text:
What are host cellular factors?
With respect to this paper:
Global Analysis of Host-Pathogen
Interactions that Regulate
Early-Stage HIV-1 Replication
What does the term "host cellular factors" mean??

Generally spoken, "host cellular factors" are proteins, receptors etc. of the host cell. In this case, they are important for the HIV infection. The authors write:

Recently, a genome-wide siRNA analysis revealed over 250 host cellular
  factors that influence HIV-1 infection.

This means gene silencing techniques where used to identify the host cellular factors which are important for the infection, you can find these results here: "Identification of host proteins required for HIV infection through a functional genomic screen."
The overall goal is to identify proteins which are important for the function and infection of HIV to understand the interaction between virus and host cell better.


text:
How to explain Genome, Genes, RNA and protein in one figure to non-biologist?
I have a presentation to do where non-biologist are attending. In order to introduce a little bit my work I have to do a quick summary on genomes. So what is a genome, a gene, an mRNA and a protein. And the best would be to have that in one figure, an easy to understand. I found this : http://dnamismatch.com/Test/wp-content/uploads/2013/07/Genes-and-genomes.png
Anyone knows other resources ?
Thanks

I'd go with using an analogy - e.g. The genome is a cookbook, each recipe is a gene, the cook is the mRNA and the product is a protein (perhaps not entirely analogous but you get the picture) - you have to find something that can adequately explain all of the four parts in one coherent and correct example. Personally I think the figure you've shown is poor (aesthetically and only roughly illustrates what genomes and genes are, not proteins or mrna)

Some info about the topic of the talk might be helpful in guiding answers here

the topic : retrovirus and cancer . So I have to introduce genomes and genes in the case of retroviral integration

There can be different ways and giving analogies would work. What is the educational background of the audience and how much time do you have for your presentation?

the audience consists of both biologists and no scientist at all.

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How does optogenetics work?
I am aware of the post here 'Optogenetics - How do microbial opsins work?'
however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to produce these light-sensitive molecules in optogenetics, and how genetically engineering the neurones is even a usable method considering it seems you would have to genetically engineer the neurons one by one. So I suppose my question is: in the trials run of optogenetics so far (with mice), how where the neurons made to respond to the light stimulus?
Also, I was wondering whether the principle behind optogenetics- controlling calls with light- could be used for other treatments e.g. to kill cancer cells?
My biology knowledge is limited to A-Level (final year of high school), however I really want to understand this topic thoroughly, so detailed but not too technical answers would be much appreciated! Thank you!
EDIT: I just wanted to add two more quick questions...

Are the light-sensitive molecules (which I now have read are channelrhodopsins) present all along the axolemma, or just the membrane of the soma of the neuron? (I hope I used those terms correctly!)
Wikipedia says that these channelrhodopsins are non-specific (with some exceptions: The L132C mutation (CatCh) increases the permeability for calcium and generates very large currents.[17] Mutating E90 to the positively charged amino acid arginine turns channelrhodopsin from an unspecific cation channel into an anion channel. This chloride-conducting channelrhodopsin (ChloC) inhibits neuronal spiking when illuminated with blue light.[18]). How then can these channels work, if any cation can diffuse any way through the channel?

I'm not too familiar with optogenetics in neurons, but I've seen part of a talk about it, and I think they had to run fiber optics through the brain to get the light to specific areas. I assume getting light to other sites in the body would also need fiber optics, if it wasn't close to the skin.

Fiber optics are not needed :) will try writing up an answer later. So to grasp your level of knowledge, do you know the following terms: viral vector, transformation, photoreceptor, neuron, retina, optic nerve. You can just call out which you don't know.

@ChrisStronks Unfortnately I am unfamiliar with several of those terms! Viral vector (although I am guessing it is just the inactive virus that injects the DNA strand into the cell), transformation, photoreceptor (but guessing that these are just light-sensitive cells like rods and cones. I don't really know how these work though...).

Expecting your answer @ChrisStronks. Please talk a little about it's uses too

@ChrisStronks so if you have the right wavelength of light at high enough intensity you can just beam it through the body? Maybe the fiber optics were used to get specific areas of the brain.

Short answer

Optogenetics can be used to make cells responsive to light. One striking use of this technology is to restore vision in the blind by making the surviving neurons in the retina light-sensitive. This can be done by transfecting the retina with genetically engineered viruses that induce the expression of bacterial channelrhodopsin proteins in retinal neurons.

Background
I will explain optogenetics by focusing on one of the most striking applications: to make the blind see. In humans light is sensed by photoreceptors in the retina (see further reading #2). Rods infer grey-scale vision (i.e., night vision), while cones provide color vision when there is enough light available. Rods and cones contain light-sensitive proteins: the photopigments. The pigment in rod photoreceptors is called rhodopsin, in cones they are referred to as cone pigments, which are used for color vision. When light hits the rods and cones, the photopigments catch the light and activate a cascade of second messenger reactions, eventually causing hyperpolarization of the membrane. This hyperpolarization in turn activates secondary neurons in the retina, which eventually carry the receptor signal to the brain, where it is processed and used to generate a visual percept.
Light sensing across single-celled and multicellelar animals is mediated by two large families of proteins: the opsins. Opsin genes are divided into two distinct superfamilies: microbial opsins (type I) and animal opsins (type II). The rohodpsin and cone pigments found in humans belong to type II. Among other differences, type I opsins are bound to ion channels, while type II is not. Type II opsins therefore need a battery of intracellular second messenger molecules to operate. In contrast, the type I opsins, being channel proteins, directly cause intracellular changes by changing the membrane potential upon activation due to ion flow. Type I opsins, being channel proteins are referred to as channelrhodopsins.
In retinal degenerative diseases such as retinitis pigmentosa (RP) the photoreceptors degenerate and patients eventually loose their vision. The secondary neurons in the retina, however, partly survive. As explained above, these secondary neurons are responsible for processing the photoreceptor signal and sending it to the optic nerve. Hence, although RP patients miss the photoreceptors, the rest of the visual pathway is ready to rock! Hence, somehow these neurons should be activated. There are a battery of approaches to do just this. Retinal implants activate the neurons directly by electrical activation (see further reading #3).
Optogenetics (Fenno et al., 2013) is another approach where the secondary surviving neurons are made photosensitive, thereby bypassing the photoreceptors by turning the secondary neurons into photoreceptors. The neurons are made photosensitive by making them express channelrhodospins. This is done by injecting a viral vector into the eye such that the virus infects the retinal cells. Instead of a viable virus, however, it is tinkered aound with and the only thing the virus does is incorporate the channelrhodopsin into the genome of the neurons, which start to express it.
Channelrhodopsins are cation channels, and therefore, upon light activation, they allow positively charged ions (notably Na+, but also Ca+) into the cell. This depolarizes the neuron and can induce action potential firing (see further reading #1). Action potentials is the neuron way of transmitting signals to the brain. Hence, by activating the secondary neurons through channelrhodopsin transformation, they start sending light-induced neural activity to the brain. The brain will handle this input as if evoked by photoreceptors and hence will interpret it as light-evoked visual stimuli.
With regard to cancer: It has been shown that expression of channelrhodopsin and illumination of whole-mice resulted in diminished subcutaneous cancer cell counts (yang et al., 2013).
With regard to your first added question: dependent on the exact peptide regulatory sequences added to the protein, or by using viral vectors specifically targeting axons, expression of channelrhodopsins can occur wherever one likes.
Your second added question: Cation channels activate neurons, anion channels inhibit them. This means you can play around with different variants to control neurons at will.

References
Fenno et al. Annu Rev Neurosci 2011;34:389–412
Yang et al. Cell death and disease 2013;4:e893

Further reading
 1. Action potentials and neurons: how-do-the-brain-and-nerves-create-electrical-pulses
 2. Photoreceptors: parallels-between-pixelized-image-and-the-human-retina
 3. Retina and retinal implants: does-the-retina-encode-visual-information-like-a-bitmap-or-an-svg

Too good! Real nice answer.

@OneFace - Thanks! Your appreciation is welcomed - as you indicated elsewhere - the answers that take most of your time get the least upvotes, at least so it seems lol

Nice answer. But you would still need fibre optics to activate the specific neurons. In the comments you said it is not necessary. Can you clarify that point?

@WYSIWYG If you use this technology for retinal repair, then light that enters the eye will activate the transgenic cells that express channelrhodopsin

@OneFace only in the retina. Optogenetics is usually (till now) used to study neurons in the brain; to stimulate those neuron optical fibres are required. However optogenetics can be used in other cells too by using opsin-GPCRs. Mitochondia expressing rhodopsin has been shown to produce ATP in the presence of light. See this post.

Addition to the previous answer.

How to express channelrhodopsins in neurons?

Other than the method involving direct viral injection, as described in the previous answer, these proteins can be expressed in specific cells by making transgenics (by using promoters that will express the downstream gene in only specific cells).

How does it work?

When a neuron is made light sensitive by ectopic expression of channel-rhodopsins, then they can be made to "fire" (generate action potential) by simple illumination. Fibre optics are used to illuminate specific neurons in the brain. See the image below:

Are the light-sensitive molecules (which I now have read are
  channelrhodopsins) present all along the axolemma…

They would be expressed everywhere but their expression on the axons can be limited because of myelination. It is possible to make certain proteins express in the dendritic region. This requires localization signals called zipcodes (this process is still not understood very well).

