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Reason for conversion of glucose to fructose in glycolysis
In glycolysis, glucose is converted to glucose 6-phosphate so it can not diffuse out of the membrane. Then it is converted to fructose 6-phosphate.
Why is this? Perhaps it makes it less stable so it is easier to break down into pyruvate?
That is just a guess, is anyone able to provide more information about this?

Don't guess. Please do some research before posting basic questions that can be answered by reading a text book of biochemistry. For example Chapter 16 of Berg et al. online.

However as I do not think either of the answers (including the one you accepted) are adequate, the point is less obvious than I imagined.  I have therefore provided my own answer.

Clarifying the question
The pathway of glycolysis starts a hexose (glucose), but at a certain point — the aldolase reaction — two molecules of a triose are generated, then interconverted to the same triose, after which the pathway continues to pyruvate, generating net ATP. These triose molecules each carry a phosphate, which, as the poster mentions, prevents them diffusing through the cell membrane, so the hexose precursor needs to carry two phosphates. Thus the question “why is fructose formed?” can be restated as:

“Why is the hexose precursor of the two triose phosphates fructose 1,6-bis phosphate, and not simply glucose 1,6-bis phosphate?”

Short Answer
The chemical structure of glucose is not suitable to form a bis-phosphate compound that can yield interconvertable triose phosphates in the biochemical reactions the cell employs.
Fuller Answer with Chemical Details
First consider the linear and cyclized structures of relevant phosphate derivatives of glucose and fructose:

Glucose 1,6-bis phosphate may be unfamiliar: it is found in cells in low amounts and may have some regulatory function. Inspection shows that, because the aldehydic group is at the 1-position of glucose, a phosphate can only be added at that position after cyclization generates an alcohol there. Once glucose 1,6-bis phosphate has been formed it cannot convert to a straight-chain structure, unlike fructose 1,6-bis phosphate where the ketonic group is in the 2-position. (Hence none is shown.) This is the key point.
Now let us turn to the triose–hexose interconversion, which is necessary for both glycolysis and gluconeogenesis, which ever originated first. This has two requirements:

That the triose phosphate molecules can react with one another to
form the hexose carbon backbone (easier to consider the reaction in
this direction).
That if different triose molecules are required they can easily
interconvert from (or to) a single triose.

Requirement 1 is satisfied most easily in biological systems by an aldol condensation such as the aldolase reaction (also found in the Calvin cycle) in which the nucleophilic carbon of an enolate attacks the carbon of an aldehyde.
Requirement 2 can be satisfied by the isomerization of an aldehyde (like glyceraldehyde 3-phosphate) to a ketone (like dihydroxyacetone phosphate).

The fact that a ketone like dihydroxyacetone phosphate has the potential to form an enolate (shown above) explains the particular suitability of these trioses in relation to the aldose reaction:

[Taken from Chemistry Libre Texts.]
The initial product of this reaction is, of necessity, a linear hexose 1,6 bis-phosphate — with the fructose as the hexose as its carbonyl is at C2. After the fructose 1,6-bis phosphate has lost the phosphate at the C1 position it can isomerize to glucose 6-phosphate (with the C1 position free to form an aldehyde) in a similar manner to the triose phosphate isomerization.
So it is not just the symmetry of fructose (noted by the poster in a comment) that is important — but the structure of glucose itself. Glucose 1,6-bis phosphate is not, of course, the only sugar that can become ‘locked’ in its cyclic form. For example, the deoxy-ribose rings in the backbone of DNA cannot linearize because the bases are attached to the C1ʹ where the aldehydic group was originally.

Avoiding diffusion is one reason to phosphorylate glucose, the other is that it is removed from the osmotic balance between inside and outside of the membrane, so it can be transported at a high rate.
The Glucose-6-phosphate can then be used as a substrate for different pathways, namely glycolysis and the pentose phosphate way, and (depending on the organism) also be converted into glycogen and starch for further storage.
The reason for the phosphorylation lies further downstream in glycolysis: The isomerization by the glucose phosphate isomerase and the subsequent second phosphorylation into Fructose-1,6-biphosphate make the conversion and dedication of the molecule into the glycolysis irreversible.
Fructose-1,6-biphosphate is then cleaved by the aldolase into two C3-units: Dihydroxyacetone phosphate (DHAP) and Glyceraldehyde 3-phosphate (GA-3-P). GA-3-P is converted into DHAP, so that downstream only one metabolite needs to be processed.

Very good response thank you, in addition I finded out that fructose 1,6 biphosphate is somewhat more "simetrical" than glucose-6-phosphate, if it wasn't isomerized it would only form 1 usable substrate, the other would be slightly off shape and wouldn't fit in enzymes further in the chain, I not sure if this is accurate, but it sounds logical.

@RafaelFranco - please don't thank people - upvote the answer if it's useful and accept it when it answers your question. That way other users can immediately assess the impact of the answer.

So what part of your answer is to the question of “why fructose?”. I quote: “Then it [glucose 6-phosphate] is converted into fructose-6-phosphate, why is this?”

If there is no glucose there is no need for glycolysis: I deduce from this truism that – at some early stage in the evolution of metabolism – a pathway resembling gluconeogenesis must have arisen before glycolysis. This is just another way of stating the obvious fact that autotrophy must have preceded heterotrophy.
If the aldolase reaction for triose → hexose evolved around glyceraldehyde 3-phosphate/dihydroxyacetone phosphate then perhaps the involvement of fructose 1,6-bisphosphate was dictated by the underlying chemistry of the aldolase condensation, and the steps to glucose followed from there. Note that the main carbon fixation pathway in photoautotrophs does indeed use this process: carbon fixation by RuBisCO generates 3-phosphoglycerate and the subsequent action of triosephosphate isomerase and aldolase generates fructose 1,6-bisphosphate.
So, my main point is that seeking the underlying design principles in the glycolytic pathway may be futile: glycolysis represents the catabolic use of a sequence of reactions that originally evolved for the purpose of anabolism.

Disclaimer: I have probably read this idea somewhere but I have no recollection of where. If anyone can point to an authoritative version of this please do so.

The anonymous downvoter strikes again.

Alan, regardless of whether gluconeogenesis or glycolysis came first (interesting — you should post this as a separate question) the question is remains — “why is there a fructose hexose stage between the triose and the glucose hexose?” That is the essence of what the poster is asking, even if he is coming at it from glycolysis.


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Do bacteria exist which live exclusively on non-organic matter?
Are there bacteria which consume exclusively non-organic matter? Meaning that they do not require organic matter from other organisms to stay alive and reproduce? A completely pacifistic bacterium.
Or phrased differently, are there bacteria which can stay alive and reproduce indefinitely with only non-organic matter present (plus sunlight or thermal vents etc.)?
I'm asking specifically, to name one or more bacteria species which can do this.

Welcome to Biology.SE!  It is expected that you will do research on your own before asking questions here — in particular you would benefit from reading up on bacterial ecology — there are hundreds if not thousands of examples of such organisms easily found.  For example you could start with the wikipedia article on autotrophs: https://en.wikipedia.org/wiki/Autotroph. –––––––– For details on how to use this site, please check out the tour: biology.stackexchange.com/tour and then the help pages on how to ask questions on this site: biology.stackexchange.com/help/how-to-ask. Thanks!

Could you clarify your question. What do you mean by non-organic? A chemical definition would be compounds that contain carbon. However, all organisms contain carbon which ultimately comes from carbon dioxide. Do you include photosynthetic bacteria? If so, just look them up on Wikipedia etc. And what on earth do you mean by pacifistic? Are you under the impression that most bacteria survive by killing and eating other bacteria? This is a science site — you need to choose your words carefully so they convey precisely what you mean.

Sulfate reducing bacteria get their energy converting sulfate to hydrogen sulfide. They are relatively common and may have been the source to turn some oil/gas deposits "sour". Specifics in Wikipedia.

But that’s answering only half the question. How do they get the C to use the energy to build their myriad C-containing structural components?

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How does a cell distinguish left from right?
Although the human body is mostly left-right symmetrical, it consistently has asymetries. The heart is consistently slightly to the left side of the body. The liver is consistently on the right side.
This is quite perplexing when we consider that the human body has developed from a single cell. It seems like a single cell is mostly left-right symmetrical. A single cell could be oriented any which way in the womb, and it is unclear how the developing body would "know" which way is left or right.
So, how is it that the body develops the clear assymetry. Can anyone explain this interesting phenomenon in layman's terms?

You are hitting nerve of many biophysics researchers here :) This phenomenon is called Symmetry Breaking is part of active research.

Developing symmetry is is just a matter of Homeotic genes creating axial patterning, genes that produce a chemical gradient across a cell or group of cells. This is how developing organisms orient individual cells, up, down, left, right, anterior, posterior, medial, lateral, are all just gradients of different chemicals, the cells can detect the difference in concentration one one side or the other to orient itself. Most of these start getting produced when the embryo is only around a few cells so there is not much room for ambiguity.  Later more homeotic genes are added to create gradients for things like segments and limbs. Note polarity is often exhibited in a single cell, even in single celled organisms, this is a chemical gradient that orients the inside of the cell, this can easily be turned into orientation of dividing cells.
As for why things move away form this symmetry that's easy, evolution can mostly only work with what it has, evolution is about good enough not perfection.  Often good enough creates a kluge, a rube goldberg type solution then descendants then get stuck with. The earliest vertebrate ancestor pikaia is completely symmetrical even down to the gut,  A fish is nearly perfectly symmetrical, with the only deviation being to increase the length of the gut without increasing the length of the fish, which would waste a lot of material The solution is to coil and pack the intestines instead of having a straight line. This does not just happen in vertebrates you can see these solutions again and again in mollusk, insects, and even echinoderms, keeping the body compact while making the gut longer means asymmetry. As Some organisms progressed further and further away form the "fish" body plan alteration would result in asymmetry. Lungs for instance force a big asymmetry because you are taking what was a simple one way path into two divided systems, blood now has to return to the heart twice before making a complete circuit. More energetic animals specialize even further abandoning or partitioning part of the circulatory system to close off these two parts entirely so they can have high pressure blood flow without exploding their lungs. Now asymmetry is not a bad thing limbs and sense organs stay symmetrical because there is a stronger evolutionary pressure to keep them symmetric, moving with asymmetric limbs wastes a lot of energy (try running with only one shoe on).

