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Why can't our eyes smoothly transition from side to side without focusing on a moving object?
Why are we not able to slowly and smoothly look from side to side, or up and down in a single and smooth transition, given that we are able to do this if our eyes are focused on a moving object?

Experimentator here! 1) I am not necessarily focussing on a moving object. 2) even in the complete darkness I failed to transition smoothly from side to side.

@remi.b I don't think it's possible to not focus on anything. We always have a destination in mind, even if we're staring at a blank wall! Consider why you are moving your eyes: you're testing if you can smoothly transition from side to side - that's two points -with nothing in between them. Of course you can't transition smoothly from max left pane to, max right pane. However, if we use our neck to guide our vision (maintaining central vision) we can do so very easily.

"If we use our neck to guide our vision" isn't that the same effect as staring at something moving? I don't know if you meant that as an attempt to transition from side to side without staring at something moving. I could be understanding that wrong though i guess.

@Hooplehead24 I believe that by "maintaining central vision", what R.Doto means is maintaining fixated focus on a point while moving the head. This statement then is certainly true, but irrelevant if I understand accurately that your question pertains to doing so without a focal point.

@R.Doto "I don't think it's possible to not focus on anything." It is actually, but it's not natural under normal circumstances. Try this experiment: Close your eyes and imagine that you feel the sensation of a hair tickling your nose, or hear the sound of a tiny fly buzzing directly in front of you. Then open your eyes and "look" for it. If only for a brief moment, your searching eyes are focusing into a place where there is nothing to see. With patience, calm, and practice, it is possible to even maintain focus on a relatively fixed point where there is nothing. It's a very odd sensation.

Short answer
Smooth pursuit is driven by retinal slip, which is determined by external input registered peripherally in the retina.
Background
The smooth pursuit system is a system designed to minimize retinal slip, i.e., the movement of an image across the retina. Saccades are rapid eye movements meant to fixate quickly on a new target (Purves et al., 2001).
Both movements are readily apparent when sitting in a train and staring outside; the eyes focus on a distant object and pursue that object. Once it exits the field of view, the eyes target a new object via a saccade and smooth pursuit is again initiated (the train window phenomenon).
Saccades can be triggered both involuntary (due to a sudden, unexpected stimulus) and voluntarily (Walker et al., 2000).
The smooth pursuit system cannot be voluntarily controlled, barred in some highly trained observers (Purves et al., 2001). Instead, it is guided by eye movements dependent on the movement (slip) of the fixated target on the fovea (Thier & Uwe, 2005). Hence, this system is controlled by external stimuli, not by internal ones. Retinal slip can of course be voluntarily manipulated by moving the eyes away from the target, for example by moving the head. The smooth pursuit system detects this by registering retinal slip, and keeps the eyes fixated on the target, through smooth pursuit which is involuntary.
References
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates (2001)
- Thier & Uwe, Curr Opinion Neurobiol (2005); 15: 645–52
- Walker et al., Exp Brain Res (2000); 130: 540–4

+1 Excellent answer. Given that this "highly trained observation" is possible (which I can corroborate), I still favor the idea that the involuntary nature of smooth pursuit is probably more from the force of deeply ingrained and continually useful and rewarding habit than actual neurological hard-wiring. (Visual tracking is a skill acquired after birth in our species.) Still because this skill and habit is pretty much universal in acquisition and application (excepting the visually impaired), I think the answer you have given here is functionally accurate. Thanks.

@MarkBailey, thanks! Smooth pursuit is indeed an acquired skill, but most of the visual capabilities are, for that matter. For example, depth perception is acquired afaik, but still hardwired in adults. I have to admit Purves et al. don't provide a reference to the primary literature on voluntary smooth pursuit. However, the book is pretty good.

Your eyes are attempting to see; not merely move. The muscles that move your eyes are voluntary. You control them, but think about how you usually command them. Whether sudden and reactive or careful and deliberate, you think about where you want to be looking and make your eyes look there. There is no functional purpose in looking without seeing, and seeing involves tracking specific features, focusing. It requires quick movement between multiple points of focus to gain information efficiently.
Compare this to the movement of your fingers. That movement can be smooth and fluid even though multiple muscle groups have to work together to make it happen. When you command the movement of your finger, you have a body-map that gives you a detailed idea of where your finger is, and how it is connected to you. You can be aware of its location with reasonable precision even if you can't see it. When it is necessary to move it with smooth, fluid motion, your muscle movement is guided by your internal body-map, and usually your eyes, confirming the motion. In contrast, you have very little concept of the actual position of your eyes within their socket, probably because it's not generally very useful information.
Positioning your eyes precisely, independent of what they are looking at is actually counter-productive. Doing so costs you the ability to see, as you can demonstrate to yourself by crossing your eyes, which, incidentally, is probably your best chance at achieving the sort of smooth movement you are referring to.
Probably the most significant reason you can't move your eyes smoothly is what you have practiced consistently for most of your life. With your motor muscles, countless various activities have required some degree of precise, smooth movement. During those very activities, what are your eyes doing? They are only moving smoothly if they are focused on a single point in motion - either a point on your body, or a point on an object which you are moving. Otherwise, they are bouncing from point to point, gathering information to measure whether your muscles need to adjust to accomplish the smooth movement you are attempting.
When you were born, your motor muscles were not proficient with smooth action either. Think about how a newborn baby jerks their limbs around, sometimes even clobbering themselves with their own hands, and then getting upset about being hit. As a toddler grows toward primary school age, they gradually learn to control muscle movement, but still have trouble when a situation demands very precise movement. Practice, for years, is what ultimately brings graceful movement. But no one ever naturally practices graceful eye motions (not independent of focusing on an object), because such movements are not useful for seeing.
References:
Body Map Concept: This concept is something you can demonstrate to yourself by moving around in the dark or by performing a task that you cannot see directly, like writing or typing, with your hands hidden from view. Here is a fascinating RadioLab discussion on phantom limbs which relates closely to this concept.
Motor and Eye movement: The Wikipedia article on Eye-Hand Coordination provides some context around the way eye and motor movement correlate.
Childhood development: Smooth pursuit is an acquired skill early in life (Van Hofsten & Rosander, 1997), which I can back up with personal observations of my 3 boys growing up.
Smooth Eye Movement: I have verified every statement I've made on this topic via personal experiment. I can move my eyes between more and less cross-eyed quite smoothly, which demonstrates that the muscles in the eye are entirely capable of smooth movement on command. It is clear as I do this, however, that not being able to focus on objects while crossing my eyes is an important part of the process. Otherwise, the instinct to focus on something and see it clearly overcomes my ability to control the movement. I have also learned to move one eye at a time from left to right - again, beginning in a cross-eyed state. This is not nearly as smooth, but the practice contributes to my understanding of the nature of voluntary movement of the eyes. Observation of the blind also contributes to conclusions in this area. A person who has been completely blind for a while will often exhibit the kind of smooth motion you describe (in addition to jerking movements), as does a close friend of mine who sees nothing but complete blackness after his optical nerve was destroyed by a bullet.
Cited paper

Van Hofsten & Rosander, Development of smooth pursuit tracking in young infants. Vision Research vol.37, Iss 13, 1997, Pages 1799–1810

This was a great explanation. Is there a source for this information? Correct me if I'm wrong but, going by what you said, a person should be able to "train" their eyes (eye muscles?) into smoothly transitioning. Is there evidence to support this? I wonder if there would also be an explanation from the perspective of how the brain works with the eyes.

@R.Doto While comments such as yours are not banned here, tearing down others without any support for your allegation is not a productive use of this forum. By what definition of "fact" do you disparage these statements?

@R.Doto Direct experiment, especially when the method is given for others to verify the results is among the most primary sources of all facts. It can be relied on with greater trust than hundreds of internet references if you or someone you know can repeat the experiment. In this case, I can accept that not every person will have the patience to verify these results directly, but put it to a group of people you know (including at least a few adults) and someone will be able to reproduce much of what I've described. (The independent eye movement thing took me months to learn though.)

@MarkBailey personal "direct experiments", unless run with strict relevant controls and peer-reviewed by unaffiliated third parties, are simply anecdotes. Please cite some actual published studies in reputable journals to support your claims.

@MattDMo If enough contributing members see this comment, we can peer-review this right now: Everyone, please upvote this comment if (and only if) you are able to verify at least two of the following: 1) You can move your eyes relatively smoothly without focusing on any moving object by beginning from a cross-eyed position. 2) Very young children are less able to move motor muscles smoothly. 3) Your eyes jerk quickly between different focal points during eye-hand coordination. or 4) You are able to locate and utilize body parts with some precision even if you can't see them.

Saccades are not necessarily under conscious control, which does contradict your first paragraph. I think some references would be useful to support your answer.

@MadScientist All muscles can twitch involuntarily, but that doesn't make them an involuntary muscle. But I agree; I do need better references. I'm actually in the process of generating a reference right now, and your assistance is hereby invited. In the name of science, do a couple of the experiments. Then upvote the comment above. No one can even see it right now.

At this point I'm not sure if your answer is correct or not. The issue seems to be primarily with your sources (as I'm sure you are aware of at this point). This question contains a great example of using references in an answer. http://biology.stackexchange.com/questions/937/how-many-times-did-life-emerge-from-the-ocean

@MarkBailey I'm not sure if you are understanding what we're trying to explain. You cannot do home experiments and use it as proof. Even more so, your results would never be open to opportunity to be published as there is no proof or data collected with high precision equipment by professionals in that field of academia. Period.

I do have to say some referencing would be place; anecdotes are welcome, but only to add to more credible sources. Especially your voluntary smooth pursuit is questionable without a source. I have added a reference to the developmental issue. Hope that helps.

Also: blind folks often have nystagmus as you rightfully say, but drifting gaze is unknownst to me. Citations would be in place.

@Christiaan I read the chat between you and Mark. While it sounds like there is actual damage to the nerve in this case, could there also be conversion disorder at play, given the trauma of the event? If the optic nerve is destroyed, obviously there is nothing that can be done, but might this also relate to the persons ability to be able to perceive ideas and memories by tapping into their visual cortex, so as to "see" their thoughts? That might be helped through therapy.

@AMR Well, he often sees in his dreams. In fact, that frequently makes him lucid, because he knows very well in his dreams that if he can see, it's not real. But yes - extraordinary trauma of the event.


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Can fireflies species be identified with their wavelength?
I was wondering if we could ID male fireflies using their wavelength? A bit like how we use UV light to ID species of scorpions.