How then can these channels work, if any cation can diffuse any way through the channel?

Chr2 can conduct Na+, Ca2+ and K+. Its conductivity for sodium is higher than that for potassium. When the channels open the higher inward flow of sodium would trigger action potential (AP). Moreover Calcium also helps in strengthening the AP. Though the channel can conduct Li+, the ion is not present in the extracellular fluid. Usually the nonspecific channels are not used.

Also, I was wondering whether the principle behind optogenetics-
  controlling calls with light- could be used for other treatments e.g.
  to kill cancer cells?

Light (as lasers) is used for killing cancer cells but it does not involve optogenetic techniques. You would need to genetically modify the cancer cell first.

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Two mice heterozygote and black are reproduced. Find the probability of getting the filium dark and heterozygote
Well, here's what I did: P: Aa*Aa
F1: 1/4 AA, 1/2 Aa, 1/4 aa, SO the answer is 1/2, but out teacher did this:
AA(1)    Aa(2)    aa(1) and she said we divide the number of filium for the phenotypes number and get 2/3. This is the probability. I don't get it.

why didn't you ask your teacher to explain when you didn't understand

You know in India it is very unlikely a student will ask a teacher about something (s)he does not understand. In many cases I have found out that the teachers themselves don't properly understand what they teach. The language is a huge barrier @WYSIWYG

@OneFace (a.k.a CRags :P) That is a problem with the education policy. We cannot do anything about it. We also cannot do a background search of a user before answering the question. Plus, you cannot generalize this for an entire country.

What is a "filium"? I would assume Latin for "children", but it isn't even correct Latin.

Okay so in your teachers answer there are four offsprings. . You used all offsprings when you made the division so 2/4 = 1/2.Your teachers 2/3 comes from the fact that 3 out of four is black, but only 2 out of that 3 black is heterozygote so 2/3 is good by this logic. I think that your teacher's logic faulty because you have to take into consideration all the offsprings. Basic genetics and Mendel's law tells us that crossing two heterozygotes with independent alleles result in a 3:1 ratio in phenotype separation in the next generation with 1:2:1 genotype separation -- that is what basically both of you have wrote. The fault is in the getting the probability - basic maths tells us that in an independent experiment, the probability variables have to sum up to one. In your teacher's logic this basic rule is not kept, because finding homozygous non-dark offspring would be one (there is only one non-dark filium and that one is homozygous). So by this logic all filium are non dark-homozygous, but then what about the others. I hope you see the problem with that logic.


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Why does cucumber skin kill ants?
I recently read that cucumber skin is an effective repellent for some ants:

Set out cucumber peels or slices in the kitchen or at the ants' point of entry. Many ants have a natural aversion to cucumber. Bitter cucumbers work best.
Source: Natural Insect Pest Control

See also: How to Use Cucumbers to Prevent Ants from Entering the Home
But when I tried it out they died instead. What made this happen?

Please include the source of your information. Where did you read this?

There you go @OneFace

It's always good to include the source, especially when asking about things that are not commonly known.

Under what circumstance did the ants die? If possible, post a photo of the dead ants near the cucumber skin.

@MarchHo Sorry , cant post a photo since this was done a few days back .

Was an edit necessary ?

I think the ants aren't killed but they are forced to move out because the Cucumber slices are just disabling the ants pheromone tracking system there by forcing them to withdraw from the location.

Cucumber contains a compound called trans-2-nonenal (reference 1 and reference 2) that repels insects. This particular compound (reference) has can also be used in insecticide foams for repelling ants (reference)


text:
What is the minimum eye?
What is the minimum eye which confers some evolutionary advantage?
By minimum I mean anything less than this has no advantage whatsoever and therefore is not favored by natural selection.
By eye, I mean not just a light sensor but also infrastructure which converts the light stimulus into an advantageous response.
Ideally would like a clear unambiguous before/after case especially on the infrastructure between the mutated protein and the cell's response mechanism which translates this into a survival advantage.
(I assume Opsin proteins floating around the cytoplasm by themselves confers no advantage without some kind of other infrastructure)
please also provide an estimate of the number of coordinated DNA base pairs which needed to change to confer this advantage so that a proper probability estimate can be done.

An opsin protein attached at the membrane of cells exposed to light with a standard biochemical cascade allowing for example to regulate the expression of a gene will potentially be beneficial. Would this answer your question?

@Remi.b wouldn't this need a custom cocktail of chemical cascade to convert the light impulse to something useful (we are after all talking about a cell without an eye). The details of this cascade is really my question. which includesalso the details of how the impulse would be converted to something advantageous

@Remi.b will check out these links. thanks. looks complicated. wish there was something which addresses this specific question.

I moved my comments into an answer. I think that all the links directly address your specific question. Or I may not understand your question. Maybe the last link on the structure and function of the opsin gene is the information that you're specifically seeking for. I am not sure.

I think "eye" needs to be quite strictly defined before answering is possible.

@ChrisStronks I agree. Not knowing what the OP is meaning by "eye" made the answer difficult to write and make it quite generalist and approximative. But I am not sure what the question is anyway. I think the OP struggles with how an opsin protein works.

@Remi.b yes agreed totally. I upvoted your answer as I agree that your description is the simplest *light sensor *, however, an opsin system alone may not be categorized as an eye.

@ChrisStronks right. you'd need other infrastructure converting it to an sight sensation/reaction which is really what this question is about

Is this question inspired by that Darwin quote that creationists seem to love?  Because if so that was totally taken out of context, see here.

@augurar no it was my own thought. can be applied to the emergence of all new information. not just the eye

I think that you are expecting for some complicated system while such things are not necessarily involved. You basically just need a protein that is light-sensitive and some cascade of signal transduction. A light-sensitive protein is just a protein which conformation is changed in the presence of photons of a given wavelength. This cascade of signal transduction can be very standard. It doesn't need to be anything extraordinary.
Consider a mutation that turns a given protein into a light-sensitive protein. Such mutant protein could easily still activate the same cascade (and eventually regulate the expression of the same gene) and may eventually be beneficial. A visual signal (presence/absence of photons of a given wavelength) directly affect the conformation of the protein which in result can activate a whole cascade. The cascade doesn't need to have evolved after the protein had acquired the ability to response to photons. You may want to dive into the details of how the structure and function of the opsin proteins.
This article describes how an ancestral non-light sensitive protein (coded in GPCR gene. The proteins are also called serpentine) evolved into a light-sensitive protein (opsin). The article also link to other articles that discuss this transition.
There are several types of light-senstive proteins in different kingdom, including plants and bacteria that don't have nerves.
You can learn more about the cascade of transduction on wikipedia (here or here for example). You may want to learn more about opsin proteins and learn more about light-sensitive proteins.
Wikipedia page: Evolution of eyes > Early Eyes will probably interest you as well. Depending on the definition you use for "eye" (note, "eyes" have evolved independently 50 to 100 times), Planarian might be a good example of a species that have a primitive eye.

thank you but I am looking for an actual working example. either way, thanks for the links

Are you looking for a species that has a very primitive form of "eye" (eye taken in the strict sense of animal eye I suppose)?

no i am looking to understand what is involved in jumping from no eye to minimum eye

Do the sentences (in my answer) not answer your question? Consider a mutation that turns a given protein into a light-sensitive protein. Such mutant protein could easily still activate the same cascade (and eventually regulate the expression of the same gene) and may eventually be beneficial.

There is now a small paragraph (the second paragraph) about how a single mutation that offers the ability to sense light might be beneficial. Let me know if it still doesn't answer the question.

if you could provide a detailed example yes. but merely stating this does not. need something unambiguous. something scientific which can be put to the test

I linked an article that describe a specific example (see edited answer). Does it answer your question?

will need to research all these links. thanks. ideally would like a clear unambiguous before/after case

If I may say something that has nothing to do with the subject of the discussion; it sounds like you don't need this info for research purpose or whatever (otherwise the question would have been much clearer from the beginning) but that you arrived on this site almost ready to refuse any explanation one could give you. People who does that often end up protecting their first opinions toward any explanation by digging always further a possible way to refute the evidences even going to the philosophy of knowledge (or of logic). I'd advice not to make the mistake to be "primarily opinion based".

Enjoy the readings!

I have a hard time to understand what you would call a "clear before/after scenario". I think you either expect a an observation with a methodology that one with very little knowledge in biology can understand (in which case, we could sum up this point of view to "I don't trust your answer because I am not able to understand your answer") or an observation where the mutation would naturally occur behind our eyes, which is of course extremely unlikely to ever happen. But in the second case, I don't really understand what difference that would make.

I don't see how this answers the question. I agree that it is possible for one protein to mutate into another. What I am asking is about the other infrastructure which translates the light's effect on the protein into a minimal sight response. regarding what you wrote that the existing cascade could be reused, can you provide details or better yet empirical evidence for this? ex an experiment where a microorganism without any kind of sight had opsin proteins injected or mutated in its cell menbrane and this offered minimal sight. without this your answer is useless to me. but thank you anyways

i also dont see how this answers the question. the OP is asking for a minimum eye with the minimum accompanying infrastructure. maybe this should be a comment.

