text:
How do I make conclusions from the autoradiograph of a Southern blot?
Here's another question taken from "Concepts of Genetics," Klug et al (10ed), revolving around a paternity test. PCR and a Southern blot were carried out in order to determine whether 3 chimpanzees (lanes 3, 4, 5 in the blot below) were the "legitimate" offspring of 2 potential parents (lanes 1 and 2).
The question makes a point of saying that the primers used to bind to the chimp DNA originates from humans, and that they "flank highly polymorphic sites in human DNA that result from variable numbers of tandem nucleotide repeats." My first question is what exactly does "flanking" mean in this context? It sounds to me like the human DNA "mirrors" the chimp DNA, and so makes it good enough to use as a primer, but I'm not sure.
I've come across a few other examples not in the text about how to infer whether a potential parent is indeed a parent based on whether the offspring's lane contains bands found in both the maternal and paternal lanes, which leads me to believe I can rule out the chimp in lane 5.
I'm given five answers to choose from to decide which of the offspring, if any, are legitimate:

None
A only
A and B only
Not enough data; more polymorphic sites should be examined
No conclusion can be made because "human" primers  were used

Main questions: Does that fact that we're using human DNA as primers cause any problems? Do we know enough from this blot to determine paternity?

For your first question, the sentence could be rewritten as: "are on either side of highly polymorphic sites in human DNA that result from variable numbers of tandem nucleotide repeats."

Okay that makes much more sense, thanks for clarifying.

A Southern blot needs to be probed with labeled DNA. It is not clear from your description what the origin of such a probe would be. Nor are Southern blots typically used to resolve and detect such short pieces of DNA--in fact you would need an extremely high percentage of agarose in a gel to achieve this resolution. That suggests it is actually a polyacrylamide gel, and therefore unlikely to be a Southern blot.  The fact the the primers match sequences in the Human genome is irrelevant.  The question is about using VTNR as dominant genetic markers to "fingerprint" genomic DNA samples.

As @canadianer pointed out in the comments section flanking sequence is a sequence that is immediately near the target on either side. Since chimps and humans are closely related and the sequence different is minimal (according to this paper its approx 4% for the entire genome)  so using human primers is totally fine.  Now if take a look at the picture of the gel:
 The answer is 2. only A because only this offspring has a variant in large amount (that can be determined from the width of the band) that can be acquired from both parents and in this case chimp A actually did inherit the 136bp variant from both parents.
For chimp 4 either parent can be the same (as for chimp A) from the two because it has the 136bp variant as well ( that can be inherited either chimp one or two), but has a different one that cannot come from chimps 1 and 2.
As you said chimp 5 can be ruled out instantly because it has a large band that cannot be found in either of the two parents.


text:
Does breathing air containing 3% carbon dioxide gives you a headache?
As far as I know, breathing air containing relatively high levels of CO2 may get you a headache.
I also know that CO2 level in the fruit bodies of peppers can reach levels as high as 3% at certain stages in development (Blasiak, 2006). So clearly it is possible in a natural setting to achieve these high level of CO2, at least in a micro-environment like around the locules of pepper seeds developing in its fruit.
So I was wondering, if we would have to breath air containing 3% CO2, would get a headache if we breath it in?

Do you have the source?  If not, it's hard to know what the number is referring to.

The source: J. Blasiak et al., JASHS 131, 164 (2006). http://journal.ashspublications.org/content/131/1/164.short

To close-voters - I edited the question during the close-vote process to reflect the linked article posted by OP. Please re-consider when voting to close when you your decision on the previous efforts of others as question is changed.

totsha - feel free to change my edits, or roll back when the edited question does not reflect your intended original question any longer.

Of course there is a natural setting with even more carbon dioxide: inside the alveoli in the lungs (5.3% carbon dioxide.)

http://en.wikipedia.org/wiki/Carbon_dioxide#Toxicity
"In concentrations up to 1% (10,000 ppm), it will make some people feel drowsy.[83] Concentrations of 7% to 10% may cause suffocation, even in the presence of sufficient oxygen, manifesting as dizziness, headache, visual and hearing dysfunction, and unconsciousness within a few minutes to an hour.
...
Occupational CO2 exposure limits have been set in the United States at 0.5% (5000 ppm) for an 8-hour period.[90] At this level of CO2, International Space Station crew experienced headaches, lethargy, mental slowness, emotional irritation, and sleep disruption."
So according to this, yes you could breathe it, and yes, you would get a headache."

It would take a lot of peppers to get 8 hours worth of pepper air.

Where there's a will there's a way!

source: Stack Exchange

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

sort: votes


text:
Does ale give less of a hangover than a lager?
I got into an argument surrounding beer type and hangover. Apparently there is a opinion that ales give you less hangover than lagers do (considering same alcohol content consumed).
My understanding is that a hangover is nothing more than dehydration caused by alcohol. More alcohol per unit of mass - more dehydration.
Is there any biological evidence to show that the same amount of alcohol consumed (with a different type of yeast) per same body mass would have different effects?

Is there evidence other than the assertions by the posters that they do in fact cause a greater hangover? The question cannot be answered if the effect does not in fact exist.

@MarchHo that is essentially what I am looking for, some scientific explanation (or thesis or source) that would confirm it or dismiss it.

Not a direct answer to ale vs. lager, but there certainly is evidence that different alcoholic beverage types have different hangover effects, although the effect size is probably small

@oreo I am not sure if that study would qualify since it is purely subjective. The researchers asked the participants how they feel. The same feeling in the bourbon drinker to the vodka drinker may have been rated weaker since we don't know if it is true or just different tolerances to discomfort. Maybe the vodka drinkers could handle discomfort better so rated all hang over effects weaker.

@dustin Yes, you're totally right about "Hangover Intensity" as  subjective measure, but the study that Wired refers to gave participants vodka vs. bourbon vs. placebo randomly, so I don't see any reason to think that tolerances to discomfort would be different among the subject groups.

@oreo it is like sensitivity to pain though. Some people are total fine when they receive a 2 inch laceration and others going into shock over the site of blood. With the alcohol drinkers, I would like to see the vodka drinkers be giving bourbon and the vice verse a. If they then say it isn't worse or is worse depending on the group, one could then say it is plausible that dark liquor is worse.

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Decreasing Solubility as Solvent Moves Higher in Paper Chromatography
In paper chromatography, as the mobile phase (I used 1:9 acetone/petroleum ether) climbs higher and higher, will the solubility of the solutes decrease as the solvent moves higher? I speak mostly about the beginning, when the solvent just begins to climb up the paper. Will the solutes travel right at the solvent front at the beginning, and then start to lag behind (and separate) as the solvent front moves higher?

The solubility of the solutes is the same at all points in the chromatography process. The solutes are clustered together at the beginning (at the solvent front) because none of them has moved very far yet. The reason for the separation of the solutes isn't that they become less soluble, it's that the solutes are moving at different speeds, like cars in an auto race:
  _______
 /____/SF\___
 |_,._____,._)
---`'-----`'--
  _______
 /____/S1\___
 |_,._____,._)
---`'-----`'--
  _______
 /____/S2\___
 |_,._____,._)
---`'-----`'--

At the beginning, both cars (solutes) S1 and S2 are even with the solute front car (SF) because the race (chromatography) has just begun. However, over time, the SF car outpaces S1 and S2 because it is moving faster.
                     _______
                    /____/SF\___
                    |_,._____,._)
                   ---`'-----`'--
         _______
        /____/S1\___
        |_,._____,._)
       ---`'-----`'--
              _______
             /____/S2\___
             |_,._____,._)
             ---`'-----`'--

And at the end, you get great separation:
                                                                _______
                                                               /____/SF\___
                                                               |_,._____,._)
                                                              ---`'-----`'--
                        _______
                       /____/S1\___
                       |_,._____,._)
                      ---`'-----`'--
                                           _______
                                          /____/S2\___
                                          |_,._____,._)
                                         ---`'-----`'--

(Thanks to retrojunkies.com for the ASCII car)

Great analogy to explain the answer! +1

Another helpful concept is RF, which is the distance traveled by the solute divided by the distance traveled by the solvent front. A very soluble compound may have an RF close to 1, so you'd only be able to see a difference between it and the solvent front after a significant distance.


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Do "non-human" animal like cat, dog, bird or fish think about future while sleeping?
I don't think "non-human" animal like cat, dog, bird or fish think about future while sleeping.
I think when sleeping, the "non-human" animal will feel rather think about anything. I think when sleeping, the "non-human" animal will feel  their breath just like when we are meditating. So, when we meditate we will feel our breath like "non-human" animal that are sleeping.
Do "non-human" animal like cat, dog, bird or fish think about future while sleeping?

I'm not sure we know enough about animal thought to even begin to answer this question.

Issue with your question
This question is full of terms that don't have a proper definition in Biology. I don't think there is any clear definition in the verbs "feel" and "think". Also, I don't fully understand what the differences between feeling or thinking (whatever that means) when sleeping matter for the question of whether some animals "think" (and its variants) about future while sleeping. I am not sure either what "thinking about future" really means. One doesn't know the future, he can imagine it and in some cases it is kinda complicated to really know whether a set of thoughts are encompassed within the concept of "thinking about the future". I vote to close for primarily-opinion based. Finally, your question might eventually be a better fit on CognitiveScience.SE.
Theory of Mind
You might be interested in the Theory of Mind (ToM). Having the ToM (I know it is weird formulation, ToM is not a theory per se) means having the ability to 1) be aware (might have various definitions for "aware") of its own existence and 2) be aware that others also think and have intentions and 3) more importantly be aware that others might be aware that you think and have intentions.
It is pretty hard to investigate whether an animal has the ToM. Here is a list of species (and lineages) where ToM has been found (or thought to exist at some level). The list is probably not exhaustive and the difficulty to accurately define ToM and awareness make those pretty arbitrary.