Image sources.

Sorry but I don't think this is right answer. It is not matter of 'just' Homeotic genes. There are lot of factors which plays important role in symmetry breaking even before these genes are expressed. One of the earliest symmetry breaking even is asymmetrical cell division (long before even tissues are formed). There are lots of hypothesis currently which explains this including maternal mRNA deposition, cilia rotation, external chemical gradient, uneven protein distribution etc.

This question could easily be construed as too broad if addressing every form of symmetry and asymmetry in biology. I was trying to restrict myself to the specific examples the OP gave. vertebrate symmetry and organ asymmetry.  If you want to address other occurrences feel free to create an answer.

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What genes in a plant determine whether a stem is erect or climbing?
I was randomly reading this Wiki article on Jasmine and this question crossed my mind after reading the following lines:

Jasmine can be either deciduous (leaves falling in autumn) or evergreen (green all year round), and can be erect, spreading, or climbing shrubs and vines.

How can a plant be both erect and climbing at the same time?
I have looked for genetic mechanisms related to this, correlating environmental or other stimulus with this phenomenon, but have not found a satisfactory explanation.
So how does this occur?


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Stability of the chromosomes of thermophilic bacteria
We know thermophiles — generally archaebacteria — can survive high temperature, but their genomic DNA also contains hydrogen-bonded nitrogen bases. Why don't they collapse like ordinary hydrogen bonds?

The stability and replication of the DNA of thermophiles is an interesting problem, for which there does not appear to be a single unequivocal answer. However the way you express this question is unfortunate: the hydrogen bonds in the DNA of thermophiles (which include some eubacteria as well as archea) are the same as those in any other genomic DNA. The question is, rather, why the strands of the DNA do not dissociate. This is not really my area, but as there have been no other answers I shall summarize what I have learned from the literature.
A review that was the starting point for this information is:
D.W. Grogan, Hyperthermophiles and the problem of DNA instability Molecular Microbiology (1998) 28(6), 1043–1049.

One obvious possibility would be that the genomes of thermophiles have a high percentage of GC, as GC base-pairs have three hydrogen bonds, whereas AT base-pairs have only two. However, this is NOT the general case.
It has long been known that the melting temperature (the temperature at which 50% strand-separation has occurred) is increased by increased concentration of cations. It has been suggested that this could be a factor, especially in those thermophiles that are also extreme halophiles.
In eukaryotes genomic DNA is condensed into chromatin by the interaction of the basic histone proteins. These proteins are not found in prokaryotes, but different basic molecules, polyamines, have been observed that are more abundant in thermophilic than mesophilic bacteria. As they have been observed to protect DNA from thermal denaturation in vitro, it has been proposed that they may also perform this function in vivo.
Type I topoisomerases that introduce positive supercoils into DNA (‘reverse gyrases’), occur in hyperthermophiles examined but not in mesophiles, and it was suggested that this could stabilize the DNA. However, the Grogan review presents a body of evidence that casts doubt on whether this is, in fact the case.
In addition to strand-separation, the genomes of thermophiles face the problem of increased damage to their DNA. Although, again, the situation is complex, it appears that they have evolved more extensive and active systems of DNA repair to deal with this.

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Where is the H+ ion in this step of glycolysis coming from?

(from Fundamentals of Biochemistry by Voet, 5th ed.)
In this step of glycolysis, I'm not seeing where the $\ce{H+}$ ion on the product side is coming from. It seems to me that the G3P's aldehydic H is replaced by phosphate, and that H is given to $\ce{NAD+}$ to make NADH. So where is the extra $\ce{H+}$ coming from?

Look at what you are substituting  OPO for

I've reverted the question to its original. Clearly the answer to the question needs to take into account the ambiguous nature of the equation, which does not make it clear whether it is meant to be a stoichiometric representation of the reaction occuring on the enzyme (which must involve discrete species) or adherence to a convention (which I assume, like Berg et al. is not explained) in which Pi is used to represent the fact that the reactive species (orthophosphate?) is in equilibrium with other phosphate species. Thanks @tomd for putting me right here.

Although texts such as Berg et al. tend to refer to inorganic phosphate, $\ce{P_i}$,  as orthophosphate ($\ce{PO4^{3-}}$), the term inorganic phosphate is used because in aqueous solution at pH 7.6 several phosphate species exist, the predominant one being $\ce{HPO4^{2-}}$. If this is regarded as $\ce{P_i}$, then it is the source of the $\ce{H^{+}}$, and the equation balances.
Note added by David:
On checking I find, in contrast to Berg, Lehninger’s book defines $\ce{P_i}$ as monohydrogen phosphate ($\ce{HPO4^{2-}}$), and Fersht actually writes the equation of the reaction (16-1) with $\ce{HPO4^{2-}}$ rather than $\ce{P_i}$.

Ok, so do most sources assume $\ce{P_i}$ as being $\ce{HPO4^{2-}}$ or as being $\ce{H2PO4^-}$? It seems like the source of my image assumes $\ce{P_i}$ is $\ce{HPO4^{2-}}$.

Take a look at this link: http://www.statemaster.com/encyclopedia/ATP-hydrolysis .  It is about ATP hydrolysis which also releases Pi (the phosphate ion) but notice the resonance stabilisation. I think this is what anongoodnurse is meaning

This is very muddled. You are mixing up solubility and ionization, and if you want to discuss this you have to put the charges on.

@RickBeeloo No, the question is about the stoichiometry of the equation, it has nothing to do with resonance stabilization. In the link you cite the equation is balanced.

@David - I am not tech savvy enough to include both the superscript charge and the subscript. However, in truth, in cells, Pi does not exist as PO4-3. And ultimately, the H+ does, indeed, come from the solution, which has a number if weak acids and bases.

@tomd - I suppose it depends on exact definitions of inorganic phosphate. I'm glad you added your own answer.

I'm not sure that it's the right answer, but what it seems to me you are arguing seems better expressed as follows. Orthophosphate (3–) may be counterbalanced by N+ or K+ in solution, but will be in equilibrium with a much greater amount of the monohydrogen acid (2–). If orthophosphate is removed an almost equivalent amount of this acid will dissociate regenerating the orthophosphate, but also a hydrogen ion. This hydrogen ion could be the one in the equation. If this is what you intend I can edit your answer with the charges shown.

@David - I agree with what you say. If you can write in mathematic (I can only write English), I would be happy and grateful for your improvement to my answer, however you want. Many thanks.

I've now edited your answer. Do modify or revert it if you are unhappy with any aspect of it.

@David - Thank you, it's good.I looked at how you wrote it. It's like reading nonsense words (I could never have done it.) Again, thanks!

No problem. I've added a short additional note and regard your answer as correct.

Although an answer that I have contributed an edit to has been, rightly, accepted, I decided to add my own answer to clarify a couple of points.

The equation in the question is what is known as a biochemical equation, not a chemical equation. As this IUPAC document notes:

Chemical equations are written in terms of specific ionic and elemental species and balance elements and charge, whereas biochemical equations are written in terms of reactants that often consist of species in equilibrium with each other and do not balance elements that are assumed fixed, such as hydrogen at constant pH.

One should not, therefore, expect Voet’s equation to balance.

The 1974 paper of Buehner et al. on the crystallization of glyceraldehyde 3-phosphate dehydrogenase includes the following (net reactants in yellow, hydrogens in orange):

…which answers the question.
It is interesting that the IUPAC document defines Pi as orthophosphate, although this is irrelevant to the question at hand as none of the old papers I have looked at use the abbreviation Pi.

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Effect of pH, temperature and enzyme concentration on Km
I understand that enzyme concentration doesn't affect Km since the Michaelis–Menten equation is based on the steady state approximation which requires high levels of substrate compared to enzyme (that's why changing enzyme concentration is negligible compared to substrate concentration and therefore there is no apparent change in Km).
But what about change of temperature or pH? It is known that change in those parameters can change enzyme activity, but does this actually change kinetic parameters like Km?
Why should I think not? Because the same explanation that says that change in enzyme concentration doesn't affect Km should apply here. There is a lot of substrate anyway and therefore there should not be an apparent change in the Km?
Another issue which makes me think so: In all the biochemistry literature that I have encountered Km and Kcat appears for each enzyme with no indication of the temperature or pH for which those values were observed (not in Lehninger, nor Wikipedia or other textbooks).
I have not been able to find a detailed consideration of this point.

Wikipedia: “The value of Km is dependent on both the identity of enzyme and that of the substrate, as well as conditions such as temperature and pH.”

Michaelis constant is defined as $$K_\textrm{M} = \frac{k_{-1}+k_2}{k_1},$$ where $k$s represent the rate constants for the reactions $$\mathrm{E+S} \;\;\underset{k_{-1}}{\overset{k_1}{\longrightleftharpoons}} \;\;\mathrm{ES}\; \overset{k_2}{\longrightarrow}\;\mathrm{E+P}.$$ Rate constants can generally be expressed by the Arrhenius equation: $$k(T) = A(T)\exp\left(-\frac{E_a}{RT}\right).$$ Because the parameters $A(T)$ (pre-exponential factor) and $E_a$ (activation energy) are generally not equal for all three reactions, the change in temperature does change the value of $K_\rm{M}$.
When measuring the enzyme kinetics and calculating $K_\rm{M}$, one has to explicitly state at which temperature the experiments were performed. This is probably not mentioned afterwards in the textbook because it is not of significant importance to the surrounding text and concepts.
Here you can find an article example with the measurements of enzyme kinetics at different temperatures. You can clearly see the change in $K_\rm{M}$.


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Why is glycine considered a nonpolar amino acid but a polar molecule?
Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?
Also, is the backbone of a protein nonpolar?

