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Thoughts precede neuron firing or vise-verse?
I am at the verge of submitting a paper on 'scientific explanation of reality' to an international philosophy body. First submitted draft was returned by the evaluation expert, asking me to re-submit it, after re-checking the validity of my  assertion that 'science (biology) believes that neuron firing always precedes thought'. Can any one provide answer on biology's clear stand on above question ?

how do you define "thought" biologically?

see the "materialism" philosophy debate. biologists are more agnostic on this, a position not really required for biological work. maybe a better fit on [philosophy.se] or [cogsci.se]. there is possibly some data from neurobiology specifically brain imaging studies that does impinge on the question.

I would suggest doing reading on corollary discharge to answer part of your question.

i'd be surprised if you could find a neuro-scientist who didn't go at least this far.

this should be on the neuroscience stack. Voting to close until you migrate it.

@John — the question is too old to migrate, and the original poster hasn't been seen in the last seven years.

I think the only way to interpret these kinds of questions biologically is to assume that "thought" means "the perception of a thought occurring." The perception of a thought, like all perception, arises from neuronal firing.
The interesting biological (rather than philosophical) questions arise when we look at the relationship between the neural firing that gives rise to the perception of intent to act and neural firing that carries out the "intended" actions.
This paper is relevant. The authors are trying to argue that the initiation of a motor action comes before the perception of intent for that action. I'm not a cognitive neuroscience person, though, so I'm not very familiar with their techniques and personally have a hard time determining if they draw valid conclusions.

I didn't read the paper that you linked, but the reaction time literature supports that assertion as well.  See some of the papers in the early 2000s by JF Kalaska.  The work is done in primates, so it's difficult to gauge "perception" of the movement.  I'm sure there's been human work since then, I just haven't looked for it.

You've stumbled on an old and unanswered question that is still debated--- bordering on the issue of Free Will. The reason it is still in the realm of philosophy is because current experiments don't allow direct testing of which neurons give rise to specific thoughts. This area of consciousness is fraught with difficulties and we just can't get at an answer.
Now for a more philosophical answer.
All consciousness is generated by the brain so every thought must come from neuronal firing necessarily. The difficulty lies in the fact that thoughts themselves cause neurons to fire and one is never thoughtless so we are reduced to the chicken and the egg problem if we continue down this path. However, assuming we come from a thought free state- for example deep coma-- the first thoughts we have are indeed generated by neuronal firing so your assertion is correct.

Original thought is not perception. Perception is response to the afferent, reacting to something. Original thought is efferent not reactionary but inventive. This is the conundrum, chicken or the egg. Dennett would support that the egg creates the chicken in order to create another egg.  The egg that creates a rooster is well on the way to independent inventive thought (free will).

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Does antibacterial soap work chemically?
Normal soap requires scrubbing, does anti-bacterial soap require scrubbing too? Since it (I assume) works chemically, can I produce the same cleansing effect without lathering with soap and using anti-bacterial soap instead? It could save me a lot of time showering in the morning.

The point about scrubbing with soap is usually not to get rid of bacteria (which colonize your skin anyway) but to get rid of dirt. I am not sure, if it is really advisable to always use a real antibacterial soap, since the bacteria on our skin are not doing any harm. It will probably irritate the skin.

most antibacterial soaps contain triclosan, which would work just on application. However, the objective of bathing is not just to get rid of microbes but also to clean the dirt, dust, oily sebaceous secretions etc and therefore scrubbing is still important. If you have rashes/cracked skin then you can avoid scrubbing..

How does "waiting a minute or two" as opposed to "scrubbing for a minute or two" change the time it will take you to shower? How long do you scrub for?  Why in the world do you shower using antibacterial soap? Depending on the soap that can be dangerous and is almost certainly unnecessary and very likely counter productive.

What the comments are trying to say might go something like this.
The antibiotic triclosan that's used in almost all 'antibacterial' products works pretty quickly - by interfering with several processes in the bacterial and fungal membrane.  It doesn't need much more than contact to work.
That being said, the longer your exposure to the antibiotic, the more thoroughly it will work.  Triclosan can penetrate the blood stream through the skin.  If you have soap suds scrubbing may or may not get the triclosan into more contact with a greater surface area as it diffuses into the skin, but probably won't affect the substantial effect it has killing surface bacteria and fungi/yeasts.
Its worth noting that the FDA doesn't recommend the use of antibacterial soap or other antibacterial products.  Soap itself is a powerful agent for killing bacteria and other microorganisms and biocides like triclosan probably encourage the emergence of antibiotic resistant strains which present a medical risk to people.

This is a very good question, and a very important topic in the healthcare and biological world.  It is something that everyone should consider, as the answer is not as self-evident as it may appear.  The responses here are excellent.  I would like to add a few things from a healthcare perspective.
This is the WHO recommendation on how to wash your hands.  It is in agreement with the CDC recommendations. This includes use of antibacterial soaps.
The reason for friction in handwashing is as Chris and WYSIWYG said: removal of oils, dirt, bacteria and other things accumulated in the crevasses of your skin and nails (including microbes and biological residues).
Regular soap on its own is a surfactant; it is a molecule with a polar end (and a non-polar end.  It basically dissolves in both oils and waters.  It is perfect for removing oils and rinsing them off in water.  Detergents such as soaps are cell membrane disrupters, and as such, it is capable of rupturing cell membranes of many microbes on its own.
Shigeta is right-on with the FDA recommendations to not use antibacterial soaps.  They are completely unnecessary is most situations and actually do harm by putting selective pressure on bacteria strains to become stronger by killing off all but the most resistant ones, which then breed and overgrow.
In daily use, alcohol foams are a convenient way to sanitize if soap and water are unavailable, but it's often overused.  Soap and water are better in the daily environment, and always better before eating, because alcohol does not kill spores nor denature toxins.
Overuse of antibiotics in general is the reason why MRSA and other multi-drug resistant bacteria have emerged, and these are extremely dangerous because they are so difficult to treat.  We're struggling to catch up with antibiotics to kill the newly emerging strands.  There are cases I have seen where all efforts to treat an infection failed due to resistance.  So I guess I'm saying all this to emphasize that yeah, it's important to not go overboard on antibacterial cleansing :)  /end soapbox.
Well, one more quick thing - I do want to add that healthcare settings are slightly different.  The use of antibacterial soap in hospitals is approved for the purpose of reducing the microbial load on skin between patients, to reduce transmission as much as possible.  Alcohol foams have been found to be comparable, but are insufficient in several cases (such as spores). (See the CDC for more info on alcohol foams: http://www.cdc.gov/oralhealth/infectioncontrol/faq/hand.htm#a3).
In daily use, alcohol foams are a convenient way to sanitize if soap and water are unavailable, but it's often overused.  Soap and water are better in the daily environment, and always better before eating, because alcohol does not kill spores nor denature toxins.
References for following information:  I personally have been involved in patient counseling discussions in clinic with a patient and an attending physician (a supervisory teaching doctor) discussing best practices in hygiene.  This includes two dermatologists, two Emergency physicians, an OB/Gyn physician, and a pediatrician - and all concur:
For general washing in the shower, unless you sweat a great deal or are exposed to dirt and chemicals, the majority of your exposed skin does not require extensive scrubbing to become clean.  In fact, scrubbing can irritate skin, worsen dry skin, or exacerbate conditions such as eczema.   Warm water, normal soap (or even better for sensitive skin / eczema, moisturizing body wash like Dove), and a soft washcloth are completely sufficient. If using a pouf or exfoliator, only apply light pressure, never aggressive. Armpits, groin, and feet do require more attention, but hard scrubbing is unnecessary.
Interestingly (and hopefully not TMI in this post), I learned from the OB/Gyn's patient counseling that it is unnecessary (and actually irritating to the mucous membranes) for women to use more than warm water to clean between the labia majora. I looked this up and found supporting information for this. Other genital surfaces should be washed well, but as mucous membranes, that area has a self-cleaning system of secretions.  This is similar to the strong recommendation for women not to use vaginal douching - it upsets the balance of natural bacteria (flora) in the vaginal canal.
The WHO handwashing instructions:

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Hypovolemia and orthostatic hypertension
What is the physiological mechanism behind the occurrence of orthostatic hypertension in the presence of hypovolemia?

it would really be helpful if you could like to some external references for terms like this :)

Orthostatic (=postural) hypertension is an excessive increase of blood pressure upon standing up. Hypovolemia is a reduced total blood volume (i.e. lack of plasma). This question is perfectly on-topic.

The pathophysiology of orthostatic hypertension has not been elucidated. It is believed it involves activation of the sympathetic nervous system [1], vascular adrenergic hypersensitivity and diabetic neuropathy [2]. High levels of plasma atrial natriuretic peptide and antidiuretic hormone were observed in children [3].
Hypovolemia causes:

baroreflex-mediated increase in muscle sympathetic nerve activity [4]
release of epinephrine and norepinephrine [5]
activation of renin-angiotensin axis [5], thus increasing ADH levels

All these reactions result in vasoconstriction and blood pressure raising. But not up to absolute hypertension.

Orthostatic hypertension is diagnosed by a rise in systolic blood pressure of 20 mmHg or more when standing [6].

This is possible. A raise of 20 mmHg from hypotension could result due to vasoconstriction.

References:

Fessel J, Robertson D. Orthostatic hypertension: when pressor reflexes overcompensate. Nat Clin Pract Nephrol. 2006 Aug;2(8):424-31. doi: 10.1038/ncpneph0228. PubMed PMID: 16932477.
Chhabra L, Spodick DH. Orthostatic hypertension: recognizing an underappreciated clinical condition. Indian Heart J. 2013 Jul 5;65(4):454-6. doi: 10.1016/j.ihj.2013.06.023. PubMed PMID: 23993009.
Zhao J, Yang J, Du S, Tang C, Du J, Jin H. Changes of atrial natriuretic peptide and antidiuretic hormone in children with postural tachycardia syndrome and orthostatic hypertension: a case control study. Chin. Med. J. 2014 May;127(10):1853-7. PubMed PMID: 24824244.
Ryan KL, Rickards CA, Hinojosa-Laborde C, Cooke WH, Convertino VA. Sympathetic responses to central hypovolemia: new insights from microneurographic recordings. Front Physiol. 2012 Apr 26;3:110. doi: 10.3389/fphys.2012.00110. PubMed PMID: 22557974.
Wikipedia contributors, "Shock (circulatory)," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Shock_(circulatory)&oldid=612494727 (accessed June 26, 2014).
Wikipedia contributors, "Orthostatic hypertension," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Orthostatic_hypertension&oldid=603984647 (accessed June 26, 2014).