Chimpanzee
Orang-outan
elephants
dolphins
corvids
some parrots
bee-eater

Btw, your list of lineages is funny by the fact that you seem to weight equally two relatively closely related domestic species (cat and dogs) and two gigantic taxa that are fishes (fishes do not represent a monophyletic group) and birds


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Is [O2] different in a 5 mL liquid media?
Is there a drastic difference between top and bottom of the tube, with no stirring?

I believe there is. As you can see in the image below, strictly anaerobic bacteria can survive in liquid medium in test tubes, herefore they will migrate to the bodem of the medium to avoid Oxygen. Also you can see that microaerophiles, which require an oxygen percentage of approximately 2-10% (versus approximately 20% in normal air), will be able to survive below the surface of the medium.
So yes, there is a drastic change, seeing as obligate aerobic bacteria can surive at the surface of the medium, and obligate anaerobic bacteria can survive at the bodem.

To this I have one caveat to add. Namely that these tests are normally done in standard test tubes (approximately 9, 22 or 28mL depending on size), which would most likely contain more medium. So I am not absolutely sure, nor have I found any specific information on oxygen gradients in 5mL tubes. You could test this by performing the experiment in described in the figure in your tubes with 5mL medium and see what happens. Then you will definitely know.
Hope this helps!


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Magnetic-activated cell sorting vs. FACS
When sorting cell populations it is possible to use either magnetic-activated cell sorting or fluorescence-activated cell-sorting (FACS). I am wondering when you would choose either technique and what the pro's and con's of each technique are.
As FACS sorts cells one by one, I can imagine magnetic-activated cell sorting is a faster process. So I guess if time is an important factor this could be used to base your decision on. Also by sorting cells one at a time I assume FACS is a lot more precise, and will lead to less 'contamination'.
So, are there other factors at play here that can influence the choice of magnetic-activated cell sorting over FACS, and what are the pro's and con's of these techniques respectively?

Well for one, MACS only works with surface exposed antigens.

@canadianer assuming one would want to use live sorted cells in their subsequent experiment(s), FACS has the same constriction.

@MattDMo Presumably a genetically expressed fluorophore should allow sorting without the need for fixation/permeabilization.

@canadianer true, I hadn't thought of that. I'm an antibody guy, so I usually think in that direction :)

Exactly as canadianer said, GFP sorting is very common.
MACS is much faster, which can also help with viability (especially if the cells are very sensitive) especially when it comes to working with large cell numbers. CliniMACS, for example, is routinely used to isolate CD34+ hematopoietic stem and progenitor cells precisely for those factors (time and viability)

Magnetic-activated cell sorting (PDF download), or MACS, is a procedure developed by Miltenyi Biotec to separate cells from complex mixtures using antibody-coated magnetic nanoparticles. The antibodies are specific for certain cell surface markers, either expressed on your population of interest (positive selection), or expressed on undesired cell types (negative selection). After adding the antibody-coated beads to the cell mixture and incubating, the suspension is added to a special single-use separation column affixed to a magnet, to which the beads stick, while unlabeled cells flow through. If performing a negative selection, the flow-through is your population of interest and the bound beads and cells are discarded. If your cells of interest are bound to the beads (positive selection), the column is washed several times to make sure unbound or weakly-bound cells are washed through, then the column is removed from the magnet and the cell-bead complexes are eluted.
In fluorescence-activated cell sorting or FACS, the initial complex cell mixture is first labeled with one or more cell surface marker-specific antibodies that have been conjugated to fluorescent dyes. Cells can also be analyzed that express one or more recombinant fluorescent proteins in conjunction with a gene of interest, allowing for selection of cells without using antibodies. After incubation and wash steps, red blood cells are lysed, if analyzing whole blood. The reason for RBC lysis is shown below:

Without lysis, the RBCs overwhelm the cytometer, as they make up around 95% of the cells in human whole blood. White blood cells (leukocytes), on the other hand, only make up 0.1-0.2% of cells, and lymphocytes between about 15 to 50% of leukocytes.
The cell mixture is then analyzed on a cell sorter such as a BD FACSAria.

From: https://commons.wikimedia.org/wiki/File:Fluorescence_Assisted_Cell_Sorting_%28FACS%29_B.jpg
The cells pass in single file past one or more laser beams, which excite the dyes and cause them to fluoresce at a certain wavelength. The user can then use gating to select the combination and intensity of colors they are interested in, and when a cell meets the criteria, it is given an electrical charge, and electro magnets direct it into a collection container.

So what are the pros and cons of each technology? MACS separation generally is quicker than FACS staining, and a greater number of cells can be processed at one time (sometimes orders of magnitude more, depending on instrument and protocol). If you are, for example, looking to purify large numbers of CD4+ T cells from whole blood, MACS may be the better choice of the two (although I prefer the RosetteSep system for that particular requirement). MACS doesn't require a rather expensive dedicated instrument, although automatic platforms are available if needed. On the downside, most MACS-qualified beads are mostly only available from Miltenyi, so if they do not have beads with your particular marker of interest available, you will need to do the conjugation yourself, at the expense of time and possibly precious antibody while you optimize conditions. Fluorescent-conjugated antibodies are extremely common, and available from practically innumerable companies, so unless you are working with a self-generated antibody it's much more likely that you'll be able to find one for FACS quite easily. There are MACS beads that contain antibodies directed at certain fluorophores, so you can use flow antibodies for MACS, although optimization is likely still necessary. Finally, MACS separation is only an option for cells that have your marker of interest expressed on the cell surface.
One of the major advantages of FACS is multicolor staining (depending on the instrument you're using). This makes it much more straightforward to purify potentially rare populations that are only differentiated by their combined expression of a number of surface markers, necessitating multiple gating steps. If this were to be accomplished by MACS, you would need to go through multiple rounds of purification, something that could take longer than FACS, and not necessarily be feasible, as a certain number of cells are required for each MACS run. With FACS, these rare populations (which may only be tens or hundreds of cells per million) can be collected just as easily as more common ones. Also, as mentioned above, there are more antibodies available for flow/FACS than for direct MACS. Additionally, FACS allows for sorting of cells expressing GFP and relatives, letting you collect populations based on internal markers.

Thank you, this is a great answer! I have one question about something you wrote in the second paragraph. Why do you have to lyse the RBC when analyzing whole blood?

@Wolgast see my edit above for a detailed explanation. Basically, RBCs make up about 95% of all cells in blood, while white blood cells are only 0.1-0.2%. They just overwhelm the cytometer.

That makes sense! It seems like something I should have thought of myself! Thanks for the extra explanation!


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Energy consumption of a resting synapse
What is the energy penalty of maintaining rarely used synapse?
I'm wondering if forgetting is cheaper than remembering unnecessary details.

Short answer is yes, of course. Maintaining a healthy synapse is very energy-consuming process.
Let me first note that forgetting as we know it is more complicated than just pruning of synapses. It might involve rearrangement of proteins in pre/post-synaptic membrane and near it, local de-regulation of local protein synthesis, decrease in synaptic mRNA content and epigenetic change of transcription.
Secondly, average energy spending on a synapse, if it is not being used too often, includes mainly maintaining of membrane potential at resting -80mV level. Cellular membrane is a leaky barrier, so that without ion pumps, such as $K^+/Na^+$-ATPase, potential will quickly go to zero. Maintaining and recycling neurotransmitter pool also require energy.
Action potentials itself are passive processes, its generating does not require energy. ATPase will have to maintain potential at rest and keep it from fluctuating.
You can read this review for more: Synaptic Energy Use and Supply (Neuron, 2012). It generally describes where energy comes from and how it is being used.

Let me first note that forgetting as we know it is more complicated than just pruning of synapses. Yes. You took the comment right out of my mouth.


text:
Surface Power Density of Fluorescing Reaction
I am looking to find out what is the ballpark power density of a fluorescing PCR reaction using a SYBR Green or Taq Man dye might be. Is it on the order of $E_e=1mW/cm^2$, less or more? Any help of data would be useful.

shouldn't amount of light you detect depend on the excitation power? and total volume, and geometry of reaction volume?...

@aandreev Yes it would, I'm sure things like the amounts of reactants would also play into this. With that said, is there any ballpark for any currently used devices on the market?


text:
The ring formation of ringworm
I know ringworm is caused by a fungus on the skin, nails or scalp but what causes the rash to form as a ring instead of like a normal spread out rash?

Maybe the fungal spore infects 1 point in the skin, and the hyphae spread out through the skin in a circular pattern. The ring would be where the edge of the hyphae is.

dermatophyte fungi
Ringworm is caused by a several species of Trichophyton fungi (T. rubrum, T. tonsurans, T. interdigitale, and/or T. mentagrophytes); and a couple others are well known (Microsporum canis, and Epidermophyton floccosum).
The ring pattern is not unique to ringworm causing fungi. (Fairy) Rings are totally common with fungi because mycelium grows outward from the center; and as the mycelium grows, the inner mycelium often dies (from starvation, age, attack by immune system?, or it is cannibalized) leaving only the outer ring of mycelium, which may continue expanding.