@AlwaysConfused please read the text that appears when you start to write a new comment - "Use comments to ask for more information or suggest improvements. Avoid answering questions in comments." You have been doing this a lot lately. Please stop.

@AlwaysConfused That's fine for a short hint but your comments just get too long, spanning two or three comment boxes. If you have time for such a long comment then better give an answer.

@AlwaysConfused Please take heed of MattDMo's comment. StackExchange has a particular model for particular reasons. If you answer in a comment you break this model. The question is marked as unanswered and there is no way for anyone to up- or down-vote your comment/answer so that other readers can get a feel of whether the answer is likely to be correct. I feel very strongly about this and have made my views clear in an answer to http://meta.english.stackexchange.com/questions/2653/why-are-answers-being-posted-in-the-comments-on-the-question/8171#8171

I have altered your question by adding in my assumption that glycine is only considered non-polar in the context of proteins. This allows me to answer it more clearly.

The first part of your question illustrates a common confusion of beginners between the physiochemical properties of free amino acids in solution, and the properties of that part of an amino acid that remains after it has participated in a condensation reaction to form part of a polypeptide. They are different. (It was for that reason that I modified the question to make it clear that the ‘consideration’ of glycine as nonpolar applies to it in its protein context.)
I have prepared a diagram to clarify.

As can be seen on line 1, all free amino acids at physiological pH are charged because of the pKa of the  α-amino and α-carboxyl groups (proline, as an imino acid is the exception). The chemical features common to all amino acids are shown in blue, for the second amino acid, and the unique feature — wherein amino acids differ — is shown in red.
To show amino acid 2 in the context of a polypeptide chain, I have condensed it with two other amino acids (1 and 3) to produce a tripeptide (line 3). (This is the situation most amino acids in a long polypeptide chain will be in, as there are only two that will be at the ends.)
You can see from the colouring that what is left of the amino acid in the protein — the amino acid residue — has lost the charges of the α-amino and α-carboxyl groups, which have become parts of peptide bonds. (A molecule of water is removed in a condensation.)
The properties that a particular amino acid endows to a protein are those of the ‘R-group’— R2 in the diagram. In the case of glycine, R is H, so that in the context of proteins we regard glycine as a non-polar amino acid (The C-H bond has a negligible dipole.)
Don’t confuse R with residue. It is a side-chain, designated using a common chemical abbreviation.

The second question was “is the backbone of the macromolecule nonpolar?”.
No. The backbone of a protein has partial charges on the oxygen and nitrogen atoms of the peptide bond, as shown below. This is because it has a partial double-bonded character. These partially charged atoms can (and frequently do) form hydgrogen bonds, either with another part of the backbone (secondary structure such as α-helix or β-sheet) or with polar side-chains.

I'm just converting @alwaysconfused's comment into answer (with a bit of more details).
Yes, glycine does have a dipole moment (15.7 D), but when it comes to biochemistry, then the dipole moment on the side chain is considered. Since the structure of glycine is:

H2N - CH2 - COOH   <--->   H3N+ - CH2 - COO-

So the side chain is:

-H-

which has, obviously, 0 dipole moment. Thus glycine, though polar, is considered non-polar in protein structures.

Source

Glycine has no side chains.
In a neutral solution; not forming a peptide bond, glycine has the following the following structure

H3N+ - CH2 - COO-

which is polar because of the -ve and +ve charge.
Once it forms a peptide bond with another aminoacids (aa), it becomes in the following form:

aa-----H2N - CH2 - CO ------aa

As you can see, it doesn't have any charges on it since the amino group and the carboxylic acid group formed bonds with another 2 amino acids.

@David: Pentavalent carbon corrected.


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Why was not RNA completely replaced by DNA when the RNA world evolved into a DNA and protein world?
If DNA just has a slightly different chemical composition from RNA, why can't DNA act as a catalyst and why hasn't it replaced RNA? Here, I am talking in terms of evolution, shouldn't evolution just replace all the RNA with DNA?

Welcome to Biology.SE! One thing that needs to be made clear at once is that evolution doesn't work to make things perfect, if something works, it is okay even if it can be improved. Yes, DNA works as genetic material for higher organisms, but RNA is useful too for temporary things like transcription.

This is also an opinion-based question because it is asking about a hypothetical situation. From the [help/dont-ask], avoid asking subjective questions where … you are asking an open-ended, hypothetical question: “What if ______ happened?” We expect answers to be based on verifiable facts and references, along with subject-related expertise. While this is an interesting question, unfortunately it is off-topic.

DNA doesn't do much it is just the storage media for RNA information. RNA does all the work.

I don't know what this question was before editing, but it seems nothing to do with evolution and good traits and bad traits. It is about the chemistry of DNA and RNA and so is quite valid in that context. I shall edit out the traits stuff and ask you evoutionists to leave this as a molecular biochemistry question.

OK. That was a bit extreme. It is about evolution, but it is not speculative. You can look at the function of the molecules and analyse the chemical advantages of the different alternatives.

A related question is Why do some bad traits evolve, and good ones don't? Basically a strong selection pressure is necessary to filter out a trait.
Having said that, there is no strong argument in support of transcription being disadvantageous.
RNA has unique properties that makes it suitable for certain functions. RNA can adopt different secondary/tertiary structures that an equivalent ssDNA cannot. One of the reasons is that GU wobble pairs are stable in RNAs but not in DNA thereby allowing structural flexibility to the former. See https://chemistry.stackexchange.com/a/35224/5295
RNA also has a high turnover because of different RNAses. If there was DNA instead of RNA for carrying temporary messages and there were equivalent DNAses to increase the turnover of the "mDNAs", then the genomic DNA would also become susceptible to degradation by these DNAses, which would cause genomic instability. You can argue that protein synthesis could directly begin on DNA as a template instead of mRNA. I guess that it would crowd the DNA and clash with replication. Even transcription machinery clashes with the replication machinery; this is called Transcription Replication Conflict which leads to genomic instability. A hypothetical situation in which there are multiple ribosomes on a DNA, is likely to have higher chances of the conflicts with replication than transcription-replication conflicts, thereby causing higher degree of genomic instability. I am assuming so because a large number of ribosomes need to simultaneously be progressing through the gene in order to produce sufficient amount of corresponding protein (like in case of polysomes).
Another possibility is based on the RNA world hypothesis. If it is really true that RNA preceded DNA as a functional as well as a hereditary molecule then it is difficult to get rid of all RNAs that easily. Even if most of the functions of the archaic RNAs were taken over by DNA and proteins, they are still performing some vital functions. To replace RNA from these roles, an alternative should exist which performs much better than the RNAs.
These are just guesses. An absolute reason can not easily be attributed to many biological observations. This is because we do not know the actual evolutionary trajectory of how things happened. However, what is important to keep in mind is that evolution does to proceed towards some kind of global optimum. Evolution does not "aim" for perfection.

The argument in this question is based on the false premises that a slight difference between two macromolecular structures is an unimportant difference, and that any importance or lack of it for that difference will have the same weight for different functions.
The slight differences between DNA and RNA gave DNA certain advantages as genetic material — for example it is less subject to alkaline hydrolysis and therefore can make longer stable genomes. It will only replace DNA if its chemistry does the job better — for other functions of RNA, this is not generally so.
RNA was largely replaced as a catalyst — but by protein, not DNA, something one can rationalize chemically because there were a wider variety of groups for catalysis etc. in the 20 amino acid side-chains of proteins.
RNA was retained for functions in which either its extra sugar hydroyl group or acid lability conveys and advantage over DNA (e.g. mRNA), or replacement by DNA would seem to convey no advantage (e.g. ribosomes). I am not an expert on catalytic RNA, but I understand that the 2'-OH is involved in the acid–base catalysis.
In conclusion, if you talk about biological molecules, you need to think about how their chemistry affects their function. If you have no chemistry, go away and learn some or restrict yourself to some non-molecular area of biology.
Footnote
I have an answer to a related question here: Why don’t different organisms have nucleic acid genomes containing different bases and sugar?

There are actually DNA enzymes, but they are artificially created -> https://en.wikipedia.org/wiki/Deoxyribozyme


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What causes the variable/conserved structure in the 16S rRNA gene?
See the image below for a visual representation of the 16S rRNA gene. It is composed of conserved and variable regions however I can't see to find a reasoning for why this is the case

Thanks

Are you talking about the variablility/conservation and structure of the RNA or of the gene (which would presumably include other parts of the DNA)? If it's just the rRNA, you should remove references to the gene, as this is confusing. (Also, it's "its", not "it's" for the possessive of it, the pronoun, and other pronouns except one.)

It would also be useful if you could indicate your source so that an answer can be addressed appropriately. What have you read about conserved or variable regions?

I added an image to try to be more specific to the question. I'm talking about the gene, but obviously that impacts the RNA/protein and everything else.

Thanks: that helps. I used  to follow the literature on rRNA structure and will dust off my papers (so to speak) and get back. I must say I have never seen a diagram like that — where did you find it?

OK. Found a related paper myself and answered the question.

The structure of ribosomal RNAs involves double-helical stems, on the one hand, and loops or junctions, on the other. A comparison of small-subunit rRNAs of different sizes shows that, despite increasing complexity, a basic core structure exists. The is illustrated in the diagram below is adapted from Brimacombe, Trends in Biochemical Sciences (June 1984) 273–277.

From a structural (3D) point of view, both stems and loops are conserved, but as far as the nucleotide sequence is concerned, the helical stems are less conserved than the loops and junctions. This would appear to be because the main function of the helices is structural — so an A–U base pair can generally be replaced by a G–C (or U–A or C–G) base pair, whereas the loops are involved in interacting with various species — tRNA, initiation, elongation and termination factors, ribosomal proteins and the 50S subunit — which may involve more specific bases.
The main thrust of research on ribosomal structure (and what has interested me) is the relation of structure to function, but Carl Woese realized that, because of its ubiquity, rRNA was an excellent molecule for phylogenetic studies. Although, if one compares, say, mitochondrial ribosomes with mammalian ribosomes the sequence conservation is small, with different strains of bacteria it is much larger. This has led microbiologists interested in bacterial phylogeny to analyse the best regions for comparison in 16S rRNA, in terms of their degree of conservation, resulting in the concept of variable and conserved regions in the diagram in the question. (I find this terminology rather unfortunate because of its similarity to the totally unrelated immunoglobulins.) It appears that this is due to van de Peer et al. (1996), from whose paper I reproduce the figure below.