@user813801 On one hand the OP is asking for the minimal number of changes for an "eye" to be beneficial. I showed that very few changes can lead to sensitive abilities. Now if the OP were not to consider the thing I described as being an eye (but he seems to not complain about that), the thing I described would still makes sense in order to describe the adaptive valley that the OP assumed to exist between having no eyes and having an eye. I would agree though that the absence of definition of what is an eye make the question confusing

if you dont understand the question, then clarify before giving a bunch of links to peripheral issues

@user813801 Criticisms about the sense of the questions have been made below the question and there are currently 4 lose votes. I prefer avoid editing the post myself to clarify it as I am afraid the OP would feel like I change the sense of its post. I just thought I would do my best and give an answer to a somehow unclear question.

the OP made changes to the question to address all those points

A mutation that lets a non-light-sensitve protein be light-sensitive would already have all the necessary infrastructure, since it would still have whatever cascade the original, non-light-sensitive protein used.  Generally speaking, no additional infrastructure would be needed.

the article you reference says: "the origin of phototransduction in animals MAY have involved the alteration of only a single component...Taken together, these data support a view that the origination of animal phototransduction, and by extension of animal vision itself, involved the evolution of an existing CNG-based cascade into a functionally new cascade, founded by a novel opsin lineage of light-sensitive G-protein-coupled receptors." how much change is this? please give as much details as possible. thanks

Please continue this discussion in chat.

Comments are not for extended discussion; this conversation has been moved to chat.

A relatively simple proto-eye is the pineal gland. It has been considered to be the third eye and it is involved in circadian rhythms in man, it is involved in thermo regulation, and in reptiles and amfibians it is in fact directly light-sensitive.
However, it is not an eye as such, because the pineal does not convey topographical information about the environment to the brain. It is more of a light sensor in reptiles and amfibians. However, it is a sensor embedded in the central nervous system of higher organisms including humans. As such, it is not just a light sensor, but an endocrinic organ involved in the light-based entrain of endogenous circadian clocks present in various organs. It has been implicated to be an integral part of the visual system in early life:

hypothetic four-eyed protovertebrate. Source: Vigh et al., 2002
The hypothetical system in the picture is not so much different from the lancet fish today, a 'living fossil'. In early life, and reptiles and amfibians today, the pineal is directly light-sensitive and thereby entrains the circadian clock directly via endocrinic functions. Synchronizing the circadian clock helps organisms to adapt to the environmental light periods, in other words prepare diurnal creatures to wake up in the morning and get ready to hunt etc. Hence it aids survival of various species in different biotopes (Vigh et al., 2002). In humans and other mammals with a dense, solid skull light-sensng is taken over by the retina, as the skull prevents admission of light. Here the pineal has only an endocrinic function receiving afferent input from the eye.
Reference
Vigh et al., Histol Histopathol 2002;17:555-90

thank you. can this structure be useful if it were simpler? if yes, then it is not a minimum eye.

It is useful in organisms living today, such as for synchronizing day/night cycles or for either moving towards areas that are likely to have food or moving away from areas that are likely to have predators.

@RayS. - the pineal gland is the most simple structure I know that has been called an eye, but is far more rudimentary than the eyes that re-construct the visual environment. To me, it is more than a molecular light sensor (it is an organ), but its light-sensing capabilities are not such that it generates conscious perceptions of the environment.


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Divalent cation binding to calmodulin
I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I added 2 µl of calcium (2 mM), magnesium (2 mM) and manganese (2 mM) ions respectively to three reaction mixtures and had a control that was made up to an equal volume with Tris-HCl. All reaction mixtures were made up to 10 µl with Tris-HCl. Here I ran into a problem with the waterbaths and the reactions couldn't be incubated at 37 degrees Celsius.
After I added the loading buffer to each, I added the 4 reaction mixtures to the polyacrylamide gel and electrophoresed for 45 minutes at 150 V. After this I placed the gel in Coomassie Blue stain for 20 minutes.
After the destaining process, I reviewed the gel to find that the calmodulin in the 4 lanes had migrated the same distance. I had expected the EDTA control to have migrated the furthest on the gel, with Ca2+ and Mn2+ migrating similar distances due to their similar ionic radii; making it a good substitute for the binding to the calmodulin. I was unsure of how far the Mg2+ would travel as I thought it would have a lower affinity to the calmodulin due to its binding to the N-terminus rather than the C-terminus. However, I was wondering if this was negligible in the absence of Ca2+, although now I can't be sure due to the results of the gel.
I was wondering what errors in the experimental design or process could have resulted in this? And if the experiment was run correctly, what results would be expected?
The first image is the result I was expecting. The second is the results from my gel electrophoresis.

Why add EDTA if you want calmodulin to bind ions? Are you expecting just ion binding to influence migration rate?

Binding of a cation would not change the mobility much so as to be detectable by electrophoresis.

If you want to sequester the bivalent ions, you need ways more EDTA. It complexes an equivalent amount of ions, so 1mM EDTA complexes 1mM of calcium (for example). If you EDTA solution is 1mM, but your ion solution is 2mM, this will never work.

Apologies, edits have been made to include the concentrations. EDTA was added under the instruction of my supervisor, which I did question at the time. I was under the impression that the migration would be detectable through the existing literature.

And with the EDTA being added to each reaction mixture was to sequester any divalent ions from the protein before the target ions (Ca2+, Mg2+ and Mn2+) were added respectively. I thought the ion binding at this step would not be interrupted as the ions are in a two-fold molar excess of the EDTA, and therefore could bind calmodulin and cause its retardation? Which would be picked up on the gels?

What article is that figure from? Also, you should destain your gel.

You cannot see a mobility shift in SDS-PAGE (even in this picture that is claiming so). Shift in native-PAGE is due to conformational changes upon ion-binding. Moreover it is unlikely that an ion remains bound to a protein in denaturing conditions of SDS-PAGE.

The change in gel migration distance is due to the conformational changes due to the binding of the ion, and have nothing (detectable) to do with the ionic radius of the ion.
The left image shows calmodulin with no ligand bound, and the right image shows it with calcium and peptide bound to it.

As you can clearly see, the unbound calmodulin is significantly thinner, and therefore can migrate faster through the gel. The change in charge on the protein due to cation binding in native PAGE may also affect the result.
Since the calmodulin conformational change is enhanced by both a peptide and calcium cations, as well as its phosphorylation state, it would be reasonable to investigate the contributions of these factors to your result. Reading the original paper again to see what you missed the first time may also be helpful.

Yes the left panel is apo-calmodulin, but Ca(II)-calmodulin also resembles structure in the left panel (with minor structural adjustment). The major conformational change on the right panel is a result of peptide binding, which is not part of experiment in the question.

@SYK I am pretty sure that peptide cannot bind without calcium also binding.


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Possible to remove accumulated haze on fluorescence interference filters?
I have a few different fluorescent microscopes, the two that use Mercury  lamps are older than 7 years. I notice on those that the thin film filters in the filter cubes (green, red, blue) have accumulated this haziness. Both the excitation and barrier filters seem to have this, more so on the ex filter and it's not present on the dichroic.
I've always referred to this as the filter being "burned" and my rational is that it's from the heat & intensity & low wavelengths from the Mercury lamp.  But in all honesty I don't know what it is or if it's removable and if so how? I would like to see if removing it improves my image clarity.
I know a picture would help here and I'm having trouble showing it but will keep attempting and add it to an edit for this question. However I have seen this on many microscopes if you have one with a merc arc lamp and it's getting up there in age take a look at the filters on it. Let me know if you see this too.

In fact, filters can be damaged by heat. However, newer filter coatings are less prone to heat damage [details].
For the barrier filter, it's less likely to be heat damage. The older/less expensive filter coatings do degrade slowly over time and have to be replaced.
So I would guess that the haze represents permanent, non-removable damage to the coating. You should replace the filters with hard-coated filters, which are more durable if you do ever need to clean them for some reason.
Just to be safe, you may want to get a heat filter between the lamp and the excitation filter. One caveat with the heat filter: if you are using near-IR dyes (Cy5/AlexaFluor 647) check the transmittance of the heat filter to make sure it doesn't interfere with the ~640 nm excitation.

Its probably not from heat.  Filters are basically a glass substrate with some ionic compound deposited in thin layers.  These won't oxidize at reasonable temperatures, and furthermore since you have it on the emission filter as well, its even less likely to be from the source.
More likely its just accumulated organic material from the environment.  7 years is a long time, and microscopes are exposed to a lot of chemicals and other substances which can gradually build up on optical surfaces.
Most vendors have a recommended way of cleaning their optics, but usually it involves lens paper or lint free swabs and methanol (or sometimes acetone for more durable stains).  You must be very careful though, as you do not want to scratch the filter.
Semrock for instance has a detailed guide here:
https://www.idex-hs.com/resources/resources-detail/how-to-clean-optical-filters

Thank you for this I haven't considered that strongly. However other glass on console is fine however. The excitation filters are considerably more burned than the barrier ones on the cubes. Your right about the time however. I have tried solvents but they don't remove it. I need/will get a pic up for this.

Thats interesting.  I haven't seen something like that, but if even acetone won't clear it, then I think you'll have to replace it.  Possibly its just a poorly made filter that degraded over time.

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The meaning of RNA-seq data
many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition.
As far as I understand, RNA-seq data is the complete RNA information in a cell (or all of the cells) of a species that is extracted at a certain time.
Am I correct with this definition? If yes, does this mean that by extracting all the RNA information ones knows all the RNA sequences in that species (like AUGGUCAUCAG....)? Or does it mean I have the RNA, but not the sequence?