Unfortunately the medical world doesn't spend much time on the problems that they can already solve (like with an antifungal ointment or pill), so there hasn't been much effort devoted (to my knowledge) toward answering the mechanistic questions of ring formation of dermatophytic fungi. But it is known that some Trichophyton species sexually reproduce and Trichophyton rubrum also probably does reproduce sexually (ie., plasmogamy, karyogamy, and gametangia). I don't have any grounds for mentioning it (besides logic), but sexual reproduction is probably "age" related in fungi as is growth- so, a ring may be more pronounced in an area where fungal hyphae conjugate... much like the expression of fruiting bodies of other mushrooms.

Hmm.. I too find the question interesting and the fairy rings came to my mind. The dermatophytes are keratophilic and feed on keratin. Fairy rings spread circular coz the centre is now devoid of nutrients. It is ok to relate that way but the host immune reaction should not be left unconsidered... There must be some references hidden deep in litereature :) Hope someone digs it out!

the fairy ring phenomenon may not be a good analogy. Apart from host responses, nutrients are unlikely to run out on the skin which constantly makes keratin that dermatophytes live on.
Incidentally, there are a number of infective and non-infective conditions which have a ring-like or annular morphology. Lupus vulgaris, a type of tuberculosis, mid-borderline leprosy, pityriasis rosea,  granuloma annulare and erythema annulare centrifugum, idiopathic inflammatory disorders and annular variants of lichen planus and psoriasis are some of them. So there must be more to it


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Powdered meal replacement vs regular meal
Can a person live with this alternative nutrition? Of course, assuming that eating pleasure is assumed the same.
The nutrients that contain are far better than average meal a person eats the majority of times, al least me. However, since is not solid food, do our digestive system need to work harder?
Scientific reports would be appreciated, comparing these two modes of feeding.

Are you referring to the Sci-Fi Classic movie Soylent Green?

Soylent is a powdered meal replacement product, advertised as a "staple meal" that meets all nutritional requirements for an average adult.

Probably yes, but I wouldn't look forward to bowel movements without any fiber in my diet

I've lived on it for a month with no ill impacts (sample of 1!) The bigger issue with Soylent is the protein in it is dried soy beans. I love soy beans fresh, but anyone who cooks knows that if you don't soak dried beans before cooking them you get gas. Horrible gas. Which can be corrected by taking "beano" but it makes me wonder about long-term nutritional impacts.

Thanks @futurebird, It would be great to know what were the main differences you noticed during this month. Did you miss real food? Maybe the ritual associated with eating? Let us know your experiences.

Yes you could live off a protein shake type supplement if it had the vitamins, minerals, protein, carbohydrates, and fats you would need. Would you want to? Probably not.
First thing we must determine is the protein whey or soy? If a male is consuming this meal replacement and the only protein is from soy, their estrogen levels will be elevated. In Soy Protein Isolate Increases Urinary Estrogens and the Ratio of 2:16α-Hydroxyestrone in Men at High Risk of Prostate Cancer, Dr.s Jill M. Hamilton-Reeves, Salome A. Rebello, William Thomas, Joel W. Slaton, and Mindy S. Kurzer concluded that soy does elevated estrogen in men which helped with the reduction of prostate cancer [1], but as a male, you wouldn't want to have a lifetime of increased estrogen [2].

Infertility. Estrogen is partly responsible for creating healthy
sperm. When estrogen levels are high, sperm levels in semen may fall.
This can lead to fertility issues.
Gynecomastia. Estrogen may stimulate breast tissue growth. Men with
too much estrogen may start developing larger breasts.
Erectile dysfunction. A balance of both testosterone and estrogen is
important for healthy sexual growth and development. Sexual function
may be impacted when these hormones become imbalanced. Men with high
levels of estrogen may have difficulty getting or maintaining an
erection.

So to be on the safe side, let's assume that the protein is from whey and we have one less thing to worry about. Now as for the vitamins and minerals, the Mayo Clinic states that [3]:

Supplements aren't intended to be a food substitute because they can't replicate all of the nutrients and benefits of whole foods, such as fruits and vegetables.

and there are three main differences:

Greater nutrition. Whole foods are complex, containing a variety of
the micronutrients your body needs — not just one. An orange, for
example, provides vitamin C plus some beta carotene, calcium and
other nutrients. It's likely these compounds work together to produce
their beneficial effect.
Essential fiber. Whole foods, such as whole grains, fruits,
vegetables and legumes, provide dietary fiber. Most high-fiber foods
are also packed with other essential nutrients. Fiber, as part of a
healthy diet, can help prevent certain diseases, such as type 2
diabetes and heart disease, and it can also help manage constipation.
Protective substances. Whole foods contain other substances important
for good health. Fruits and vegetables, for example, contain
naturally occurring substances called phytochemicals, which may help
protect you against cancer, heart disease, diabetes and high blood
pressure. Many are also good sources of antioxidants — substances
that slow down oxidation, a natural process that leads to cell and
tissue damage.

So you could live off of some meal replacement shake for the rest of your life but should you? Probably not.

Suggested edit: answer the question with facts, and leave out the opinion at the end. It doesn't contribute anything useful.


text:
Photolysis of Water?
In chemistry, I studied the decomposition of water as being $2H_2O_{(l)} \rightarrow 2H_{2(g)} + O_{2(g)}$. However, when water is split, the equation is $2H_2O_{(l)} \rightarrow 4H^+ + 4e^- +O_{2(g)}$. Why is that? How does $H_2$ just ionize?
Moreover, what is the mechanism for photolysis? I would have thought that splitting water molecules requires a ton of energy; yet it can be accomplished simply with light energy during photosynthesis?

Have you read about the photosynthesis in detail? I think this will explain the question.

I don't want to write the same again: http://biology.stackexchange.com/a/23829/3703 use this and read about redox reactions.

The part of photosynthesis occurs in the granum region of thylakoid region of a chloroplast when light use absorbed by chlorophyll. It is the break down of water molecule into hydrogen and oxygen under Influence of light when photons are absorbed, it causes the hydrogen to bind to an acceptor, subsequently releasing oxygen.

Water is split in chloroplasts in the light reaction of photosynthesis. Chlorophyll, acting as a photopigment, captures sunlight and transfers that energy to an electron pair of a water molecule. Under the influence of a water-splitting enzyme (George et al, 1989) it is separated into 2 protons, molecular oxygen and a free electron pair.
Reference
George et al. Science 1989; 243(4892): 789-91

The splitting of water in chloroplasts is catalysed by the Oxygen Evolving Complex. It's all about redox reactions but in general hydrogen is the less electronegative of biological elements so it is easily ionised in many life reactions.


text:
Latency differences between our senses
I would be interested in knowing how long it takes between the moment something touches our skin and the moment something is activated in the brain. Also how long does it take in total until we subjectively perceive something? And I would like to know whether this is dependent on which part of the body was stimulated (same latency for foot and neck?), or if it is dependent on the nature of stimuli (heat or mechanical). I would also be interested in that latency in the auditory and visual system. I tried searching for that but could not find what I needed due to the lack of the correct terminology.

Given your questions taken together and your comment It would be interesting to know how much delay the brain can handle in understanding causality and associating events I think you are interested in intersensory asynchrony. A well-known example where two stimulus modalities are perceived as separate while they are in fact coming from the same event is a thunder heard after lightning. This is caused by the fact that sound travels at a speed much slower than light, and hence a thunder can lag lightning by seconds.

source: NASA
In many instances, however, one event generating perceptions across stimulus modalities are actually perceived as synchronous while they are in fact offset in time due to differences in physical characteristics of the stimuli. Taking the storm as an example - when it is far away, the thunder is perceived as separate because the thunder lags by seconds. But when the thunderstorm is close enough, the auditory crack and visual lightning are actually perceived as synchronous, while in fact they are still offset because of the sound travelling so much slower than light.
So the question becomes, as you rightfully ask, what are the margins in which stimuli across modalities can be asynchronous while perceived as one event? In other words, what is the window of integration?
A review by Vroomen and Keetels (2010) describes various psychophysical studies that have examined what the minimal asynchrony is between two stimuli of different modality that lead to a synchronized percept. The following values are for simple stimuli, such as tactile taps, auditory beeps and visual flashes.

Auditory and tactile stimuli: 80 ms
Auditory beeps and visual flashes: 25 - 50 ms
Visual and tactile stimili: 35 - 65 ms

Note that these lag differences are relatively large, given the speed of peripheral neural transduction (see the other answer of Nandor Poka below). Moreover, the window of integration between more complex stimuli can be much greater. For example, the window for speech and visual information can be as large as 203 ms.  Such large windows of integration point toward higher processes playing a role in the brain.
Note that only temporal lags below 20 msec are expected to go unnoticed because of hard-wired limitations on the resolution power of the individual senses,
Hence, Vroomen and Keetels (2010) argue there must be higher processes at work in the brain that actively synchronize percepts that are offset in time, but seem to belong to one and the same event. One such mechanism is referred to as temporal ventriloquism, which means that one perceptual modality is actively shifted in time to match it with another. This effect is most pronounced in visual stimuli, in that a visual percept is actively adjusted in time to match a sound or tactile stimulus. Likely visual percepts are shifted preferably by the brain, because the visual system is the slowest of all the senses.
Reference
- Vroomen & Keetels, Att Percept Psychophys 2010; 72(4): 871-84

This is a really interesting set of questions and I'll try to answer all yet keep it compact. So first of all let's see the nerve classes and conduction speed from this and this wikipedia pages:
Peripherial nerves can be classified into three groups A, B, and C (based on their diameter).
Group A are the thickest (largest in diameter), are myelinated and have high conduction velocity.
Group A can be divided to subclasses:

'A' alpha nerves are 13-20um (micrometer) thick and have 80-120m/s
conduction velocity (this equals 288-432km/h (meter/s * 3,6) or
180-270mph (khm/h / 1,6)). These are associated with proprioception (this
subconscious sensation is responsible for us knowing how our body is positioned in 3D and where are our limbs compared to our body)

This means that in a fairly average 180 cm (approx 6 feet) tall human a stimulus on such nerve can travel the whole body of the person in 0,018s (with an average of 100m/s conduction velocity) How ever this is not the real case, I'll discuss that later.