[Figure 3 of van de Peer *et al.*The most variable positions are in red, the most conserved in blue. Absolutely conserved positions are indicated in purple. Nucleotides present in E.coli but absent in >75% of the bacterial sequences considered are indicated in pink.]


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How is Glyceraldehyde 3-phosphate converted into glucose?
In the light-independent reaction of photosynthesis, one of the products is glyceraldehyde 3-phosphate, and the Wikipedia page on the light-independent reactions states that 6 of these can be used to form glucose.  However, the Wikipedia article on gluconeogenesis does not mention this, and the Wikibooks article on gluconeogenesis only mentions the molecule glycerinaldehyde 3-phosphate (which I'm not sure if it's a typo, because I can't find any information on glycerinaldehyde).
So how does G3P actually become glucose (and is there a good reason this information is not available on those Wikipedia pages, plus the page on G3P)?

Advice to students of biochemistry
This site is concerned with biology, not with biological entries in Wikipedia. Wikipedia is a voluntary effort to which anyone may contribute, and is full of errors and omissions. It’s structure means that it is focussed on individual small topics, rather than presenting an integrated account of various areas of science. The student who wishes a balanced integrated account of a topic that has been subjected to editorial review should consult a text book. Those whose resources do not permit this should try searching on NCBI Bookshelf, which provides free on-line search-only access to old editions of texts. For biochemistry, Berg et al. is recommended.
The generation of glucose from triose produced in the dark reaction is well understood
The answer to the question can be found in e.g. Berg et al. 20.1.3:

The 3-phosphoglycerate product of rubisco is next converted into three forms of hexose phosphate: glucose 1-phosphate, glucose 6-phosphate, and fructose 6-phosphate... The steps in this conversion (Figure 20.9) are like those of the gluconeogenic pathway (Section 16.3.1), except that glyceraldehyde 3-phosphate dehydrogenase in chloroplasts, which generates glyceraldehyde 3-phosphate (GAP), is specific for NADPH rather than NADH. Alternatively, the glyceraldehyde 3-phosphate can be transported to the cytosol for glucose synthesis.

Berg et al. Fig. 20.9
The Section 16.3.1 referred to is a general treatment of gluconeogenesis, which is the same in all organisms or cells that possess the enzymes to catalyse its unique steps. (Some cells may not have — or need to have — the initial steps from pyruvate. In fact, Fig. 20.9 shows the steps to G 6-P — the only step missing is the phosphatase step that generates glucose.) There is therefore no reason to expect an account specific for plants.

Nice!  That paragraph from Berg was exactly what I was looking for. +1

Glucose is made from the trioses (3-carbon sugars) in plants according to the usual gluconeogenesis pathway.  That is, glyceraldehyde phosphate is converted to fructose-1,6-diphosphate by triose phosphate isomerase and aldolase, and then dephosphorylated to obtain hexose phosphates. Free glucose is not usually the end product in plants though; instead, glucose is coupled to ADP for use in synthesis of starch.
I'm afraid I did not find any good open-access references on plant gluconeogenesis, but it should be covered in most biochemistry textbooks.

The tricky part of gluconeogenesis is going from pyruvate to phosphoenolpyruvate. If you're starting with glyceraldehyde 3-phosphate, going backwards to glucose is easy. It's just the normal (reversible) glycolysis enzymes, used in reverse. (So if you're looking for references, look for those which say that that part of glycolysis is reversible.) -- This probably explains why it's not mentioned explicitly. People intimately familiar with central metabolism would think it "obvious" that it can run backwards.

@R.M.   Actually, glycolysis "above" glyceraldehyde phosphate is in fact not reversible, due to the phosphofructokinase step, which must be bypassed by fructose bisphophatase to be energetically favorable.

@RM — The ”tricky step“ is hardly relevant to this question as we are starting from glyceraldehyde 3-phosphate, not pyruvate. Remember that cells such as fat cells that use the pentose shunt to generate NADPH can return G 3-P to glucose via the latter half of the gluconeogenic pathway but do not possess the enzymes for using pyruvate as a gluconeogenic substrate.


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Oxidation means inflamation?
All right, I was reading article on nutrition, that focussed on content analysis of pastry-like food product for kids. I have to say that I am not sure this article would pass the imaginary smell test, although it didn't raise any serious red flags, except one.
Among other things, this article said that oxidation means inflammation. It said this in connection with use of rapeseed oil in said product, saying rapeseed oil is less saturated and therefore more likely to oxidize. It then implied, that when this oxidation takes place in the human body, it leads to inflammation.
Now I am no biology, medicine, or nutrition specialist, but if something is still stuck in my head from high school biology, it is that inflammation is the physical manifestation of our immune system fighting off infection, no? Apart of some autoimmune reactions, I don't see how ingesting rapeseed oil could cause inflammation.
So my question is this: is it really possible to safely say: "oxidation = inflammation"? Or is it total nonsense? Or is there some theory that could support such claim and how reliable is this theory? Isn't it just one of those hypothesis disguised as theories?
Said article is in Czech, otherwise I would link it for you.

EDIT: Article link here, you can try it with Google translate :)

You should link the article anyway. You have an international audience for your question. :)

OK I edited in a link :) might be of help.

Inflammation is not only a response against infection. It can also be triggered by any alteration in homeostasis. For example, high-cholesterol diet causes and increase in LDL particles in the blood, which deposit in the blood vessel's walls, causing an inflammatory response that when it gets out of control leads to atherosclerosis. Oxidative stress is associated with inflammation but I would not say oxidation=inflammation.

Oxidation does not mean inflammation. But oxidation can be a cause of inflammation.
Oxidation processes are part of normal cell metabolism (mostly in mithocondria). They lead to reactive oxygen species ($O_2^-$, $H_2O_2$ and $OH-$) which can trigger inflammation via activation of some transcription factors:

NF-κB, AP-1, p53, HIF-1α, PPAR-γ, β-catenin/Wnt, and Nrf2 [1]

The metabolic processes also produce some  antioxidants to inactivate those reactive oxygen species. But the excess of oxidants leads to oxidative stress which seem to be linked with inflammation and even to cancer [1].

rapeseed oil is less saturated and therefore more likely to oxidize

Being "less saturated" I guess it would be better, as studies have found that saturated fatty acid promote inflammation [2], while unsaturated fats decrease the production of inflammatory cytokines and reactive oxygen species [3].

So my question is this: is it really possible to safely say: "oxidation = inflammation"?

NO. By definition, oxidation is a chemical reaction in which a molecule, atom or ion loses electrons [4]. On the other hand, inflammation is a very complex process, a biological response to harmful stimuli and requires cellular interaction [5].

References:

Reuter S, Gupta SC, Chaturvedi MM, Aggarwal BB. Oxidative stress, inflammation, and cancer: how are they linked? Free Radic. Biol. Med. 2010 Dec 1;49(11):1603-16. doi: 10.1016/j.freeradbiomed.2010.09.006. PubMed PMID: 20840865.
Saturated Fatty Acids and Inflammation: Who Pays the Toll?
Alan Chait and Francis Kim
Arterioscler Thromb Vasc Biol. 2010;30:692-693, doi:10.1161/ATVBAHA.110.203984
Supplement: n–3 Fatty Acids: Recommendations for Therapeutics and Prevention:
Philip C Calder
n−3 Polyunsaturated fatty acids, inflammation, and inflammatory diseases
Am J Clin Nutr June 2006 83: 6 S1505-1519S
Wikipedia contributors, "Redox," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Redox&oldid=621442954 (accessed September 13, 2014).
Wikipedia contributors, "Inflammation," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Inflammation&oldid=625272396 (accessed September 13, 2014).

Small addition: Oxidation can be cause as well as an effect of inflammation.


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Distance matrix with different length sequences
In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, etc.) requires the sequences' length to be equal. Is there any pythonic way to get the matrix with sequences of different length? Or any other indirect way that would get us to the same result?

Without seeing your code it's kind of hard to help. This question is much more suited for [so], please ask it over there and tag it [python] and [biopython].

Use a metric that is a function of the sequence but not the sequence itself; something like GC content. Or use end-to-end alignment such as Needleman-Wunsch algorithm

I am not a python user but it seems to me AlignIO is (similar to the bioperl counterpart) for reading/writing an already existing alignment (hence the requirement of equal sequence lengths). You could align the sequences with an external tool (like e.g. MAFFT) and then read the alignment in python with the AlignIO interface.

There are two possibilities:

Do not use the sequences per se but a scalar metric of sequence similarity for distance values
Introduce gaps in the alignment. You can also do an end to end gapped alignment such as the Needleman-Wunsch and use the alignment scores for the distance matrix.


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High Glucose vs Low Glucose DMEM for Cell Culture
I've noticed that in mammalian cell culture, there are often two types of DMEM available. High Glucose and Low Glucose. Does it matter which type I use for culturing of cells (e.g. Hela or HEK293)? Which is the type people normally use?

We typically use High Glucose as cells grow faster.  One caveat is that there are concerns that certain protein modifications (specifically OGlnAc-ylation) may be upregulated in non-physiological (25mM or high glucose) media.


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Experimental evidence for the selfish gene vs. the selfish individual
In the Selfish Gene, Dawkins makes the argument that a better  view of evolution (i.e. more in accordance with experiment) is obtained if you view the basic unit of evolution to be the gene rather than the group. Having read the book, I am convinced (inasmuch as a layperson can be convinced) that group selection comes up with incorrect predictions about evolution, so is a fallacious interpretation of evolution (is this a correct interpretation of the book and is this conclusion common opinion among biologists?).
I have heard that historically, his book was part of a backlash against the then prevalent viw of group selection.
TL;DR
However, is there an experimental way to prove whether the gene-selection or individual-selection interpretation of evolution is more correct?
I hope my question is not ill-defined whilst leaving 'unit of evolution' vaguely defined.