I presumed you meant orthostatic hypotension.
Blood pressure falls on standing and is caused primarily by increased gravity causing blood pooling in the legs. This reduces venous return and subsequently cardiac output and therefore arterial blood pressure. Usually however standing doesn't usually cause a massive fall in blood pressure as standing immediately triggers vasoconstriction (baroreceptor reflex), pressing the blood up into the body again. However when there's a secondary factor reducing blood pressure such as hypovolaemia, the fall in pressure is higher than the body may sometimes be able to compensate for. This causes symptomatic orthostatic hypotension.

No I meant orthostatic hypertension, which apparently can also a symptom of hypovolemia.  For instance, look at the 5th cause on the list on wikipedia http://en.wikipedia.org/wiki/Orthostatic_hypertension.

Ah okay. Orthostatic hypertension: Sometimes the above mechanism can overdo it in whats thought to be through an alpha adrenergic system. This is rare and medical communities doubt its existence.

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Pathogenesis of Group B Streptococci and C5a
I am thinking the pathogenesis of the C5a in GBS.
I think the pathogenesis happens like

C5a-peptidase in acid environment (Sialic acid, capsule) $\to$ cleaves C'-derived Neu chemoattractant C5a $\to \downarrow$ alternative pathway of Complement.

However, this part cleaves C'-derived Neu chemoattractant C5a is not clear to me.
I think this means that C5a-peptidase cleaves Neu C5a from the previous complement reaction that inhibits the next coming alternative pathway of complement.
How does this pathogenesis of GBS happen?

I think "neu" must be an abbreviation for "neutrophil".
C3a and C5a are both chemotactic peptides that recruit cells to sites where complement activation is occurring. C5 is a substrate for the C5 convertases formed in one of the three complement pathways (classical, lectin, alternative). C5b, the other product of this cleavage goes on to form the membrane attack complex.
C5a peptidase is a Streptococcal product which destroys the C5a peptide before it can recruit neutrophils and other agents of cell-mediated immunity. Streptococci also produce an inhibitor of the membrane attack complex.


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Can too low oncotic pressure lead to Third spacing and Edema?
I know that low oncotic pressure is associated with many pathologies.
I am interested how it is associated with Third spacing.
My professor says that it can permit edema formation.
The opposing pressure of oncotic pressure is hydrostatic pressure.
So that would suggests mean that the blood pressure is too high if low oncotic pressure and thus fluid would like to go to the third spacing (not sure) and edema.
Can too low colloid oncotic pressure lead to Third spacing?

Yes it can! Its a very important cause of third spacing a.k.a. peripheral oedema, mainly due to decreased protein.
Below is a list of causes of peripheral oedema due to fluid moving from the vascular bed to the peripheral spaces gathered from the following source: http://www.patient.co.uk/doctor/Peripheral-Oedema.htm
Immobility: Increased fluid pressure from venous stasis. Varicose veins.
Obesity: Increased fluid pressure from sodium and water retention; should not to be confused with non-pitting lymphoedema.
Cardiac: Increased fluid pressure: right heart failure, constrictive pericarditis.
Drugs: Increased fluid pressure from sodium and water retention: calcium antagonists, non-steroidal anti-inflammatory drugs (NSAIDs), prolonged steroid therapy, insulin.[1]
Hepatic: Decreased oncotic pressure: cirrhosis causing hypoalbuminaemia.
Renal: Decreased oncotic pressure from protein loss, and increased fluid pressure from sodium and water retention: acute nephritic syndrome, nephrotic syndrome.
Gastrointestinal: Decreased oncotic pressure: starvation, malabsorption, protein-losing enteropathy (eg Crohn's disease, ulcerative colitis, tumours of stomach and colon, coeliac disease and other intestinal allergies).
Pregnancy: Increased fluid pressure both from sodium and water retention and venous stasis from pelvic obstruction.
High-altitude illness: Oedema of face, hands and ankles may occur.
Idiopathic oedema: Associated with cyclical high lymph volume overload, or dynamic insufficiency: usually in a woman aged 20-40 years. Variable and not related to menstrual periods. Diagnosis is based on the exclusion of other causes of oedema.
Post-thrombotic syndrome: Late complication of deep vein thrombosis (DVT) which occurs in up to two-thirds of patients. May present with pain, oedema, hyperpigmentation, and even skin ulceration. May result from remaining venous obstructions, from reflux, or both. Rate of reflux is highest during the 6-12 months after an acute DVT. It may be temporary and self-limiting or not resolve and persist at variable severity.
Pitting localised limb oedema:
DVT: Compression of large veins by tumour or lymph nodes.
Following hip replacement or knee replacement.
Local infection, trauma (including burns, which may also cause generalised oedema because of protein loss), animal bites or stings.


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Why does the slope of parent-offspring regression equals the heritability in the narrow sense?
Background
---- Notations and assumptions ----
let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $A2$ is $1-x$ because we'll consider only the case of a bi-allelic locus. Also, we consider that only one locus influence the random variable $W$ (the fitness). We will assume that the environment does not influence the fitness. We also assume random mating in order to use hardy-Weinberg equilibrium.
---- calculations ----
The mean fitness is:
$$\bar W = x^2W_{11} + 2x(1-x)W_{12} + (1-x)^2W_{22}$$
The variance of fitness is:
$$\sigma^2 = x^2(W_{11}-\bar W)^2 + 2x(1-x)(W_{12}-\bar W)^2 + (1-x)^2(W_{22}-\bar W)^2$$
We then want to calculate the covariance between father and son with respect to fitness.
Suppose first that the father is $A_1A_1$ Then the son will be $A_1A_1$ if the mother transmits an $A_1$ gene to him, an event with probability x. Similarly the son will be $A_1A_2$ with probability $1-x$. The father himself will be $A_1A_1$ with probability $x^2$. Continuing this wa it is possible to draw up a table of the probabilities of the various father-son combinations in genotype and hence fitness.
Therefore, assuming no change in frequency of $A1$ between the two generations, the covariance father-son is:
$$cov = x^3W_{11}^2 + 2x^2(1-x)W_{11}W_{12} + x(1-x)W_{12}^2 + 2x(1-x)^2W_{12}W_{22} + (1-x)^3W_{22}^2-\bar W^2$$
which also equals
$$cov = x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2$$
The correlation between the two fitnesses is found by dividing the co-variance by the variance (since the variance of sons is the same as that for fathers):
$$cor = \frac{x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2}{\sigma ^2}$$
We then define dominance and additive variance:
$$\sigma_D^2 = x^2(1-x)^2(2*W_{12} - W_{11} - W_{22})^2$$
$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$
such as
$$\sigma_D^2 + \sigma_A^2  = \sigma$$
My question
The slope of a parent-offspring regression equals the heritability in the narrow sense $h^2_N$.
Heritability in the narrow sense is defined as $h_N^2 = \frac{\sigma_A^2}{\sigma}$ (see Why is a heritability coefficient not an index of how “genetic” something is?).
We defined above that the correlation between parents and offspring is $cor = \frac{cov}{\sigma}$. So I'd expect the slope of the parent-offsprings regression to equal $cor = \frac{cov}{\sigma}$ and not $h_N^2 = \frac{\sigma_A^2}{\sigma}$
What am I missing? Is there a mistake in my background calculations? Is there a mistake in the way I defined some concepts? The answer might be much simpler than it looks like!

Man, your questions always scare me :).

Well, I think I found the very simple mistake I made…
Looking again in my equations, I realize that (for some reason) $cor = 2 \cdot \frac{\sigma_A^2}{\sigma}$
And looking at this website, I see that the slope of the parent-offspring regression is $\frac{h_N^2}{2} = slope$
Here was my mistake!

I thought the range of heritability is between 0 and 1.  But values of parent-offspring regression times 2 calculated this way can certainly be higher than 1.  Am I wrong about heritability?

@sterid Parents share 50% of their genetics with their offspring. So we need to multiply by 2. See: https://biology.stackexchange.com/questions/112552/is-heritability-just-slope


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How can promoter binding sites be determined?
I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it to be the housekeeping $\sigma^A$. However I have found out from the Bacillus subtilis transcription factor database, that $\sigma^A$ binding sites have been found in the promoters of $\beta$ (rpoB) and $\delta$ (rpoE) subunits, and a whole bunch of alternative $\sigma$ factors, but it says nothing about $\alpha$ or $\beta ^{\prime}$.
So I want to know if there is a way for me to find out, without entering a wet lab!
Firstly; how do we know that something is a transcription/sigma factor binding site? What is it about the region? And how do we know which TF/SF it is a binding site for? Could the same transcription/sigma factor have multiple different binding site motifs?
Secondly; Since the genome for B. subtilis is available, would I be able to find out binding site motifs for all the sigma factors, and then determine which is/are contained within the promoter for the $\alpha$ subunit? I.e. if I know the TF/SF sequence, is there a way of finding out which promoters it can bind to?
Finally; the main purpose of this question is to find out how rpoA is transcribed, and I know that in general sigma factors are required in bacteria for specific transcription initiation, but could it be that rpoA transcription is non-specific, and that the sigma factor is just not involved in its transcription?
Please let me know if there is anything I can do to improve my question, I can provide references if it would be a good idea. Thanks!

its hard - most of the techniques that don't involve having the protein for the transcription factor are unreliable and unspecific.