'A' beta nerves are about half as thick as 'A' alpha (6-12um) and
conduct stimulus with 33-75m/s. Among others these are linked to cutaneous mechano receptors

Alpha and beta fibers can be both afferent (sensory) or efferent (motor)

'A' delta nerves are thinly myelinated and far slower than the
previous nerves with 3-30m/s velocity. These type of nerves are linked to nociception, cold thermoreceptors and make up the free nerve endings for touch and pressure.
'A' gamma fibers are efferent fibers and with 4-34m/s velocity.

Group B nerves are preganglionic fibers (ganglions are hubs of neurons of the autonomic nervous system) and conduct stimuli with 3-15m/s velocity. Thes are 1-5um thick and myelinated.
Group C are post ganglionic fibers (leading to the organs) and belong to nociceptors and warmth receptors They're thin (0.2 - 1.5um) and non myelinated. Their conduction speed is 0.5-2m/s.
So different sensory types have different nerves associated to them, and this results in different conduction velocity of that stimuli. Thus the answer is yes there is difference in sensation lag times to different types of stimuli.
In this paper scientist tested reaction lag time to heat caused pain and found the following:

Researchers stimulated two different parts of the hand of test subjects, the thenar eminence - that is the base of the thumb, and the volar forearm - that is the same side of the forearm as the palm ( the lower part of your forearm if you imagine your hands palms down). As you can see on the graph the volar forearm has lower lag times that the base of the thumb after a certain level of stimulus.
These authors also made a control experiment to:

estimate the sum total of time necessary for central sensory processing, the decision making plus motor execution times were measured in one subject for responses to suprathreshold auditory stimuli. Auditory stimuli were chosen because primary afferent conduction time is negligible. Latencies were measured in the same way as with the thermal stimuli. The tenth percentile (point at which 10 ~ of the latencies were faster and 90 ~ were
  slower) was near 0.19 s.

So response to sound is pretty fast, but this as with the heat experiment includes the measurable response of the test subject, thus the value is higher than the actual sensation.
For the heat-pain experiment the authors concluded :

The conduction distance from the area stimulated to the spinal cord was 0.78 m in this subject. If receptor utilization time, rise time, and conduction time in the cervical spinal cord are ignored, then primary afferents that signal first pain must have a conduction velocity of at
  least 0.78 m/ (0.33 --0.19) s, or 6 m/s.

The 6/ms velocity correlates well with the A-delta nerve's conduction speed.
Also here's another diagram on the distribution of lag times to different level of stimulus:

The difference of lag times can result from the activation of differrent receptors. Temperatures around 40 degrees Celsius are more likely to activate warmth receptors only that have lower conduction velocity. The high numbers of slow (1-1,5s) response to these stimuli correlate well with the group C fibers for warmth reception. On the other hand, responses to higher and potentially more damaging temperatures, nociceptors are more likely to be activated and faster conduction of these stimuli result in lower latencies. Also the transition from high latency to low is quite smooth with increase of the temperature.
Difference in nerve conduction values are not the only thing that occurs lag in sensation. These stimuli do not travel directly to the brain from receptors, but have to be transmitted to a sensory neuron, then these have connections in the spinal cord before stimulus can be transmitted to the adequate part of the brain, and then these neurons of the brain still have to process the signal. It is important to note that lag times are different from individual to individual. Authors of this paper conducted a great series of measurements to find out effects of age, sex and height on nerve conduction velocity and it turns out that for example:

Controlling for age and temperature, the 0.17 m/s decrease in sural  conduction velocity per centimeter increase in height (0.44 m/s per inch)
  was somewhat larger than previously reported.

Also this last article has many good comparison tables of different nerves and conditions.

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


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What's a mouth ulcer/canker sore "made of", and why do they develop?
Mouth ulcers are red/white rings with a crater. They are sore and last for 7-10 days.
What I want to know is what they are 'made of' - i.e., what is the ring filled with, and why is the centre crater so sore? And why do these relatively benign and short-lasting ulcers have to hurt so much when they simply heal in a couple of days

I'm especially interested in the latter half of this question, specifically in the case of minor oral injuries. What is the mechanism by which a small wound (e.g. from accidentally biting the inside of your lip) can develop into a wide open sore that's many times the size of the original injury?

The redden area around the grayish-white indentation of the canker sore isn't filled with anything. This circular area is simply inflamed. The grayish-white area in the center is not filled with puss or anything else as well. This is an area of dead cells but underneath this layer of dead cells the tissue red [1],[2],[3].
Canker sores, Aphthous stomatitis, is an ulcer. An ulcer is a break in the membrane. That is, you have an open sore in your mouth. As with any open wound, pain and discomfort will occur but the mouth is how we consume our food. Since we intake our daily bread in this manner, what we consume can cause the pain to increase; for instance,

acidic foods
spicy foods
abrasive foods

The cause of canker sores is not entirely known, but according to the Mayo clinic [2], possible triggers are

A minor injury to your mouth from dental work, overzealous brushing, sports mishaps or an accidental cheek bite
Toothpastes and mouth rinses containing sodium lauryl sulfate
Food sensitivities, particularly to chocolate, coffee, strawberries, eggs, nuts, cheese, and spicy or acidic foods
A diet lacking in vitamin B-12, zinc, folate (folic acid) or iron
An allergic response to certain bacteria in your mouth
Helicobacter pylori, the same bacteria that cause peptic ulcers
Hormonal shifts during menstruation
Emotional stress

Canker sores may also be caused by the following diseases as well [2]

Celiac disease, a serious intestinal disorder caused by a sensitivity to gluten, a protein found in most grains
Inflammatory bowel diseases, such as Crohn's disease and ulcerative colitis
Behcet's disease, a rare disorder that causes inflammation throughout the body, including the mouth
A faulty immune system that attacks healthy cells in your mouth instead of pathogens, such as viruses and bacteria
HIV/AIDS, which suppresses the immune system


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Formation of life on other Planets
At the present time it looks as if there is no other life in the Universe other than here on Earth . If this is true then why didn't it occur anywhere else ? Is it possible for something to happen only once ? Hundreds of Billions of  other Planets have formed so whatever happened here why wouldn't it have happened again elsewhere ? It is very , very strange indeed .

Although this is an interesting question, it has few problems with it. 1, I think it's off topic (too broad / unclear what you're asking - in biology topic), and suits astronomy better. 2, there's no proof that life does not exist in some other from somewhere else (as far as I know Mars has signs that it was habitable to some extent in the past - for microbes at least) .

@poka.nandor Most often I post my questions on astronomy but I thought this fitted biology more. I know that there is no proof either way but recently I read that Scientists were scanning millions of Galaxies and could see no indication of life anywhere else. We have to keep looking and to keep an open mind but until we find some evidence it will look like we are alone in the Universe. So what I am asking is how could it , life , occur only on one world out of trillions of worlds and how strange this is if this is actually the case ?

I'M not even sure that with current technology we could tell if Earth has life, even within from our solar system.

@PeterU do you have a reliable (preferably peer-reviewed) reference to back up your statement that "Scientists were scanning millions of Galaxies and could see no indication of life anywhere else"? What were their readouts? $CO_2$? The color green? This completely contradicts the mounting evidence of large numbers of rocky, "Earth-like" planets withing a sun's habitable zone.

@poka.nandor yes, you can, with listening to radio waves, for one thing. See here for one description of how planets are evaluated for "life as we know it".

Emphasis on life as we know it... what about planets that dont have civ with radio tech...like earth did not have up until like a hundred years..i know that there are molecules you can look for that might indicate presence of life but detecting those fom millions of kms /light years...

This project tried to look for advanced alien civilizations by looking for their waste heat from other galaxies. The recent news is that they haven't found anything, but this project would probably only detect civilizations that had spread across entire galaxies and used a lot of energy. This doesn't say anything about the presence or absence of biological life on other planets. As far a good way to detect life, molecular Oxygen gas would probably be good.

Issues with the post
I agree that the question is too broad. It is not the only issue, it is also primarily opinion-based (see below for explanations). The post is also somehow unclear (see below for explanations). But here is some kind of an answer that may help you.
If you google your question you will get tons and tons of hits. There is a whole lot of videos on youtube that address this question. You may want to have a look at those and come on StackExchange to ask a more accurate question because for the moment the question is too broad.
As a first short answer to the questions...

At the present time it looks as if there is no other life in the Universe other than here on Earth

It sounds wrong (as a consequence your question would be primarily opinion based). We haven't found life. This doesn't mean that life doesn't exist elsewhere. Actually most people think that life exist elsewhere. Part of the issue behind this question is the definition of life. Often, people refers to Drake equation (you might want to read about it) which gives you the number of planets where life should exist. However, Drake equation is a speculation that has no solid grounds. It is actually pretty complicated (or impossible because we need to assume things about what the original conditions are) to calculate a probability that life occurs on a given planet. While it sounds pretty intuitive to many people (me, including) that life should exist somewhere else, there is really not much certainty.

Is it possible for something to happen only once?