Today, most evolutionary based studies are molecular.  Take a look at the neutral theory of molecular evolution

Selfish gene/selfish individual are not mutually incompatible. Old-style group-selection on the other hand is incompatible with the gene-centric (selfish gene) approach. Good question, BTW. I'll take a stab at it once I organise my thoughts on the matter, it's been a long time since I read The Selfish Gene.

I agree with @ChinmayKanchi but its often said here that this is all proven.  I haven't really found that myself - publications in reputable journals including Nature continue to appear.   But maybe someone can post their full argument? @RichardSmith?

Answering this question properly would require me to at least skim a dozen papers to refresh my memory. But essentially @shigeta is right, the gene-centric view is held by the majority of biologists, but it's not a done deal. And there's little direct evidence either way. Personally, I think the answer is probably that selection acts at multiple  levels.

My understanding of this is that the complete reference for molecular centralized evolution is The Selfish Gene itself.  I'm going to cite Alan Grafen's essay here,
Richard Dawkins, proposes that the logical, fundamental unit of evolution is the replicator.
The replicator is the fundamental unit of reproduction - whether these replicators survive or do not defines the properties of the biological system they reside in.  These words were chosen carefully because DNA sequences themselves are not replicators exactly - many individual copies make up the animals in a gene pool and the replication of one copy or another doesn't matter.  The distinction between a physical strand of DNA and the replicator is the bulk of more than one of Dawkins book.  It shows why the life of an individual means nothing to biology or evolution, how the boundaries of genes as transcriptional elements do not define the replicon (commonly misunderstood by molecular biologists).  The replicon (a genetic unit of replication) manifests a behavior or phenotype in the organism that helps it reproduce and is reproduced.  This can be cooperation with other members of your species or egg rolling or killing other sperm and is usually the result of many individual mRNA transcripts working in concert.  A given gene as defined by mRNA transcription commonly participates in multiple replicon type behaviors.
But DNA is in the mind of the molecular biology camp highly intertwined as a replicator because it is the physical medium through which the replicator is passed from one generation to another.  Without DNA, meiosis and the rest there are no replicons.  The earliest replicators were possibly simple transcripts which self replicated and not much more, but over time they have become a network of intertwined molecules working in a system.
To my understanding this is axiom more than proof.  It does not need to be proven because the physical transmission of DNA replication over time is the minimal necessary scenario to picture biology and evolution as we understand it.  The selection amongst groups of genes or groups of cells or groups of individual multicellular animals seem unnecessary given the physical framework of DNA replication.
Certainly that these connections have been shown.  The inspiration for The Selfish Gene is the confirmation of Robert Triver's Selfish Gene hypothesis with the discovery of t a terribly selfish gene which takes up the better part of chromosome in drosophila and increases its chances of showing up in the next generation by showing up in sperm more than half the time.  There are lots of other examples in the Selfish Gene and the Extended Phenotype, which answers many of the common questions about this thesis.  The literature since has been pretty productive. That being understood, its one thing to prove that something is true in biology, and another thing to prove that all other similar mechanisms are simply not true.
Yet even in Dawkins essays we see that the replicator is a bit of an abstraction some practically indefinable group of genes. Even as they each compete against each other, they create phenotypes collectively and the replicon becomes abstracted from the fundamental mechanism of replication.  The most popular example of replication Dawkins creates - the meme - has no relationship to DNA at all - a sticky idea that spreads socially and replicates in the minds of individuals.
When we look at terribly complicated but obviously advantageous behaviors, the connection between the replicator and the competition of individual genes gets muddy.  EO Wilson, having discovered pheromones and started ecology and sociobiology as disciplines still publishes group selection arguments.  Having studied social behavior in insects over his career and co-authored one of the most complete compendiums on the subject, he has put forth consistant arguments since the 70s that group selection still has a place in evolution. Unlike others, Wilson has I think always kept the conversation scientific and isn't jumping off any ideological cliffs (though responses say differently, the whole conversation is still published).
I don't see how an unbiased forum can ignore the fact that the editors of Nature still call this an open discussion.  Some may object, but calling the subject closed is overreaching I feel. There are others besides Wilson; I'm not familiar enough with the whole discussion to go into David Sloane Wilson and the rest, though they publish in reputable places.
I've started in this post since the question has been sitting around for a while. I expect others will post their corrections/objections/views - please do!  Whenever group selection is mentioned it often happens that someone will pop up and say 'this is not appropriate for a scientific discussion of biology here' but never any justification of disqualifying questions - I think that's not really scientific.  The fundamental attraction to academic thought to me is that minority voices that have legitimate observations are tolerated and often result in scientific revolutions, after which they are venerated for their persistence.
Here's a good place to tell us why some questions are beneath discussion in biology.  I personally do not agree; even if a position is intertwined by politics and religion, its the scientific value that should be judged, not by the company it keeps - lest science become just another intolerant clot, not driven by logic, observation and facts.  I ask you, why bother then?

This is a superb answer!

Agree with Chinmay, but I'll give time for your call for corrections/objections/views.

That's a good thought @Alyosha - this sort of question probably needs a conversation not a single answer.


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Is the eyes' movement discrete?
When tired and it was dark, I noticed that if I focused on a dim light source and moved my eyes fairly rapidly sideways, the resulting images that lingered for a short while were not smoothly blurred together, but were discrete.
I assume this is not due to the brain's inability to process the data fast enough or the retinas not repairing fast enough when light breaks part of them down, so I am lead to the conclusion that eyes (if not generally, sometimes) move in very small sudden jolts rather than smoothly.
Is this correct? What is the reason for this (is it due to the eye muscles being unable to sustain motion for a long time, or something to do with the mechanics of the eye)? Was this result anomalous?

There are two types of eye movement: smooth pursuit and saccadic. As the name suggests the latter movement involves quick and discontinuous movements of the eyes. Saccadic movement is used most of the time as the eyes move around analysing the current scene.
According to Wikipedia, these saccades are the fastest movements produced by the human body: peak angular speed of 900 degrees of rotation per second (this would be 2.5 full rotations of the eyeball per second, were such a thing possible).
The processing of information by the eye-brain system during a saccade is complex, and may be responsible for the effect that you report: it causes the phenomenon of saccadic masking explained in this quote from Wikipedia:

A person may observe the saccadic masking effect by standing in front of a mirror and looking from one eye to the next (and vice versa). The subject will not experience any movement of the eyes nor any evidence that the optic nerve has momentarily ceased transmitting. Due to saccadic masking, the eye/brain system not only hides the eye movements from the individual but also hides the evidence that anything has been hidden. Of course, a second observer watching the experiment will see the subject's eyes moving back and forth. The function's main purpose is to prevent smearing of the image.

I assume the advantages of smooth pursuit and saccadic movement are that the image is continuous (so no information is lost) and that the angular speed is large, respectively, or am I oversimplifying?


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Meaning of term ‘rapidly labeled RNA’
I encountered the term, “rapidly labeled RNA”, in the article: Rapidly labeled HeLa cell nuclear RNA. I. Identification by zone sedimentation of a heterogeneous fraction separate from ribosomal precursor RNA. (1966).
I would appreciate it if someone could explain to me what it means or implies.

Explanatory answer
Rapidly-labelled RNA was the RNA labelled by radioactive precursor during a short period (the pulse), terminated by swamping the system with an excess of non-radioactive precursor (the chase). This is known as a pulse–chase, and is described in the methods section of the paper cited in the question and reiterated by @SeRe as an answer. Such a pulse–chase preferentially labels RNA species that have short turnover times (i.e. half-lives of the same order of the pulse), and was thus regarded as a way of studying messenger RNA.
This strategy and its interpretation was an extrapolation from what was known about mRNA in the regulation of bacterial gene expression, but the descriptive term ‘rapidly-labelled RNA’ was used rather than ‘mRNA’ because there was no direct evidence to support such an assignment in nucleated mammalian cells. Indeed, there were major problems because the rapidly-labelled RNA in the nucleus was of a different size to the RNA that subsequently appeared in the cytoplasm, and, indeed, there was no simple precursor–product relationship between the two. In retrospect this is not surprising given what we now know about the splicing of eukaryotic mRNAs and the fact that most of them have much longer half-lives than bacterial mRNAs. However, at the time there was a school of thought that interpreted these results as evidence against the idea of mRNA in eukaryotes, and one of the purposes of the paper cited was to demonstrate that some of the rapidly-labelled RNA that appeared in the cytoplasm had properties consistent with mRNA.
The historic context
It may be necessary to explain to younger scientists that this work was done before DNA cloning, before RNA sequencing (never mind DNA sequencing), before the discovery of polyadenylation of eukaryotic mRNAs (the ‘handle’ for purifying them), in short, at a time when no specific mRNA had yet been identified or isolated (see, e.g., the Wikipedia article on The History of RNA Biology). As documented in Mathew Cobb’s excellent article ‘Who discovered mRNA?’, mRNA wasn’t really discovered but was an idea to account for the rapid response of the lac system (observed in genetic experiments) in terms of a previous unexplained labelled RNA with a DNA-like base composition observed associated with more abundant stable RNA (ribosomes) when bacteriophage infected E. coli. Subsequent work, presented in papers by Brenner et al. and Gros et al. in the same issue of Nature in 1961, in effect documented this RNA more precisely in phage-infected cells and showed that it differed from ribosomal RNA. The importance of the work of Mathhaei and Nirenberg in establishing cell-free systems for translating polyU and subsequently other artificial polynucleotides cannot be underestimated. However, it is important to recognize that the genetic code was not deciphered using genuine mRNA.
It was natural to assume the mRNA model extended to eukaryotic cells, but at that time there was no convenient system with an abundant mRNA like that of bacteriophage and so the presumed differentiating characteristic of short half-life was used, as seen in a plethora of papers on ‘rapidly-labelled RNA’. Many of these were opportunistic, claiming to document anticipated hormonal or other effects on eukaryotic gene expression. Consequently the demonstration that much of the rapidly-labelled RNA in the nucleus never reached the cytoplasmic ribosomal location had the effect of discrediting not only these papers, but the very idea that mRNA existed in eukaryotes. This may seem rather absurd today, but the foremost ‘eukaryotic mRNA denier’ (as he might be termed in contemporary parlance) was the eminent Oxford Professor of Pathology, Henry Harris FRS, who developed man–mouse heterokaryons and set out his ideas in a published monograph entitled ‘Nucleus and Cytoplasm’ (a copy of which I once possessed). So it is relevant that Warner et al. (1966) refer specifically to Harris in the discussion section of their paper, which describes work that addresses the issues Harris had raised.
If there is a moral to this story (and it is always easier to draw morals after the event) it is perhaps that Harris was happy to confusticate lack of proof with disproof in an area that was peripheral to his main concerns, and that the groups in New York — and Jonathan Warner, especially, having previously described polysomes in Alexander Rich’s lab — were prepared to accept the fact that the situation was more complicated than originally thought, but were not prepared to throw out the baby with the bath water.