@terdon could you explain it if it is possible ?

RNA-seq data usually provides a snapshot in time of the transcriptome of that which is being sequenced. Single-cell sequencing is possible, but less common than RNA-seq on a sample (containing many cells).
You are correct that RNA-seq provides one with knowledge of RNA sequences, like AUGGUCAUCAG and so on. However, one will not necessarily have information about all possible RNA sequences from a particular species. Performing RNA-seq on the same cell type of a species at two different time points, or two different cell types at the same time point, may result in different profiles for the RNA sequences you get back. It depends on which parts of the genome are being expressed by the cells in a sample at the time of RNA extraction.
The data one gets back from RNA sequencing depends on the technology and company used. Typically, RNA-seq involves using a reverse transcription step so that the sequence data you get back is actually reported as the cDNA version of your original mRNA transcripts. Usually one gets a (very large) file of sequencing 'reads'. One can either then 'assemble' these directly to form a snapshot of the transcriptome or one can map them to a known reference genome. One of the main benefits of RNA-seq is that we learn not just what the sequences of the RNA molecules are, but also their relative abundances within the sample. Knowledge of this can be particularly useful in testing or developing a large range of biological hypotheses.

+1, being able to know relative RNA abundances is an important feature

RNA sequencing occurs when you perform an RNA extraction and then sequence them, which usually involves fragmenting them.
You do in fact know all of the sequences for all of the RNA molecules that are being sequenced. I can't see an interpretation that does not result in you having the sequences of the molecules, what with it being called "sequencing" and all.

we start to know sequence of the RNA after sequencing right ?

Yes, you will only know the sequence of the RNA after sequencing. Prior to sequencing, you will only know they are fragments of RNA.


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MTHFR recessive alleles and B-vitamins
I know that being heterozygous or homozygous recessive for the MTHFR gene prevents that person from being able to process and use folate and B-12. It causes an unhealthy level of homocysteine to accumulate in the bloodstream which can cause more serious problems. Taking methylated B-vitamins, specifically Methylfolate and Methylcobalamine will prevent homocysteine from building up, but I am not sure why.
Can someone explain how this process works? I am wondering how the body uses folate and B-12 (cobalamine) normally and how the recessive MTHFR genes interfere with this process.

Folate, or rather its active form tetrahydrofolate (THF), is a coenzyme that carries a 1-carbon group. The carbon group can occur in various redox states: CH3-THF (methyl-THF), CH2-THF (methylene-THF), CH-THF (methenyl-THF) or CHO-THF (formyl-THF). These can be interconverted by a variety of enzymes, and are used by cells to synthesize a number of products, including nucleotides and methionine.
MTHFR (methylene-THF reductase) converts CH2-THF into CH3-THF. The CH3-THF form is the most abundant folate in blood, and is therefore considered the "transport" form of folate. CH3-THF is also the form used to synthesize methionine, in the reaction
CH3-THF + Homocysteine $\rightarrow$ THF + Methionine
catalyzed by methione synthase (gene symbol: MTR). This enzyme requires cobalamin (B12) as a cofactor. Actually, the reaction occurs in two steps,

CH3-THF + Cobalamin --> THF + CH3-Cobalamin
CH3-Cobalamin + Homocysteine --> Cobalamin + Methionine

Loss of MTHFR leads to deficiency of CH3-THF, causing methionine synthase to run out of substrate, and homocysteine to accumulate. Lack of the B12 cofactor also blocks methionine synthase, and it should be clear from the reactions above why supplementing with either CH3-THF or CH3-cobalamin can alleviate the problem (at least in theory). I would guess the phenotypes seen in this condition is mainly due to lack of methionine though, rather than excess homocystine, since methionine is required for a variety of methylation reactions in cells.
This is a simplified view. There are many other interactions between B12 and folate; for example, the methinine synthase reaction is needed for cells to take up and store folates, and therefore B12 deficiency can create a folate deficiency as well. See for example http://www.ncbi.nlm.nih.gov/pubmed/6115113 and http://www.ncbi.nlm.nih.gov/pubmed/10466189 for further reading.


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

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

@MattDMo You should convert that into an answer.

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

This sounds a bit too much like a homework question

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

Introns are not included in the polypeptide sequence.

This is rather a comment than an answer.

Now its an answer....


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Retina Transplant Difficulties
Why is retina transplant not as easy as the normal eye donation and transplant (I think the latter involves the cornea ) ?
This says that a new method has come up but why isnt the process similar and simple as the normal transplant ?
What are the difficulties in retina transplant ?

This is a diagram of a cross-section of the cornea:

It is an amazing but relatively simple structure, the shape of which is responsible for about 60% of our focusing power, and the clarity of which allows light to enter. It is avascular (no blood vessels), and the non-mylenated nerve endings are very tiny and present in the epithelium.
Transplanting this relatively simple tissue is easy (well, not do-it-at-home easy, but easy.) The only problem with cutting all those nerve endings is that the new cornea will feel nothing if there's dust in the eye, etc. This is a problem, but nothing compared to blindness.
This is a diagram of a cross section of the retina:

As you can see, it is not nearly as simple as the cornea. The nerves (to the left: yellow, light blue, medium blue and darker blue), which collect information from the rods and cones (pink and purple) are very numerous, and absolutely vital to the ability of the brain to interpreting information from these photoreceptors. Therefore, a cut piece of retina immediately loses the ability to send any information to the brain. To transplant it into an eye with a damaged retina would do nothing to improve vision. Also, it is not easy surgery. It's very difficult.
What has been called "retinal transplants" in the recent past have been tiny pieces of embryonic retina, about...

4 millimetre square of retinal tissue, complete with retinal progenitor cells and the retinal pigment epithelium that nourishes them. The tissues were placed in the sub-retinal space beneath the fovea, the area of the retina responsible for sharp central vision.

Note, they didn't try to connect nerves or blood vessels. And, it came from an embyro (so the supply is a problem.) The improvement in vision - which was significant in 7 out of 8 recipients (one patient going from 20/800 to 20/160) - is not long lasting, and believed to have been not from the transplanted retina connecting to the existing retina, but from the release of growth factors from the embryonic tissue improving the health of the degenerating retina.
The newest in "retinal transplants" (which might be better called stem-cell-supplied growth factors implanted in the retina) actually derives from the patient's own stem cells:

A Japanese woman in her 70s is the first person to receive tissue derived from induced pluripotent stem cells, a technology that has created great expectations since it could offer the same regenerative potential as embryo-derived cells but without some of the ethical and safety concerns. [No news yet on whether it worked.]
In a two-hour procedure... a team of three eye specialists lead by Yasuo Kurimoto of the Kobe City Medical Center General Hospital implanted a 1.3 by 3.0 millimetre sheet of retinal pigment epithelium cells into an eye of the Hyogo prefecture resident, who suffers from age-related macular degeneration, a common eye condition that can lead to blindness.

TL;DR: It's not as easy as taking cadaver retina and replacing a patients retina (that would result in immediate and permanent blindness). Whereas corneal transplantation is very easy.
Corneal Innervation and Cellular Changes after Corneal Transplantation: An In Vivo Confocal Microscopy Study
Retinal transplants see fleeting success
Japanese woman is first recipient of next-generation stem cells

Great answer +1 - but - was the transplanted material effective? Just curious :) Interesting stuff!

@AliceD - D'oh! Sorry, I've edited my answer.

That was great . +1


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Mitochondria variability per tissue in humans?
I would like to know the distribution of mitochondrial content per tissue type in humans. I understand the simple metric that energetically active or energy requiring tissues will have more mitochondrial content, however is there any study/link for a more quantitative estimate ?

Welcome to Bio.SE. You ask for mitochondrial content per tissue type? Are you asking for help in searching for a proper database or are you expecting folks to sum up every tissue type in man along with its mitochondrial content? I would suggest to specify your question.

check this out. Not able to access it as of now.

@WYSIWYG I think we convergently cited the same paper :P

@MarchHo perhaps. This is another one. Can't access this one too as of now.

BioNumbers is a great site to answer this kind of question.
This search produced a link to this paper , which has measurements for mitochondria per cell for multiple species and cell type.


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Can all biological processes be understood as computations and studied as such?
Can we understand a cell as an organic computational device? In that case the whole organism can be considered an ensemble of a large number of interacting computational devices?
If this is the case, biology can be studied using methods of graph theory, network theory, computation theory and complex systems theory.

The answer is YES, if you can do this, But you can't (at least currently) because your devices are not powerful.

If you abstract enough, anything cam be considered as a computational device. The issue with doing this with cells is the sheer number of variables.
For any given cell, the following internal variables exist:

Internal ion concentrations for dozens of ions of importance importance
Internal concentrations of hundreds or thousands of various simple organic molecules, including "raw" internalised molecules, various steps in dozens or even hundreds of metabolic processes, and metabolic end-products and by-products.
Internal concentrations of hundreds or thousands of different proteins and other complex biological "mechanical parts", as well as the states of these "parts".
The physical state of the cell - stretched, contracted, relaxed, hot, cold, etc.