Well....yes, the death of Napoleon occurred only once.... I am not quite sure what you mean with this question, it is unclear.

b What I meant with the question is, if it was possible for life to form on this Planet then how could it be that it did not happen again elsewhere ? Since life came about here that shows that it is not an impossible event and yet so far there is no evidence that it ever happened again. Is this not strange ? Maybe we might never be able to find the answer and also we don't know what could have happened in the past, or what will happen again in the future, with regards to life evolving on a Planet.

Take some time to read stuff on the subject, I cannot make a whole overview of the field, your question is too broad. Your comment has been partially answered above but I can't make much more for you. Really, just take some time to read or watch videos on the subject, there are tons of ressources on the question. You should end up understanding the issues related 1) to the definition of life, 2) to the easiness of detecting life (we haven't sent robots all over the universe yet!) and 3) to how complicated (or impossible) it is to calculate any probability of such thing to occur.

No need to down vote this answer, as there is no other practical method to answer this type of question. Another option is to close the question immediately with out trying to answer it. +1 for the effort put towards answering it although its difficult to answer.

@PeterU: May be there are millions of planets swirling with life or may be not. But so far we cant judge whether there is life exists outside Earth. May be life is not such a big deal as we think it is. Scientific and technological knowledge are developing quite faster and we can believe that this will one day guide us to some farther planet were life is going on or some body else will find us in this remote corner. All we have to do is to patiently wait for it. (cont...)

Most of our intelligent ancestors were unaware of many scientific principles and yet now we idiots know much more than them. Many more years later may be our grand grand grand sons may worry that their grand fathers(us) were unaware of the fact that we are living in a Universe full of life. May be this comment doesn't satisfy your urge but all I can offer is this. :)

@Jay , Yes, I understand what you are saying. At the present time there is no way of knowing but perhaps in the future we may know . I was just stating that it would seem to be more logical if life exists elsewhere as well as here. If it turned out that we are alone it would seem very strange somehow ?

Yes, it would "somehow" seems strange indeed. But really, you will easily find all information you need if you just google your questions. You will have an idea of what are the difficulties in estimating the number of independent origin of life and on the likelihood of actually finding life given that it exists somewhere.

@PeterU: Considering the vastness of Universe, we will never find out we are alone even if we are. We will be in constant search for it. If we found out we are not alone our plans for future will still be to found out more. Life is just like that, It will never let us RIP.


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Alder Tree Root Nodule Origins?
I recently found out that alder trees have root nodules which contain nitrogen-fixing bacteria and that alders are primary colonizers in primary succession. That leads me to this question: since there are really no fungi in the soil and since the alder is a colonizing species, where does the fungi come from? Or is my assumption that there are no fungi in the soil incorrect?

Welcome to Biology S.E.! If you need any assistance, please visit The Help Center.

Where did you hear that alder trees are primary colonizers? Primary colonizers tend to be organisms such as mosses and bryophytes. I don't know for sure, but I would be willing to bet good money that the fungi make it there long before the alder trees do

Cyanobacteria can form nodules in plants, and actinobacteria also called a sort of association which is called "actinorhyza" similar to mycorrhiza. But how could you conclude there is no fungi? fungi are everywhere, and they play a key-role in degradation of lignin etc biopolymers from plants

How you conclude that nodules contain nitrogen fixing bacteria? did you found that from experimental analysis?

Many types of bacteria can form nodules or such. In case of your alder tree root nodules; it might be some sort of Actinorhiza. See  https://en.wikipedia.org/wiki/Frankia_alni , https://en.wikipedia.org/wiki/Root_nodule , https://en.wikipedia.org/wiki/Actinorhizal_plant.

Symbiotic bacteria and fungi can come to the plant in several ways. It can come through soil (where some-other forms of propagules already exists in soil). Or it can be remain attached at the surface of seeds (or other plant propagules) and plant-debris. Sometimes they can exist inside the plant's tissues and propagules in actively symbiotic form (see https://en.wikipedia.org/wiki/Endophyte).

Any soil microbiology textbook will tell you that there are a great number of fungi in most soils. I believe there are 12 or 13 species of non-legumes capable of fixing atmospheric nitrogen. Podocarpus is one of them. Look at the roots of podocarpus and you will see nodules all along the roots.


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Non Coding DNA and its effect on evolution
I had a discussion with a friend of mine; from his understanding, bacteria and other small organisms have higher amounts of "coding" DNA and, as such, are able to evolve much faster than organisms like us.  His argument was that if bacteria are able to evolve so much faster than us, then they should have become the Apex Predators on Earth instead of humans.
I argued that the 2% of the "coding" DNA is probably as long as the 90% of a bacterium (I'm guessing at this point) and that it is the bacterium's small life span that makes it evolve so fast.  Was hoping to get clarification from someone with more experience in the field.

Well, your friends argument does indeed make no sense, which makes it kind of difficult to address. Evolution tends to drive populations to become better adapted to their environment. That in no way implies that faster evolving organisms are at the top of the food chain. Bacteria can evolve faster largely because of their short generation time.

You can do a crude calculation about the amount of coding DNA in humans based on your 2% figure. The human genome is ~3.2 Gb. 2% of that is 64 Mb. Compare to the E. coli K12 genome which is about 4.6 Mb.

I've heard the suggestion that DNA is encrypted as a protection against virus. Maybe someone knowledgeable here can say whether this is a serious possibility?

DNA isn't encrypted...

Generation time is indeed the correct answer. On top of that some bacterias do exchange genetic material (like antibiotic resistance genes) via "plasmids" and therefore can adapt even more quickly.

I reject the premise that apex predator is the pinnacle of evolution.  Filter feeders like humpback whales only survive because plankton greatly outweigh them.  Doesn't that make them, as a class, more successful?  Whales might go extinct in the near future,  but not phytoplankton.

Richard Dawkins discusses this in his book The Greatest Show on Earth: The Evidence for Evolution
Bacteria and other microorganisms, specifically Archaea, are able to exchange in a sort of 'copy and paste' genetic exchange that differs wildly from sexual reproduction.  They can even exchange genes with other distantly related species.  This, coupled with their short (compared to Humans) lifecycle, accounts for much of the difference in evolutionary rates.  Often, it makes sense to speak in terms of evolution in terms of specific genes themselves (in the case of bacteria), as opposed to evolution of the species as a whole, due to the 'copy and paste' exchange that can take place.  For Bacteria, there is something to be said for compiling a 'true' family tree for each gene separately, regardless of which kind of bacteria in which it resides.
Dawkins remarks, "The philosopher Dan Dennett has put it, 'Where the tree of life for animals is a majestically spreading oak, that for bacteria is more like a banyan.'"
Also, evolution by Natural Selection and random mutation does act on 'non-coding' DNA, just to be clear.

http://www.livescience.com/46986-human-genome-junk-dna.html
Microorganisms are often able to adapt to new environments quickly, but they lack the specialized functions of macro-organisms. Consider that the micro-organisms of macro-organisms have developed to form machinery that builds solutions to problems, rather than being retrofitted themselves to counteract new threats. Each time a bacteria needs to adapt itself to attack, whereas the specialized cells of our body can manufacture a solution on the fly rather than waiting around for a random beneficial strait to show up in the population. It would be like a small manufacturer quickly retrofitting it's production system to produce a new product. Sure, it can produce a new product, but it takes time for setup, and the company can only produce a limited number of varied products at a time, whereas a giant production company may have a huge amount of preset equipment for manufacturing a enormous variety of products with no need for retrofitting (evolution). The larger factory could have the advantage when it comes to efficient production, with quicker turnaround.
Therefore, the specialization of micro-organisms leads to nature allowing the evolution of macro-organisms as the major factories of nature.
Excess, unused (or at least non-critical) DNA is useful because it allows evolution some wiggle room. If a bacteria suffers a deleterious mutation in a vital gene, then it's obviously not fit. But, that same bacterium with can accumulate potentially useful codes in the previously unused portion of it's genome, without needing to deal with risky mutations in vital genes. And again, as microorganisms specialize, they can fabricate new proteins and such, with lower risk, and less time, compared to micro-organisms which use evolution of their genome as the sole/primary means of short term adaption.

This is not exactly correct.... non coding DNA is not "unused" as you said. Several studies have proven that non coding DNA, in most cases, is in fact regulatory DNA, origins of replication, centromeres, telomeres, etc.. Sources in case you're interested: http://www.theguardian.com/science/2012/sep/05/genes-genome-junk-dna-encode, http://en.wikipedia.org/wiki/Noncoding_DNA, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884187/

I assumed by the word "non-coding" that they meant sequences which are truly responsible for nothing. There are obviously going to be sequences that do nothing, or do something which has a completely neutral effect.

Also, there is an issue with the idea that all the genome is being used: http://www.livescience.com/46986-human-genome-junk-dna.html                                                                                The human body is pretty complex compared to wheat. Yet wheat has 5 times the amount of information? That can't possibly all be regulatory and such.

@CDB
Consider the very first organisms. They must have had SOME non-coding DNA which served no purpose, otherwise they would have had no room for growth, with each mutation destroying something critical to the function of the cell. It's VITAL that there be junk DNA initially, and after life has gotten a foothold, junk DNA can offer a competitive advantage for the reasons stated in my answer. So nature clearly has a reason to select for organisms which have non-functional and/or large amounts of non-critical information. Telomeres can shorten, and still fulfill their role.

@CDB
A mutation which extends a telomere, also allows for further mutation of potentially beneficial traits within the telomere, with less chance of destroying it's function.