They performed an experiment where they treated cells with [3H]-uridine (tritium-labeled uridine) for a short period of time (5 min). Afterwards, they added non-labeled uridine, cytidine, and thymidine in excess. So in principle, rapidly labeled RNA is radioactively labeled RNA after a short period of time.

But you haven't explained why. What was interesting about RNA that was labelled under these conditions? Why would the poster be reading a 50 year old paper about it?

But he never asked why. He wanted an explanation for the term rapidly labeled RNA. And obviously, my explanation was sufficient for him as he accepted the answer.

If your answer was only to reiterate what the poster could have read in the methods section, then you shouldn't have answered the question on that basis and the implication that the answer would have been of no general interest for biology. There is a greater general interest implicit in the question and which is a valid, but more comprehensive and comprehensible answer to the question "could you please explain it (what rapidly-labelled RNA is) to me?" If you know, please include it in your answer, if not, I will answer it myself.


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Backbone hydrogen bonds between adjacent amino acids in a protein?
Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO?
Are there any examples of such situations in proteins and how common are they?
If such bonds are rare, why is this so?

Are you talking about main-chain hydrogen bonds (i.e. from the CO and NH on the backbone) or side-chain hydrogen bonds (e.g. from serine, aspartate etc.)?

@David Yes, I am talking about the main chain hydrogen bonding.CO--HN of the backbone

The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis.

This turns out to be very rare in proteins. To understand why, one must remind oneself of the conditions for forming hydrogen bonds in proteins. For hydrogen bonds between peptide bonds these would be:

Correct distance between hydrogen of the NH and the O of the CO (too far apart — bond weak, too close — repulsion).
Near(ish) linear angle of the NH and OC.
Lack of steric repulsion of other atoms in the structure

Calculations indicated that a 2.27 helix would be less strained than the 27 ribbon:

Playing with polyglycine in Bosco Ho’s Ramachandran Plot Explorer (Rama) indicates steric repulsion still exists in this structure (white striped connectors):

I could only find one report of this structure, and that was in the artificial peptide Ac-(∆ELeu)5-NHMe, with a model using dihedral angles Φ,Ψ approx. –60°, 30° (as in the Rama simulation) shown below:

It should be noted that this position of the Ramachandran plot is at the margins of stability, and I would expect the bonding only to occur in proteins where it was stabilized by other interactions (as in this artificial peptide) and no lower energy structure were possible.


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What do different fermentation products have in common?
I met with the following question in my masters course:

What do different fermentation products have in common?

Thinking about this, I have difficulty in identifying the similarities between lactic acid and alcohol fermentation.

Although there is  no net oxidation or reduction in glycolysis, a constant supply of  NAD+ is (paradoxically) required in order for glycolysis to continue. Otherwise, the glyceraldyde-3-phosphate dehydrogenase reaction (GAPdh) could not generate 1,3-diphosphoglycerate.
So how is the NADH generated in the GAPdh reaction converted back to NAD+? Both alcohol and lactic acid fermentation regenerate NAD+ by reduction of the carbon skeleton that was oxidized in the GAPdh reaction, albeit at different 'points' in the glycolytic reaction sequence.
In alcohol fermentation, alcohol dehydrogenase acts as aldehyde reductase, reducing acetaldehyde to ethanol and NAD+.  In lactic acid fermentation, lactate dehydrogenase acts as a pyruvate reductase, reducing pyruvate to lactate and NAD+.
In both alcohol and lactic acid fermentation, there is no net oxidation or redution: glycolyis is the splitting of glucose.
Finally, we may note that the electron acceptor in both cases is 'internal'  Neither process requires an external electron acceptor such as oxygen.  The electrons removed from the carbon skeleton in the GAPdh reaction (generating NADH) are added back to the same carbon skeleton (but with different molecular arrangement) in both the ADH and LDH reactions.

Q1. What do different fermentation products have in common?
A1. They are generated in a reaction in which NADH is reoxidized to NAD+, allowing anaerobic oxidation (e.g. of glucose) to continue.
Q2. What are the similarities between lactic acid and alcohol fermentation?
A2. They both generate ATP ‘at the substrate level’ (i.e. directly in reactions, without using oxidative phosphorylation) in a sequence of reactions which involve oxidation by NADH. The end-product of the oxidation (here pyruvate) is of no further use for anaerobic generation of ATP and so it is unimportant what it is reduced to by NADH.

This is illustrated below (see also this question):

(As mentioned in the answer from @xusr, pyruvate is converted to acetaldehyde before the NADH step.)
There are other types of fermentation with different end-products — see e.g. the Wikipedia article on fermentation — but the general principle is the same.

I posted this answer, despite the late stage because I think the diagram really makes things clear, and the other answer doesn't mention ATP.

Having taught this topic at university level for many years I maintain that this is the correct answer to the question. It would be useful to others reading this if those who have down voted it explained why they thought it incorrect. This should not be difficult given the sharp focus of my answers to the two questions. Without such a discussion, how is the reader to know?

Would "all fermentations are basically methods to recycle reducing equivalents for glycolysis to continue without invoking external electron acceptors" be a good tl;dr here?

@Dunois — Apart from one thing that sounds excellent to me. However I’m not sure that there aren’t processes other than glycolysis that can be supported in this way. I’d need to check and get back to you.

That would be awesome.

@Dunois — The qualification I would make to your summary is to add in parentheses after glycolysis: "(or its less common variant, the Entner–Douderoff pathway)". If you are not familiar with this, check it out in Wikipedia. You'll see it differs in the hexose steps of anaerobic glucose catabolism, but is similar in the triose steps which generate ATP at the substrate level. Like glycolysis it needs to reoxidize NADH (or NADPH) to continue, and can do this by reducing pyruvate, i.e. the whole process is a fermentation.

Thank you for taking the time to research this. I've only heard of the Entner-Douderoff pathway in passing, thanks for the link. I think your qualification in parentheses completes and complements my statement nicely.


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Is it wrong to consider an allosteric inhibitor a non-competitive inhibitor?
Supose Caspase-1 is allosterically inhibited. Since the inhibitor is not binding in the active site but instead in the allosteric binding site, can I conclude it is a non-competitive inhibitor?

Could you give me examples, please? The link you have provided is too technical, and these concepts are still somewhat confusing.

The concepts are clearer now. I'll definitely read your links. Thank you very much.

Why are you asking this question? Why do you want to use another name for an allosteric inhibitor? In any introductory text book you will see the kinetics of what are called non-competitive inhibitors described as being quite different from allosteric inhibitors.

@tomd — perhaps you could formulate your comments into an answer. At the moment we seem to have an accepted answer that is at variance with them.

Actually, this was about distinguishing concepts which were confusing, and applying them.

No, you cannot assume that an allosteric inhibitor is non-competitive. "Allosteric" refers to the location of binding, whereas terms like competitive, non-competitive, uncompetitive, or mixed inhibition refer to how (or if) the binding of the inhibitor affects binding with the substrate.
The Wikipedia page on competitive inhibition is a reasonable source for this question.
A competitive inhibitor is one that prevents binding of the normal substrate(s) at the active site. It is possible to achieve this either by literally getting in the way by binding in the active site or by binding elsewhere, causing a conformational change that prevents binding the active site. Both cases are considered competitive inhibition because of how they influence substrate binding.

I am puzzled by your answer. The question is about non-competitive inhibition, but you quote a link to competitive to an article on competitive inhibition. Are you concluding that if an inhibitor is not a competitive inhibitor then it must be a non-competitive inhibitor? I am no enzyme kineticist, but I thought the usage of the term in enzyme kinetics was much more restricted. I cannot see the utility of calling an allosteric inhibitor a non-competitive inhibitor. I would just say it is not a competitive inhibitor. Surely it is better to use definitions related to the kinetics of inhibitors.

@David I think the title of the OP's question might be a little unclear, I read it to be "If an inhibitor is allosteric, does that mean it is non-competitive?" I answered that no, that is not always true, and used the definition for competitive inhibition as an example proving that you can have allosteric inhibition that is competitive, rather than non-competitive. I could have also gone into mixed or uncompetitive inhibition but I thought one example was sufficient.

The question was formulated this way because I didn't know an allosteric inhibitor could be competitive or even mixed.

It may be technically correct to say that an allosteric inhibitor can be (or is) a “competitive inhibitor”, but, in terms of communication and education, I would advise a more measured approach. Most students encounter the terms “competitive inhibitor” and “non-competitive inhibitor” in the context of reactions exhibiting Michaelis–Menten kinetics. Their mental image of such an inhibitor will therefore be of the type:

In discussing allosteric inhibitors I would therefore focus on the different mental model, below, in which substrate (or positive effector) and negative effector (use of this different term being deliberate) have opposing effects on the equilibrium between tense and relaxed states:

I would then go on to say something to the effect that because the relative concentrations of substrate and negative effector determine the rate of the reaction “the negative effector indirectly competes with the substrate”.