This list is not exhaustive.
It's also worth noting that the above variables may also exist for multiple separate "compartments" within the cell; vesicles, the endoplasmic reticulum and the golgi apparatus being three which come to mind immediately.
The other issue is that cells do not exist in a vacuum; the external environment plays an important role in their functioning. The human body is at any one moment existing in direct contact and interaction with the following extracellular environments:

The atmosphere (Mainly, but not only, temperature exchange)
The air within the respiratory system, including nose and mouth
Stomach contents
Small intestine contents (which would need to be considered in several segements, since the nature of the interaction changes along the path of the small intestine.
Large intestine contents
Blood
Cerebrospinal fluid (Fluid found "inside" the brain)
Extracellular fluid, or "tissue fluid" (A separate compartment for each small swatch of tissue in the body)
Lymph
Pleural fluid (Fluid surrounding the lungs; a separate compartment for each lung)
Pericardial fluid (A small amount of fluid surrounding the heart)
Joint capsule contents (A separate compartment for each joint)

...and the list goes on. Each of these compartments requires tracking of the same variables as individual cells.
This is yet further complicated by the fact that some of these compartments can't easily be considered as one big compartment, because of the importance of spatial relations. For example, the oxygen and carbon dioxide concentrations of blood (as well as the concentrations of other substances like alcohol) change centimeter-to-centimeter. Yet another issue is the fact that cells are not static in terms of their relations to each other; red blood cells move with blood flow, and experience turbulence and other effects, and other cells (like macrophages) are capable of "deliberate" movement in the blood and in tissue.
You would also have to account for physical disturbances - things like a stab wound or even a pinprick are ludicrously complex at a cellular level.
Of course, human beings are very complex organisms, and there exist much simpler organisms. You might be interested in OpenWorm, which is an attempt to computationally simulate Caenorhabditis elegans, a species of roundworm, at a cellular level. Doing so even for an organism as simple as C. elegans is a massive undertaking, as evidenced by the fact that even with the contributions of dozens of experts in their fields the project has been ongoing for some time and is yet to reach stage one.
The short version: Is it possible? Perhaps. Is it easy? Definitely not.

As a mathematician interested in biology I am very curious about informed answers, here I add mine, with the understanding that it is in no way complete and it might be very biased or ignorant as concerns biology.
We may understand a cell as a chemical and physics based program which runs itself. The cell is a computational device in the sense that the outcomes of its activity are computable functions of its inputs (a reasonable hypothesis), but more than that: at the cell level there is no distinction between the computer, the program which runs on the computer, input and output data AND the execution of the program. All is at the same level, i.e. every abstraction is embodied in a concrete chemical or physical thing.
This concreteness part adds, I believe to the difficulty, because the usual thinking in computer science is all about structuring abstractions, while in biology everything is ultimately at only one level: real, physics and chemistry embodied.
This is a claim which needs strong supporting evidence. Being a matter of principle, it cannot be proved rigorously, but it might be given a rigorous support by constructing simple proofs of principle models.
There are many computing models which are inspired by chemistry, therefore in return they can be seen as such proof of principles.
There are Chemical Reaction Networks and Petri Nets models which are more like structuring tools than real embodied models of computation, because they don't consider the structure of molecules (they are just nodes in a graph), nor the way chemical reactions happen (they are edges in a graph). They are very useful tools though and the description given here is very much simplified.
There is the CHAM (chemical abstract machine), G. Berry and G. Boudol. The chemical abstract machine. Theoretical Computer Science, 96(1):217–248, 1992. In this model states of the machine (imagine: a cell) "are chemical solutions where floating molecules can interact according to reaction rules" (cite from the abstract). In this model "solution" means a multiset of molecules, reaction rules are between molecules and they do not apply inside molecules. This is a limitation of the model because the structure of the molecule is not as important as the number of molecules in a species.
Another very interesting model is the Algorithmic Chemistry of Fontana and Buss. The main idea is that chemistry and computation are basically the same. The reasoning goes as following. There are two pillars of the rigorous notion of computation: the Turing Machine (well known) and Church's lambda calculus. Lambda calculus is less known outside computer science, but is a formalism which may be more helpful to chemists, or biologists even, than the Turing machine.  Fontana and Buss propose that lambda calculus is a kind of chemistry, in the sense that the its basic operations, namely abstraction and application, can be given chemical analogies. Molecules are like mathematical functions, abstractions are like reaction sites and applications are like chemical reactions.
The Algorithmic Chemistry is almost as closer as possible to be (proof of principle) answer to the question.
Finally I mention chemlambda, or the Chemical concrete machine, which is like Algorithmic Chemistry, but it is far more concrete. Molecules are graphs, applications and abstractions are molecules, chemical reactions are graph rewrites.
What is very interesting in all these models, in my opinion, is that they suggest that answering to the question "Can we understand a cell as an organic computational device?" is somehow relevant to the Computer Science question "How to design an asynchronous, decentralized Internet?".


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What is the mechanism behind tinnitus?
I seem to have come across two contrasting explanations for tinnitus induced by loud noises- i.e. damage to the hair cells in the cochlea.
On the one hand, I have read that damage to the hair cells results in them releasing excess glutamate, the neurotransmitter that carries the impulse from the hair cells to the neurones in the auditory nerve. This would result in the neurones constantly being excited, which I can understand would lead to constantly perceiving sound.
On the other hand I have read that when the hair cells are damaged, the auditory cortex is no longer receiving electrical impulses from the hair cells that detect those frequencies, and so the neurones start to fire (although I am not sure why no input would lead to neurones going off by themselves! Surely there must be some input to cause the initial depolarisation to cause an action potential?) and so you perceive a constant sound.
These seem to me to be two contrasting explanations. My only other guess on how these explanations overlap is that the excess glutamate being released causes death of the neurone, and therefore the neurones after that one do not receive and input and they start firing spontaneously (although again I would appreciate if someone could explain how lack of input results in neurones firing by themselves).
Thank you in advance!

Short answer

The exact mechanism behind tinnitus (ringing in the ear) is unknown.

Background
Of the two theories you pose here, to the best of my knowledge the second one is the most widely accepted. It is a generally accepted phenomenon that whenever neural systems are being deprived of input, they start seeking new input, or even generate it themselves. For example, blind folks rarely have no visual perceptions at all. In contrast, they often perceive spontaneous visual sensations. For example, many blind folks report perceiving a persistent grayish background hue. In other words, it is never black in the eyes of a blind person. They also often see spontaneous spots of light. The most striking example, however, being Charles Bonnet syndrome, where the blind person may perceive complex scenes with faces and objects (Bhatia et al., 2013).
In the case of tinnitus, the perceived sounds are mostly not complex, but repetitive and simple in nature ('ringing', beeps etc.). It is thought that the deafferented auditory cortex actively starts generating sound perceptions. However, many other explanations have been brought forward, such as spontaneous activity in the hair cells in the cochlea and spontaneous activity in the auditory nerve fibers (Luxon, 1993). I will sum up a list of potential causes mentioned in Han et al. (2009):
Peripheral mechanisms
(1) Spontaneous otoacoustic emissions
Spontaneous otoacoustic emissions (SOAEs) are small acoustic signals generated by the electromotile activity of outer hair cells (OHCs) in the cochlea. While normally inaudible, SOAEs may be perceived as tinnitus. Tinnitus due to SOAEs is mild and is more common in subjects with functional hearing.
(2) Discordant theory
Tinnitus may be induced by the dysfunction of damaged OHCs while inner hair cells (IHCs) are still intact. For example, intense noise and ototoxic agents initially damage OHCs in the basal turn of the cochlea, and subsequently, if continued or repeated, affect IHCs, because IHCs are generally more resistant to such damage. IHCs are the receptor cells for sound transduction. In contrast, OHCs work as mechanical amplifiers, enhancing weak sounds by providing up to 50 dB, which can be evaluated by measuring OAEs. When OHCs die, cells in the dorsal cochlear nuclei (DCNs) show increased spontaneous activity due to the fact that IHC input is relatively normal, but OHCs input is decreased due to damage to the OHCs. This spontaneous activity is perceived as tinnitus.
Spontaneous activity in neurons can occur through a host of mechanisms. Basically, a depolarization beyond a certain thresholds sets the neuron off to fire. In case of the disinhbited DCN neurons, the input from the OHCs is taken away. OHC input to the DCN is inhibitory,m as it is believed OHCs activate inhibitory interneurons. The exact mechanism is unknown, but a central inhibitory neurotransmitter is GABA. GABA can activate GABA-A receptors, that open up a Cl- channel, which in turn leads to Cl- influx into DCN neurons and hyperpolarization. When this input is taken away, you can imagine that DCN neurons depolarize and when this depolarization reaches threshold, the DCN neuron may increase firing Kaltenbach et al. J Neurophys 2002;88:699-714. Hence, as you question whether, in the absence of neurotransmitters, cells can fire action potentials, I say: **yes*. In fact, many neurons have spontaneous spiking activity, often with very regular frequency. These oscillating behaviors are often mediated by cation channels that gradually depolarize the cell up until its spiking threshold.
(3) Crosstalk theory
Nerve compression (e.g., due to a tumor) may cause artificial synapses to be formed between nerve fibers of the cochlear and vestibular nerve  (crosstalk). The breakdown of the myelin insulation of the nerve fibers may further enhance coupling. Hence, spontaneous activity in the auditory nerve may be generated through vestibular activity.
Central mechanisms
Some patients may still perceive tinnitus after the auditory nerve is transected. Hence, tinnitus in this subgroup must be caused by mechanisms located more centrally from the auditory nerve.
(4) Auditory plasticity theory
Damage to the cochlea enhances neural activity in the central auditory pathway, specifically in the temporal lobe in the auditory association cortex and inferior colliculus. This theory was touched upon further above in the first paragraph. Basically, when neural tissue is deafferented, it tends to look for new input or even generate activity de novo.
(5) Somatosensory system
The activity of the DCN is also influenced by stimulation of nonauditory structures and the somatosensory system has been implicated in development of tinnitus. Somatic tinnitus can develop as somtaosensory input may disinhibit the DCN.
(6) Limbic and autonomic nervous systems
The aforementioned theories cannot explain why some people suffer from tinnitus while others do not. More than 80% of those perceiving tinnitus for the first time do not associate the sound with any negative meaning and experience spontaneous habituation. However, if the first perception of tinnitus induces high levels of annoyance or anxiety by association with unpleasant stimuli or with periods of stress and anxiety, tinnitus might develop into a problem.