Perhaps it would be better to use the term junk DNA rather than non coding DNA than, seeing as most non coding DNA actually does do something. I just wanted to clear up a term that many people get wrong. As for the wheat, it's large genome comes mostly from it's many ancestors. And yes, most of that %80 non coding DNA is regulatory and such. But you are right, not all of that is vital, but there is only a very small percentage that is actually junk. Like I said, I just wanted to clear up that term.

@CDB The article I just provided states that "80%" is NOT regulatory. Take a look at introns: en.wikipedia.org/wiki/Intron Introns are coded for, but removed. SOME do NOTHING because they aren't given a chance to do so.

I was talking about wheat. Umm....introns do quite a bit, where are you getting all this?

Introns often do something. However, intron loss and gain would not be possible if they were always required or served a function. Eventually, you will have sequences which pop up and do absolutely nothing for at least a time. They do no harm, and they do no good. They simply go unused.

I never said it wasn't possible to get unused sequences, I merely wanted to clarify the misused terms to avoid confusion.

Oh...I thought you were saying unused code was not possible...nvrmind. My earlier comment was meant to be "Also, introns...", to imply a new offshoot...


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Which monkey species features two distinct male phenotypes?
I remember coming across a popular science article years ago about a monkey species which featured two male genotypes: the first were good looking males who acquired social status (as alphas or betas) within the group and could thus achieve reproductive succes. The alternative (less frequent) phenotype achieved similar fitness by adopting an outgroup (omega) lurking rapist kind of reproductive strategy.
Does anybody know which species and whose observervations I could be referring to? I'm curious to find out if this was a valid observation and if any further research has been done on this phenomenon.

Related behaviour in lizards: http://en.wikipedia.org/wiki/Common_side-blotched_lizard

Search term 'alternative reproductive strategy' for lots of related behaviors in various organisms.

Patas monkeys exhibit "sneak mating" where a male other than the resident male sires offspring. Resident males do sire more offspring than sneaker males, but both strategies do co-occur. I'm pretty sure there are other species that have a similar mating strategy as well.

Although I'm pretty sure that this is not the species I was looking for, this behaviour resembles the description in my question closely enough, so I'm accepting your answer.


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Is emergence connected to nature's transition between fractal regimes at different size scales?
A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is only true at a certain range of scales, about 0.1 - 10 meter. The forest does not look like one tree, nor does the texture at millimeter scale or the cellular structure at microscopic scale. At those scales the tree may or not be fractal, but at least it is not fractal in the same way as on the 1 meter size. Nature breaks the fractal regime after only a couple or so self-similar scales.
Are these transitions between fractal regimes studied by biology?
Are there any ideas around about how different fractal regimes might be connected with emergent phenomena? At very small scales there exists no tree, but only elementary quantum particles/waves. Macromolecules and cells and the tree and the forest each emerge as a phenomena on different size scales. I wonder if this emergence is matched by the different fractal regimes at those scales?

I think that you are mixing up the causality between fractals and emergent phenomena.
There are LOTS of different types of emergent phenomena, and only some of them are connected to fractals.  Many are instead connected to other physical phenomena like phase transitions (e.g., traffic jams) or feedback loops (e.g. dune formation).
Biology does indeed make use of emergent phenomena at many different scales. This is, however, only what we should expect from an evolutionary process that is building patterns through trial and error selection.  Critically, emergence is the formation of complex patterns from relatively simple local interactions, and these patterns are often highly robust due to the nature of the physics driving them.
This means that emergent phenomena are an evolutionary "shortcut" for achieving many kinds of useful structure. Fractal-generating programs, in particular, are a one very simple way of encoding large-scale space-filling patterns such as tree branches or blood vessels (other space-filling patterns, like hair follicles or shell patterns use different mechanisms). And remember, they typically run "inversely" in biology, starting small and growing rather than starting large and subdividing---thus the natural truncation of iterations by the limit in growing scale.
It is thus unsurprising that organisms would first "discover" fractals rather than something more akin to a human-style blueprints for encoding such phenomena, since the repeated local rule of a fractal is so much less complex. It's just that we discovered fractals later and they are less intuitive to us, so they look more remarkable to human thinkers.

Fractals are by far more ubiquituous than it may appear at a first glance, spanning essentially all the levels of organisation of living organisms; including vascular and neural networks in animals and plants, metabolic networks in bacteria, and the food networks characterizing whole communities. (See, e.g., the answers to this question for more discussion and the relevant links.) All these networks are self-similar, and one cannot really claim that there are transitions between different fractal regimes (at least, such claim is explicitly excluded by one of the postulates of the cited theory.)
That the existence of these fractal networks is an example of an emergent phenomenon (in strict physical sense, as, e.g., described by Anderson), does not cause any doubt. What is less clear is whether 1) these networks are the result a single symmetry-breaking/emergence event that modern organisms inherited from their most recent common ancestor or 2) whether organisms naturally evolve toward fractal structures as a means of increasing their fitness (the theory states that fractals lead to the highest energy efficiency).
The last paragraph in the OP suggests that the question might be posed in more general sense, of the emergence phenomena in biology. Indeed, if we start with atoms, one can treat evolution as a sequence of emergent phenomena in their strict physical definition. To give just a few steps:

emergence of simple molecules and chemical reactions between them
emergence of self-replicating polymers
acquisition of cellular membrane
emergence of multicellular organisms

This question gives links to some more or less readable discussions. Yet, it is fair to say that in terms of exact theory we have not much evolved since Anderson (although a fe succinct results were obtained, e.g., regarding teh tehrmodynamics of self-replicating polymers: here and here.)


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What has caused life to choose this unfathomably tiny subset of all possible proteins?
I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever come into existence anywhere in the visible universe, let alone on Earth. And evolutionary selection only works on stuff that exists.
Is there some chemical or other explanation, or is this an unresolved paradox in biology?
The median number of amino acids in a human protein is 375. Most are longer than 200 and maybe all are longer than 100. The 20 different kinds of amino acids can be combined to 20^375 = 10^487 different proteins which have the length 375.
If the entire crust of the Earth consisted of proteins which all were 375 long and each protein mutated once every nanosecond during 5 billion years and each mutation resulted in a protein which is unique in time and space, and there exists 100 such "protein Earths" around every star and 1000 billion stars in each of 1000 billion galaxies in the visible universe, it still only adds up to something like 10^100 proteins. Adding 10^37 years until the last star remnant has cooled down to less than 1 Kelvin, doesn't change this picture, almost all of the possible proteins will literally never exist anywhere. Even if I'm off by a factor a million on each of those numbers, only one in 10^300 of all possible median length proteins could ever exist.
Since our mind-bendingly small subset of possible proteins supports life, shouldn't we expect that many many (as in 10^300) other potential subsets of different proteins would do so too? And can we conclude that if DNA/protein based life has originated somewhere else, it will not have even one single protein in common with us or with any other independent origin of life? Or is this focus on proteins somehow invalid?

Sentences "...evolutionary selection only works on stuff that exists." and
"What has caused life to choose this..." Look like "Life suddenly started to use arbitrary set of proteins, like guy who buys some tools in nigh-infinite shop" and it's not true - it has everything to do with evolution.

@Mithoron If mutations are random, then the median protein can mutate to 10^487 different new proteins. Less than one in 10^300 will ever happen anywhere, and still that works fine for life! Maybe 10^200 other mutations would have worked fine too? Or are we that lucky? Evolution has nothing to do with selecting proteins which never exist. Evolution only kicks in given this ridiculously small subset. I wonder if any known mechanism can explain this selection of protein varieties.

This question is a bit like shuffling a deck of cards and asking why they ended up in that particular order. They just are by chance.

@CactusWoman And having to conclude either that you got a one-in-a-10^100 straight flush, or that almost any hand given would have been as good. Doesn't matter much how proteins mutate, they will cause life anyway.

@LocalFluff Proteins don't mutate. Genes mutate. Individuals are selected. Species evolve. Even when genes mutate they could not do so every nanosecond. The phenomenally large amount of radiation that could cause every gene on earth to mutate every nanosecond--I've got that correct? That is akin to your gedanken experiment?--would obliterate life on earth in less than a second. No life, no endless pool of 375 amino acid long proteins. When we say that there are 10^6 different protein sequences on the planet--is that your assertion(?)--that is misleading, they don't have 10^6 functions.

"Maybe 10^200 other mutations would have worked fine too?" Yes they would have. Luisi (I strongly suggest you to ree his work if you are really interested in this topic) made a good point on that. There are plenty of studies showing that purely random proteins have high probability of having function, it turned out, for example, that for a given environment (buffer condition), a consistent percentage of random protein will collapse into a folded structure and have some biochemical reactivity.

The answer is chance or, even better, contingency.
About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the scaffolds and functionalities have been. It is true that protein-based life could be evolved somewhere else, and it is true that the overall sequence space evolved somewhere else would be different from the one evolved on this planet. However, I would expect to find almost the same palette of biochemical reactions that we have discovered on our proteins.
I would suggest reading the work of P.L. Luisi here. He makes really good points on this issue.

+1 for the sequence - scaffold comparison. Good insight,

Would chunk copying of DNA also bias against protein diversity in terms of what is easy to generate (first mover advantage) and perhaps in terms of error containment?

That is not a logical answer. Evolution has no relation to which "scaffolding" would be optimal, since evolution never ever can test and select any protein which is better than 10^100 or so times worse the actual theoretical optimum, for a protein which exactly consists of a medium number of amino acids. "Chance" is not the answer. "Chance" is precisely what is utterly defeated by these grotesque monster numbers!