This might be a bit broad; I don't know. There are many species of fireflies, with different flashing patterns and intensities; some male fireflies don't even bioluminesce. Though the luciferin may be slightly different among species, I would doubt (but have no evidence) that it is different among sexes of the same species. It's much easier to tell which are males by their location and flash patterns.

In short: Yes it should be possible, but probably not for all species and as @anongoodnurse said there are probably easier methods of species-identification.
Elaboration:
I know (but could not find a reference) that there are currently hyperspectral cameras that are able to capture bandwidths as small as 2 nm.
And there are differences in the emission spectrum of fireflies.
Firefly luciferase bioluminescence color can vary between yellow-green (λmax = 550 nm) to red (λmax = 620). ( https://www.ncbi.nlm.nih.gov/pubmed/2801227 ) There are currently several different mechanisms describing how the structure of luciferase affects the emission spectrum of the photon and effectively the color of light emitted. (https://en.m.wikipedia.org/wiki/Luciferase)
However, it is likely that there are closely related species of firefly that have no (or very small) differences in emission spectrum. These will not be identifyable with spectral imaging.

Do you think we could ID individual in one species using wavelength ? Putting a set-up of those camera and then use Capture-recapture model to estimate population size ?

@NicoCoallier I don't know but I doubt that the spectral differences within a apecies are large enough. But there is only one way to find out...

very interesting stuff

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Does light from the left visual field reach the temporal left retina?
A diagram of the visual pathway is shown here. Light from the left visual field reaches the left nasal retina and the right temporal retina. On the other hand light from the right visual field reaches the right nasal and the left temporal retina.

The optic fibers from the nasal parts of the retina cross, whereas the fibers from the temporal hemispheres don't. This configuration leads to the projection of the left visual field to the right occipital cortex and vice versa.
My question is, why can't light from the left visual field reach the temporal left retina and vice versa? I have illustrated this in the picture below with blue arrows.

Obviously, if it would, it would interfere with the normal pattern of projection. Now my question is what prevents light from the left field of view reach the left temporal retina? Or is there some overlap between the visual fields?

Very interesting and well researched question +1d. I hope you get a few more upvotes.

@Christiaan Just wanted the answer! Not the upvotes. Thanks :)

There is overlap between the left and right visual fields, as shown in Fig. 1. This overlapping part is referred to as the binocular field of view. The monocular field of view (FOV) is 160o (w) x 175o (h), and the binocular FOV is 200o (w) x 135o (h). The region of binocular overlap is 120o (w) x 135o (h) (Kolb, 2016). The visual disparity in the binocular FOV of the both retinal projections forms one of the most important depth cues that allows us to estimate the distance of objects.

Fig. 1. The left and right visual fields have an overlapping area, the binocular visual field. source: Harvey Mudd College
Fig. 2 below shows why only a certain part of the visual fields overlap. Firstly, the retina has a finite size and secondly, the anatomical location of the pupils restricts the angles of the visual field. The most eccentric parts of the left visual field simply cannot reach the temporal left retina (and vice versa), because the angle of the pupil with respect to the retina simply doesn't allow for it. The same holds for the most central part of the left FOV, which cannot reach the nasal part of the right retina; it can only project to the the temporal right retina because of the restrictions due to the localization of the pupil, the retinal size limitations, as well as the nose blocking a certain part of the FOV.

Fig. 2. The left and right visual fields have an overlapping area, the binocular visual field. source: Ohio State University
Reference
- Kolb, Facts and Figures concerning the human retina. In: Kolb et al (eds). Webvision, The Organization of the Retina and Visual System. Utah University (2016)

But one doubt remains. If the fields of view are overlapping, a lesion in the visual pathway like, lesion 2 (bitemporal hemianopia) in the picture in the question - shouldn't be so well defined/ straight line. Is the picture wrong in showing the visual defect to be etched out so clearly?

@Polisetty - the picture is valid and the symptoms are indeed pretty much as depicted, as the retinal hemispheres are divided in half.

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How many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’?
Based on what we learned on condensation reactions, how many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’
I had an online biology quiz with this question, and I thought it would be one molecule for each nucleotide, for 11 total. The answer I have been given is 10. I feel like I am missing something obvious.

I just wanted to point out that the net generation of water is 0 since, for every condensation reaction of two nucleotides by RNA polymerase, there is a subsequent hydrolysis of pyrophosphate by pyrophosphatase.

To amplify what @canadianer wrote seven years ago, RNA is made from nucleotide triphosphates condensing with the 3'OH end of a nascent chain to give pyrophosphate. No water is generated. So the correct answer is 0, regardless of the fate of the pyrophosphate. I notice that a Google search for images of the reaction features one from Researchgate showing a NMP reacting to give water. This is a RNA ligase reaction. Only NTPs or NDPs participate in RNA synthesis. The nonsense generated by problem questions to students!

It's one for every phosphodiester bond formed. 11 nucleotides, but only 10 bonds needed to join them into an oligonucleotide:
1  2  3  4  5  6  7  8  9  10 11
N--N--N--N--N--N--N--N--N--N--N
 1  2  3  4  5  6  7  8  9  10

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Manufacturing of Bio Molecules
Can we Manufacture bio molecules say e.g. the simplest Sugar, C12,H22,O11 the way we do with any other mechanical component. So, we know all about the Structure and arrangement of Atoms in Sugar - so do the design send the commands to the manufacturing machine which will use C,H and O elements and put them in them specified order !
If it's not doable today, what's the reason? -
1. Our lack of understanding of the Structure of Sugar atoms  or
2. The specialized method which will put nascent atoms into the configuration of Sugar. Are people anywhere in the world trying to work this way? Please give references.

If that is meant to be sucrose, that isn't the simplest sugar. Technically I think it would be glyceraldehyde (C3) which makes the task a little easier. If you want a cyclic molecule maybe ribose, C5.

This is more about chemistry than biology (synthetic chemistry to be exact) and should be moved to Chem.SE in my opinion.

I agree with Armatus on that one, I'm afraid. You'll have better luck on the chemistry site.

this question needs more detail - its not going to make more sense to chemists. what is it we don't know about molecules like sugars?

Dear Shigeta, my question simply means that, do we know enough to create molecules like Sugar from scratch. I am not talking about synthesizing. Or is it that we know all the details, but it is not possible because of technological limitations (it may or may not be practical, I am not bothered). I am talking about possibilities and am keen to know the limits!

There are literally millions of biomolecules.  Some of them we know the structures and chemical properties of others we know nothing about.   I'm going to focus on sugars.  It would be too broad a question probably even to list all biomolecules, much less describe how their chemical synthesis would be performed.
The good news is that industrial manufacturing of biomolecules is done for thousands of compounds and even available.  Certainly chemical synthesis of sugars is possible and even available but is very expensive and often produces side products compared to fermentation processes or extraction from plants say.
Sugars, for instance glucose are very similar, but if you look at this structure you will see that the four OH (alcohol) groups could point up or down.  Any manufacture of glucose would have to get each one of these bonds exactly right.  This is D-glucose, which is commonly available as extracted with water from sugar beets and sugar cane.  I can buy 10 pounds of it at the store for less than $10.

Compare with L-glucose, which is synthesized by a chemist.  Its available (though not really recommended for human consumption because its got impurities and doesn't necessarily pass FDA definitions of purity to be a food) at the cost of $87 per gram.
So the answer is probably best put like this: who would pay \$87,000 for a bag of sugar when they could pay $10?  Cases where one would have to pay a company to produce a biomolecule, its going to cost...

Great answer, but my impression was that the question was about some sort of nanosynthesis.

why not write it up Alan?  there seem to be more than one way to read the question...

I don't have an answer to my reading of the question.

Thanks friends for your inputs. As Alan Boyd has mentioned, my question has to do with the methods available to manufacture. I am aware that synthesis is cheaper, but I want to know, if there is a system/machine which takes various aspects of the design of complex molecules (the knowledge gained through structural an functional studies) as input and gives the desired molecule as output. The machine has nano scale control to fix things at the right place and uses elements as the manufacturing material. Also, please give references to such work.

nano scale is not enough of a description in itself to answer this question, i still interpret the nano scale manipulation would still be a small scale of synthetic, enzymatic or fermentation methods.  we have no demonstrated way of making most biomolecules... there are practically an infinite number of them.  do you have a reference?

In short, no, molecules aren't synthesised that way. This is because the common atoms that in biomolecules (C, O, H, N, P) don't occur as individual atoms in nature and it would be extremely difficult (and unnecessary) to keep them in a single-atom state ready for assembly into a molecule in some way.
However, chemists are able to synthesise almost any kind of biomolecule desired by performing different routine reactions in a targeted fashion. The efficiency of production and the purity of the product obtained can vary extremely, but in principle any biomolecule up to a reasonable size could be synthesised chemically that way - as long as the desired product is itself chemically stable.
While theoretically, the repertoire of reactions you can do that way might be limited, there is no machine that does them routinely according to a program you put in, because there are too many variables that need to be adjusted depending on the current aim of synthesis and much more flexibility is needed than such a machine could provide.
I'm waiting for a reply from my chemistry friend on a few examples of those reactions.

authors: مهدي محمد الصباري


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Are there seeds intended to feed eaters?
Seeds are meant to survive digestive systems of the animals that disperse them. Are there seeds meant for a creature, who will digest most of the seeds for nutrition and disperse only a minority of intact seeds?

Doubtful because it would decrease the probability of that species remaining extant. Typically traits that would drive a species to be less competitive or less demographically fecund are traits that are heavily selected against in a population/community due to competitive pressures. Still, I think it's an interesting question, and anything is possible! It's fun to think about instances in which this could possibly happen and why...

@theforestecologist Not much of a botanist here, but...isn't that essentially what a fruit is (or a nut?)? I mean, I guess the OP is maybe asking for something more specific than that, but it seems like a fruit is essentially taking the role of the digestible part of the seed, and nuts are fruits that some animals bury and disperse and then only eat some of them - of course with the distinction that those dispersed, uneaten nuts never pass a digestive system.

"Meant" is the wrong word to use here.  (IMHO, anyway.)  But consider that almost all plants produce far more seeds - perhaps hundreds, thousands, or more - than they need to perpetuate themselves.  So if some animal is enticed into eating the seeds, digesting most, and dispersing a few (perhaps enclosed in a handy packet of fertilizer), then evolution has created an effective dispersal method.