References
- Bhatia et al. Delhi Psych J 2012;15:423-4
- Han et al. J Clin Neurol 2009;5:11-9
- Kaltenbach et al. J Neurophys 2002;88:699-714
- Luxon, BMJ 1993; 306:1490-1
Further reading
- Action potentials in the absence of neurotransmitters: how-does-optogenetics-work

Thank you for your reply! I was just wondering: in the discordant theory section, you said that 'cells in the dorsal cochlear nuclei (DCNs) show increased spontaneous activity due to the fact that IHC input is relatively normal, but OHCs input is decreased due to damage to the OHCs' Do you have a link explaining how this spontaneous activity occurs? I just don't get how there can be an action potential firing in a neurone without some kind of initial stimulus... Thank you!

@21joanna12 - the Han article is open source and that one cites the relevant articles. Basically it is disinhibition playing a role. Also note that many, many neurons in the auditory system display spontaneous spiking activity.

I have read the Han article and looked up spontaneous activity of neurones and disinhibition, but I still cannot find an answer to my question. I simply do not get how an action potential can fire along a neurone without the initial depolarisation to reach the threshold voltage initiated by the neurotrannsmitter...

@21joanna12 - Other processes can depolarize a neuron. If you look at your other question, biology.stackexchange.com/questions/30203/…, you can see in the answer posted there that channelrhodopsins are also able to depolarize a neuron up to the point of spiking without one neurotransmitter being involved. I have explained spontaneous activity in the DCN in my answer.

There are neurons that fire by themselves. For example neurons in the RAS (reticular activating system) fire spontaneously by themselves and are responsible for arousal (alert non sleepy state).

@OneFace - Absolutely - many do. A background firing rate basically doubles dynamic range - it can also go down then. See my first comment here lol

I don't know if a neuron has this mechanism, but the electrical activity of heart which is also spontaneous is due to activity of special channels among which there is one called "hyperpolarization activated potassium channels". This channel activates when the SA nodal cells get hyperpolarized and causes sufficient depolarization to cause an action potential. @21joanna12

Yep Ih channels.


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Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?
I am running Paradigm on a matrix of mRNA expression. I read

Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM." Bioinformatics 26.12 (2010): i237-i245.

and also the help section in the web application. However it is not defined which format is best-suited for mRNA expression. Using log$_2$-ratios instead of log$_2$ data format gave me different results.
Thanks


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How do parrots stabilize their field of view without moving their necks while walking?
Based on my search online, I have found some theories which try to validate the activity of some birds (like pigeons) which involves moving their heads and neck while walking. These theories include - Assistance with balance, Providing depth perception, Sharpening their vision. Also, most of the studies state that similar to our eye movement, they need to move their heads along with their eyes to stabilize their surroundings visually.
If the above mentioned hypothesis is true, then how do some birds which do not move their heads while walking, manage to visually stabilize their surroundings and balance themselves?

why can't you just Google your question ?

I googled it, and found some possible reasons as to why the birds have to bob their heads while walking, but I did not find any theories about why some don't do so. Also, I think that finding interesting answers and rational discussions here on Stack Exchange from real knowledgeable people here on Stack Exchange can be quite enlightening for some people  with much less effort online. So repeating the same answer (which is found online),maybe in more detail, if the question wants something more, which is not found easily, it should be answered. Even if you say so, I will modify the question.

You can include your research results or any details you want to share in order to get a clarified answer, but a question with only two sentences and without even mentioning what you know about this so far, can make everyone believe that it is a home work type. Re framing the question may help. In future please feel free to use our Helpcentre

Edited. Is it OK?

@a.aniq This question is still so broad. Tell me do you have an answer for why the gaits of different animals are different or why dogs wag their tails but monkeys do not?


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Protein PTM site prediction
Is there any in silico analysis method to predict post-translational modification sites on a given protein?

There are actually a lot of these sites available, I have used some of the one listed below. Additionally there are some huge list of other services available in this field from ExPASy, you can find it here and the Center for Biological Sequence Analysis, which can be found here.

ExPASy - FindMod
The Eukaryote Linear Motif resource for Functional Sites in Proteins
Phosida


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How do we know if the folding@home project results are right?
Some of us are involved in the folding@home project, spending time, money, and resources.
I would like to know the answer to two main questions:

How do we know we fold it right? I mean, these models used in folding calculations. Is it probable that in a decade we will find that all these results are nil and void?
Do we have any example that these calculations were practically applied anywhere?

https://en.wikipedia.org/wiki/Folding@home, also http://www.reddit.com/r/askscience/comments/r93i6/has_foldinghome_really_accomplished_anything/

the reddit link is quite interesting. Apparently there is someone that used F@H results for real drug development

in silico modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally.
From the Folding@Home website:

Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions. Since then (2002-2006), Folding@home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others. In 2007, we crossed the millisecond milestone by simulating a protein called NTL9, and the 10 millisecond barrier in 2010 with ACBP.
More recently (2006-present), we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer’s and Hunntington’s Disease. You can learn more about our results and peer-reviewed scientific achievements on our Papers Page.

As they say, you should check out their research contributions for how it's being practically applied.
You may also be interest in this article for the science behind and prospects of protein folding prediction: Bowman GR, Voelz VA, Pande VS. 2011. Taming the complexity of protein folding. Curr Opin Struct Biol 21(1):4-11. At least try reading the conclusion for a less technical overview.

In the coming years, making quantitative comparisons between theory and experiment should further deepen our understanding of processes like folding and allow us to refine simulation methodologies and parameterizations.

Looking to the future, it will perhaps be in the application of this knowledge to numerous related problems, such as protein misfolding (relevant for numerous diseases [2]) and protein dynamics associated with function (such as enzymatic activity [74]), where advances in protein folding will continue to yield insight and impact for many years to come.

It is from the Taming the complexity of protein folding.  first quote talks about refining MD simulation, does it mean the folding we do now will be rejected because of more precise methods?

Second quote - that's what I asked in my original question, where the knowledge was applied? I would like to see a research of treatment for any disease which was based on folding data and then verified by other means

Research contributions - I didn't read all 118 items but looks like it contributed mostly to modeling. something like "lets fold to make folding better", this is not the outcome I expect from project of this scale

I will try answer your question directly.

How do we know if we fold it right?
A. If you're interested in only the end product pf folding -- the 3D structure, then this is the subset of the folding problem called the structure prediction (from sequence alone).
a. We can verify the structure experimentally by determining the 3D structures by NMR or crystallography. In fact, the CASP competition withholds newly solved structures and see which algorithm comes out the closest to the experimental structure.
b. Based on Anfinsen's hypothesis, we can calculate the free energy of folding, and the structure that has the lowest energy among the assembles is probably (but not necessarily) the folded state.
B. If you're also interested in how exactly the protein folds, including its folding rate, plausible intermediates etc.:
a. You can experimentally determine the folding rate although the computed folding rate is often off by several order of magnitude.
b. Some interactions, esp non-native interactions (aka. interactions between amino acids that are only observed during folding but not in the final folded structure) can be verified by carefully designed NMR experiment.

1b. Yes it is possible. Adjusting the force constants and force field in molecular dynamics (MD) (the core engine of Folding@Home) so that the calculations converge to consistent and sensible results is not trivial.

If you mean the method of calculation, then yes, MD has a wide range of application outside the field of protein folding. Besides the improvement in MD algorithm and necessary approximation, it also facilitates some advances on calculation on more specialized hardwares e.g. GPU and programmable array.

2b. If you mean the end of product of computation model, then probably no, but one example came close. A model determined purely computationally (aka. ab initio), although still not as useful as an experimental structure, was close enough to facilitate the experimental determination of that structure (by a method called molecular replacement in X-ray crystallography)

A certain fold of a peptide string can be validated or ruled out if other experimental data is available. Some other techniques to infer protein structure are X-ray crystallography (requires pure protein that will crystallize) and single particle analysis.

As I understand crystallography is quite complex and expensive how  much of simulations were verified with crystallography to prove it right?

It's not really my field, but there are databases of protein structures, with annotations for each structure how it was obtained.


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enhancers in cell-type-specific signatures
I was reading an article in nature : Epigenomics: Roadmap for regulation and was confused by the definition or/and interpretation of enhancers.

Enhancers are activated through interactions with transcription
  factors, which recognize and bind to specific DNA sequences within the
  enhancer region. Bound transcription factors recruit co-regulators,
  many of which deposit or remove modifications on histones. […]
  Enhancers that are active in cell-type-specific epigenomic signatures
  are typically highly enriched in DNA sequences to which
  lineage-determining and signal-dependent transcription factors bind.