Evolution doesn't know indeed which scaffold will be optimal and it will never try all the possibilities, but this is not the point. My point is, that given an infinite number of sequences you do not end up with an infinite number of functions nor domains. Most of the infinite sequences will fold in few main scaffolds, with more or less the same shape and will end up having very similar biological functions.

Let's consider a very easy protein to make an example, the GFP. The only function it has is to be fluorescent. Many variants of this fluorescent protein are known, all with a different sequence. The sequence may vary a lot, however all the proteins ends up having the same main structure and function. Now, all the variants differ for absorption/emission spectrum and for stability under different conditions. These factors will be selected by evolution but it will depend from case to case whether  a red fluorescent protein will be more advantageous of a green one for example.

Will all the fluorescent protein variants be tested by evolution on our planet? Nope! Does exist a better, more stable and more efficient GFP in the universe? Probably. So the "optimal" you refer to is always a local optimal, local in time and in space, i.e. that particular protein have an advantage now, in that environment and for that organism and it will not be the best solution ever anyway. That is the contingency! and it is mostly governed by chance... That is what evolution is about.

I'm not sure I understand the question. You've elegantly demonstrated that only a tiny fraction of all protein sequences could possibly exist, but then asked why only a tiny fraction of all protein sequences do exist. Your conclusions about independent origins of life having no proteins in common are accurate, but also consider that you as a human being have not even a single protein in common with the bacteria in your yogurt (I mean you do, but they have slightly different sequences).
As far as which protein subsets make life, there are demonstrably thousands of sets of proteins that support life. Each genetically distinct individual has a slightly different set of proteins, most of which support life.
As far as how many of these subsets exist, that's unknown. Maybe aliens use only ribozymes based on RNA molecules. Maybe they have a different set of amino acids, or a silicon backbone to their proteins, or what have you. Until we find alien life(or perfect abiogenesis in the lab) the total diversity of life-like things is unknowable.

I thought all life on Earth shared some genes, even me and the bacterial yogurt I eat at breakfast. But maybe none of that is expressed as proteins? And is it really "demonstrable" that thousands of sets of proteins support life? And what has "thousands" got to do with the orders of magnitude involved here? This is not about thousands, it's about one in a trillion of a trillion of a trillion of a trillion of a trillion of a trillion of a trillion of a trillion of a trillion. At the very least. For the median length protein which keeps you and me alive and happy.

again, it is not the sequence that matter in this case but the "protein domain". To make an easy analogy, think about a car, has 4 wheels and an engine and have one main function. Now you can think of trillion trillion trillion different cars, each of a different colour, a different shape, a different size, different setups... do the math and you will find that the numbers are huge. However the function will be always more or less the same. So in other planets, with other combinations of pieces, always the same kind of machines will arise. Proteins are molecular machines.

You and a yogurt share many genes, but the sequences are not identical. Metaphorically you both have a steering wheel but it is a different steering wheel. Maybe slightly smaller or with a leather inset or whatever. Does the same thing but isn't identical.

@alec_djinn Are you sure that all 'life' has precisely the same set of molecular functions? 'RNA world' life would be similar to life that we recognize, but the vast majority of the proteins would have completely different functions, or not be proteins at all. 'RNA world' life is also the most similar to familiar life we can conceive of, and there's a statistical certainty alien life would be more alien than we can conceive of. 'The same kind of machines' needn't necessarily arise.

@ Resonating Well, if we talk about "chemistry based life" then yes. Whatever set of molecules you choose, there will be common problems to solve to have life, like how to store information, get energy flow running etc... In a molecular scenario these problems are solved by coupling chemical reactions (oxidations, reductions, bonds formation etc...) in larger pathways. If those pathways are catalyzed by proteins, nucleic acids or other molecules it doesn't matter and may vary from life form to life form. Don't you think?

You ask why living things use the proteins they use, and not something different.
It's mainly because they must do something that works, and they have found something that works OK.
Each protein serves one or more functions for its cell. If it changes at random, probably it will change into something which does those functions less well. Because it has been selected for thousands of generations to get something that works well, and so most of the alternatives are worse.
Many mutations have no effect. But if you have 300 proteins and you have a change in each of them, chances are you will not live so well. And if your son has another change in each protein, he will probably do worse than you. It won't take many generations before your descendants can't compete and die out.
So each change is a gamble. If you don't make any changes, then eventually something which does change will do better and will drive you extinct. But if you make too many changes your descendants will do worse because of them. Ideally you would make just the right number, to balance the weighted odds of  damage from bad changes versus benefit from good changes.
For many organisms, the rate of change is down somewhere around 1% -- 99% of the time they get no change when they reproduce.

Since our mind-bendingly small subset of possible proteins supports life, shouldn't we expect that many many (as in 10^300) other potential subsets of different proteins would do so too?

Sure. And we have tended to find some that we could get to from where we were before. Point mutations tend to happen in small steps. You change an amino acid to a similar one. The genetic code is a Gray Code, often mutations have no effect, or hydrophobic amino acids are replaced by other hydrophobic ones, amino acids are replaced by others of similar size, etc.
Some of the best enzymes might be things that have nothing else good similar to them, so that they are very hard to evolve to.
Science fiction writers have sometimes written about life that has evolved for different times, and they usually suppose that the more-evolved one will simply and easily outcompete the ones that have not had so long to discover better ways. That isn't necessarily so. Human beings transported back to the Silurian Period might eat well (once they figured out which seafood is poisonous) and might not be eaten by anything (but they might get mobbed by centipedes if they sleep, and be unable to make hammocks out of cooksonia, and have no trees to hang the hammocks from either). They still may not thrive. Half a billion years evolving to fit into a different ecosystem might not be that useful after all.


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What is the most reliable tumour suppressing gene for NSCLC?
I was looking at some tumour suppressing genes that can be helpful in diagnosing lung cancer (particularly NSCLC - Non-small-cell lung carcinoma) at an early stage. I came across a few such as p53, etc. However, as a beginner (and someone who has never pursued higher studies in biology), I do not have much knowledge as to which is the most reliable and the most extensively documented tumour suppressing gene for NSCLC.

Welcome to Biology SE! I took the liberty to edit your question to resolve the abbreviation. You can revert my edit any time if you wish.

The first resource I would look at would be the TCGA publication on NSCLC which can be found at this location. The first figure shows the most frequently mutated genes. TP53 rises to the top as most frequently mutated gene in the cohort studied, however, one also sees on the list KEAP1, NF1, ARID1A, SMARCA4, RB1, and CDKN2 as commonly altered tumor suppressors TSGs. You will want to take into account copy number data and mutation data in the frequency count in cohort also. Another issue to check in the data set is stage of the tumors in TCGA. You mentioned 'early stage' in your query, but if all the samples in TCGA are recurrent then it may not be appropriate for your question. The cBioPortal resource allows you to look and manipulate the data and I encourage you to look at that resource. It is very well done and shouldn't have too much of a learning curve. You will be able to put in TSGs and get back the freq of mutations. They may also have information on stage so might be possible to filter for only those samples. There are also a couple of text-mining resources that you can ask queries through pubmed to get back gene lists or to link gene lists. One tool is Glad4U (search this name in google) which allows you to type a query such as: "tumor suppressor AND early stage NSCLC" and it will return a ranked list of genes. Ranking is based on co-citation. However, one must check the returned list to make sure the genes returned are TSGs. A listing of putative TSGs can be found here. The second resource is CoCiter v2.0. On the Gene-Term search you can rank the lists of TSGs against search terms and it will return a ranking of the TSGs most associated with your search term. Hope this helps.

Thanks a lot. I was looking for such an answer for a long time. I'll go through all the sources that you have listed


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Literature that demonstrates organisms have a competitive advantage in numbers
I'm studying two bird populations that are competing against each other for a resource: Population A and Population B.
Population A is present in much higher numbers than Population B, and as a consequence, I think that Population A has a competitive advantage over Population B.
I'm looking for literature that demonstrates that when one population is present in higher numbers than the other population, the population present in higher numbers has a competitive advantage. Can anyone point me in the direction of literature that demonstrates this?

This is not necessarily true. Take for example elephants and aphids that both feed on the same plants (competition for the same resource). It is not necessarily the case that relative quantities are linked directly to competitive advantage.

I don't see your logic that the more abundant species need to have a competitive advantage (I assume that populations A & B are referring to different species), at least without more information. There is often a negative relationship between body size and population density, and there are many other things that are affecting population abundances. Why are you assuming that competitive advantage is the key factor? Are they directly competing for the same resource? What type of resource are you referring to?

I have found these papers:
http://www.sciencedirect.com/science/article/pii/S0169534713002322
http://www.sciencedirect.com/science/article/pii/S0040580912001360
http://www.ncbi.nlm.nih.gov/pubmed/19416834
http://www.ncbi.nlm.nih.gov/pubmed/21930936
The last two argue that larger groups have better "problem solving" capability, and this is a clear advantage in competition.

Can you please expand your answer beyond just dropping links? This is not helpful, even if the articles might be...

He asked for papers and I gave him links to pertinent scientific publications... However, the main point is that in a larger community there is higher chance of finding solutions to problems. In case of birds, bigger is the swarm and easier will be to solve issues. This in general gives a reasonable advantage. So if two groups of the same species (or very close) are in competition the bigger group have greater chance to prevail.

Chris - answer is helpful because I asked for papers


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Is it possible to knock out a gene in adults?
gene knockout is mainly used in creating newborn animals... right? Well can you do it to already-adult animals or humans so that they themselves would experience change in their body and not just their off springs?