There's a very interesting case of mutualism between the species Homo sapiens and Oryza Sativa (also Triticum aestivum...). The humans have bred the plants to produce highly nutritious seeds, much greater then non-adapted species, and in return the humans save a small fraction of the seeds and will cultivate the plant for many generations.
It goes further then that in that humans also will protect their mutualistic plant partners from other invasive species and cultivate them, ensuring their mutual survival.


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What is name of the red eyed rabbit or hare, found in Himalayan region?
Is it Rabbit or Hare?

The eyes are red in colour.
These animals are habitat of Himalaya.
The pictures are taken in Dowhill Park, Kurseong, West Bengal, India.

Perhaps a bit underwhelmingly, those are Himalayan Rabbits.
https://en.wikipedia.org/wiki/Himalayan_rabbit
The pure white fur and red eyes are usually a sign of albinos, but in this case it's actually a trait of the entire species.

[They] can only produce eumelanin under a certain temperature and they cannot produce pheomelanin at all.

Thank you for the identification. It's strange that the Wikipedia page doesn't have the classification. I have a question though, the article is saying a breed of rabbit. What does it mean? A species of rabbit?

It means a species of rabbit, yes. Of the genus Oryctolagus.

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Information and image of Genus Acesina
I am searching for image and information, like distribution etc of the genus Acesina. The Taxonomic tree is:
Kingdom:        Animalia
Phylum:         Arthropoda
Class:          Insecta
Order:          Lepidoptera
Superfamily:    Papilionoidea
Family:         Lycaenidae
Genus:          Acesina

According to Catalogue of Life this genus has the 4 species. I haven't found any information by searching web, even the species are extinct or not! Any pointer would be appreciated.

@kmm thank you for the information. Can you post your comment as the answer, so that I can accept it.

Also described at  http://en.wikipedia.org/wiki/Acesina

The genus Acesina has been revised and is now part of the genus Arhopala. The wikipedia page for Arhopala has some additional information on this genus.


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How many nucleotide pairs code one gene?
As I know three nucleotide pairs (triplus) code one gene.  But I have found next information in  the "Molecular biology of the cell" by Bruce Alberts:

Mycoplasma genitalium:  it has only about 480 genes in its genome of 580 070 nucleotide pairs.

But 480 genes * 3 ~ 1500 nucleotide pairs.
Where I have made mistake ?

you said 480 multiplied by 3 equals to 1,500 but it actually equals to 1,440...

Please quote a source for your statements in a question. If you had done so you would have realized that your statement about nucleotide pairs and genes was incorrect nonsense.

You seem to have some confusion, so let's clear things up.
A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.
Each gene consists of nucleotides bound together, which are interpreted by the cellular machinery in groups of three, called triplets.
DNA is first transcribed into messenger RNA (mRNA), which is then translated into proteins.
Each triplet codes for one aminoacid not one gene! In fact genes are not "coded" by anything, they are the code!
Now, what I just wrote is extremely simplified, there are other important details that I omitted, but hopefully it cleared your doubt.
To give you some further detail: not every single nucleotide in a gene will code for an aminoacid. There are regulatory elements such as the promoter of the gene, which allows the enzymes that transcribe the DNA to attach to the gene (essentialy it says: "hey, start transcription right here!"). Similarly, enhancers and silencers can tune up or down transcription of the gene.
In eukaryotes there are big stretches of DNA called introns that are not coding for anything but have big importance for regulating transcription. In fact a single mRNA can be used to code more than one protein, using a process called alternative splicing.
There are also regions of DNA that code for RNA sequences not translated into proteins at all, but which have all sorts of regulatory functions in the cell.

In addition to the above answers, one needs to first understand the difference/relationship between a Gene and the genetic code. The genetic code is written in triplets (3 nucleotides) and one triplet of nucleotides codes for one amino acid (a.a) except the Stop "triplets" or codons(UAA, UAG, UGA in nuclear DNA)
Now since one protein/polypeptide is made up of more than one amino acid and that one gene codes for a specific protein, the gene will be a set of triplets.
SUMMARY
Gene = Protein.
Protein = a.a + a.a + a.a...
One a.a is coded for by 3 nucleotides(triplet)
Thus a Gene will have many triplets and hence nucleotide pairs depending on its size.
You can Calculate again now
Knowledge about the process of transcription (formation of mRNA from DNA) to translation gives a better and deeper insight.
Hope that was helpful?
Regards
Lubega Jason (Biomedical scientist; Molecular & Cell biologist)
Makerere University - Uganda

Why are you multiplying 480 * 3?  Do you think every gene is only 3 bases long?
If the average protein length as 500 amino acids, every gene would have on average 1500 nucleotides.  480 genes 1500 bases long = 720,000.  So the proteins of m.genitalium  must be smaller than that on average, but that's realistic.

This assumes that there are no overlapping genes.


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Perception of artificial light - flickering
I noticed something strange a couple of years ago. I was walking down the street at night, when it struck me that the street lights were flickering. But, when I turned to take a direct look at the light source it did not flicker any more. In other words, when the light is not the main focus of your eye, it can flicker.
From then on, I started to focus on these flickerings and they are everywhere. Street lights, lights in a house, but also computer monitors or even projections on a screen. Again, the flickering only happens when you do not look directly at the source.
Does anyone have an explanation for that? Is it the brain's fault, or the eye's?

It's difficult to give an exact answer without actually observing the light and performing measurements. I have a theory, though.
Your peripheral vision is hyper-sensitive to changes in light - an evolutionary trait that provided quicker reactions to predators sneaking up on you. As such, even the tiniest fluctuations in light can be registered with your peripheral vision; much more so than your primary field of vision. In this case, it may well have been that the light was flickering very subtly, or at a very high frequency, which your primary field of vision could not pick up. When your peripheral vision was in play, it immediately spotted the flicker.
This is reliant on a principle called the flicker fusion threshold, which essentially states that there is a threshold of various light properties (including flicker frequency, colour, intensity, etc.) at which an eye begins to distinguish a steady light from a flickering one. Research has demonstrated that species who have high rod density are good at picking up flickering, whereas species with low rod densities have a much poorer threshold. Cone density doesn't seem to factor in very much, since flickering is primarily a change of intensity rather than hue.
This transfers into the human eye, since we have a high rod density (and low cone density) at the edges of our retinas, i.e. in our peripheral vision. If you had the eyes of another species (as creepy as that would be) with a high rod density, you may well have been able to detect the flicker quite easily with your primary field of vision.
To directly answer your question - yes, I believe this is primarily the "fault" of the eye, rather than the brain. The brain has a role in identifying the flicker at a subconscious level, in terms of fight or flight response, but the eye is responsible for providing the elevated sensitivity at the peripheral.

Thank you for your answer! I figured the same: the peripherals of your eye is more sensitive. But it's so strange that you cannot see it when you look directly at it. Thank you for your answer +1. Will see what others have to say about it!

I believe this answer is correct; but I think it's worth emphasising that these things are actually flickering. It's not an illusion; if anything the absence of flicker when directly observing is the illusion.


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Relation between goose bumps and temperature
As we all know, cold weather will cause us to have goose bumps. I honestly don't know why (1), because our skin contracts?
Apart from that something quite contradicting happened this morning. I was taking a hot shower and it was so hot that I suddenly felt that I had goose bumps. Not because it was cold, but because it was so hot. How can this happen? Because of a sudden change in temperature the skin goes haywire? Or aren't goose bumps related to temperature in a way, but is a sort of safety reflex?

Oh dang I highly suspect that Ca++ ions are binding troponin on actin filaments and blocking the action of tropomyosin thereby exposing cross-bridge binding sites and promoting the hydrolysis of ATP to an inorganic phosphate and a diphosphate.

Goose Bumps (a.k.a. - Goose Pimples) are caused by the Arrector Pili muscles in your skin:

Their purpose is to increase the distance from epidermis to the top of the follicle, and increase the area between follicles. This has the effect of increasing the amount of air trapped between the hair and surface of the skin. In other mammals the end-result is an increase in the insulatory properties of their fur, meaning they will stay warmer or cooler depending on their current needs.
Another function in our mammalian cousins is to simply appear larger, and thus more of a threat to any predators or dangerous animals. Much like the shoulder and lower back hair on this dog:

Thermoregulation in humans has evolved since our furrier ancestors; we sweat to cool off, and shiver to keep warm. We also use tools and weapons, can create fire, and have other ways to communicate our lethal capabilities.
Goose Bumps are the human body utilizing old instinctual reflexes in the proper situations, but we lack the thick mattes of hair our ancestors had for the reflex to have any significant effect. They're a fun Easter-egg, a leftover that doesn't do us any harm and are an easy way to tell if someone is cold or scared - which might be useful under the proper circumstances.

Great answer! Will wait for a day or two before accepting. Give other peeps a chance as well. :)


text:
How come that we "feel" it when someone's watching us
The question is relatively easy (the answer however..). We all know this feeling "being watched" and more often than not this is a real thing. If someone is staring at us from the side or from the back we sort-of "feel" it and we evenf eel the direction where it's coming from.
I can't seem to find a plausible answer for this though:

We actually see the people staring from the corner of our eyes - false, I tested this thoroughly and it also happens when your eyes are closed or someone's behind you.
Eyes don't send out energy (or "beams") as far as I know. They "receive" light but don't send any out, except for reflection.

So, what causes this strange phenomenon?

I'm wondering if carbon dioxide, body odour, infrared radiation could have an effect. I wouldn't be too surprised if the spiritual realm was at play somehow either.

I think that this question would be a better fit at the Cognitive Sciences StackExchange.

This may be a better fit on the Cognitive Sciences SE [cogsci.stackexchange.com]

You do not have evidence of this "phenomenon" happening. What you do have is the impression of it happening.
So a better question is: what are the biological correlates of the "being watched" feeling. Or better yet: when you feel being watched, on average, is someone actually watching you?

possible duplicate of What portions of the brain have drastic changes in activation when we "sense" someone is there?

(answer to both questions is the same, I think)

To quote the University of Sidney site:

People often think that other people are staring at them even when
  they aren't research led by the University of Sydney has found.
When in doubt, the human brain is more likely to tell its owner that
  they're under the gaze of another person, researchers from the
  University of Sydney and The Vision Centre reveal in a recent article
  in Current Biology.

Also, from the scientific paper:

We presented participants with synthetic faces viewed under high and
  low levels of uncertainty and manipulated the faces by adding noise to
  the eyes. Then, we asked the participants to judge relative gaze
  directions. We found that all participants systematically perceived
  the noisy gaze as being directed more toward them. This suggests that
  the adult nervous system internally represents a prior for gaze and
  highlights the importance of experience in developing our
  interpretation of another’s gaze.