First of all, I take your point about the previous post being too technical.  On this occasion, there will be no equations and no diagrams.
When dealing with reversible enzyme inhibition, we are mainly concerned with the meaning of four terms: competitive, uncompetitive, non-competitive and mixed. As I said above, the literature is very confusing to the point of making relatively simple concepts appear very complex, and the confusion often arises from the meaning of the term 'non-competitive'.
First things first: reversible inhibitors are best classified by their effects on two kinetic constants rather than by the mechanism that gives rise to a particular inhibition pattern.  The two kinetic constants are kcat and kcat/ Km. (So why not kcat and Km? This is discussed in a previous post, but the short answer is that it is simpler:  Km is often a very complex kinetic constant). We can distinguish two 'limiting' cases. (i) A competitive inhibitor effects kcat/ Km but not kcat and (ii) an uncompetitive inhibitor effects kcat but not kcat / Km. (iii) We can also now distinguish a third case where both kinetic constants  are affected. Let's call this one non-competitive inhibition.
The confusion in the literature arises because some authorities call non-competitive inhibition as defined above mixed inhibition, and (to really screw things up), they consider non-competitive inhibition  a special case of mixed inhibition where both kinetic constants are changed to the same extent!  For the purposes of this answer, I am not going there as I think what you mean by non-competitive is as defined in (iii) above. In any event, this is how Cleland, the leading authority in this field, defines non-competitive inhibition.  In other words, 'mixed' inhibition is banished from this answer from this point on.
We could be a little bit more adventurous here and say that a competitive inhibitor only effects binding of the substrate to the enzyme and that an uncompetitive inhibitor effects only the catalytic step. Or, we could say that a competitive inhibitor effects only the apparent second order rate constant for the combination of enzyme with substrate (which the enzymologists call kcat/ Km) and that an uncompetitive inhibitor effects only the apparent first order rate constant (which the enzymologists term kcat).  But that is becoming too abstract. But perhaps you can see where I am going? There are only two limiting cases,  one affecting substrate binding and one affecting catalysis, and a combination of both.  It really is as simple as that.
Having got the nomenclature mess out of the way, I will now attempt to answer your question: if an inhibitor does not bind to the active site can we conclude it is a non-competitive inhibitor?
IMO, the answer is an emphatic no. An allosteric inhibitor (one which binds to a site other than the active site) may be competitive, uncompetitive or non-competitive.
As Bryan Krause put it , a  competitive inhibitor  prevents binding of the normal substrate(s) at the active site, but there is no requirement that the inhibitor bind to the active site. Binding of the inhibitor at the allosteric site may cause a conformational change that prevents substrate binding, for example.
The same argument applies to uncompetitive inhibition.  A simple mechanism that gives rise to uncompetitive inibition is where the inhibitor cannot bind to the 'free' enzyme but binds to the enzyme-substrate complex.  And of course binding to the allosteric site might not be possible unless substrate is bound.

The confusion had arisen from the unawareness of those constants. I didn't know an allosteric inhibitor could be competitive or even mixed. Thanks a lot.


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What determines whether a regulatory T cell suppresses a naive T cell binding the same antigen-presenting cell?
Here's what I learned about how regulatory T cells work:
There is a self-recognising naive T cell around.
A regulatory T cell that recognises the same self-antigen binds the same antigen-presenting cell as one of these T cells.
It suppresses activation of the naive T cell.
However, let's say the antigen-presenting cell is presenting foreign antigen on some of its MHC molecules. The naive T cell binds the  antigen and there happens to be a regulatory T cell nearby binding a self-antigen on the same antigen-presenting cell.
Does the regulatory T cell suppress the naive T cell? Is it just do with proximity, or do both cells have to bind the exact same antigen?

There a strong implication for a feedback loop mechanism for IL-2.
If a Treg is bound to an APC, it downregulates IL-2. It will then require exogenous IL-2 to be maintained. This IL-2 comes from a nearby naive T cell which is also binding a self-antigen. When that happens it upregulated IL-2. When it upregulates IL-2 and dumps it to all nearby cells which are then taken up by the nearby Treg. That causes Treg to continue its normal function by suppressing all nearby cells. It's an IL-2 negative feedback loop. It's all about proximity. What you are suggesting is not feasible since T cells recognise APC cells by MHC class II which are loaded by phagocytosis, meaning that the self-antigen has to be taken from outside of the cell. That means the APC would have to engulf two different self-antigens and displayed them on separate MHC class II which I guess is probably possible...
Check out this paper and figure 2:
http://www.cell.com/cell/pdf/S0092-8674(08)00624-7.pdf


text:
Polydactyly and its genetics
One of my friend was saying that her aunt (father's sibling sister) was having polydactyly but none of her cousins (her aunt has two daughters) is having it.
What is the chance that my friend's children inherit polydactyly?
(considering that her partner nor anyone in his generation exhibit polydactyly)

if polydactyly is autosomal dominant (Wikipedia), then effectively zero.

Polydactyly can be dominant or recessive. that is

A single copy of the mutation/s involved result in the phenotype
vs
Both copies of the gene must be mutated to result in the phenotype

When two random people who don't have polydactyly nor a family history of polydactyly have a child, there is around 1/548 (0.18%) chance that child will be polydactyly because the parents were carriers without knowing it, and a 1/11.7 (8.54%) chance the child is a carrier of a single copy
If the aunt's polydactyly is Dominant, then your friend's father hasn't inherited it (he isnt polydactyly) and just has the normal population chance of being a carrier.
In the case of Dominant polydactyly, assuming your friend has a partner with no history of polydactyly, your friend and her partner have the same chance as average of a polydactyly child (1/548)
If the aunt's polydactyly is recessive, meaning she has two copies one from each parent (you friend's grandparents), there is a 1/130 (0.76%)chance your friend's child will have polydactyly (4.2 times more likely), and a 1/4.5 (21.4%) chance of being a carrier (2.6 times more likely)
I'll quickly go through the working/
if you're interested:
Given that the grandparents are both carriers (needed for the aunt to have two copies), then your friend's father has a 2/3 chance of being a carrier of a single copy (1/3 chance no copies, 0/3 chance having two copies because he isn't polydactyly).
Your friend's mother has the usual 1/11.7 chance of being a carrier.
The chance of your friend inheriting a single copy is (chance passes from father) + (chance passes from mother) - (chance of getting two copies)
=0.6600/2 + 0.0854/2 - (0.33*0.0427)
=0.3727 - 0.0140
= 0.3586
35.9% chance your friend carries one copy
Your friend has 1/2.8 chance of carrying and 1/5.6 of passing it on
Friend's partner has the 1/11.7 chance of being a carrier and the 1/23.4 chance of passing it on
Therefore their child has
=0.1793*0.0427 (chance friend passes on * chance partner passes on)
=0.0076
=1/130 chance of having two copies, having polydactyly

=0.1793 + 0.0427 -(0.1793*0.0427) (chance any copies - chance two copies)
=0.2143
=1/4.7 chance of one copy a 2.5 times increase risk

That's a really detailed answer. Good one and thanks for simplifying the confusing parts. But can you add any reference? It will help me accept your answer.


text:
What is inside the male’s body in the space where females have the ovaries and the uterus?
The male penis and scrotum are external, whereas the female sex organs are placed "inside" the body. As females have the bladder, rectum etc.  just like males, does this mean overall females have a larger volume of organs? Is this why females have wider hips — because the male penis and scrotum are external appendages just like female breasts?

The ovaries and uterus are pretty small except for the uterus during pregnancy. Just for comparison, think of how your intestines take up a significant fraction of the abdominal cavity, but the actual space they take up completely depends on how much food etc is in there - that variation from hour to hour is going to be a lot more than the volume of the female reproductive organs when not pregnant.

@BryanKrause I guess you could extend your comment (and use keywords like phenotypic plasticity) into an answer if you want to.

@Remi.b Not really my area besides a familiarity with abdominal anatomy necessary to pluck arteries out of an animal model, so I'll let someone else take a stab at it, just hoping to redirect the question asker a bit: probably the more interesting question to think about are the female specializations for pregnancy and delivery (humans and animals), rather than space for the organs generally.

You are asking multiple questions here. I would suggest that you restrict your question to the pelvic region, as your question title says. Each organ would have sex-based differences. We cannot cover all that in a single post.

Oh cool @WYSIWYG I'll make the second paragraph into a separate question.

Wider hips in females is not contributed because of large volume of organs.
Broadening of the hip bones happens as a feature of the female pubertal process, and estrogens (the overwhelming sex hormones in females) cause an enlarging of the pelvis as a piece of sexual separation. Consequently females for the most part have more extensive hips, allowing labor.
However, I found this article from International Business Times that states >>

Women have not evolved wider pelvises despite it being difficult and
  dangerous to give birth – yet they may have developed some physical
  features that help during labour.
Barbara Fischer, from the University of Oslo, has found a link between
  pelvis shape and statue and head circumference of both baby and
  mother.

There was, however, no sufficient evidence to back this article, but it is quite an interesting approach otherwise.
Males are not needed to have any extra organs, but females have just more space in the pelvis region. That space can be linked to idea of uterus expanding to hold the fetus during gestation as mentioned by @BryanKrause.

the article is a poor understanding of a study on the size of the birth canal portion of the pelvis, the pelvis as a whole is still wider. a big red flag is it is the an article in business times about evolutionary biology.

mostly nothing, males have narrower pelvises. The prostate, seminal vesicle, and basal anchorage of the penis do take up some space.


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How does a ribosome move along mRNA?
I've been reading around Wikipedia recently trying to learn more about various biomechanisms. I’m intrigued by ribosomes — with how small they are, they’re basically chemical machines from what I can tell. I’ve got the general idea of what they do, which is nicely illustrated in the super common GIF below:

My question is how this happens, on a molecular/chemical scale. Even in the GIF, the way the mRNA is being so mechanically fed through the ribosome at the exact-right times seems so deliberate, and I can’t imagine a chemical process that does this so well. It seems like we know the exact protein by protein structure of a few types of ribosome; as such, I naively assume we can work out exactly why and how it does each thing it does. I’m sure it's not a simple question — if it's not really answerable in a stack exchange question, then I guess my question becomes where should I read to learn this.

