mapping with ChIP and is likely also applicable to what you're studying.
Also, do you know why there are two sets of reads (red and blue)? I would venture a guess that they are taken from opposite strands. In other words, they are reads of the same DNA region taken from different directions. That might help clarify what's going on.
To conclude:

DNA is not extracted from a single cell. In usual procedures it is
always from a collection of cells or from tissues.
The overlap in TF associated reads arises because of the TF bound
sequence coming from different cells in this collection.
Each DNA piece is amplified and clusters are formed in the NGS
sequencers (for the ease of detection);
In a homogeneous cell collection i.e. all cells are of same type, the
variability in the read position usually arises because of
flexibility of binding sites (i.e TF wont exactly bind to at a
certain locus). Also, as previously mentioned the variability can
arise during the technical procedures.
In case of heterogeneous tissues the variability arises because of
different biochemical status of different cells. Strictly speaking
there is always some heterogeneity even in an apparently homogeneous
tissue but tissues such as brain are highly heterogeneous
In the case of nucleosomes the positioning is not exact because the
sequence contribution to the position is very minimal. Certain
nucleosome positions are tightly maintained for e.g. around the TSS
(transcription start sites) whereas in other regions the positioning
is fuzzy because of the dynamic nature of the chromatin.

I added conclusions to summarize your answer.

Thank you. I think was missing is that a TF may bind 'around' a binding site. I was thinking suppose you have a DNA seq ATGCGCTATATCGAT but you have a thousand of these since there are 1000 cells. TF binds to TATAT so when we crosslink and "digest" we get rid of everything surrouding it. Then we have TATAT left. Then we can break this up to TA, TAT since NGS readers can't read long seq. Now we have a bunch of TA, TAT floating around. If we align all of them up, we shouldnt see the picture I posted, but we should see a "ladder". This is not true, but do i have the process right?

Your transcription factor may bind to TATAT but it may protect much more than that. For example, prokaryotic RNAP binds the core promoter at -10 and -35 (which is about 29 bp) but protects about 70 bp of DNA. Thus, you'd likely get more than just TATAT. Also, I expect that no NGS could actually sequence a fragment so short. Maybe I'm not understanding what you're getting at.

The example seq I used was supposed to be a very long DNA sequence. The binding site TATAT was supposed to be 150 - 900bp long. Still too long for NGS, so we breakup TATAT into shorter fragments TA and TAT.  And I wanted to see where my understanding had gone wrong.

So that's not quite how ChIP-Seq (Chromatin ImmunoPrecipitation and Sequencing) works. First, you start out with a large number of cells per sample (preferably on the order of 107 or more - the more sample, the more immunoprecipitations you can do to different targets) and do whatever it is that you're going to do to induce transcription factor binding - expose cells to drugs, treat with cytokines, grow in different conditions, or simply compare two types of cell populations - normal vs. cancer, etc. After a certain period of time, determined by your experimental setup, you cross-link the cells with 1% formaldehyde, which fixes everything in place, including transcription factors bound to DNA. The cells are then broken apart by incubation in a detergent-containing buffer, and nuclei are harvested. After washing, the nuclei are either incubated with micrococcal nuclease (MNase) to digest DNA into strands of 1-5 nucleosomes in length (150-900 bp), or sheared by mechanical ultrasonication, hopefully leaving strands of the same length.
Once you have your DNA strands, you add antibodies to specific targets - either certain forms/post-translational modifications of the histone proteins that make up the nucleosome, or to specific transcription factors or TF families. The antibodies bind to their targets, and are enriched by incubating with (generally magnetic) beads that have the antibody-binding protein Protein G covalently attached to their surfaces. The beads are washed with low-salt and high-salt washes, then the formaldehyde cross-links are reversed and the chromatin is eluted from the beads in an elution buffer at high temperature (65°C) with vortexing in a thermomixer. Any remaining protein is removed by digesting with Proteinase K, the DNA is purified using a spin column, and you now have your enriched, purified DNA sample ready for sequencing.

Source
Antibody binding and enrichment of known sequences is often first analyzed by regular PCR, just to ensure that everything worked. Once your sample has been validated, it is then prepared for next-gen sequencing. We are now near Step 1 of your illustration above. The read lengths of some instruments may be shorter than the average length of the fragments you prepared during the ChIP step (150-900 bp), so during the library construction phase they are further broken down into shorter strands before having the common primer templates ligated to them (if that's the technology you're using). Even if the instrument allows you to use the full length of your DNA strands, you need to remember that the sample is the aggregate DNA from millions of cells, and they didn't all break after MNase digestion in exactly the same way.
After amplification and reading, you are then left a large number of short sequences, which need to be compared to a reference genome and aligned:

Source
Since we've already enriched for certain regions of DNA by using the antibodies which bind to DNA-bound or -associated proteins, there will be a larger number of similar overlapping reads in enriched areas, allowing us to tell where the histone, transcription factor, or other protein was bound when the sample was originally cross-linked.
Hopefully this all makes sense to you. I based my description of the ChIP protocol on Cell Signaling's SimpleChIP products, which I've found to be of quite good quality and reproducibility (no, I don't work for them!).

Thank you. I can not express my sincerity and appreciation for typing that out for me. Just a couple of questions: 1) what does " enriched by incubating with..." mean? In other words, what does enriching the DNA do?

When you introduce the antibodies to the sample, they bind the target protein but the complex is still in solution. The beads allow effective purification of the complexes by concentrating them on the beads, which are easily isolatable. 2) The NGS reads correspond to the red regions in the bottom image. Each 'line' is a single isolated DNA fragment which is sequenced from both ends to produce the 35 bp reads and then aligned to the genome. 3) That's essentially correct.


text:
T-cells Question
T-cells are important for efficient vaccination since they have:

A. T-cell receptor (TCR)
B. CD4+
C. CD8+
D. Memory

My gut is telling me it's A since the TCR would recognize the antigens but I want to make sure. Thanks!

Can you add some reasoning as to why the other options are not correct? A is wrong, by the way. Think about vaccination, and what its goal is. When do we get vaccinated, and why? What is it trying to do?

@MattDMo Thank you for the response. So after thinking about what a vaccination does, I realized that since it recognizes and remembers invading antigens and tries to prevent them from causing harm that D would make the most sense. As for eliminating CD4+ and CD8+, they seem more of a short-term choice whereas memory would be more long-term for efficiency. Sry for my ignorance, I'm an electrical engineer taking my first bio course in a while

no worries, I just wanted to get you to think a little more deeply, and it looks like you did. Great job!

You should choose D, vaccination is about memory.

vaccination is injecting the low or non-toxic substances that having a pathogen's identifying characteristics into human or animal body. When the animals exposed to the non-injurious pathogens, the immune system will produce a protective material, such as immune hormones, physiologically active substances and specific antibodies. When the animal re-exposure to this pathogen, the animal's immune system will follow its memory and create more protective material to prevent damage from the pathogen.
So choose D

I think T cell when presented to antigen (here vaccine) will produce memory T cell, which on next encounter with the same organism may act much faster and efficiently .so i think the correct answer is option D