I don't have a definitive answer, but I can perhaps offer some insight. Given the necessary function of rpoA, I would be willing to bet that SigA is the factor responsible for its transcription, so I will focus my discussion there.
Predicting promoters without experimentation can be very challenging given their immense variability. The idealized core promoter consists of a -10 region, a spacer and a -35 region. Recognition of the promoter by a sigma factor is done at the -10 and -35 regions: each sigma factor recognizes a different consensus sequence. Bacillus subtilis SigA recognizes the consensus sequences TTGACA (-35) and TATAAT (-10). They key word there is consensus however, as it is rare that a promoter will actually contain these exact sequences. In reality, 3/6 nucleotides matching could be considered reasonable. Between the -10 and -35 regions is a spacer with conserved length. In the absence of transcription activators, SigA requires a 17 +/- 1 nucleotide spacer. This is due to thermodynamic constraints. Very briefly, promoter melting (at -10) is dependent the angle between the -10 and -35 regions. Given the helical nature of DNA, this angle is in turn dependent on the distance between the -10 and -35 regions. If the angle is just right, the untwisting of the DNA to align the promoter elements and thus allow sigma binding provides the energy to melt the promoter. If the angle is too large, the regions can never align. If the angle is to small, alignment will not provide enough energy for melting. Complicating this are non-standard core promoters and various flanking sequences that all play a role in transcription initiation. As a direct answer to one of your question, a single sigma factor can bind to many different DNA sequences with some conserved regions.
Fortunately, the B. subtilis genome has been sequenced. Your search for the promoter might involve looking for the -10 and -35 regions 5' to the rpoA gene. This however doesn't take into account that rpoA might be part of a polycistronic operon and thus under the control of a promoter further upstream. Suh et al. (1986) did basically this and reported:

Our DNA sequence analysis suggests further experiments to study regulation within the rpoA region. Because inhibition of polycistronic message translation by free protein S4 is one of the chief controls of alpha operon expression in E. coli (16, 23), the apparent absence of S4 from the B. subtilis alpha region suggests different regulation. Although the close coupling of the rpsM and rpsK genes in our sequence (Fig. 3) supports the notion of a translational coupling similar to E. coli, the putative rpoA promoters in the relatively large intercistronic distance following rpsK are also different (28, 29). However, the apparent absence of a rho-independent terminator in this region could indicate that significant transcription occurs from additional upstream promoters in B. subtilis as well as in E. coli (28).

Albeit this is an old paper, but I was unable to find more recent studies in my quick research. Basically they compared the B. subtilis rpoA gene to that of Escherichia coli, where it is located in an operon with ribosomal proteins rpsM, rpsK, rpsD and rplQ (under the control of a single promoter). They found both similarities and differences. They were able to find two possible SigA core promoters in the region between rpoA and rpsK (the next gene 5' to rpoA in B subtilis). There was also a relatively large distance between the two genes, suggesting that they are not part of the same operon. Furthermore, they were able to find a ribosome binding site (Shine-Dalgarno sequence) between the hypothetical promoters and the translation start site. On the other hand there is no transcription terminator between rpsK and rpoA which suggested that a promoter further upstream regulated rpoA expression. After their sequence analysis, they suggested that further experimentation was required.
In conclusion, it's hard to find promoters just by looking at the sequence. Even if you do find a possible promoter, it's impossible to say whether or not it is utilized without experimentation. That said, given that the alpha subunit is necessary for cell function, that the rpoA gene appears to be transcriptionally tied to ribosomal proteins (which are also necessary for cell function) and that SigA is the predominant factor in log phase B. subtilis, I feel that it is very likely that SigA is ultimately the factor responsible for rpoA expression
I also thought I'd mention that there are various online bioinformatics tools that attempt to predict promoters, but I will not comment more on them because I have not used them.


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What's the difference between an embryo and a fetus?
The most I've been able to come up with is that fetuses are embryos slightly farther along in their development. Is that correct?

Yes, you are correct. You can read the wikipedia article about an embryo:

An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the >time of first cell division until birth, hatching, or germination. In humans, it is called an >embryo until about eight weeks after fertilization (i.e. ten weeks after the last menstrual >period or LMP), and from then it is instead called a fetus.


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How do we know that everybody's DNA fingerprint is unique?
How do we know that everybody's DNA fingerprint is unique?
I know, I know, everybody's DNA is unique.
But when we do DNA fingerprinting, we're looking at very specific regions of high variability.
How do we know that just by chance, two people's DNA could be the exact same in the spot(s) we're observing.
With real fingerprints, uniqueness is (almost) guaranteed (I believe it's a 1 in 64 billion chance) because they are developed by physical stresses on the fetus in the womb.
Is there any similar mechanism/affect that acts on these non-coding/highly variable sections of DNA?
Thanks!
evamvid

Yes, the fact that they are highly variable. I don't have the numbers at hand but while it is theoretically possible for two DNA fingerprints to be identical, I would expect a similar or smaller probability of this than for "real" (let's call them digital) fingerprints.

@terdon one meaning of the word digit is finger :)

@user13107 yes, that's why I used it.

Essentially, for the same reason we "know" that no one is going to be struck by lightning 100 times. It is possible but highly unlikely.

First, remember that identical twins actually have the same genotype. So its not exactly true that everyone has a unique genome.
But to get at the heart of it, you're asking how I can be sure that I have a different genome than you, or even than say my brother. And moreover you're asking how these differences are obvious enough that they can be detected without whole genome sequencing.
The answer is that there is no mechanism to ensure differences, but that the differences arise from the enormous variability of our genome. Look at the major histocompatibility complex, or MHC, a cluster of genes that affect our immune system.
Just to simplify things, lets focus in on four genes in this cluster: HLA-A, HLA-B, HLA-C and HLA-DRB1. According to this site there are 2579, 3285, 2133 and 1411 alleles for each, respectively. If we make a naive assumption that each of us received a random assortment of these genes, that makes 2579 x 3285 x 2133 x 1411 = 25,549,791,000,000 possible combinations. The chance that we both have the same combination is then about 1 in 25 trillion, just considering 4 genes.
But wait, you say, surely some of these genes are not equally likely and surely they segregate together, making this chance much smaller. You would be right. But this consideration stops mattering very much when you account for the rest of the variable regions. They combine multiplicatively, so considering a fifth gene with only 2 possible alleles brings the possible combinations to 50 trillion.
If you consider just a few more genes, the numbers get unthinkably high. This pretty much ensures that, even considering a small sequence, we can be sure that the genetic fingerprint is unique.

That said, you would need to compare one very large number to another to evaluate overall uniqueness. For example, although there are only 6 or so billion people in the world (i.e., approximately 10^9), The relevant divisor for overall uniqueness would be the number of possible pairwise comparisons between people (e.g., around 10^17; which is much larger than a trillion).

Identical twins don't have identical genotypes.  They have very similar genotypes, but there will typically be a few dozen base pairs that differ due to mutations.  These usually won't be in the regions used for DNA fingerprinting, though, and will require full-genome sequencing to spot.  A complicating factor is that the error rate for sequencing is similar to the mutation rate, so you 'll need to sequence multiple times to be sure you're seeing the actual mutations.

Thats not true. Twins do not have exactly the same genotype, since they occured some individual variations. Its possible though, that the standards used for genetic fingerprinting in crime scenes is not precise enough to differentiate twins. This has happened in Germany and led to the release of a subject from prison as he couldn't be distinguished from his twin brother. With more test points (which was not allowed at this time) the differentiation woud have been possible.

Possibly partly offtopic, but I'd like to add that when using dna fingerprint as evidence of identity in a legal investigation, the odds become smaller due to combination of human factors and reduced accuracy. There is the twin issue already mentioned, but in addition there are laboratory errors and the possibility of contamination with other evidence. Samples may be damaged in other ways as well, and dna samples can be planted.
In the analysis done by Jonathan Koehler, it was found that around 1.2% of tests used in this context gave out an incorrect match. Additionally, in this other study by him it was found that the way results are presented has a considerable impact as well.


text:
Gap junction turnover
Gap junction proteins, connexins, are known to form intercellular hemichannels, between two adjacent cells. These junctions are maintained cell adhesion proteins (cadherins), yet the turnover of connexins is fairly rapid. As these connexins are being turned over, do the replacement connexins re-form the channel at the same location as previously existing channels, or is the pattern stochastic? Put another way, if we know cells in culture have formed gap junctions, and for any one cell, does it have different connected neighbours with time?

This is an interesting question.
Reading this two articles linked below, it seems very much that the connexins are turned over and degraded with the channel more or less staying at the same place (the figure is taken from the first paper, but the second has a similar):

Following this, the connexins are synthesized and then subjected into the ER and then the Golgi for proper protein maturation and oligomerization into hemichannels (misfold proteins are subjected to proteasomal degradation). They are then exported from the trans-Golgi in small vesicles to the cell membrane, transported to the sarcolemma where they form complete gap junction channes with hemichannels from another cell. Single channels aggregate into gap junction plaques.
The connexins are degraded in the proteasome and the lysosome. It is discussed that post-translational modifications as phosphorylation and ubiquitination play an important role here.
The degradation seems to take place at the formed channels. This was tested in two ways: When the export of new proteins to the membrane is inhibited, then the connexins in the membrane and the junctions get lost over time. If the proteasome is inhibited, the number is growing. And when both pathways are inhibited (export and degradation) the number is approximately constant. See paper 3 for more details.
This shows that the process of forming the junctions and degrading the connexins is a permanent and that cells, which form junction with each other stay in the same place.
References:

Connexin Expression and Turnover
Pathways for degradation of connexins and gap junctions
Degradation of connexin43 gap junctions involves both the proteasome
and the lysosome.

Oh, thats right. I wrote it different first. Thanks for the notification.


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What causes skewed lanes in a DNA gel electrophoresis experiment?
In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)?