So you, and I, overestimate how often people is staring at us.
For details, see: http://sydney.edu.au/news/84.html?newsstoryid=11335 and https://www.cell.com/current-biology/retrieve/pii/S0960982213003321

I would guess hearing plays a part, as a powerful human sense  that works in 360 degrees.
Just as a hypothesis, I'd imagine that small sounds help you sense people behind you, and that this, plus chance, plus the very human capacity to see meaning in random events, gives the impression that there's a way to sense that someone not just behind you but actively looking at you.
In our every-day experience (that is, not in an artificial experimental setting), there are a lot of ways to bias our observations / data collection. For instance,

a half-conscious glance behind you is quickly forgotten (data discarded) if you realize it was just somebody strolling past, but remembered (data retained) if you see someone staring fixedly at you. This will spuriously increase your positive results (that is, the impression that "every time I look behind me, my sense that someone is looking is confirmed")
on the other hand, if someone is staring at you from behind, but you don't notice, you also do not retain that negative data, because, by definition, you didn't notice. So there is a strong effect that is spuriously decreasing your negative results.

So, as Brandon Invergo mentioned, we'd like to see a testing protocol along the lines of a blindfold and earphones playing white noise on the "senser", and the "watcher" behind the senser staring or looking away at random intervals, and a large number of trials.
This is not to diminish the fact that some people have much better situational/interpersonal awareness than others (say, a ninja vs. me), but I really imagine that this is more an effect of cognition (putting together small cues from hearing/peripheral vision/smell etc.) than of any difference in sensation.

I think the phenomenon should be studied separately in two conditions it happens (though in one of them it only happens subjectively):

When it happens outside of the peripheral vision, e.g. when your eyes closed, or  someone's behind you
When it happens within the peripheral vision (approximately 180), i.e. corners

For the first part, I agree with Sherin quoted the scientific paper "People often think that other people are staring at them even when they aren't".
But for the second part, we often experience that when we stare at people from the corners, they turn their heads and say "What ?". Perhaps recognition of this corner staring has something to do with extra foveal perception and of course the emotional part of it would be the emotional salience of being stared at. And because this extra foveal perception is less accurate than the perception in eyes' focus, it may result in false perception of "being watched" too. It's worth to mention that, because "eyes", "faces", and "staring" really have a high emotional valence for us,maybe we became very adept in recognition of them in our peripheral vision through many years of accumulative experience (I'm a fan of information processing approach to cognitive development). For more information about extra foveal perception, you may take a look at the seminal research carried out by Henderson (2003), "Human gaze control during real-world scene perception".


text:
How does hair grow and is it similar to how grass grows?
If I recall correctly, nails (finger nails or toe nails) grow by adding matter at its base. So for instance, if you would draw a dot at the very bottom of your nail, it would end at the top in a couple of weeks.
I was wondering how this works with hair. Is new hair added at the bottom and the old hair 'pushed' away? Or does hair consist of layers that always try to get further and further (that would mean longer hair is thicker than shorter hair). And is this wayof growth similar to how grass grows?

In hair and nail growth new cells are added to the bottom. These cells are produced at the follicle. There are three stages called:

Anagen : active growth
Catagen : end of active growth
Telogen : total stop of follicular growth

I don't know what you mean by like grass but both nails and hair have a first in first out order.
Feathers present a contrasting case: the outermost portion is the most recent. Feather growth is relatively more complex. This article is a nice read on feathers.

Well, does grass grow in a similar manner? First in, first out?

plants grow differently.. the tips grow.. its opposite to hair growth

And all hair cells are all dead cells...


text:
what is knob heterochromatin?
I am reading a paper which discusses Maize Genome Structure. Descriptions of the  structure is given in the papers introduction.
I know about heterochromatin "heterochromatin stains intensely, indicating tighter packing. Heterochromatin is usually localized to the periphery of the nucleus"
but, could someone explain what is knob heterochromatin?
thanks for help.

Here's a good summary of knobs, which says that they are "typically telomeric," "tandemly repeated DNA sequences [that] appear as distinct, heteropycnotic regions located at certain sites on specific chromosomes and look much like beads on a string" and are involved in:

increased recombination
neocentromere activity
preferential segregation
chromosome breakage and chromatin loss
sex differences in recombination

The introduction to this paper gives some of the same information.

I found it in this article :

Heterochromatic knob
  A chromosomal region that can
  be identified microscopically as
  being darkly stained compared
  with surrounding chromatin.
  DNA sequence analysis has
  shown that knobs often contain
  highly repeated DNA
  sequences. They were
  described initially in the
  1930’s by McClintock during
  her studies of maize
  chromosome structure

If you copy a paragraph verbatim from another source, please indicate this clearly by naming and linking the source and using a blockquote. Else one might get confused about which parts of the answer you wrote yourself, and which are taken from other sources.


text:
Are glycoproteins and glycolipids present only on the cell surface membrane?
I haven't read this being stated explicitly, however whenever I read about proteins and glycoproteins this seems to be implied. For example, in this Wikipedia article,

Lipid and proteins on the cell membrane surface often have short carbohydrate chains protruding out from the cell surface, known as glycolipids and glycoproteins.

My question is, is this the case? And if so, why would they only be present on the cell surface/plasma membrane. Would they not be useful elsewhere in the cell for example for vesicle trafficing as receptors for targetting sequences?
One idea I have is that, to the best of my knowledge, the enzymes for glycosylation are present in the endoplasmic reticulum and Golgi lumens (oligosaccharyl transferase in ER, etc) so glycosylation would only occur on the part of the protein/lipid that is topologically outside of the cell, however this brings up more questions:

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.
Why would there not be glycosylation enzymes on the cytosolic side?

This journal article has some information on glycolipids: "Membrane lipids: where they are and how they behave.".

Since you asked three questions, I'll answer them one by one.

Are glycoproteins and glycolipids present only on the cell surface membrane?

No, glycoproteins have many functions and are certainly not restricted to cell membranes.
Some examples of glycoproteins in blood include fibrinogen, antibodies, miraculin, etc. See this:

Fibrinogen (factor I) is a glycoprotein in vertebrates that helps in the formation of blood clots.

For a more detailed list of glycoproteins, see this wikipedia article.
On the other hand, glycolipids are found only on cell membranes. See this:

Glycolipids are lipids with a carbohydrate attached by a glycosidic bond. Their role is to maintain stability of the membrane and to facilitate cellular recognition. The carbohydrates are found on the outer surface of all eukaryotic cell membranes.

This does not exclude glycoproteins from sticking into certain organelles (i.e. on the other side of the membrane to the cytosol) which is also topologically equivalent to the cell exterior.

Glycoproteins, or any proteins, after they are completely processed , don't just float around in the cell and reach their appropriate place. Its obviously not that proteins 'know' where to go, but they are actually taken to their appropriate places. This is known as protein targeting. See this:

Protein targeting or protein sorting is the biological mechanism by which proteins are transported to the appropriate destinations in the cell or outside of it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases.

There are differences between cell membrane and organelle membrane, which makes them distinguishable for targeting factors.

Why would there not be glycosylation enzymes on the cytosolic side?

Glycosylation is a post-translational modification or proteins.

Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Only certain proteins require glycosylation, that is why they are translated by ribosomes connected to golgi apparatus or endoplasmic reticulum. If glycosylation enzymes are present everywhere in the cell, then every protein that encounters them would get modified and, possibly, non-functional. Thus, there are special compartments in the cell for such purposes.
EDIT: To answer the questions you asked in comments:

are there any glycoproteins found elsewhere inside the cell? For example in the mitochondria?

We aren't sure about that yet. There have been a couple of studies to find out whether there could be glycoproteins in mitochondria, one of which is this:

Isolated intact mitochondria selectively incorporate monosaccharides from nucleotide diphosphate monosaccharides into protein. Fucose, mannose, glucose, and galactose were incorporated by the mitochondria into glycoprotein; xylose was not. Structural integrity of the mitochondria was not necessary for the incorporation of monosaccharide into glycoprotein; mitochondria broken by homogenization also incorporated monosaccharide. The monosaccharides incorporated into glycoprotein were localized in the inner mitochondrial membranes, the same membranes which contain the protein into which leucine is incorporated by the isolated mitochondria.

If there are glycoproteins in mitochondria, they could be at many other places too inside a cell.

does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm?

Glycoproteins are not required inside cell (I, or maybe nobody, knows why). Their main function is as receptors or secreted products, thus they are not found inside a cell. However, glycosyltransferases can behave as dynamic glycoproteins and hence are found inside cells. See this:

Glycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based.

Metroplex thank you for your reply. I still have a question though; so glycoproteins can be secreted as well as being destined for the plasma membrane, but are there any glycoproteins found elsewhere inside the cell? For example in the mitochondira? I know there will be glycoproteins present inside vesicles which have just come from the plasma memebrane, and these will be returned. But what about glycorproteins being specifically targetted to regions in the cell which are not the plasma membrane and are not excreted?

Question 2: Also, I understand now why glycosylation enzymes would not be present inside of the cytoplasm, however does this not seem a bit of a shame for the cell? I mean, does the cell not sometimes need glycosylated proteins inside of its cytoplasm? How would it get these proteins in its cytoplasm? It seems impossible, unless they were to be transported in from the ER lumen or from outside of the cell through chennel or carrier proteins, but I have never heard of a channel, carrier big enough to achieve something like this...

I hope you find the modified answer helpful. Please add the above questions too in your main question.


text:
Could there be a pathogen which does not activate an immune response?
In order for the immune system to be stimulated to produce antibodies, there must be a surface protein of the invading pathogen which binds to a receptor on B cell surface somewhat loosely. We need this first step for the initiation of the somatic hypermutation phase to produce specific antibodies.
But what if there is a pathogen which does not have such a surface protein? i.e. its surface proteins, if it has any, do not bind with sufficiently high affinity to surface proteins on existing B cells to trigger further aspects of the immune response.
One may argue that this is unlikely to be the case because:
a) naturally occurring pathogens evolve from existing ones, so the changes in the antigens will generally be minor. A new strain will have surface proteins that are similar enough to those of an existing strain for some loose affinity to present antibodies in the host.
b) I think, though am not at all sure, that pathogens need to invade cells to be dangerous.I'm not entirely sure what the nature of a pathogen which cannot invade cells would be. Perhaps not a pathogen at all? In any case, if the starting assertion is true, the dangerous pathogens have a surface receptor which binds with surface proteins on cells to enter them. What if many antibodies are based on the same proteins? (Though I have trouble believing this because the natural agonists of these cellular receptors are some biologically relevant and useful proteins, which we would not want an immune response to. For instance, a generally accepted mechanism of entry of SARS-CoV-2 into cells is by binding the ACE2 receptor, which has angiotensin II- a vasoconstrictor peptide- as an agonist.
So my questions are:
a) Could we synthesise a pathogen which has no surface proteins but which nevertheless does harm in some way? How could it do this harm?
b) Can we make a pathogen which has surface proteins such that it can enter cells or do damage that pathogens normally do, but goes undetected by the immune system?
In the above I have assumed that surface proteins (or perhaps also other surface molecular- maybe carbohydrates will do- are necessary for activating the immune response. If this is not the case, please let me know.