As far as I know enhancers are the DNA sequences to which TFs bind, and then everything including co-activators complexes bind to basal TFs on the promoter.
I am confused by the last line:

Enhancers that are active in cell-type-specific epigenomic signatures
  are typically highly enriched in DNA sequences to which
  lineage-determining and signal-dependent transcription factors bind.

They state, that in DNA sequences to which TFs bind the active enhancers are highly enriched. For me it sounds strange because the definition of enhancers says that these are the DNA sequences to which TFs bind. And of course enhancers are enriched there because otherwise they would not be called enhancers. As for me they are trying to say that active enhancers (by definition TFs bind to them) are highly enriched in enhancers region to which TFs bind.
Does it make sense or not?

You nailed down what enhancers are (canadianer give a good explanation too, while not answering the question in my opinion).
For understanding the authors statement you first need to know that:

Lineage-specific and signal-dependent transcription factors are specific classes of transcription factors. Those are TFs that require external signals for activation.
All enhancers are not always accessible. This depends on the epigenetic marks, and subsequently histones binding, around those regions. If, for example, an enhancer is in a region of tightly packed DNA (i.e. heterochromatin) it will not bind any TFs and is therefore not active.

What the authors where trying to convey is, in my opinion, that active enhancers are highly enriched in DNA sequences specific for signal-dependent TFs. In other terms, the cell's identity is given by a combination of 1) epigenetic regulation of gene expression via a) a certain pattern of active enhancers and b) chromatin state of genes in conjunction with 2) signal-dependent transcription factors.
In summary this means that the cell identity is not only described by signal-dependent TFs but also by the active enhancer pattern. And this therefore implies that one might be able to predict TFs necessary to determine a specific cell's identity as stated in their next sentence:

Therefore, the delineation of a particular cell's active enhancer repertoire provides a powerful means of predicting the transcription factors required for that cell's identity.

I hope this helps.

Enhancer is a just a term for a regulatory region distant from a gene that contains specific sites where transcription factors bind. As it happens, a single enhancer can contain DNA binding sites for multiple transcription factors.
For example, an enhancer called TESCO, which regulates a gene called SOX9 (involved in sex determination) has binding sites for many different proteins (confirmed or putative): SRY, SF1, SOX9, ESR1, FOXL2 and likely many more that I haven't heard of. This allows complex regulation of SOX9 through protein-protein interactions.


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How does de-myelination occur in multiple sclerosis?
From what I understand, only the oligodendrocytes are affected in multiple sclerosis, and they are attacked by T cells which cross the blood-brain barrier. This leads me to two questions:

How is the blood-brain barrier affected in MS that allows T lymphocytes to cross the barrier?
Why do the T lymphocytes attack the oligodendroccytes? And when they do, what is the mechanism for de-myelination?

Thank you in advance!

Q2 is likely some kind of autoimmune disorder, which is very difficult to study.

T-cell migration to the brain is very limited and occurs at a very low level in healthy conditions, however during diseases the number of T cells passing through the blood-brain barrier is elevate due to increased expression of traffic signals and adhesive molecules.
I've found two good articles on how T-cells migrate through blood-brain barrier:
J Neural Transm (2006) 113: 477–485
Molecular mechanisms involved in T cell migration across
the blood–brain barrier, B. Engelhardt
and
 D. W. Miller, “Immunobiology of the blood-brain barrier.,” J. Neurovirol., vol. 5, no. 6, pp. 570–578, 1999.
During T-cell maturation, those that react too heavily to antigens of the body are killed to avoid having T-cells that would kill the body's own cells. But in rare cases this process fails and auto-reactive T-cell get released from the thymus (This short paper is good for starters). So the (simplified) reason why T-cells attack oligodendrocytes is that they falsely recognize them as pathogens, and therefore kill them. The loss of oligodendrocytes results in loss of myelin sheats.
Also in this paper (it holds many info on demyelination and multiple sclerosis) it is shown that even non-specicfic T-cells can open the way for antibodies through the blood-brain barried, and this results in extended demyelination.


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Why is amyloplast produced by some plant cells but not other cells?
For example I know it is produced in Potato's and fruits and its purpose is to synthesize glucose in to starch through polymerization. But why is it only present in some cells? Is it only present in cells with higher glucose content?

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Just a guess: fruits/seeds need starch for the nutrition of the seedling. For tubers I guess it is better to differentiate chloroplasts to amyloplasts in regions where there is no light exposure (chloroplasts won't be able to carry out photosynthesis). This differentiation is controlled by plant hormones and light exposure also has a role.

amyloplast is just another form of chloroplast. The portion of a potato tuber (while attached to plant) gets light (have some unexposed position from ground) turns green.

Amyloplasts are non pigmented organelles responsible for plant sugar storage, release and gravity perception (or tropism). This being the case they are commonly found in root caps (for gravity) and storage sites like tubers, fruits and grains.
So due to cell differentiation, it is not possible for these plastid organelles to be present in all cells the same way chloroplasts (another type of plastid) is not present in the stem (with the exception of small plants and succulents) and most of the root cells (Reece Urry et al, 2011).
Reference
Reece J.B., Urry L.A., Cain M.L., Wasserman S.A. et al (2011). “Campbell Biology 9th ed” Pearson Education, Inc., publishing as Pearson Benjamin Cummings, 1301 Sansome St., San Francisco, CA 94111.


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What proves that speciation is a pairwise process?
I have been asked this questions by many biology students and even non-biologist without a pretty straightforward answer to give. We are quite accustomed to phylogenetic trees where a common ancestor becomes two different species and these new species become, each one, two more. But, Why is not possible that a species might divide in three different species? Or four? Or more?
What arguments support this conception of the evolutionary process? Also, if somebody has a good article explaining this, please provide me with the link or citation so I can refer my fellow biology students to it.

Speculation: consider what tends to cause speciation — either some barrier (fully or partially) divides a population, or a selective pressure favours different extremes of a group.  With each of these, speciation will be binary unless two such barriers or selective tensions arise simultaneously.  So you’d expect it to be unusual for that reason, but you can also imagine situations which would cause it, e.g. a large flood wipes out most of a population (of a sedentary species), and the remnants form three or more isolated groups.

possible duplicate of Does a fully-resolved phylogenetic tree have to be dichotomous?. See also Evidence & discussions of hard polytomy

I offer this perspective in addition to what WYSIWYG has provided.
Phylogenetic trees are tools to model what has actually happened, or what some evidence implies has happened, to a population of entities that exchange genetic material.
These models fail, for instance, when describing the phenomenon of horizontal gene transfer since a tree is acyclic by definition. Consider a viral genome that has integrated into a host genome. The host now contains DNA from its ancestral lineage and the viral lineage. This process cannot be modeled by a tree.
Some founder population that is susceptible to exogenous genetic transformation may give rise to many distinct lineages, some of which your species concept may qualify as "new" species.

+1 This is an important point. I wonder what can be commented about this case in which a virus integrates in two different locations in two different individuals of a population and this leads to phenotypic differences between them (a sort of speciation). This also qualifies as a case of two species coming from one because of anisotropic horizontal gene transfer.

It is not impossible that a species can give rise to more than two lineages simultaneously, but it is just highly unlikely in certain cases.
If you assume that a point mutation in the DNA gives rise to a lineage then the number of two different mutations happening simultaneously (in two different individuals from the population) and also getting fixed, would be low for a small population. In any case a single DNA won't give rise to two different mutants. However this number would increase with increase in population size.
In such cases (small population) two separate events can be assumed rather than a single event that gives rise to two mutants. However, if the time difference between the occurrence of these two events cannot be determined (or it is too small compared to other timescales) then a single event can be assumed.
Phylogenetic trees can have nodes with multiple branches if the distance between all of them is the same (as in the abovementioned example; the distance between all of them is 1).
So I think it can be said that the likelihood of simultaneous formation of multiple lineage increases with population size.

I agree that the total ordering of events that give rise to new species (lineages) would give a total ordering to the branches in the tree or graph representing the speciations. The last statement may be true only if the probability of speciation-event-mutations increases with population size, like in the case where it were equiprobable and non-zero for all individuals.

@mcg256 The likelihoods actually won't change. But the number of mutants will increase with bigger population.


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What is NK-cell compartments?
with respect to the paper:
Adaptive reconfiguration of the human NK-cell compartment in response to cytomegalovirus: A different perspective of the host-pathogen interaction
What is meant by NK-cells compartment? I searched Google but couldn't find a proper text that would help me understand what it means.. Google search shows papers which has this term, but I need to understand what it means before reading the paper. Please help.

I agree that you need to know the basics. But I got answers to your term on googling. Here's one: NK Cell Compartments and Their Activation by Dendritic Cells. Read the first two paragraphs.

In my very brief search, it appears to refer to the expression of specific surface markers.

@anongoodnurse You can post that as an answer. This is not that obvious to be classified as homework (someone VTCed this as homework).


text:
Reasons why living fossils exist?

A living fossil is a living species (or clade) that
  appears to be similar to another species otherwise known only from fossils,
  typically with no close living relatives.

A living fossil is considered as a successful organism, which has made its way through many  major extinction events. Also, the morphology of living fossils resemble some species of organisms which we know only through their fossil remains.