(These images were samples that I took from an online activity we did for class)

These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, which still contain too much salts from the PCR reactions. This can also happen to only a few bands as seen here. Overall these are still pretty nice and clean gels, I have seen much worse.
Other reasons which cause uneven gels are cases where the acrylamide is not mixed good enough (causing the gel to have different concentration and thus causing different running conditions), uneven warming (although this was usually preventing by the gel heating system) and leaky gels where the electric field was not completely even.

Could please elaborate on why too much salt from PCR can lead to this ? Thanks!

The different salt concentrations cause different conditions for the currents which flow through the gel. When the conditions are not uniform, then the field is not uniform, which causes the transported nucleic acids to not move uniform. We could call it a "disturbance in the force" :-)

@Chris's suggestion is very possible, high salt characteristically shows this towards the end of the gel. But there are additional suspects. This looks like it's just an agarose gel, Correct? I've seen a few things cause this including the gel not being level, the gel shifting during during it's run the percentage of agarose not being uniform and the temperature jacking up towards the end. If you do it again keep an eye on your amperage during the second hour or so.
But first, try doing a quick PCR cleanup on a column (be sure to get one that will not loose your smaller fragments) or alternatively a phenol extraction followed by an ETOH precipitation will purify your reaction; and the force will be with you.

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


text:
Biopython error
>>> from Bio import SeqIO
>>> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
... print(seq_record.id)
  File "<stdin>", line 2
    print(seq_record.id)
        ^
IndentationError: expected an indented block

First I import the sequence and then whenever i try to print using this
" print(seq_record.id)"
        ^
I get this error
IndentationError: expected an indented block
how can I preent that need help..

This question appears to be off-topic because it is about a bioinformatics software development issue.

basic python question. I suggest a quick search on stackoverflow.com

Biopython is a module of python and the language is structured in the same way.
This particular example does not make it clear how and where to find the files and extract the data you want. First, you need to download the file and put it in a place where python will find it. Below I have an example where I was able to extract the record id. I first set up a fasta file for my code to go through and then it adds the data to a list (seq = []). The "with open" line joins my data files together. The line ends with a ":" to signal to the program that there is a block of something to do in the next line. Indentation is important in python and after a ":" the next line is indented 4 spaces.
from Bio import SeqIO

data_dir = 'data' #folder where my data files are
data_file = 'ampk.fasta' #name of file I want to get data from

seqs = []

with open(os.path.join(data_dir, data_file), "rU") as f:
    for record in SeqIO.parse(f, "fasta") :
        seqs.append(record)
        print(record.id)

Hope this helps!

okay I will try and let you know


text:
What cell types produce immunoglobins and where are those cells found?
I know B cells found in bone marrow produce immunoglobin G.  But IgM is produced in mucosal cells at least in the gut.  Can you find immunoglobin expressing cells in other tissues in the human body?  Are B cells or IgG mRNA ever found in blood or tissues?

I think the antibodies produced in the gut are from lymphoid cells in Peyer's Patches http://en.wikipedia.org/wiki/Peyer%27s_patches , so B cells again.

First: B cells do not produce antibodies, but rather they synthesise the B cell receptor. This may sound a bit picky, but is not, since the B cell receptor is anchored in the membrane of B cells and not secreted. Its this receptor which recognizes antigens and causes the production of highly specific antibodies (including somatic hypermutation and all related processes).
Antibodies are produced by plasma cells (and that basically the only thing they do), which are differentiated from activated B cells which have undergone the selection process on the given antigen.
IgM is the first set of antibodies produced by the mature B cell, later on this often changes to IgG (different heavy chain, same antigen recognition site) by class switching.
The secreted antibody is IgA, which is found basically in all body fluids and is also secreted into the different mucosas of the body. It has two subtypes: IgA1 and IgA2 with A1 mostly present in the serum and A2 mostly secreted (see: "IgA subclasses in various secretions and in serum." for details).
IgA is made by plasma cells which are located in the lamina propria adjacent to mucosal surfaces. For details see thesetwo papers:

Intestinal IgA synthesis: regulation of front-line body defences.
The polymeric immunoglobulin receptor (secretory component) mediates
transport of immune complexes across epithelial cells: a local
defense function for IgA.

B cells (and also plasma cells) are found in the blood, they are then called peripheral cells. B cells have to be present outside the lymphatic tissues (not only bone marrow but also lymph nodes and the spleen) to be able to get in contact with antigens. Upon contact with an antigen they move into the adjacent lymphatic tissue.
You will not find IgG mRNA in the blood, as this will trigger immune responses. And it has no function outside of the cell.

thanks for the answer chris.  My immunology stopped at one lecture about clonal selection!

You`re welcome. It has at least some use that I learned this stuff. :-)

I find immunology to be particularly confusing - too many cell types doing only somewhat specified things...

@shigeta: immunology has many exceptions.. that makes it a little bit confusing

ha- i sometimes wonder if immunology has any rules! :)

Thats why I like immunology. It is not simple and you can find something new more or less every day. :-)

I know the thread is a bit old, but as per the terminology at least Kuby uses, Immunoglobulins come in two forms. The membrane form and the secreted form. The membrane form is the BCR, while the secreted form is the antibody. There is a difference in structure (the membrane one's got more hydrophobic residues) and a more interesting explanation of how they are differentially expressed. Why I bring this point up here is that, all IgA,D,M,G,E can be either secreted or membrane bound. Secreted here is from the cell and not necessarily into bodily secretions. A bit of semantics, but still.... :)

"B cells have to be present outside the lymphatic tissues (not only bone marrow but also lymph nodes and the spleen) to be able to get in contact with antigens."  This is a misunderstanding. Naive B cells come into contact with antigen in secondary lymphoid organs. Antigen is concentrated there by follicular dendritic cells, which allows for the necessary cross linking. Naive B-cells are not antigen presenting cells. In their naive state, they cannot be activated by antigen outside of lymphatic tissues.


text:
Length differences between physically interacting proteins
What can be said on the length differences between interacting proteins? Are they usually of similar sequence lengths or not at all?

What do you mean by length difference? Interacting proteins which are different in size? And why should this be a problem? Additionally: Proteins fold into a 3D structure, which is much more important for protein-protein interactions than the size.

Each protein has a sequence. Sequences have lengths (amount of amino acids). Some proteins interact by forming physical bonds to each other. I'm asking if something can be said about size differences between interaction proteins. E.g. - usually very small proteins would not connect with each other, but only with a bigger protein.
This is not "a problem". I'm simply wondering because I want to understand what would be a good descriptor for proteins when trying to model physical interactions.

I think that if you did an analysis of this it would be dominated by interactions involving the same protein (dimers, trimers). Apart from that I know of no bias towards similar sizes.

@Uri it seems like you mean to ask about 3D size rather than sequence length, is that correct? In other words, you are using sequence length as a proxy for some 3D size property.

No, I'm asking about sequence length.

This is just a gut feeling, but I would assume that sequence length is largely independent. In very large proteins, usually it is only one domain that interacts with a given binding partner. That domain can be a tiny fraction of the size of the protein. Eg. Nup358, a 358 kDa protein that has multiple domains that independently interact with Ran, a 25 kDa protein.

Just for reference, here's a question that actually asks about size: http://biology.stackexchange.com/questions/2965/what-role-does-a-proteins-size-have-on-protein-protein-interactions?

At least in a human protein interaction network, it appears that proteins indeed mostly bind to proteins of similar sequence length. Consider the figure below, based on analysis of a human protein interaction network from the Protein Interaction Network Analysis (PINA) platform. In the data set, the median relative protein size (the largest amino acid sequence length divided by the smallest in each interacting pair) was 1.9, the maximum value was 293.6 and the 99th percentile, which is the cutoff for the plot, was at 15.2.

Edit: As per stords comment below, you get essentially the same result for a random network:
In this case, the network was generated by picking two proteins at random from the original network, creating an interaction between them, and repeating until the random network has the same number of interactions as the original.
Immediately, it might look like the PINA PIN is dominated by random interactions. I would run some network analysis to determine its characteristics, but seeing as it's a rather large network it would take more time than I have right now. The results are similar for two additional networks with interactions in Saccharomyces cerevisiae and Caenorhabditis elegans respectively downloaded from PINA. Note that all three networks have been constructed from databases with varying levels of curation (See the original publication for PINA:  http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html). As such, many of the interactions might not be biologically meaningful.
Taking into account the above, you might want to define "interacting proteins" more precisely. One might expect that a better curated network only containing interactions with a known function or effect might give a different picture. However, using a more strigently constructed human "functional interaction" network published by Wu et al. (http://genomebiology.com/content/11/5/R53, FIs_043009.txt in Additional file #3) still gave a similar result.
Method: I made a Python script to calculate the relative amino acid sequence lengths for all interactions in a human protein-protein interaction network (PIN) available from PINA ((http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do). The network file is located at: http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.sif. PINs for other organisms are also available at the same site and many other places. The script can be used with any PIN in SIF format using UniProt identifiers.
The script can be downloaded here: https://github.com/jarlemag/misc-bioinformatics/blob/master/ProteinInteractionNetwork.py
The most time-consuming part was downloading the sequence lengths from UniProt. To avoid having to do that, the protein sequence lengths can be saved to and loaded from a text file.  The list of protein sequence lengths is here: https://github.com/jarlemag/misc-bioinformatics/blob/master/protlengths.txt To create the figure, place all three files in the same directory and run the script using Python 2.7.
Keep in mind that the PIN data may not be entirely reliable.

Did you in any way correct for the natural distribution of protein sizes? There are many fewer large proteins than small proteins, so just by random interactions I could imagine a plot like this.

No, I took a very simple approach - suggestions for improvement are certainly appreciated. How would you do that, specifically?

I'm not very good at statistics, so take my advice with a grain of salt, but what I would do is simulate this kind of plot, but just use random interactions between proteins  in your dataset rather than using known interactions. If the random plot looks the same, then the effect is likely due to the natural length distribution. If the random plot looks different, then the effect is likely real. Its qualitative, and I'm sure that there is a better way, but its quick and would be informative, I think.