"I think, though am not at all sure, that pathogens need to invade cells to be dangerous."
True in the case of viruses and some bacteria.
Hiding within the cells of the host is the intracellular pathogenesis.
But other "tricks" are possible. Four examples:

biofilms
surface proteins that "catch" antibodies
fast mutation of surface epitopes, like the (in)famous HIV
using host molecules (the HIV again)

Source: Extracellular Immune Avoidance (LibreTexts)
Also interesting: How bacterial pathogens colonize their hosts and invade deeper tissues (Microbes and Infection
Volume 17, Issue 3, March 2015, Pages 173-183).


text:
What was the first known flower meant for a flying pollinator insect?
I think flower ancestors were colorless and sugarless. The first flower then chanced upon using insects by attracting them. Has this flower been discovered and from what ancestors did it evolve from?


text:
What is carbon in the soil?
I often see the term "carbon in the soil" (example) but I cannot figure out what it is. It's a positive goal too - people want agricultural techniques that do not deplete it.
What form does this carbon exist in and what are the major sources? How does it help plants and other organisms who use the soil?

CaCO3 can be a major constituent of soil, i.e. Chalk, so mountains can be made of carbon in large amounts. Environmental Scientists study mountain weathering's effect on the climate, with sulphuric acid and absorption of CO2 carbonic acid into alcaline soils. Carbon in the soil conversely, refers to carbon fixing by plants adding to the soil, and plant matter being consumed and returning to the air. There is mineral and organic carbon. soil technically is not often mineral, it is normally a living matter of organic and mineral.

It refers to organic carbon, i.e. the carbon present in proteins, carbohydrates and other molecules as consequence of the metabolism of living creatures. Carbon rich soil is an indication that microorganisms, insects, and worms are living in the soil. They are the basis for the soil ecosystem and boost the flow of nutrients that ultimately will support plant growth. A soil with low content of organic carbon indicates that it's a harsh environment where living organisms struggle.
Some articles on the matter:
https://en.wikipedia.org/wiki/Soil_microbiology
http://www.nature.com/nature/journal/v501/n7468_supp/full/501S18a.html
http://mbio.asm.org/content/6/2/e02527-14.full

How does agriculture deplete it?

Why the downvote?

@aitchnyu It depends on many factors. The use of chemicals for pest control of fertilizers may affect the ecosystem, for example, causing a cascade of reactions that it's hard to predict. Also, intensive cultivation may deplete the soil nutrients too fast, "starving" the biota.

If you take an average soil sample, it contains lots of organic matter, unless it is completely mineral like desert sand. Oganic matter always has C, H, O elements, and often N. Peat bogs for example, are classed as a type of soil and can contain almost only organic matter, with many kilos of carbon per cubic meter, rainforest soils are sometimes meters of peat, it can catch fire due to carbon content. Humus in forest soils is also mostly organic. If carbon fixing life is removed from a carbon rich land, soil carbon will often slowly return to a mineral state, often as a function of temperature (hot soil mineralizes faster) carbon products get turned into simpler more volatile lower energy compounds, by being eaten by biota and respired as CO2.

Carbon in the soil would be what's left of anything that died in there, or any animal feces.
Carbon in the soil may possibly benefit bacteria that live in the soil, which may fix or otherwise convert nitrogen, but the plants don't use it.
However, let's imagine a dog is walking around and dies. It will rot into a gooey paste as maggots eat it, and then will liquefy into a putrid mess and eventually what's left of it will turn to dirt.
The dirt will have lots of carbon in it, which bacteria will probably use,
The dirt will have lots of minerals in it, which the plants DO use
They get their carbon from co2.


text:
How is the brain kickstarted during development
The brain is a complicated beast, that operates (generally) by electrical activity. During development, all cells originate from the a single "cell": the zygote.
At some point during development, the cells will begin to form into the specialised cells of the brain. But how does the brain activity start?
Is there some process that gets things going, akin to jump starting a car? Specifically, I'm referring to the mammalian (and more specifically human) brain.

Given the right set of molecular machinery, neurons can start firing spontaneously. No kickstart needed.

If nothing else, touch, temperature and other sensory neurons will start firing in response to stimuli detected by the embryo, which will start firing impulses into the brain.


text:
Book recommendation: protocols and recipes handbook for molecular biology / biochemistry
I'm a 5th-year PhD student in chemical biology. I've mostly been doing computational work, so my bench skills are rusty. To help me, I'd like a handbook of common techniques -- transformations, ELISA, protein purification, DNA extraction, SDS-PAGE, column chromatography, etc. I'd especially like a collection of recipes for buffers, etc.
I can find some protocols, but it's hard to find ones covering the more basic methods, and I'd like something cohesive. And there's something satisfying about an actual book.
I found these (and browsed through them in an HHMI library once):

https://www.amazon.com/Kathy-Barker/dp/0879697083/
https://www.amazon.com/Lab-Ref-Handbook-Reagents-Reference/dp/1936113791/

But they're pretty out of date! Most of the techniques are still valid, but I know many have been superseded. There are still a lot of radioligand assays (which are now uncommon in most labs).
So, can anyone recommend a book that could help someone relearn basic techniques?

My experience is that techniques are almost most often taught by hands-on, one-on-one training -- you find someone who knows the technique and ask them to show you, but COVID-19 distancing protocols make that nearly impossible. (The good news is that I often have the lab to myself and an underused supply of chemical stocks and reagents.)

Not a book recommendation but you should check out : https://www.protocols.io/ As someone with a computational background, I'm not the happiest about the about the way they write the protocols but they are definitely legit.

The extremely old-school answer here would be Maniatis' Molecular Cloning. They put out a new edition every decade or so, there is one from 2012 that is updated.
To get an idea of the book's impact in molecular biology, see this review from their website:

“In every kitchen there is at least one indispensable cookbook...Molecular Cloning: A Laboratory Manual fills the same niche in the laboratory (with) information to help both the inexperienced and the advanced user. (It) has once again established its primacy as the molecular laboratory manual and is likely to be found on lab benches...around the world.” ——Trends in Neurosciences

Likely there are more streamlined books out there at this point (this book runs at 3 volumes), but it's hard to see how to dispense with Maniatis.
It includes recipes for buffers etc. (see end of listing below). It is a little lighter on protein techniques, though, so I don't think you will find e.g. ELISA in there, though you will definitely find SDS-PAGE.
Here is a current chapter/protocol heading (you can scroll through the monospaced text). I had to delete a bunch of subheadings to make it fit under 30K characters:
Volume 1
Chapter 1: Isolation and Quantification of DNA1
Protocol 1: Preparation of Plasmid DNA by Alkaline Lysis with SDS: Minipreps
Protocol 2: Preparation of Plasmid DNA by Alkaline Lysis with SDS: Maxipreps
Protocol 3: Isolating DNA from Gram-Negative Bacteria (e.g., E. coli)
Protocol 4: Precipitation of DNA with Ethanol
Protocol 5: Precipitation of DNA with Isopropanol
Protocol 6: Concentrating and Desalting Nucleic Acids with Microconcentrators
Protocol 7: Concentrating Nucleic Acids by Extraction with Butanol
Protocol 8: Preparation of Single-Stranded Bacteriophage M13 DNA by Precipitation with Polyethylene Glycol
Protocol 9: Plating Bacteriophage M13
Protocol 10: Growing Bacteriophage M13 in Liquid Culture
Protocol 11: Preparation of Double-Stranded (Replicative Form) Bacteriophage M13 DNA
Protocol 12: Isolation of High-Molecular-Weight DNA Using Organic Solvents to Purify DNA
Protocol 13: Isolation of High-Molecular-Weight DNA from Mammalian Cells Using Proteinase K and Phenol
Protocol 14: A Single-Step Method for the Simultaneous Preparation of DNA, RNA, and Protein from Cells and Tissues
Protocol 15: Preparation of Genomic DNA from Mouse Tails and Other Small Samples
Protocol 16: Rapid Isolation of Yeast DNA
Protocol 17: Using Ethidium Bromide to Estimate the Amount of DNA in Bands after Electrophoresis through Minigels
Protocol 18: Estimating the Concentration of DNA by Fluorometry Using Hoechst 33258
Protocol 19: Quantifying DNA in Solution with PicoGreen
Chapter 2: Analysis of DNA81
Protocol 1: Agarose Gel Electrophoresis
Protocol 2: Detection of DNA in Agarose Gels by Staining
Protocol 3: Polyacrylamide Gel Electrophoresis
Protocol 4: Detection of DNA in Polyacrylamide Gels by Staining
Protocol 5: Detection of DNA in Polyacrylamide Gels by Autoradiography
Protocol 6: Alkaline Agarose Gel Electrophoresis
Protocol 7: Imaging: Autoradiography and Phosphorimaging
Protocol 8: Recovery of DNA from Agarose Gels Using Glass Beads
Protocol 9: Recovery of DNA from Low-Melting-Temperature Agarose Gels: Organic Extraction
Protocol 10: Isolation of DNA Fragments from Polyacrylamide Gels by the Crush and Soak Method
Protocol 11: Southern Blotting
Protocol 12: Southern Blotting: Simultaneous Transfer of DNA from an Agarose Gel to Two Membranes
Protocol 13: Southern Hybridization of Radiolabeled Probes to Nucleic Acids Immobilized on Membranes
Chapter 3: Cloning and Transformation with Plasmid Vectors157
Protocol 1: The Hanahan Method for Preparation and Transformation of Competent E. coli: High-Efficiency Transformation
Protocol 2: The Inoue Method for Preparation and Transformation of Competent E. coli: Ultracompetent Cells
Protocol 3: Easy Transformation of E. coli: Nanoparticle-Mediated Transformation
Protocol 4: Transformation of E. coli by Electroporation
Protocol 5: Cloning in Plasmid Vectors: Directional Cloning
Protocol 6: Cloning in Plasmid Vectors: Blunt-End Cloning
Protocol 7: Dephosphorylation of Plasmid DNA
Protocol 8: Attaching Phosphorylated Adaptors/Linkers to Blunt-Ended DNAs
Protocol 9: Cloning PCR Products: Addition of Restriction Sites to the Termini of Amplified DNA
Protocol 10: Cloning PCR Products: Blunt-End Cloning
Protocol 11: Cloning PCR Products: Making T Vectors
Protocol 12: Cloning PCR Products: TA Cloning
Protocol 13: Cloning PCR Products: TOPO TA Cloning
Protocol 14: Screening Bacterial Colonies Using X-Gal and IPTG: -Complementation