Your question and tags are fine in principle, so I'm deleting your remark about them. Your supposition that this is a simple question is completely wrong. It is the animated gif that is simple, not least because our knowledge of the process is based on static views of the ribosome. The reality is extremely complex and requires one to read original papers in detail. I doubt anyone could summarize what is known here. I'll see if I can find a decent recent review to point you at.

I've modified your question a little more (restricted the title to a single question and specified messenger for the RNA — mRNA). And give an "answer" with some references.

I agree with David. The exact mechanism cannot be explained here. You need to read the articles/papers on the structural biology of the process. It is also not very easy to understand even for biologists who are not working in that field.

Disclaimer
It is not clear to me that requests for references are on-topic here. In general I would think not, as they are subjective and not about biology per se. I therefore solicit neither votes for, or acceptance of, this answer. I would have used the comment area to provide references, but there isn’t really enough space, so I decided to flesh it out into what follows.
Overall perspective of elongation in protein synthesis
The main concern of the question is the movement of mRNA during translation, so I shall focus on elongation (rather than initiation). Most of our detailed knowledge of the ribosome is based on static ‘views’ of the ribosome at different stages, although there is a paper (reviewed in Nature by Ehrenberg) in which the dynamics have been deduced from millions of time-resolved electron microscopy images. I doubt whether that is what the animation in the Wikipedia article is based, however.
After an introduction to the subject from Wikipedia, I strongly recommend graduating to a good text book. Text books have the advantage over Wikipedia that they are comprehensive, integrated, professionally illustrated and sent out by publishers for review. Berg et al. is probably as detailed as you will find in a general text, the 2002 edition is available online (as are others such as Alberts et al. and Lodish et al.) through NCBI Bookshelf.
Figure 29.24 of Berg et al. provides a static general view of elongation:

You need the associated text to understand this properly, but the step at which the mRNA is thought to move with respect to the ribosome is the penultimate one in the diagram: translocation.
Unfortunately you can’t just read through books on NCBI Bookshelf — you have to search for particular topics. But Chapter 29 of Berg et al. is what you need, and the links to the relevant sections are:

29 Introduction
29.3
29.4
29.5

How exactly does the mRNA move?
The details of the individual steps in protein synthesis are being deduced from examination of high-resolution structures of complexes at different stages. For the student who as able to go beyond the accounts in general textbooks, a review such as that published in 2009 by Schmeing and Ramakrishnan is perhaps the next port of call. But, chemical virgins beware, this is structural biology, and there is no simple answer that you can scribble on a table napkin!


text:
Do all multiple sequence alignments employ global alignment algorithms?
Multiple sequence alignments are usually done between sequences of similar length, which resembles best a global alignment. However, I'm not sure at all what the algorithmic background would be in such case. Is it essentially a global or a local alignment when one performs a multiple sequence alignment?

Global or local alignments mean to align parts of the sequence or the whole sequence, whilst multiple alignments is how many sequences to align (one or more than one). They are not mutually exclusive terms. See "what is the difference between local and global sequence alignments?"

It is dangerous to generalize, as different multiple sequence alignment (MSA) programs may well employ different algorithms. However as the objective is to align many sequences along their whole length, and all MSA programs of which I am aware present the results as such, it is difficult to envisage anything other than global alignment being employed.
For the widely used Clustal W and X, this is certainly the case. Clustal employs a progressive alignment algorithm which involves the heuristic assumption that the most closely aligned sequences by pairwise alignment are a valid basis for the order in which progressive multiple alignment is performed. The initial pairwise alignments (which are used to produce a guide tree) use dynamic global alignment, as does each progressive alignment step, although this alignment is to a profile of previously aligned sequences, and uses context-dependent scoring.
There is an extensive Wikipedia article on MSA and one of the original Clustal papers is freely available on-line. The excellent book by Durbin et al., Biological Sequence Analysis, contains a chapter on the topic.

Just as James said these terms are not mutaully exclusive.
you statement is not correct:

Multiple sequence alignments are usually done between sequences of
  similar length

It really depends on what you want to achive with your MSA (multiple seqeunce alignment). First some brief explanation about local and global alignment(the difference between these two is described previously in this question):
 local alingment: trying to match a portion of your sequence of interest with another sequence, this could be done with MSA think about BLAST. Using BLAST you are performing a local sequence alignment with all the sequences in the database. When using this local alignment you are focusing on parts which overlap between your sequence with those in the database --> clue about domains e.g.

global alginemnt: the matching of the whole sequence with another sequence, which DON'T have to be equal in size. When using a global alignment with sequences of different length e.g. what will happen is that depending on the  algorithm that is being used (Needleman–Wunsch), there will be gaps inserted to match those sequences over the whole length.

Some practical examples when to use which alignment:

Making profiles of a group of proteins --> global alignment
Intersted in homologous proteins --> most of the time you use a local sequence alignment especially when you know the homologs are quite distance, so there is not much sequence similarity.
searching proteins which could have simillair function --> local alignment, BLAST will give you the proteins which have same domains e.g. or the same structure when blasting againt the PDB database, which can give you major clues about the function of the protein of interest.

NOTE that these suggestions are just some examples, some people will prefer an other option.

Rick, English may not be your first language, but that doesn't excuse your not using a spell checker. If you can set your browser language to English (Firefox allows me to switch to French etc), most will spell check entered text. Otherwise, copy the text into a word processor such as Word, select it all, set the language to English (British of course ;-) ) and run a spell check.

Thankyou I will try that! , indeed it will spell check my typed words to my browser language(Dutch) So if I type an english word it will change or split it to make it look Dutch so changing my browser setting would fix that problem (I hope) @David

Multiple sequence alignment is a very complex task and there are several approaches depending on what you are looking for.
A global alignment might find the overall closest region. However, it is a well known problem with the lengths. If sequences lengths are very different this can be generate bad alignments.
Local alignment is seeking for the best matching regions along sequences.
It is well known that some genomic regions tend to accumulate more mutations than others. For this the idea of domains is suggested. The main idea behind (and to make it simpler) is like performing several local alignemnts in order to get the optimum alignments for different regions of you sequences.
There are many algorithms that implemented very different methods to do so: from pairwise alignments to HMM profiles.
I would recommend to read this article.


text:
Warm water bath
Why is it advised to take bath in warm water when we are sick?I know that as homeotherms we need to generate metabolic heat to adapt to the environment temperature.But what is the mechanism by which it makes people feel better(except those who are allergic to it)?

Why someone likes bathing in water at some particular temperature is just based on personal choice. Some people like cold water. Some people are also allergic to bathing in warm water.

1) A hot bath, or soak in hot water raises our body temperature. Several benefits of this rise include:  Improved blood circulation, Improved lymph circulation, increased metabolism and calmer nervous system.
2) During this increased temperature your body releases endogenous opioid peptides, which are primarily endorphins.That’s why you might feel like a new person after a hot bath!(reference)
It apparently also takes your feeling of loneliness away (reference)

It is a myth that sweating detoxifies you. See for example, http://www.uamshealth.com/?id=12247&sid=1

@ChrisInEdmonton thx for pointing that out

@TheLastWord Can you edit your answer then, please? It is a good answer, except for the detox stuff. I promise to upvote it if you fix that ;-)

@JohnEye I edited it


text:
Do humans have the hyaloid canal, after all?
Most Google Images results for "eye anatomy" are pictures of eyes that don't have the hyaloid canal while some do (proof). Do humans have it, after all, or not? :)

Yes, humans do have the hyaloid canal.

Schematic diagram of the human eye (reference)
For function and other information, please refer to this journal article.

What, in your opinion, justifies that it is missing in the vast majority of eye anatomy images? I don't even remember seeing it in my high school biology textbook.

@user132181 Can you send me links to a few such images?

Look at the mentioned Google Images search.

@user132181 I would have to say that most of them are showing you the full eye while you get to see the Hyaloid canal if you go for a cross-section view. In full eye images, the hyaloid canal would not be marked.


text:
What is this crawling next to my house?
I just found this outside my house while walking the dog. I was thinking it's some kind of slug? It's been raining a lot lately and today, so maybe that has something to do with it being on the pavement. I live in South Central Indiana, US. When it wasn't stretched out, I'd say it was 2-3 inches long.

It's definitely some sort of slug. I would suggest you link the images directly in the post using the image tags. I would edit it for you if I knew the direct URL for the images, not just the imgur links. I would also suggest you posted your approximate location so we can narrow down options for specific species of slugs. Since I'm not a slugologist, I can't help much more than that.

@user137 The precise term is a malacologist

You'll actually find them, or their tracks, quite commonly on the sidewalk or pavement in the early morning just before sunrise. I imagine if it was raining it might have gotten washed onto the pavement or it may have gotten there searching for higher ground. In the US they are generally considered a pest and can consume crop plants very quickly. I don't actively treat my lawn for them but if I find them I take the opportunity to not let it back into my yard.

It could help if you were to say what country / region you're in ...

Based on another post, the OP is in Indiana.  Or at least was 2 years ago...

It looks as though it has a keel along it's back (the area behind the mantle shield.)
If so (and I think it is), it would be a keelback slug, the coloration strongly suggesting a leopard slug (Limax maximus):

Coloration varies but the general pattern is a spotted spotted mantle sheild about a third of its length in size, with a striped tail.
The major doubt I have is the size. It looks smallish in the photo. Leopard slugs are very large. Perhaps it's a juvenile.

I suspect the keel is just an artifact of the way ansarob took the photo. If ansarob is in the Midwest USA, that's almost certainly a leopard slug. It's hard to tell scale from the image but it looks as if it's retracted into a defensive posture which might explain its lack of length.

+1; definitely looks like a leopard slug to me and as @RobertKaucher says above I think the apparently small size is an artefact of the camera angle.

Yes, this is the leopard slug. It's native and relatively common in my country, but it has been introduced to North America.