Seems like you might be right. I've updated my answer.

On the topic of PIN quality, the following articles may be of interest: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683745/, http://www.nature.com/nmeth/journal/v6/n12/full/nmeth1209-934.html


text:
Is cancer a defect of the immune system?
Is cancer due to a defect in the immune system?

No, it isn't. Although cancers have to escape the immune system, they usually don't affect it, except for B cell lymphoma, but this doesn't make it an immune system disorder. Disorders of the immune system are diseases like SLE.

Please try and do some research before posting. At least explain why you think that cancer would be an immune disorder. As it stands, your question is like asking whether McDonald's makes cars. Unless you give some reason why you think it might be a car maker, the question makes very little sense.

This question appears to be off-topic because it is a wild stab in the dark with no research or any indication of why the OP might believe this to be the case.

@terdon: So, the question is too broad?

Yes, too broad and also too basic. We expect users to do research before asking, a cursory reading of the 1st paragraph of wikipedia's entry on cancer would show you that it is "a broad group of diseases involving unregulated cell growth" and not an immune disorder.

I think this is a fair enough question, a suppressed immune system can result in higher susceptibility to cancer. The immune system kills mutated cells as well as foreign pathogens. There is a lot of high level research into the development of cancer and its link to the immune system.

I agree with @Spinorial one role of the immune system to prevent cancer. If it cannot fulfill this task, then it is the main cause of cancer, and not the mutations of cancer cells. Afaik. there are immune cells which actively defend cancer cells, so I think cancer can be called as immune disorder.

It can be named an immune system limitation or imperfection though, not disorder. Disorder is something that is out of order, and there is no such normal immune system that can beat cancer. Not in humans at least. Still don't understand why the question is downvoted. Users are very rude here and tend to downvote every question they consider not interesting.

@ZAB Thanks. I've edited my question accordingly.

How the hell is this question off topic? How cancer relates to immunity is not on topic for Biology? What is this SE even for then?

@DanielGoldman If you can, please cast a vote to re-open. thanks

Cancer is uncontrolled division of abnormal cells. This is caused by mutations in a cell which causes a cell to divide more frequently and the lack of control by intracellular AND extracellular mechanisms. The extracellular mechanisms include growth inhibition by hormones, local factors, contact and also the immune system.
These cancerous cells could be immune system cells and then, in that respect, the cancer could be considered an immune system disorder. Or the cells could be of different origin, but due to the lack of a functioning immune system (particularly NK cells), the cells may divide uncontrollably whereas otherwise they would've been tagged for immune or self destruction. Or a cancer may be caused by a virus; in this situation an immunocompromised patient is more susceptible to a cancer caused by this oncogenic virus. In these cases the risk of cancer is increased due to a compromised immune system. So cancer risk may be increased in these circumstances but cancer still is not an immune disorder.


text:
how cells make other macro molecules?
We know that the nucleus of the cell is the White House of the cell and its DNA is the president and it commands to make protein. So my question when DNA only codes for protein and enzymes,after the birth of a new cell where does the cell get lipids and carbohydrates to make membranes, organelles, water, ions, plasma membrane etc ...?

Molecules like complex lipids and carbohydrates are all synthesized by a special class of proteins that catalyze chemical reactions, called enzymes. Since the information of these proteins is coded for in the nucleus, you can imagine that ultimately the synthesis of these molecules does boil down to the genome.
The basic building blocks that the enzymes use to synthesize complicated molecules come from things you eat. Of course, we eat things that were once alive, and so the molecules that we get have been built up through enzymatic processes in the organisms we eat.
Ultimately, the "pre-organism" source of most of our molecules is CO2 from the air. Plants and photosynthetic algae have proteins that allow them to use the energy of the sun to reduce the carbon, making useful compounds such as glucose.

so imagine the first cell of the universe the begining of the world where the cells got there other molecules??

Looks like in the beginning of the world there were a lot of organic molecules available (since there wasn't bacteria to eat them). The cells only began building them after a long process of natural selection. http://en.wikipedia.org/wiki/Abiogenesis


text:
What is the creature with the lowest neuron count that demonstrates cognition beyond reflexes?
I'm under the impression that nematode worms just perform the same scripted actions over and over again in response to specific stimuli. They have 302 neurons. Chimpanzees display problem solving capabilities, as do other mammals with smaller brains (cats, for instance with ~ 1 billion neurons). You might say that bees demonstrate something more than reflexes when they communicate the location of nectar sources to the hive (~ 960,000 neurons).
What's the creature with the lowest number of neurons to demonstrate something more than mere scripted actions? I would imagine its somewhere between a bee and a nematode worm...

How would you demonstrate that human cognition cannot be boiled down to scripted actions? Your question seems to assume its answer.

Depending what you mean by cognition, it could be zero.

Indeed, C. elegans nematodes (which are the ones you are talking about) do not show cognitive responses. AFAIK, Drosophila melanogaster is also able to learn and display some quite complex behaviors, but no cognitive functions. I believe the "simplest" organism known to display what could be called "cognitive" functions is the honeybee (see for example this article).
But as to your question:

to demonstrate something more than mere scripted actions

I would also ask "what is a scripted action?" and to what extend a complex, cognitive response from a monkey or a human isn't also scripted (though through many different interacting pathways)?

Ahh I guess I'm looking for learning or extremely basic problem solving. So, honeybees definitely learn. If two creatures are fighting and trying to anticipate each others moves, this would also fall under my definition of cognition, as this is not hard-coded genetically.

I wouldn't say learning is the criterion. In fact, nematodes can learn (see http://learnmem.cshlp.org/content/17/4/191.long).
The ability to "anticipate each others moves" seems a bit hard to quantify in real life. I think the criterion would rather be "abstract learning". While drosophila can learn (by appetitive and aversive conditioning), honeybee can learn patterns, "concepts" to take the word of the article. They can then transfer what they have learned in one situation to a new situation they have never seen.
Also, their "waggle dance" is flexible, and they can have a cognitive map.

What's a cognitive map?

You can find definitions in several articles [1,2], and a more general one on Wikipedia [3]. To summarize, it's a mental representation (e.g. from their spatial environment), which allows them to make plans and find novel solutions to a problem (e.g. find a new path to reach a goal). So it's not just "if the odor comes from the left, I go left", the bees "understand" where they want to go, and manage to find a way to go there. −−−−−−−−− [1] http://www.pnas.org/content/102/8/3040.full [2] colinallen.dnsalias.org/Secure/TCA/gould-final.pdf [3] https://en.wikipedia.org/wiki/Cognitive_map

So why do you say that Bees demonstrate a cognitive map, but Flies do not? Is it just that we haven't researched it yet, or do we know for sure?


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What is the significance of and biological mechanisms demonstrated in lac operon?
I would appreciate it someone could explain clearly how the genes in the lac operon of E coli are activated to allow the bacteria to metabolize lactose?
The part that I really don't understand is the activation of the lac operon.  A good answer would make clear to me how the introduction or removal of lactose from the envirnment activates and deactivates the different genes there.
Also, what are the specific functions of each of the genes (lacA, lacI, lacY, lacZ).
I am in AP Biology and I will not see the light of day again if I do poorly on this test. Please help!

You'll have to be more specific about which aspects of the lac operon you don't understand, currently this question is far too broad.

There are many good youtube animations and videos which might help you !

just trying to help - I made some edits to illustrate what they want.  Feel free to roll them back if you don't like them.

The lac operon in E coli is a set of four genes which work together to allow the bacterium to make use of lactose for energy. An Operon is a set of genes which are co-transcribed on a single mRNA, controlled from a common promoter.  While operons are nearly always found in bacteria, eukaryotes (and viruses that infect eukaryotes) do have some sets of genes organized into operons.
lacZ and lacY is the business end of the lac operon. They are the only 2 genes necessary for lactose usage in the cell.
lacZ codes for beta-galactosidase, an enzyme that cleaves the lactose disaccharide into D-galactose and D-glucose.  Most of know that glucose is an important source or energy via the glycolysis pathway, which is highly connected energy usage in the cell.  Galactose is readily converted by an enzyme (galactose mutarotase) into glucose, making lactose an efficient source of energy.

lacY codes for a protein found in the cell membrane called lactose permease which pumps lactose into the cell from the outside using the proton gradient inside the cell for its motive force.
The lacA gene codes for an enzyme which transfers an acetyl group to galactose, which may prevent the buildup of galactose in the cell.
The way the operon works is more important than what it does.  the lac operon was one of the first examples of transcription regulation every studied.  lacI is not in the lac operon, but it is the single gene which controls whether the operon is copied to RNA from the chromosome.  lacI is translated to the lac repressor protein (LacI), which binds to one of three sites in front of the lac operon.
lacI is a repressor gene - when it is active, it prevents the lac operon from being transcribed into RNA.  LacI is a tetramer - four copies of the protein form a complex.  LacI binds to allolactose, a derivative of lactose, when it is present in sufficient quantities, which then causes it to release itself from the chromosomal DNA, allowing transcription to occur and the lac genes may be expressed.


text:
Genetics independent assortment?

As indicated in this question, what do you think is is the best explanation for the observed progeny, is it because distance between genes affects recombination frequency? My main concern is question b).
Any help would be greatly appreciated thanks in advance!!

Until now, it looks good. When you are looking at basic mendelian gene linkage problems like these and you find out that the chi square analysis rejects your hypothesis, it means that there is linkage. In that case, you should have a case where your two recombinant genotypes have an approximately equal number of progeny and your two parental genotypes also have an approximately equal number of progeny. In your case, 220 is about 230, and 270 is about 280.