Chapter 4: Gateway Recombinational Cloning261
Protocol 1: Propagating Gateway Vectors
Protocol 2: Generating an ORF Entry Clone and Destination Clone
Protocol 3: Using Multisite LR Cloning to Generate a Destination Clone
Panel: Gateway Recombinational Cloning261
Panel: Basic Principles and Applications of Gateway Cloning262
Panel: Disadvantages of Gateway Cloning and Alternative Cloning Systems264
Panel: Generating Gateway-Compatible Vectors280
Chapter 5: Working with Bacterial Artificial Chromosomes and Other High-Capacity Vectors281
Protocol 1: Small-Scale Isolation of BAC DNA and Verification by PCR
Protocol 2: Large-Scale Preparation and Linearization of BAC DNA
Protocol 3: Examination of BAC DNA Quality and Quantity by Pulsed-Field Gel Electrophoresis
Protocol 4: Two-Step BAC Engineering: Preparation of Shuttle Vector DNA
Protocol 5: Preparation of the A Homology Arm (A-Box) and B Homology Arm (B-Box)
Protocol 6: Cloning of the A and B Homology Arms into the Shuttle Vector
Protocol 7: Preparation and Verification of the Recombinant Shuttle Vector
Protocol 8: Electroporation of Competent BAC Host Cells with the Recombinant Shuttle Vector
Protocol 9: Verification of Cointegrates and Selection of Resolved BAC Clones
Protocol 10: One-Step BAC Modification: Preparation of Plasmids
Protocol 11: Preparation of the A Homology Arm (A-Box)
Protocol 12: Cloning of the A Homology Arm into Reporter-Shuttle Vector
Protocol 13: Transformation of the BAC Host with the RecA Vector
Protocol 14: Transfer of the Reporter Vector into BAC/RecA Cells and Selection of Cointegrates
Protocol 15: Growth of S. cerevisiae and Preparation of DNA
Protocol 16: Small-Scale Preparations of Yeast DNA

Chapter 6: Extraction, Purification, and Analysis of RNA from Eukaryotic Cells345
Protocol 1: Purification of Total RNA from Mammalian Cells and Tissues
Protocol 2: Isolation of Total RNA from Zebrafish Embryos and Adults
Protocol 3: Total RNA Isolation from Drosophila melanogaster
Protocol 4: Total RNA Extraction from Caenorhabditis elegans
Protocol 5: Total RNA Extraction from Saccharomyces cerevisiae Using Hot Acid Phenol
Protocol 6: Quantifying and Storing RNA
Protocol 7: Precipitation of RNA with Ethanol
Protocol 8: Removing DNA Contamination from RNA Samples by Treatment with RNase-Free DNase I
Protocol 9: Isolation of Poly(A) Messenger RNA Using Magnetic Oligo(dT) Beads
Protocol 10: Separation of RNA according to Size: Electrophoresis of RNA through Agarose Gels Containing Formaldehyde
Protocol 11: Separation of RNA according to Size: Electrophoresis of RNA through Denaturing Urea Polyacrylamide Gels
Protocol 12: Transfer and Fixation of Denatured RNA in Agarose Gels to Membranes
Protocol 13: Transfer and Fixation of Denatured RNA in Polyacrylamide Gels to Membranes by Electrophoretic Transfer
Protocol 14: Northern Hybridization
Protocol 15: Dot and Slot Hybridization of Purified RNA
Protocol 16: Mapping RNA with Nuclease S1
Protocol 17: Ribonuclease Protection: Mapping RNA with Ribonuclease and Radiolabeled RNA Probes
Protocol 18: Analysis of RNA by Primer Extension

Chapter 7: Polymerase Chain Reaction455
Protocol 1: The Basic Polymerase Chain Reaction
Protocol 2: Hot Start PCR
Protocol 3: Touchdown PCR
Protocol 4: PCR Amplification of GC-Rich Templates
Protocol 5: Long and Accurate PCR (LA PCR)
Protocol 6: Inverse PCR
Protocol 7: Nested PCR
Protocol 8: Amplification of cDNA Generated by Reverse Transcription of mRNA: Two-Step RT-PCR
Protocol 9: Rapid Amplification of Sequences from the 5 Ends of mRNAs: 5-RACE
Protocol 10: Rapid Amplification of Sequences from the 3 Ends of mRNAs: 3-RACE
Protocol 11: Screening Colonies by PCR

Chapter 8: Bioinformatics541
Protocol 1: Visualizing Genomic Annotations with the UCSC Genome Browser
Protocol 2: Sequence Alignment and Homology Search with BLAST and ClustalW
Protocol 3: Designing PCR Primers Using Primer3Plus
Protocol 4: Expression Profiling by Microarray and RNA-seq
Protocol 5: Mapping Billions of Short Reads to a Reference Genome
Protocol 6: Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding)
Protocol 7: Discovering cis-Regulatory Motifs

Volume 2
Chapter 9: Quantification of DNA and RNA by Real-Time Polymerase Chain Reaction631
Protocol 1: Optimizing Primer and Probe Concentrations for Use in Real-Time PCR
Protocol 2: Constructing a Standard Curve
Protocol 3: Quantification of DNA by Real-Time PCR
Protocol 4: Quantification of RNA by Real-Time RT-PCR
Protocol 5: Analysis and Normalization of Real-Time PCR Experimental Data

Chapter 10: Nucleic Acid Platform Technologies683
Protocol 1: Printing Microarrays
Protocol 2: Round A/Round B Amplification of DNA
Protocol 3: T7 Linear Amplification of DNA (TLAD) for Nucleosomal and Other DNA < 500 bp
Protocol 4: Amplification of RNA
Protocol 5: Direct Cyanine-dUTP Labeling of RNA
Protocol 6: Indirect Aminoallyl-dUTP Labeling of RNA
Protocol 7: Cyanine-dCTP Labeling of DNA Using Klenow
Protocol 8: Indirect Labeling of DNA
Protocol 9: Blocking Polylysines on Homemade Microarrays
Protocol 10: Hybridization to Homemade Microarrays

Chapter 11: DNA Sequencing735
Protocol 1: Preparing Plasmid Subclones for Capillary Sequencing
Protocol 2: Preparing PCR Products for Capillary Sequencing
Protocol 3: Cycle-Sequencing Reactions
Protocol 4: Whole Genome: Manual Library Preparation
Protocol 5: Whole Genome: Automated, Nonindexed Library Preparation
Protocol 6: Whole Genome: Automated, Indexed Library Preparation
Protocol 7: Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing
Protocol 8: Preparation of an 8-kb Mate-Pair Library for Illumina Sequencing
Protocol 9: RNA-Seq: RNA Conversion to cDNA and Amplification
Protocol 10: Solution-Phase Exome Capture
Protocol 11: Automated Size Selection
Protocol 12: Library Quantification Using SYBR Green-qPCR
Protocol 13: Library Quantification Using PicoGreen Fluorometry
Protocol 14: Library Quantification: Fluorometric Quantitation of Double-Stranded or Single-Stranded DNA Samples Using the Qubit System
Protocol 15: Preparation of Small-Fragment Libraries for 454 Sequencing
Protocol 16: sstDNA Library Capture and emPCR
Protocol 17: Roche/454 Sequencer: Executing a Sequencing Run
Protocol 18: Validation
Protocol 19: Quality Assessment of Sequence Data
Protocol 20: Data Analysis

Chapter 12: Analysis of DNA Methylation in Mammalian Cells893
Protocol 1: DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection
Protocol 2: Methylation-Specific PCR for Gene-Specific DNA Methylation Detection
Protocol 3: Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis
Protocol 4: High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation
Protocol 5: Roche 454 Clonal Sequencing of Bisulfite-Converted DNA Libraries
Protocol 6: Illumina Sequencing of Bisulfite-Converted DNA Libraries

Chapter 13: Preparation of Labeled DNA, RNA, and Oligonucleotide Probes943
Protocol 1: Random Priming: Labeling of Purified DNA Fragments by Extension of Random Oligonucleotides
Protocol 2: Random Priming: Labeling of DNA by Extension of Random Oligonucleotides in the Presence of Melted Agarose
Protocol 3: Labeling of DNA Probes by Nick Translation
Protocol 4: Labeling of DNA Probes by Polymerase Chain Reaction
Protocol 5: Synthesis of Single-Stranded RNA Probes by In Vitro Transcription
Protocol 6: Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers
Protocol 7: Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension
Protocol 8: Labeling 3 Termini of Double-Stranded DNA Using the Klenow Fragment of E. coli DNA Polymerase I
Protocol 9: Dephosphorylation of DNA Fragments with Alkaline Phosphatase
Protocol 10: Phosphorylation of DNA Molecules with Protruding 5-Hydroxyl Termini
Protocol 11: Phosphorylation of DNA Molecules with Dephosphorylated Blunt Ends or Recessed 5 Termini
Protocol 12: Phosphorylating the 5 Termini of Oligonucleotides Using T4 Polynucleotide Kinase
Protocol 13: Labeling the 3 Termini of Oligonucleotides Using Terminal Deoxynucleotidyl Transferase
Protocol 14: Labeling of Synthetic Oligonucleotides Using the Klenow Fragment of E. coli DNA Polymerase I
Protocol 15: Purification of Labeled Oligonucleotides by Precipitation with Ethanol
Protocol 16: Purification of Labeled Oligonucleotides by Size-Exclusion Chromatography
Protocol 17: Purification of Labeled Oligonucleotides by Chromatography on a Sep-Pak C18 Column
Protocol 18: Hybridization of Oligonucleotide Probes in Aqueous Solutions: Washing in Buffers Containing Quaternary Ammonium Salts