To do so would be considered gene therapy. It is possible, but obviously far more difficult due to the number of cells involved.

To knock out a gene in an adult animal requires knocking out the gene in each individual cell. Could we do it? We have the technology to do it in a single cell. Will anyone do it to all 3.7 trillion cells in the human body? Definitely not anytime soon.

a conditional KO would make more sense, and that's actually what gene therapy tries to achieve. But basic mechanisms between KO and gene therapy are very different.( except for Crispr, I think)

Woa yea thats a lot of cells! Can a conditional KO mean KO in limited area(s)? Like just in the spinal cord, brain or another organ or something. Sounds easier than 3.7 trillion cells

Even gene knockout in newborn animals is extremely difficult. Your only chance to get a complete knockout in all cells is probably at the single celled zygote stage. Knocking out, or down, expression in certain cells in an adult is possible, but gene delivery is still pretty difficult and results aren't guaranteed.

you can try KO in subset of cells. Why bother with all $10^{10}$ cells if you are curing liver or something. Also lower chance of propagation some unwanted, off-target genetical effect down the family tree.

Another option for adults is a gene knockdown instead of a knockout.  Knockdowns involve changes at the RNA level instead of the DNA changes of a knockout.  The challenge is to get the reagent used to cause a knockdown into the cells of an adult organism (this is an active area of research).  Knockdown reagents include siRNA, PNAs, phosphorothioate oligos and Morpholino oligos.  Some are in clinical trials now.

Actually, Cas9 system might be a possible method to achieve your aim in the future, research teams are trying to utilize cas9 in vivo, which means maybe someday we can doing some genetic modification in body cell precisely. However, this is only a future direction and we still can not say its fit for a knockout.(Patrick D. Hsu, Eric S. Lander, and Feng Zhang, (2014) Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 14(6): 1262-1278)
And for editing some cell gene in a limited area, some research are on going for therapeutic purpose (Liqun Zhang et al.CFTR Delivery to 25% of Surface Epithelial Cells Restores Normal Rates of Mucus Transport to Human Cystic Fibrosis Airway Epithelium), but haven't seen research are trying to built KO cell in vivo.

thats all true, albeit speculative. Current Cas9/CRISPR efficiency is very low. around 10% for creating indels/knock-outs and around 0.1% for targeted genome integrations. In vitro you can get away with it because you don't inject/transfect single animal/cell. But in adult there should be some shotgun-like transfection with following selection. Which is very risky endeavor.

@aandreev Newer approaches increased the efficiency quite substantially, look at this post. It's again in vitro and I hardly see how that can be translated in vivo as such but I am confident this will greatly improve in the future. Also off targeting is still an issue for using CRISPR as a clinical treatment. A lot of work is being done in finding the best ways to predict the best sgRNAs for both efficiency and specificity. In essence I agree but I have good hopes.

i do have good hopes. However, paper you cite (NHEJ inhibition etc) seems to me like a novel way to screen: instead on neomycin authors rely on fact that cells with non-repairable NHEJ will most likely die. Hence increase in efficiency.

@aandreev. Nope, NHEJ and HR are two competing DNA repair mechanisms and it's not due to cell dying but rather HR being favored hence increased efficiency.

@cagliari2005 isn't it trinity: cell death/severe mutations, HR, NHEJ? sorry for off-topic, just to wrap up

@aandreev. CRISPR induces nicks in the DNA (to which extend this can be lethal depends on the guide RNA and where nicks are created). Gene, or DNA region, deletion/insertion is achieved exploiting homologous recombination. NHEJ will simply repair the nick without any modifications of the DNA therefore by disfavoring NHEJ an higher efficiency of genetic modification is achieved as now the cell is "forced" to use HR to repair the DNA. The 1st figure in the post shows that cells lacking CRISPR complexes survived (2nd lane)  to the Src7 treatment but are of course not modified.


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Which sequence assemblers I can use to compare different paradigms?
I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (Greedy, OLC, De Bruijn).
I have done my initial research but I don't know which assembler to use for comparing paradigms. Most of them are designed for real world usage, where there are many different factors to consider, but in my case the problem is more like a Computer Science problem: Reconstructing an array of symbols from it's fragments.
If there is no hope, I will try to implement them myself but I want to avoid that since it will very likely to be error-prone and slower than real world implementations.
Thanks!

Well, if I understand correctly, you would need at least three assemblers, one for each of the "paradigms" you wish to evaluate. Do you have a dataset of DNA reads to use as input? What exactly do you hope to determine? Off the top of my head people usually want to minimize the length of time that it takes and maximize the accuracy. Additional variables include the number of compute cores and amount of RAM required. Of course the estimated dollar cost may also be germane. There are very likely several review articles out there that have already made side-by-side comparisons like this.

Velvet is a De Bruijn graph based assembler, the original Staden package usues the OLC method as far as I know, an I think you can write a greedy one for yourself, as I don't know any software that uses that approach.

an article on comparison of OLC and De Bruijn assemblers: http://bfg.oxfordjournals.org/content/11/1/25.full

http://www.sciencedirect.com/science/article/pii/S0888754310000492 this paper may also help. It reviews different algorithms.

@mdperry: Yes, you understand correctly. I initially thought using Human Genome at gutenberg and creating random sequences, then I will cut them into reads. I hope to measure the lengths of the contigs and calculate their distance to initial sequence. Also I want to measure implementations resource (time, processing power, memory) usage. At the end, I want to repeat these tests as coverage and count of repetitive sequences changes.

@poka.nandor: Thanks for the information and the links! I'm currently reading them.


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Do sodium channels keep renewing themselves with new subunits made by genes?
genes make alpha beta gamma subunits (proteins) to be used in making sodium channels... If I understand correctly? And so, since the genes keep making those subunits, does that mean new sodium channels are continuously being made with those proteins till you die?
In other words, if those genes suddenly stop making the subunits in your 50's or something, your sodium channels will disappear or stop working? (Probably unrealistic, but theoretically...)

This is your second question about sodium channels that seems to show some misunderstandings about genetics, gene expression, and protein expression. So far, you've just used the term "sodium channel", I suggest you read the wiki page, then ask about a specific sodium channel, or at least offer more details. I am also having trouble understanding what you're asking. Are you asking if 1 gene makes multiple copies of the protein it codes for (it does) or are you asking if 3 individual protein subunits make multiple proteins (they don't).

Please do some research on protein turnover. Sodium channels, or any other protein or protein complex, are not just created early in life, then stay where they are until the organism dies. Cells are constantly dying and being replaced, and within a single cell proteins are constantly being degraded and new ones made. For some proteins the half-life is seconds or minutes, for others it can be hours, days, or longer, but eventually it all gets renewed. I suggest you do some more background reading on cell biology - Molecular Biology of the Cell is a good start.

You are asking about two different processes: turnover (degradation) of mRNA and turnover of proteins.  In a typical mammalian cell the mRNA half-lives of stable messages approach the length of the cell cycle (e.g. 24 hr). One mRNA could be translated around the clock if needed. The resulting proteins will also have a measurable half-life, and that will vary with the protein and the cellular conditions. If a cell ran out of protein and its mRNA there is often a feedback loop that activates transcription of the structural gene back in the nucleus.

Feedbacks are not essentially always present.

You should really study the basics before asking specifics about a particular protein. I am not voting to close the question, however.
DNA catalyses the formation mRNA (transcription) which in turn catalyses the formation of a polypeptide (translation); RNA polymerase and ribosome are co-catalysts respectively.
A functional protein may have many polypeptide chains as in the case of Sodium channel (or even haemoglobin). The function of the protein complex may be compromised if:

The polypeptides chains are not formed
The polypeptide chains are not associating properly

The former can result either because of a block in translation or a block in the transcription. These blocks can also arise because of active regulation in response to a certain condition; this is a temporary change.
Mutations can lead to loss of function by either causing transcription/translation blocks or abolishing interaction between different polypeptides.
In a cell all biomolecules are continuously formed and degraded. The rate at which they are degraded is called the turnover. If a steady level has to be maintained then turnover rate should be balanced by the formation rate.
When formation is abolished then different biomolecules will disappear at a speed proportional to their degradation rates.
If the mutation causes a loss of association of polypeptides then non-functional proteins will replace the functional ones with rate proportional to the degradation rate. (NOTE: Formation rate of a protein is proportional to the available mRNA).
Most intracellular and membrane proteins have high turnover. Extracellular structural proteins such as collagen have a relatively low turnover. So if sodium channel gene stops transcribing the effects would be felt very soon.


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Why can I see a light flicker when it's in my peripheral vision?
When I'm looking at an old CRT monitor or a worn fluorescent lamp, but not directly in the center of my gaze, the light from it seems to flicker. When I focus my gaze onto the monitor or lamp, the flickering stops.
Why can I see a light flicker only when it's in my peripheral vision?

Your retina contains both rods and cones. Cones are color sensitive, slow, and concentrated near the center of your field of vision. Rods are "light" sensitive, fast, and concentrated near the periphery. You want to be able to respond quickly to a threat "in the corner of your eye" without needing to see the color of the threat.
This is nicely explained by this diagram (source: http://hyperphysics.phy-astr.gsu.edu/hbase/vision/imgvis/retina.gif)

So when you see a CRT in the corner of your eye, your rods respond quickly enough that you can tell the light of the CRT is flickering. As you turn your gaze towards it, you get the higher resolution, color rendition of the cones - and lose the temporal resolution.

This explanation doesn't work in daylight, when rods are saturated. See also: Why is peripheral vision not bleached by daylight?