(source: k12.ny.us)
This image is just like your problem. I want you to imagine that b+ and b represent A and a in your problem and that vg+ and vg represent B and b in your problem, respectively. You start out with an AaBb crossed with an aabb. On the gametes line, it lists all of the possible gametes of this cross. On the line where it describes testcross offspring, we see a situation very similar to yours. In this case, AaBb = 965, aabb = 944, Aabb = 206, and aaBb = 185. We have our two pairs: AaBb/aabb and Aabb/aaBb. Sound familiar?
The recombinant offspring are defined as the offspring that do not have a genotype of either parents. The reason this is important is because you need a crossover to get a recombinant. The closer two alleles are together on the same chromosome, the harder it is to get one of the alleles to cross over without the other one crossing over with it.
Let's clarify. This means that if the alleles are closer, you get less crossovers. All recombinant exist because of a crossover. Therefore, the closer two alleles are, the less recombinants you get.
Quick note: the formula for the distance two alleles are from each other is expressed by this formula:
100(recombinant frequency) / (total offspring) = distance apart.
This is consistant with everything we have said, because as recombinant frequency decreases, distance apart decreases as well.
Another way to explain it: on the gametes, AB and ab really like to stay together, as they are LINKED. It is very difficult to separate them. That is why there are more AaBb and aabb; they only require the gametes AB and ab.
Apply the formula to find out how far they are apart. I think you can figure out the rest from here. I want you to try and answer the question.
Hope this helped! :)

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


text:
Promoter in the lac operon
Here is the question:
Suppose an experimenter becomes proficient with a technique that allows her to move DNA sequences within a prokaryotic genome. If she moves the promoter for the lac operon to the region between the beta galactosidas gene and the permease gene which of the following would be likely?
Here is the answer:
Beta galactosidase will be produced.
My question to you is: why is this so? I have no idea where this conclusion came from.
Thanks.

The question doesn't make any sense. Apparently before there is any manipulation there is already an intact lac operon present. Is it the lac operon or the lac operator that is being moved? And under what conditions is the production of beta-galactosidase being measured?

Unfortunately, I know nothing more about the question than you do. This is a test question that just doesn't make sense.

If you can, I would ask the test writer to explain.

Since @biogirl has given an answer, I'll add my opinion:
β-galactosidase would be expressed but the permease and transacetylase would not.
The operator lies adjacent to/slightly overlaps the promoter, upstream of the lacZ gene. Binding of the repressor to the operator blocks the promoter, and induction of theoperon involves the repressor leaving the operator unoccupied. If you precisely excised the operator and transplanted it between the lacZ and lacY genes then I think the promoter would be constitutively expressed leading to β-galactosidase synthesis, but the operator would block the polymerase from transcribing the permease gene. In this view the operator would be acting more like a terminator.
Then, if an inducer was added it would relieve the effect of the transplanted operator and the downstream genes would be transcribed. It's even possible that this experiment has been done sometime in the last three decades.
added later:
The OP has now edited the question in such a way as to make my answer, and the answer from @biogirl, nonsensical. The original wording referred to moving "the lac operon" not "the lac promoter", hence my question in a comment asking "operon" or "operator"?
I'll leave my answer here, but this question is now so compromised that I advise everyone to just forget about it.

I'm inclined to agree with this answer. I know that the distinction between the lac operon being a distinct domain from the lac operon has been known since at least the early 1970s. The lac promotor/operon regulatory region is also known to be leaky, suggesting Alan's answer is correct.

I believe the answer should be that permease is expressed.

As you can see from the image, if the operator is moved between Z gene and Y gene, Y gene should be expressed and permease should be made.


text:
Evolution (Reductionism)
My recent post was tagged as unclear so I wanted to re frame my question. Though I am a layman, I would love to read books and find the stuff, if I get an overall picture of intelligence factor. My question is, how come evolutionary mechanism of protecting ones species made them adapt to their environment ?
The answer comes by the genetic mutation, the switch genes and so on. But how are these cells intelligent to cause such mutation ? For instance, cells don't have intelligence of their own, so presented a situation where in you have to see, but have no eyes, or have to walk but have no legs, how come cells know that they have to work against gravity and develop such structures and hollow bones in birds to make the flight easier ? Does it mean that nature is intelligent ? How come matter itself create gravity, space etc., on one side, and creating beings to overcome it ? Isn't the matter altogether ? If that's the case, imagine a thought experiment, where in we all have dangerous predators which are 4D beings. So since our cognitive and visual percepts  are just designed to perceive 2 dimensions at a time, we being 3D creatures. So over thousands of years, since we have to live and survive, would we develop a vision that can see 3D ? It would be amazing then. It then means that there is an intelligence factor in nature that tells the creatures how to change !
Please do answer, and again repeating I want to hear, how Genes know that they have to work against gravity, or develop a particular efficient thing, that can solve the problem. Otherwise it's as if Genes permute infinitely, and then develop all possible models, and only those which serve the purpose will stay.
Please do clarify.
Thanks !

Hi! It's wonderful that you are thinking about evolution! Could you clarify on what you mean by evolutionary mechanism of protecting ones species ?

if Genes permute infinitely, and then develop all possible models, and only those which serve the purpose will stay. appears pretty close to what is actually happening.

@biogirl, Thanks so much for your reply. I was mentioning that, in the sense, that evolution always occurs to safe gaurd one's species.

@SatwikPasani, Great ! Thanks ! Then do you mean that they permute infinitely ? Isn't it a bad model to explain the underlying enigma ? Someone said, seeing universe as a dice play, or someone throwing marbles on ground is not a good way of looking at it. As Einstein said, God doesn't play dice.. Continued

+1,"But what has convinced many people, including myself, that one should take models with extra dimensions seriously is that there is a web of unexpected relationships, called dualities, between the models. These dualities show that the models are all essentially equivalent; that is, they are just different aspects of the same underlying theory, which has been given the name M-theory. Not to take this web of dualities as a sign we are on the right track would be a bit like believing that God put fossils into the rocks in order to mislead Darwin about the evolution of life. - Stephen Hawking

@Iyengar Hmm! The statement you are saying(regarding the benefit to species) implies a misconception. Evolution does not happen to safeguard members of a species. It happens at the individual/at the genome level. If an old spider "sacrifices" itself,in principle, it is not so that a competitor of the spider species is reduced/ the species do not face overcrowding. There has to be a selfish advantage to the spider.

I also strongly recommend the book - The selfish gene by Richard Dawkins which explains the common concepts of evolutionary biology in an interesting way !

I think we may be missing a piece from Darwin's original hypothesis.
An outline of the first 4 chapters of Origin of Species form the kernel of the Theory of Evolution:
1: Variation under Domestication
2: Variation under Nature
3: Struggle for Existence
4: Natural Selection

Really you can't reduce evolution to less than variations; competition (struggle) ; selection.  that's about as far as you can go and still call it evolution.  Even genetic algorithms which don't use living organisms at all have these 3 steps.
Most people don't have an issues with Variation any more.  At one time it was thought that individual variations were not important, but now most people understand that one water bug might have significant individual differences from other water bugs and its not just people who look at each other and marvel at individual traits.
The struggle for existence was difficult for people to accept at the time, but its simply that most living things don't make it.  Darwin had noticed that each spring that a typical bird pair might have 3-4 eggs in their nest but if you do the numbers it tells a story of how much of a struggle life can be even if we don't see it on a walk in the woods.  If all eggs reached maturity and reproduced, a single pair of birds would generate enough birds to cover England in about 40 years.  That's just a squeak under 3.5^40 without death from old age.
The struggle for existence hints how competitive Selection is.  In their breeding lifetime, to have a static population of birds, a breeding pair produces 2 breeding offspring out of perhaps 14 eggs lain.
It's a given that genes don't know that they have to do anything, but if they don't work well they will not be seen again. Their host dies from a developmental issue, falls and hurts itself doesn't display the right plumage, isn't fast enough to catch its food, is so slow that it gets eaten, its seed falls on soil it cannot germinate in, etc etc.
The list is endless as to the things that can go wrong in the wild and would cause an individual to be removed from the gene pool and they don't produce offspring. All of the important qualities that genes need to have is mysteriously embedded in what we call the environment - the earth, the air, the water the behavior of other living things decide whether most genes make it or not.
If you need any more evidence that intelligence has nothing to do with evolution, then look at human beings... not getting along well with other living things well now - is that smart?
An example of selection
Since it was requested, let me expand and give a very simple example of random selection that I've always liked (Disclaimer: maybe because I made it up as far as I know!).
Take a box of 100 coins.  We want all 100 coins to be heads up, but we can't individually flip any of the coins over: we can only shake the box.  Note that when we shake the box - nothing is thinking or acting consciously.  Genes do permute randomly and, for all reasonable approximations of infinity, infinitely, but they tend to stick around when something works.  This makes evolution seem unnaturally quick to respond.
Method 1: shake the box, looking every time. There are 2^100 combinations.  Getting terribly lucky we'd have to shake the box 2^97 times before we accidentally caught a box of all heads up coins.  That's random chance.
Method 2: if we remove the coins that are heads up every time we shake the box, we'll be shaking the box 8 times or so.  That is similar to a strong selection case in evolution: the coins which are heads up are like traits which have an advantage so they stay around.  Its striking how efficient this can be and how many tremendous changes can happen in a short time if there is selection and advantage.
Note that we have plenty of bad traits here (tails up); they show up all the time - with great frequency.  They just don't stick around because the struggle for existence is so challenging.
You can further get an idea of weaker selection if you can imagine that instead of the heads always staying heads, you have a little stickiness on the tails of the coins.  80% or 60 or 52% of the time these coins stick and stay as heads.  It still will not be long before you find that the coins are mostly heads.  10 20 or 30 shakes of the box rather than 8.
Where do new traits come from then?
So taking all this and thinking about how new traits like eyes which had not been
seen before, the same blind and random process applies.  It is better not to think of humans and human traits - we're the product of over a billion years of selection and evolution!   Think how primal traits at the bacterial level emerge.
Below is a picture of salt pools in the San Francisco Bay.  Evaporation increases the salt concentration in the pools and as they become inhospitable, halophilic (salt loving) bacteria take over.