Chapter 14: Methods for In Vitro Mutagenesis1059
Protocol 1: Random Mutagenesis Using Error-Prone DNA Polymerases
Protocol 2: Creating Insertions or Deletions Using Overlap Extension PCR Mutagenesis
Protocol 3: In Vitro Mutagenesis Using Double-Stranded DNA Templates: Selection of Mutants with DpnI
Protocol 4: Altered -Lactamase Selection Approach for Site-Directed Mutagenesis
Protocol 5: Oligonucleotide-Directed Mutagenesis by Elimination of a Unique Restriction Site (USE Mutagenesis)
Protocol 6: Saturation Mutagenesis by Codon Cassette Insertion
Protocol 7: Random Scanning Mutagenesis
Protocol 8: Multisite-Directed Mutagenesis
Protocol 9: Megaprimer PCR-Based Mutagenesis

Chapter 15: Introducing Genes into Cultured Mammalian Cells1131
Protocol 1: DNA Transfection Mediated by Cationic Lipid Reagents
Protocol 2: Calcium-Phosphate-Mediated Transfection of Eukaryotic Cells with Plasmid DNAs
Protocol 3: Calcium-Phosphate-Mediated Transfection of Cells with High-Molecular-Weight Genomic DNA
Protocol 4: Transfection Mediated by DEAE-Dextran: High-Efficiency Method
Protocol 5: DNA Transfection by Electroporation
Protocol 6: Analysis of Cell Viability by the alamarBlue Assay
Protocol 7: Analysis of Cell Viability by the Lactate Dehydrogenase Assay
Protocol 8: Analysis of Cell Viability by the MTT Assay

Chapter 16: Introducing Genes into Mammalian Cells: Viral Vectors1209
Protocol 1: Construction of Recombinant Adenovirus Genomes by Direct Cloning
Protocol 2: Release of the Cloned Recombinant Adenovirus Genome for Rescue and Expansion
Protocol 3: Purification of the Recombinant Adenovirus by Cesium Chloride Gradient Centrifugation
Protocol 4: Characterization of the Purified Recombinant Adenovirus for Viral Genome Structure by Restriction Enzyme Digestions
Protocol 5: Measuring the Infectious Titer of Recombinant Adenovirus Using TCID50 End-Point Dilution and qPCR
Protocol 6: Detection Assay for Replication-Competent Adenovirus by Concentration Passage and Real-Time qPCR
Protocol 7: Production of rAAVs by Transient Transfection
Protocol 8: Purification of rAAVs by Cesium Chloride Gradient Sedimentation
Protocol 9: Purification of rAAVs by Iodixanol Gradient Centrifugation
Protocol 10: Purification of rAAV2s by Heparin Column Affinity Chromatography
Protocol 11: Enrichment of Fully Packaged Virions in Column-Purified rAAV Preparations by Iodixanol Gradient Centrifugation Followed by Anion-Exchange Column Chromatography
Protocol 12: Titration of rAAV Genome Copy Number Using Real-Time qPCR
Protocol 13: Sensitive Determination of Infectious Titer of rAAVs Using TCID50 End-Point Dilution and qPCR
Protocol 14: Analysis of rAAV Sample Morphology Using Negative Staining and High-Resolution Electron Microscopy
Protocol 15: Analysis of rAAV Purity Using Silver-Stained SDS-PAGE
Protocol 16: Production of High-Titer Retrovirus and Lentivirus Vectors
Protocol 17: Titration of Lentivirus Vectors
Protocol 18: Monitoring Lentivirus Vector Stocks for Replication-Competent Viruses

Volume 3
Chapter 17: Analysis of Gene Regulation Using Reporter Systems1335
Protocol 1: Assay for -Galactosidase in Extracts of Mammalian Cells
Protocol 2: Single Luciferase Reporter Assay
Protocol 3: Dual Luciferase Reporter Assay
Protocol 4: Using ELISA to Measure GFP Production
Protocol 5: Generation of Cell Lines with Tetracycline-Regulated Gene Expression

Chapter 18: RNA Interference and Small RNA Analysis1415
Protocol 1: Preparation of siRNA Duplexes
Protocol 2: RNAi in Mammalian Cells by siRNA Duplex Transfection
Protocol 3: RNAi in Drosophila S2 Cells by siRNA Duplex Transfection
Protocol 4: Preparation of dsRNAs by In Vitro Transcription
Protocol 5: RNAi in Drosophila S2 Cells by dsRNA Soaking
Protocol 6: RNAi in Drosophila S2 Cells by dsRNA Transfection
Protocol 7: Analysis of Small RNAs by Northern Hybridization
Protocol 8: Analysis of Small RNAs by Quantitative Reverse Transcription PCR
Protocol 9: Construction of Small RNA Libraries for High-Throughput Sequencing
Protocol 10: Preparation of Antisense Oligonucleotides to Inhibit miRNA Function
Protocol 11: Inhibiting miRNA Function by Antisense Oligonucleotides in Cultured Mammalian Cells
Protocol 12: Inhibiting miRNA Function by Antisense Oligonucleotides in Drosophila S2 Cells

Chapter 19: Expressing Cloned Genes for Protein Production, Purification, and Analysis1481
Protocol 1: Expression of Cloned Genes in E. coli Using IPTG-Inducible Promoters
Protocol 2: Expression of Cloned Genes Using the Baculovirus Expression System
Protocol 3: Expression of Cloned Genes in P. pastoris Using the Methanol-Inducible Promoter AOX1
Protocol 4: Preparation of Cell Extract for Purification of Soluble Proteins Expressed in E. coli
Protocol 5: Purification of Polyhistidine-Tagged Proteins by Immobilized Metal Affinity Chromatography
Protocol 6: Purification of Fusion Proteins by Affinity Chromatography on Glutathione Resin
Protocol 7: Solubilization of Expressed Proteins from Inclusion Bodies
Protocol 8: SDS-PAGE of Proteins
Protocol 9: Analysis of Proteins by Immunoblotting
Protocol 10: Methods for Measuring the Concentrations of Proteins

Chapter 20: Cross-Linking Technologies for Analysis of Chromatin Structure and Function1637
Protocol 1: Formaldehyde Cross-Linking
Protocol 2: Preparation of Cross-Linked Chromatin for ChIP
Protocol 3: ChIP
Protocol 4: ChIPQuantitative PCR (ChIP-qPCR)
Protocol 5: ChIP-chip
Protocol 6: ChIP-seq
Protocol 7: Generation of 3C Libraries from Cross-Linked Cells
Protocol 8: Generation of ChIP-loop Libraries
Protocol 9: Generation of Control Ligation Product Libraries
Protocol 10: PCR Detection of 3C Ligation Products Present in 3C, ChIP-loop, and Control Libraries: Library Titration and Interaction Frequency Analysis
Protocol 11: 4C Analysis of 3C, ChIP-loop, and Control Libraries
Protocol 12: 5C Analysis of 3C, ChIP-loop, and Control Libraries

Chapter 21: Mapping of In Vivo RNA-Binding Sites by UV-Cross-Linking Immunoprecipitation (CLIP)1703
Protocol 1: Optimization of Immunoprecipitation Stringency for CLIP
Protocol 2: UV Cross-Linking of Live Cells and Lysate Preparation
Protocol 3: RNase Titration, Immunoprecipitation, and SDS-PAGE
Protocol 4: 3-Linker Ligation and Size Selection by SDS-PAGE
Protocol 5: Isolation of the RNA Tags, 5-Linker Ligation, and Reverse Transcription PCR Amplification
Protocol 6: Sequencing of RNA CLIP Tags
Protocol 7: Gel Purification and Storage of RNA Linkers

Chapter 22: Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays1761
Protocol 1: Generating Yeast One-Hybrid DNA-Bait Strains
Protocol 2: Generating Yeast Two-Hybrid Bait Strains
Protocol 3: Identifying Interactors from an Activation Domain Prey Library
Protocol 4: High-Efficiency Yeast Transformation
Protocol 5: Colony Lift Colorimetric Assay for -Galactosidase Activity
Protocol 6: Yeast Colony PCR

Panel: Reagents and Buffers1811
Panel: Tris Buffers1828
Panel: Good Buffers1829
Panel: Phosphate Buffers (Gomori Buffers)1830
Panel: Phenol1834
Panel: Equilibration of Phenol1834
Panel: Phenol:Chloroform:Isoamyl Alcohol (25:24:1)1834
Panel: Deionization of Formamide1834
Panel: Blocking Agents Used for Nucleic Acid Hybridization1836
Panel: Blocking Agents Used for Western Blotting1836
Panel: Commonly Used Techniques1843
Panel: Siliconizing Glassware, Plasticware, and Glass Wool1843
Panel: Preparation of RNase-Free Glassware1844
Panel: Hemocytometry Counting1846
Panel: Viability Staining1847
Panel: Precipitation of Nucleic Acids with Trichloroacetic Acid1849
Panel: Removing Ethidium Bromide from DNA1851
Panel: Disposing of Ethidium Bromide1851
Panel: Decontamination of Concentrated Solutions of Ethidium Bromide (Solutions Containing >0.5 mg/mL)1851
Panel: Decontamination of Dilute Solutions of Ethidium Bromide (e.g., Electrophoresis Buffer Containing 0.5 g/mL Ethidium Bromide)1852
Panel: Commercial Decontamination Kits1852
Panel: Detection Systems1855
Panel: Ethidium Bromide1855
Panel: Methylene Blue1857
Panel: SYBR Dyes1857
Panel: Chemiluminescent Labels1860
Panel: Chemiluminescent Enzyme Assays1861
Panel: Commercial Reagents, Kits, and Luminometers1863
Panel: Horseradish Peroxidase1865
Panel: Digoxygenin1869
Panel: BCIP1873
Panel: AMPPD1876
Panel: Immunoglobulin-Binding Proteins: Proteins A, G, and L1879
Panel: General Safety and Hazardous Material1885

While a little out of date, I do like it. (I found an old copy.)

I know you are asking for books, but for up-to-date basic overview of how some methods work - I would try websites or YouTube instead of textbooks...
One good website is BiteSizeBio. They have their own section for 'how to articles' and educational webinars. Otherwise I would also try YouTube. If you search in YouTube for basic techniques like 'how does the ELISA method work?' or 'principles behind SDS-PAGE' then you will find a lot of instructional movies. There is also the 'the protein man's blog' for purification of proteins, some analysis but also some DNA things.