What is the reason for a particular type of species to become a living fossil; is the engineering of this particular species extraordinary, in that it can survive any selection process encountered thus far?
Is there not enough selection pressure exerted on this species in order to force it to change morphologically?
Have these organisms modified themselves, so that currently their morphology seems to be similar to a fossil organism?

wasn't every fossil once a living fossil?

@aandreev: The term "living fossil" describes an organism which is alive today and it has great resemblance with some ancient creature(which is luckily fossilized). Every fossil we found are remains of living organisms and not remains of fossil :)

I don't think there is a reason to it. The other species in the clade just perished. If we kill all apes and monkeys (just keep one body in a museum) then we will become living fossils too.

"Is there not enough selection pressure exerted on this species in order to force it to change morphologically"…… This is not how evolution happens. They don't adopt a morphology because of selection pressure. The pressure selects certain traits which may include a particular morphology.

Of course the selection pressure changes the morphology. These are just two different ways of saying the same thing.

I think living fossil is a fairly meaningless term, since there will be fossils of extinct species out there resembling many living species.
Species which are the sole survivor of a clade were simply the most successful, I suppose. If you are wondering: why has a species remained the sole survivor of a clade for a long time without speciating again - perhaps the niche it occupies isn't very conducive to speciation, e.g. mass synchronised mating. Perhaps we just don't recognise the different species of e.g. horseshoe crab which exist, for what they are.

@WYSIWYG: However selection pressure can favor morphological changes by selecting particular traits. More selection pressure is exerted on a morphological trait makes it more susceptible to change. So lesser selection pressure could make the morphology immutable.

@Teige: " perhaps the niche it occupies isn't very conducive to speciation". Your words seems marvelous but HOW ?

There's a paleontologist from the University of Chicago called David Raup who wrote a book on extinction: "The disturbing reality is that for none of the thousands of well-documented extinctions in the geologic past do we have a solid explanation of why the extinction occurred... We have many proposals in specific cases, of course: ... These are all plausible scenarios, but no matter how plausible, they cannot be shown to be true beyond reasonable doubt. Equally plausible alternative scenarios can be invented with ease". so it seems we may have to admit our ignorance in this

One part of your question betrays a serious error:

Is there not enough selection pressure exerted on this species in order to force it to change morphologically?

Actually the reverse is true; constancy of form can only be maintained in the presence of continuous selective pressure. It's just that this is stabilising selection that acts to maintain the existing form rather than push the organism to new morphologies. In fact, most selection acts in this manner. This shouldn't surprise you: organisms are typically well adapted to their environments so changes are more likely to reduce fitness than increase fitness.
It's also worth noting that although living fossils show little morphological change they can continue to show change at the molecular level at rates as high as, or higher than, other organisms - e.g. (May et al 2007; Cao et al 2013).

Good point about molecular vs. morphological evolution.

@Jack Aidley: Consider an organism which is well adapted to its environment, if a change happens it makes the organism shifted to a reduced fitness state(as you mentioned). Then if a morphological alteration could bypass the fitness reduction and make it more fit. How is this statement invalid by your perception ?

@Jay: I'm sorry but I don't understand what you're asking?

TL;DR: Living fossils are the children of long-dead fossilised creatures that were good at being alike, other animals are the children that were good at being different.
The boring answer is that living fossils are around because nothing has happened to make them go extinct.
The more exciting answer is a tale of intrigue and lies stretching back hundreds of millions of years:
The lie that is the 'species'
The notion of a species is, of course, a lie. It's a useful lie, and one without which the equally useful field of taxonomy would be impossible, but a lie all the same. Every living thing is ultimately a unique individual unto itself. We group these individuals up and call them things, according to things that are more or less arbitrary, and we arrange these groups into bigger groups and fill books upon books with this method, because it makes it super easy to get a good overview of how life developed.
However, if we want to understand the details, we have to see past species, and look at the lineages.
The shark, our ancestor1
One such lineage that is of interest is that of the shark. Sharks are ancient: They are roughly as old as plants, and older than almost all land fauna. They are vicious, unrelenting killing machines, and all but perfectly suited for being this, with their sleek shape, their conveyor belts of teeth, and rough skin. At some point way back when, however, the lineage of sharks split in two: One branch that leads to fish, amphibians and eventually dinosaurs, squirrels and dolphins, and one that leads to sharks. The forebear to all these things were the early cartilaginous fish of the Cambrian ocean.
To answer the question as posed, we have to compare the success factors of the two lineages.
Why sharks are still around as living fossils
The real answer here is that, in a very real sense, they aren't. Modern sharks are no more alike their long-dead forebears than squirrels are. However, the biological niche inhabited by sharks (apex predator) is a successful one, and sharks, already existing in this niche, have had successful children, made more successful by being superficially and behaviourally alike to their parents, and so, the modern shark presents as a living fossil.
Why shark contemporaries are not still around as living fossils
The real answer here is that, in a very real sense, they are. Morphological differences aside, squirrels are no more different from their long-dead forebears than sharks. Rather, crowded niches have made generation upon generation of increasingly squirrely animals more successful by being superficially and behaviourally different from their parents, and so, modern squirrels have arisen.

Edit: Footnotes:

The shark is not in fact our ancestor, rather Cambrian early jawed fish are. The image of a shark is however far more evocative and easier to talk about.

"The shark, our ancestor" can you provide some reference for your claim that fishes are evolved from sharks. Also there is no reference for any of your claims, so how can I accept your answer ?

@Jay Sure, let me get right on that.

@Jay And there I've specified more exactly our relationship with sharks.

" the lineage of sharks split in two: One branch that leads to fish, amphibians and eventually dinosaurs, squirrels and dolphins, and one that leads to sharks". Here do you meant the shark instead of "Cambrian early jawed fish".

@Jay The statement "The lineage of X split in two: One branch that leads to Y and one branch that leads to Z." is equally valid for literally any known living things X, Y and Z, which is largely the point of the answer. The details of which creatures are descent from which really aren't important to this answer. Besides all of which, whether we are descent from sharks is really a subjective matter: If you follow the lineage of sharks backwards, parent-to-parent-to-parent you'll find that it's damn hard to place a hard line on where 'early jawed fish' end and 'sharks' begin.

So you must have mentioned these X,Y and Z and not sharks because the fellow readers will be misguided by this fact. Also finally, in the question I have pointed out three facts(in bullets), to which one do you agree as the reason behind this process or could your suggest a new one. :)

Let us continue this discussion in chat.

While we are at that, the concept of multicellular organisms is a "useful lie" too, as they are actually just a complicated colony of unicellular organisms.


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What do trans-fats do when in human body?
Trans fats cause health problems, especially to the heart.  https://en.wikipedia.org/wiki/Trans_fat#Health_risks
My guess is that all effects happen because trans-fats are inherently toxic as the body never evolved to process them. But then L-glucose has no harmful effects, even if it cannot be digested.
So how are trans-fats processed in the body differently, and where does all the harm happen?

The closure based on homework is a bit harsh - OP showed the parallel between L-glucose and I checked the wiki page and it is indeed unintelligible when one is interested in the mechanisms in which trans facts cause harm. I deem this a valid, interesting and sufficiently researched question.

In Ascherio & Willen (1997) it is mentioned that, and I quote:

[...] Trans fatty acids increase plasma concentrations of low-density lipoprotein (LDL)
  cholesterol and reduce concentrations of high-density lipoprotein (HDL) cholesterol relative to the parent natural fat. [...] [T]rans fatty acids increased the plasma ratio of total to HDL cholesterol nearly twofold compared with saturated fats. On the basis of these metabolic effects and the known relation of blood lipid concentrations to risk of coronary artery disease, we estimate conservatively that 30 000 premature deaths/y in the United States are attributable to consumption of trans fatty acids.

The US Heart Foundation explains in more layman's terms the same principles:

Trans fat is a type of unsaturated fat that behaves like a saturated fat because of its chemical structure. It increases our risk of heart disease by increasing the “bad” LDL cholesterol, while also lowering the “good” HDL cholesterol in our blood.

And from the Better Health Channel Australia we learn why LDL is 'bad':

Too much cholesterol circulating within LDL in our bloodstream leads to fatty deposits developing in the arteries. This causes the vessels to narrow and they can eventually become blocked. This can lead to heart disease and stroke.

Reference
Ascherio & Willen, Am J Clin Nutr 1997;66(suppl):1006S-lOS.


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Why is an increase in the amount of oxygen in the atmosphere favorable for life?
I have followed the David Attenborough series on 'First life' and heard, that an increase in the amount of oxygen in the atmosphere, as it took place just before the Cambrium, is generally favorable for life and also enables the evolution of larger organisms.
Why is that so? Is it because aerobic respiration had a better conversion rate to energy?

I think you are right - O2 allows more energy to be released from fuels in less time, allowing warm-blooded animals to develop and thrive in colder climates. However, this was only possible through large-scale adaptations to eliminate oxygen radicals in the body. Oxygen is about the most reactive compound around and therefore potentially lethal. Hence 'generally favorable form life' seems to be an invalid statement. In fact, you could envision the abudance of plant life killing life instead of supporting it.

@AliceD Indeed, see https://en.wikipedia.org/wiki/Great_Oxygenation_Event.

Because it's favorable for the process of aerobic respiration which requires O2 to produce ATP, which is the little power storage unit.
With a bigger concentration of O2, it was possible to produce more ATP, should you evolve in that direction and you needed that constraint to be removed.