The pools are colored because these bacteria have an ancient mechanism which allows them to harvest light to pump the salt out of their bodies and help create energy as well.  The light is harvested in one well documented case by a retinol molecule which absorbs blue light.  Retinols are a variation on vitamin A and must be quite ancient.
Yet a similar molecule, retinal, is used in human eyes as the light sensor there.  A similar protein holds those light sensing molecules in both human and halophile as well. While the structure of the eye and the nervous system that processes information into the brain all came later, you can see at one point the interaction with a bacterium with light became so useful that once it evolved, it has stayed in the gene pool since the days of bacteria to be the light sensor.  Vitamin A is the product of a biosynthetic pathway that very easily makes a variety of molecules.  The light sensing genes that used them evolved once, but variations on it sense light in our eyes today.

+1, @shigeta, Thanks for your answer. Anyway, it answered my question, but I didn't understand how genes adapt themselves to the environment ! I mean how can they create eye to grasp light and other things. How do they know that ? Where does the interaction start from ? For instance take beings without eyes, how did they get eyes from ? What caused the genes to create such structure ? How are they intelligent on their own ?

On a side note, loved this very comment of you. "I believe that biology and other stackexchange sites should welcome newbies and encourage dialog about science, evolution, technology and etc, not kick them back down the stairs when questions are not worded quite right. " Love to see that day, where in people in scientific field encourage layman, and where the knowledge is free. Thanks a ton !

Hi @Iyengar - yes welcome to biology.stackexchange!  Richard Dawkins wrote an entire book called the 'blind watchmaker' to try to dispell this idea that genes are active participants somehow.  let me expand the answer a bit.

The most wonderful piece of example, I have ever read. Can't stop voting it as perfect answer. You should seriously consider writing up articles and giving expositions for layman, which will benefit people like me ( You can look at my background in about me ). I would love to stay in touch and can't thank you enough. Can we exchange emails ? Do you have website ? @shigeta

Hi Iyengar - thanks - i use stackexchange to sharpen my writing skills and i teach classes locally here.  I've updated the url on my profile - you can contact me through the info there. anyway i'm glad you like the answer!

I read your answer many times, and it's so useful. But still there is some doubt, because you didn't comment about the thought experiment I have stated. So in the beginning cells had no eye. How did they understand that they have to develop something related to photons and absorb them, there by encoding all the distance ? So isn't it a very complex phenomenon, and it has something to do with nature's interruption as well ? Sorry if I am sounding foolish. @shigeta

Hi @Iyengar.  there is no answer that will remove doubt I find. Evolution is not intuitive to people and its a process to understand it.   Nevertheless I'll add a paragraph about this case explicitly.  Its getting a bit long though. go ahead and ask other questions if you are still curious.

Now, I got the overall picture. Can't be a clearer picture than this, unfortunately I can up-vote only once. I was asking this question to my friend as well, who is doing his PHD in biology. He said, it's impossible to explain in an hour. I challenged him, and showed this to him, which is less than say 1000 word. He was flabbergasted. People like you should be there in every field, to bridge the gap between experts and layman, there by bringing science to common man. Thanks so much @shigeta

youre welcome! One of the best ways to learn is to explain to others. stackexchange is a good place to learn to write and challenge yourself on things you don't understand...

This is a superb answer! Clear, well-written and just detailed enough. Plus, that picture of the salt pans is just gorgeous! Let me echo the OP and say I wish I could upvote this more than once!

You know what, I can upvote this more than once. @shigeta: bounty coming your way in 24 hours.

hey @ChinmayKanchi - thanks - I really appreciate that you like my writing.   Lets all talk more - post some more questions..  surely there are other issues.  Common questions are; 'If its selecting fit individuals, why can't evolution make us able to digest any kind of food/super strong/ live forever?'  'if we're always competing, why do people form civilizations and cooperate?' 'are people still evolving? is selection still operating?'  there is a lot more about the evolution of eyes too - that's been a hot story.   etc etc

@shigeta: I'm a biologist myself, so I don't often have questions I can't answer with a quick Google/Pubmed search. Re evolution of the eyes, I remember that Walter Gehring gave his last pre-retirement talk at our University. Best talk I've ever been to! It was only rivalled by this fantastic woman who came to gave a talk about explosives and actually blew things up during the talk :D

Hey @ChinmayKanchi well maybe you would like to write that one up? if I ask will you post?  biostack needs a nice reference to it. PAX8, crystallins etc... its one of the best stories of this kind of evolution around...

Too long for a comment:
Evolution and mutation has nothing to do with intelligence and is not influenced by the cells itself. It happens by chance and if the mutation turns out to be beneficial (or at least not harmful for the moment) it will be a selection advantage.
Something to think about: If a mutation in an enzyme which is responsible for Glucose metabolization allows bacteria to also metabolize another sugar (lets say Galactose) with the same enzyme, this will not change anything for the moment. If these cells are living in a substrate where glucose gets a limiting nutrient but which contains still a lot of galactose, these bacteria will have a growth advantage and overgrow the other strain. Eventually the strain, which can only metabolize glucose will disappear completely.
Evolution is also a very gradual and slow process. So it is not boom suddenly birds appear on the sky, it is a process which took millions of to happen. All the things which allow birds to fly (hollow bones, feathers and so on) developed slowly.
Genes do not know anything, since they have no consciousness. They are "simply" building blocks. They also don't solve any problems, they are only expressed, not more.
It is like you write, genes acquire mutations, which allows changes in function or morphology. As stated above: This is a slow and steady process with a lot of dead ends.

Wonderful ! What about my thought experiment ? Any answer/comment to that ? Thanks so much +1. @Chris

@lyengar: I expanded my answer.

Nature isn't intelligent, genes aren't intelligent, and evolution doesn't have a purpose or a goal.
Mutations are random, and roughly 97% of them are deleterious while roughly 0.03% are advantageous for the species. This is the first prerequisite of evolution.
The second one is differential survival. An organism with a better chance to survive or reproduce (because of a random mutation which was advantageous) will have a better chance of passing on that trait to his offspring.
We're talking about billions of years, and billions and billions of organisms, and that's how complex structures evolve. The most notable example would be the eye. First, by random chance, an organism evolved a light receptor cell and had a better chance to survive. Then there were several light receptor cells, then there was a chamber, and so forth. Eventually you have the eye as we know it. It took billions of years.

No.  That can't possibly be right.  The vast majority of mutations are NEUTRAL, or nearly neutral.  See Bromham & Penny (2003)

There is an average of 2.2 new deleterious mutations per human zygote, and 0.02 new advantageous mutation per human zygote.

Citation?  How does that compare to the # of neutral or nearly neutral mutations?

A mutation is an error, to put is simply, and you are correct that some of them have no visible effect. But you misunderstood the paper you linked to.


text:
How to avoid air bubbles while pipetting?
I get air bubbles while pipetting small volumes. How can I avoid them ?

You can try to be slow?

You have to pipet up slow and make sure your tip is (and stays) completely submerged in the solution. On the other hand it shouldn't be put in too far.

You're still pipetting too fast, you should move the piston slowly and evenly to avoid air bubbles. Also make sure that you wait a second or two for the liquid to rise before moving the tip out of the liquid reservoir.
Pipettes can also behave rather weird with any liquid that differs significantly in any physical property from water, e.g. very viscous solutions.
You can find a few more tips in this document from Eppendorf or this one from Thermo Scientific.

Sometimes with very viscous liquids (such as detergent solutions), it may be necessary to slowly "rinse" the inside of the pipette by doing a full pieptte up and down of the liquid before an accurate amount will be drawn.


text:
parallels or replicates?
I am writing an article where I describe real-time PCR experiments. My collaborator, after reviewing the article, consistently replaced the word "parallels" with "replicates". Are they not synonymous?
I prefer the word parallel, because, in the context of PCR, it implies that these three identical experiments were performed in the same real-time PCR run (and not consecutively).

Can you give a couple of examples of the text in question?

Replicates is certainly more common usage in general. If you wish to emphasise that these replicates were performed in the way that you describe perhaps say "replicates run in parallel".

Parallels is not as good a word imho - you can run several concurrent experiments and call them run in parallel. replicates are the same experiment.

In any case, parallels won't work, you want experiments run in parallel which is not the same thing. Parallels cannot be used that way.

The explanation I got when learning how to do qPCR was that you need run both replicate experiments and parallel experiments to get publishable data.
Replicates (or biological replicates) would be qPCR runs on independently collected samples. That does not count your control vs your experimental groups. So for my work I had to collect 3 sets of control tissue and 3 sets of experimental tissue from independent sets of animals (in my case 3 generations but for mammalian work I think three different animals would be ok).
Parallel does imply that you ran the the samples together in the qPCR machine. I think the standard is that for each sample in a particular replicate you need to run three qPCR reactions in parallel. So in total you need to run 9 wells of qPCR reactions for each test group.

Technical replicates show that the technical integrity (pipetting, master mixes, detection) is consistent, which biological replicates show that the effect you are measuring is genuine and happens not by chance. Usually you do three technical replicates per run and sample and repeat an experiment three times independently.


text:
All flowering plants gives fruits. Why does jasmine flower plant not yield fruits?
My question is actually my long term doubt. I have seen most of the flowers turning into fruits. But why not this jasmine flower?

I'm sure they do, unless some genetically modified to hinder fertilisation. Interesting are Banana & sugarcane plants.

They do make berries - they are red to violet. See here.

Flower gives rise to seeds and fruits which are the ways through them the plant distributes the seeds.
Here, one should differentiate botanic term "fruit" and general common meaning of the word "fruit" which are not the same.
Botanic fruit can be subtle, not fleshy and come as a grain or pods.
Jasmine fruits are black berries.


text:
How are viruses weakened to be suitable for vaccination?
I understand there are two kinds of active vaccination

Injecting complete viruses that are weakened to not cause the disease being vaccinated against
Injecting only antigen particles of viruses that the body creates antibodies for. So the disease can't arise, not even in a weakened form.