An additional recommendation would be https://www.jove.com , the journal for visualized experiments. Explains different experiments and methods through videos.

Some protocols are not going out of style anytime soon, such as:
Frederick M. Ausubel, Roger Brent, Robert E. Kingston, David D. Moore, J. G. Seidman, John A. Smith, Kevin Struhl (2002) Short Protocols in Molecular Biology. Wiley, 1512pp. Check the Appendix sections for buffer formulations, etc. My copy is torn into pieces due to heavy use.
If you need the up-to-date form, then I recommend the subscription to Wiley's Current Protocols in Molecular Biology.


text:
Smoking, cancer, correlation between quitting smoking and increased immediate risk
There is "proof" out there today that suggests smoking is directly linked to cancer. I cannot argue against that, for the evidence in favor appears strong, and the evidence against is lacking. I'll happily sit here and agree that smoking increases the risk of cancer. This question, however, is not about how smoking increases the risk of cancer, rather how stopping smoking might increase the risk of cancer.
Consider what I know so far:

Cancer is caused by mutant cell growth.
Mutant cell growth is believed to be caused by chemicals in the smoke
Smoking itself stunts growth, thus slowing the cell growth rate

If the growth stunt is severe enough that it will reduce the cell growth rate by 20%, one might assume this would take some weeks (let's say 8 weeks, sounds reasonable to me, though I lack knowledge of the subject) to recover. This will likely be some scale and will gradually decrease to somewhere near 0.
Further to this, the risk of cancer is not directly related to the lung, but it is believed to be caused by chemicals entering through the lung into the blood, and travelling around the body, causing cancer in various organs.
Consider that the cell growth is probably linked (in the lung, at least) to chemicals "surrounding" the existing cells, this explains why smokers run short of breath. This partially explains the growth stunt side of smoking. Perhaps this happens body-wide, I don't know.
Then consider what will happen when one stops smoking. The cell growth rate will begin to radically and unexpected increase as the growth stunt is suspended, meanwhile chemicals will still exist in the blood and organs which will be perverting cell growth causing mutant (cancerous) cells. At this point the body is unprepared and settled into its routine of slowly generating cells, but now it is generating them faster and is struggling to keep up. Energy is lacking in areas, and there is further cause of mutant cells to grow and even to be allowed.
Surely, given this reasoning, it might be understandable that stopping smoking increases the immediate risk of cancer, though reducing the long term risk?
Does anybody know, or can anybody find reasonable proof that any part of this argument is flawed? Is there any research to suggest that there is or is not an immediate increased risk? The one thing that people never mention in the side-effects of quitting is the risk of immediate body failure through a variety of means (I've known people to come with flu-like symptoms then find they have cancer weeks later). Is this really unexplored? Or is the nanny state trying to hide it from smokers to prevent them from damaging their health further?

I think solid evidence of this going to have to come from an animal model, because you couldn't really need to do the experiments required in humans.  One important note is that smoking tends to only slow proliferation in the lung epithelium [mechanism debated], not systemic cell division.  The carcinogens that are introduced into the blood through smoking are found through out the body, so your hypothesis is probably limited to lung cancers only.

Interesting that there is still a glimpse of hope at the end of this tunnel. What I'm really thinking is that although there are some very dangerous chemicals in tobacco smoke, there may also be some very useful ones. Maybe these could be applied properly, and instead of being used to scare people away from smoking, be used instead to try to treat cancer and perhaps other similarly developed disease. People are always so negative, there must be benefits to tobacco, in similar scale to what people suggest about cannabis.

To summarise your argument, cancer is a disease characterised by uncontrolled cell division of mutant cells. Smoking decreases cell division, thereby smoking decreases risk of cancer. Furthermore, stopping smoking increases growth rates, thus there's an immediate rise in risk following smoking cessation.
Cancer is NOT caused by cell division. Smoking does NOT cause cancer by cell division. That's the flaw in your argument. What's happening is that cell division ISN'T being controlled. Let's propose that smoking does indeed stunt normal cell growth. The carcinogens in tar from smoking are still floating around causing mutations in the DNA. Most of DNA doesn't code for very much, but some parts of it codes for genes which control cell division. If these genes mutate then cell division is no longer controlled by these genes and hence there's uncontrolled cell division a.k.a cancer. Once these cells are dividing in an uncontrolled fashion, smoking isn't going to limit their growth. That's because this cancer has developed in the presence of these toxins that limit it's growth and despite this it's still managed to occur.
And then that cell growth stunting may actually be causing cancer to occur. White blood cell function is impaired by smoking, these cells usually target cancerous cells and destroy them. Without being destroyed, there's a higher chance of cancer.
And then I could go further, usually cells grow older and die. Maybe smoking by stunting growth of these cells leads to cells that last longer than they should. These cells accumulate mutations and become cancerous, where else they otherwise would've been recycled.
Smoking however has been linked to improving the symptoms of some diseases. Just not cancer.

Interesting take on it, though you have slightly contradicted yourself. Cancer is caused by uncontrolled cell division, understood. But you previously said cancer is not caused by cell division. Well, one of those statements must be untrue, and one must assume the first is that. I was looking at cessation devices, and considering how much more productive these may be if they were combined with some chemicals which, similarly to tobacco, could stunt cell growth over the period in which the smoker still retains nasty chemicals from the cigarette smoke. Do you still believe this is not plausible?

To further that, it would make sense that cell division being limited by chemicals in cigarette smoke is also likely to stunt growth of cancerous cells. Unless this is being performed by the body reacting and trying to control cells in a manner to which it has become accustomed, the chances are this is being done by the chemicals in smoke itself, which as far as I'm aware operate on most human tissues. If that's the case, how unlikely is it, really, that those cancerous growths cannot be stunted similarly to regular cells? Unless the mutation is incredibly severe I suspect unlikely.

You've interpreted my answer incorrectly. Cancer is defined as uncontrolled cell division, but its caused by ONE cell which has mutated sufficiently to divide uncontrollably. This cell mutates because of tobacco which damages DNA. Smoking most likely does stunt growth of cells. However this increases the chance of cancer as healthy parts of the body are likely stunted more than cancer cells. These healthy parts include white blood cells. Without stunting these white cells could eradicate the one cancer cell before it divides uncontrollably. If things still don't make sense, let me know.

One thing is pretty clear and needs not to be debated I think: Smoking is pretty unhealthy and can cause cancer. I see a number of misconceptions here:
First you assume, that a slower cell division is something you want to have. Most cell of the adult human body do no divide at all (or only at relatively low rates). Some cells have higher proliferation rates belong to the hematopoietic system, the gut, the mucosas of the body and the skin. These cells need to be able to proliferate in order to fulfill their function. Other cells are dividing to replace cells which went into apoptosis or had to be replaced, but this can not be compared like the growing rates of kids.
Then, cell growth is highly restricted and controlled for good reasons. I did a short search for articles describing slower cell growth by smoking. What I found does not favor the idea that slowed cell growth might be beneficial. This paper for example ("Cigarette Smoke Induces Cellular Senescence"), shows that lung fibroblasts are going into senescence and are not able to do necessary proliferation for lung maintanence.
Then, even if cancer is defined (among other things) to be a fast proliferating, uncontrolled growing mass of cells, its not enough to simply let cells grow, to be able to call them cancer cells. To be able to grow as a cancer cell, the cell needs to change genetically and pick up a number of mutations which allows them to escape the security programs of the body. These are apoptosis and the immune system and its not an easy task. Most cells with the potential to become cancer cells get caught on the way. For the way, how cells become cancer cells, this webpage is pretty interesting.
Stopping to smoke does not cause more problems for you body, it reduces them. The number of dangerous substances delivered to your body is reduced, as is the chance for them to cause harm (lower concentrations). It will take quite a while to get rid of them though, for tar in the lung this can take several years.


text:
Plateletpheresis for hemophilia
Plateletpheresis is seperation of platelets from whole blood and putting the leukocytes and erythrocytes back into the blood.
If the person donating platelets does not have hemophilia than could a hemophilia patient get a periodic transfusion of platelets from a non-hemophiliac platelet donor so that his hemophilia is less severe whether it is hemophilia A or hemophilia B?

Wikipedia has a nice page on clotting disorders  - it shows Hemophilia isn't a defect/deficiency of platelets, but rather due to defective clotting factors in the plasma.  When platelets are transfused, they have a very short half-life and are used for acute support in  disorders like Bernard-Soulier syndrome

but platelets are transfused along with plasma aren't they since platelets and plasma are hard to separate? If so than if someone gets a plasma transfusion with platelets which still qualifies as plateletpheresis from someone without hemophilia and the person getting the transfusion has hemophilia it should lower the bleeding from something as simple as bumping on something.

Indeed, under US standards, an apheresis platelet product contains platelets in donor plasma.   But hemophilliacs are typically treated using plasma-derived or manufactured ("recombinant") clotting factors since that addresses the actual underlying basis of their condition.

yes I know but clotting factors are in the plasma so wouldn't it make sense that a non-hemophiliac donor of plasma if it donates blood to a hemophiliac that the clotting factors within the donor plasma would lower the risk of bleeding for much longer than those manufactured clotting factors?

Plasma contains antibodies that can cause transfusion reactions, so giving bulk  plasma requires cross-matching.  Instead, the fraction of the plasma enriched in the clotting factor needed to complement the deficiency in hemophilia, or recombinant factor is used.   Re duration of effect, in plasma the factor is at x1 concentration.  A plasma fraction could be x1,000 and recombinant x100,000. In the 80s hemophiliacs in Canada got HIV from plasma fractions.  Since it contains no pathogens, recombinant therapy is best.


text:
How do plants know to grow towards the light?
Plants lack a central nervous system. How do they know to drop leaves in full shade and to curve stems towards the current light source?

Welcome to the site. Please visit the [help]and take a [tour]. In particular pay attention to the homework page.  You might want to investigate phototropism.

Plants are not sentient beings, and do not “know” anything. If you chose to post here please use scientific language.

The curving of stems towards light sources is called phototropism.
It is a hormonal phenomena that responds to light. Just like human beings, plants have hormones in them.
The hormone that makes plant respond to light is auxin. It is a type of growth hormone, causing growth in the parts where it accumulates, and it does so in regions away from light. So, when a plant faces the light, auxin accumulates and causes growth of the side which is not facing the light. Thus, excessive and uneven growth leads to the plant to bend towards the the light.

+1 Wait so this means plants have endocrine system. There's so much to learn in this world!