I am wondering how the viruses for vaccination are weakened. Is this simply a process where randomly parts of the virus DNA/RNA are taken out and tested on animals, and as soon as it is sufficiently weakened, it is considered suitable? Or is this an analytical and systematic process?
I am wondering because some popular vaccinations (including that against measles) can still (very rarely) cause fatal complications. Which made me think whether it's systematic or just "accelerated mutation and selection".
I'm interested in an answer for layman, if that is possible at all.

There is a Wikipedia page on the topic of attenuated vaccines.
Basically the idea is that the virus is grown on some sort of foreign host such as cells in culture, eggs or an animal. This selects for mutant viruses, present in the original population, which are pre-adapted to the new host (so that they grow better). By repeating this process several times it is possible to develop a new variant of the virus which grows poorly in the original host (i.e. humans) but is still able to stimulate an immune response. The resulting antibodies, will recognise a subsequent infection by the original disease-causing virus as long as the viral component responsible for the immune response is still present in the attenuated virus that is used for vaccination.

So simply the fact that the virus now replicates in a foreign host is enough to ensure that it no longer affects humans? I would have expected that there needs to be some sort of selection for strands which do not make humans sick, but obviously the only way to do that would be to try the mutation on humans which is not possible for ethical reasons.

There are basically three classical possibilies:

Using an attenuated virus as Alan described in his answer
use only parts of viruses (here mostly proteins, which are displayed
on the surface of the virus and which can be recognized by the immune
system)
inactivated viruses (here often formaldehyde is used, which changes
parts of the proteins, the formaldehyde is then cleaned away to have
the vaccine free of it)

The part you describe about using DNA from a virus is done these days. It is called "reverse vaccinology" and uses conservation analysis between different strains (this is also used for bacteria) to get a vaccine which covers as much different strains as possible. For the vaccine, proteins are selected which are conserved as good as possible and which show no similarities to human proteins (you don't want to induce autoimmunity). Candidate proteins for a vaccine are then expressed biotechnically and tested if they work.
Complications in vaccinations (which are really rare, for measles the chance for complications is 3-4 orders of magnitude lower than when actually get the disease) are usually due to allergic reactions.


text:
Can Listeria monocytogenes endotoxin act as an A-B toxin?
I think no, but I am not sure since Listeria is Gram-positive and probably has lipopolysaccharide (exception among Gram positive bacteria).
Can Listeria monocytogenes' endotoxin act like exotoxin A-B?
(In which component B lets component A inside the cell and component A causes the toxicity.)

Considering great research we did after the answer was accepted, I should add important information about the topic. The old (and accepted) answer follows in "" marks for the sake of clarity.
We found that in spite of the earlier reports, the newest ones failed to find endotoxin-like structure in the Listeria born material. Most academic discussions about the issue say there is no such thing called "listeric endotoxin", thus I gave a right answer to a "compromised" question.
I should say that question is still brilliant because it promoted great research and should be an important source for everyone looking for information about listeric "endotoxin"

Listeria endotoxin is not a protein. Thus, is lacks enzymatic activity
  and acts indirectly by binding to sensitive receptors on macrophages.
  Thus, it can not cause lysis itself.
Considering AB-exotoxins, A-subunit is a protein that has enzymatic
  activity (responsible for toxin action)  and subunit B has no
  enzymatic activity (protein responsible for binding to receptors).
Thus, the answer to your brilliant question is NO, Listeria endotoxin
  cannot act as AB-exotoxin being nonprotein and non enzymatic
  substance.
Also, don't be confused with Listeriolysin O, which is listeria's
  eXotoxin protein which is pore-creating protein.

Just to add some important relevant information to the answer from @Ilan.
There is no evidence for the presence of endotoxin/lipopolysaccharide in Listeria.
There was an early report of the presence of LPS (Wexler & Oppenheim, 1979) but this was contradicted by a later study (Maitra et al., 1986). The endotoxin activity of Gram negative bacteria is strongly associated with the lipid A moiety of the LPS. Lipid A is synthesised from N-acetylglucosamine in a three step pathway encoded by the genes lpxA, lpxC and lpxD. I obtained the sequences for the corresponding E. coli gene products and conducted BLAST searches against the Listeria monocytogenes genome with these results:

lpxA - best hit E=0.11
lpxC - no significant hit
lpxC - best hit E=1e-04
the last hit is to a 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase whereas the E. coli gene encodes a UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase. The similarity in the sequences seems to be because they are both members of a large superfamily of acyltransferases.

I conclude that Listeria monocytogenes does not not synthesise lipid A and therefore has no LPS, and no endotoxin.
Wexler, H., and J. D. Oppenheim. 1979. Isolation, characterization, and biological properties of an endotoxin-like material from the gram-positive organism Listeria monocytogenes. Infect.Immun. 23:845-857.
Maitra, SK et al. (1986) Establishment of beta-hydroxy fatty acids as chemical marker molecules for bacterial endotoxin by gas chromatography-mass spectrometry. Appl. Env. Mic. 52: 510-514

Thank you for the addition! I corrected Ilan's answer accordingly.

I"m away from sources now, but I met sources said endotoxin exists

@ilan I tried pretty hard to find any references, so I'll be interested to see what you found.

No problem, will look for the sources later.

@AlanBoyd I tend to agree that Listeria does not produce endotoxin at all. However, multiple sites and even USMLE examination board state it does produce endotoxin. I found older articles than you did, so at this moment I upvote your answer as important one. Although my answer was right, but the question itself was probably biased and compromised.


text:
What's the point of glycolysis in fermentation?
In order to initiate glycolysis, 2 ATP are necessary. In the glycolytic process, you generate an additional 4 ATP, which results in a net gain of 2 ATP.
If you don't undergo glycolysis, however, then you have an extra 2 ATP not being used. If you do glycolysis, you still got only 2 ATP. Am I missing something here?

replace "ATP" with "money" and you have a financial system - they do plenty well :)

Turning 2 ATP into 4 ATP isn't good?

you said that glycolysis generates net 2 ATP. That means 2 ATP in excess of what you started with. Plus @Chinmay and Satwik's answers

Suppose the cellular pool has $x$ATP before starting glycolysis. In the initial phosphorylation steps, we use up two ATP to get the total tally at $(x-2)$ATP. The following steps yields $4$ ATP which brings the final total to $(x+2)$ATP.
Assuming the cell is performing fermentation, the two additional $NADH$ formed will not be contributing to any ATP gain. And hence we earn a total of $2$ ATP in excess of the already existing amount.

Actually, the NADH contributes to ATP gain in many fermentative systems.

@ChinmayKanchi You might be correct. But I guess the OP's concern is limited to cases where substrate base phosphorylation is the only source of ATP.

Remember that glycolysis yields 2 NADH as well as 2 net ATP. This NADH can be used to a terminal electron acceptor to produce an end product with a net gain of ATP. End-products of fermentation can include lactate, acetate, butyrate, propionate and ethanol, all of which generate different amounts of additional ATP.
The exact pathways involved vary according to the organism, but anywhere between 1 (or even 0.5) and 4 additional ATPs can be generated, even without the involvement of oxygen. In the case of aerobic respiration of course, the NADH feeds into the electron transport chain and yields ATP.
EDIT: It's perhaps worth noting that the 2 ATP is gained. See @SatwikPasani's answer for the math.


text:
eye myopia power changes with brightness
Is there a condition where myopic power changes with ambient brightness. When I drive in the morning in bright sunlight my power is -4.0; however when I wear the same -4.0 glass in the evening (dusk time and night) I cant see properly. The images are blurred. I have to change to -5.0 glass. However the same situation does not happen in my right eye which has a constant -5.0 power in both daylight and night. I have observed this for many years (15+).

NIGHT MYOPIA -  is a tendency for eyes to become near-sighted in dim illumination.  There are multiple theories explaining the phenomenon, most of them are related to accommodation or chromatic shift in scotopic light conditions when to light is focused before the fovea thus worsening the existing myopia.
Citation:

In dark adaptation the eye becomes more sensitive to shorter wave
  lengths (Purkinje shift- In the light-adapted eye the region of
  maximal brightness is in the yellow; in the dark adapted eye, the
  region of maximal brightness is in the green),and visual acuity
  depends on parafoveal blue cones. Shorter wavelengths come into focus
  in front of the retina, and this chromatic aberration accounts for
  some of the relative myopia that a normal eye experiences at night;
  much of the remainder is due to an increase in accommodative tone in
  the dark.  It is also called dark focus of accommodation, or tonic
  accommodation, or resting state of accommodation. Consequently, a
  measurement of the refraction (i.e. the determination of appropriate
  optical glasses to obtain good vision on these distant objects) gives
  the result that the eye is myopic. Night myopia can reach values of up
  to about - 4.0 D. Night myopia decreases with age31 and therefore it
  can be of special importance for young drivers at night. In one
  experiment with people aged 16 to 25 years, 38% had night myopia of -
  0.75 D or more, and 4% had – 2.50 D or more. Cause of Night Myopia:
Spherical aberration (The optical effect of the larger pupil decreases
  the depth of focus) Chromatic aberration. Parkinje shift Ciliary spasm
  At low light levels there is a change of the biochemistry of imaging
  on the retina: in bright light the receptors in the retina are cones
  with higher image acuity, and imaging of colors, whereas in low light
  the receptors in the retina are rods with reduced image acuity, and
  imaging of black and white only. The transition between both states,
  i.e. to get maximum sensitivity when moving from the bright to the
  dark, doesn't happen immediately, but takes some minutes33. This is a
  problem e.g. when driving a car in sunlight and entering a tunnel. The
  low light imaging by rods in the retina can be further reduced by a
  lack of vitamin A and zinc Symptoms:
  1. Blur vision only in low luminance.
  2. Feeling discomfort while maintaining fixation in low illumination level.
  3. Difficulty in night driving.
  4. Hallows around light.

While this link may answer the question, it is better to include the essential parts of the answer here and provide the link for reference.  Link-only answers can become invalid if the linked page changes.

@SatwikPasani thanks for your constructive comment. The  answer changed appropriately.