text:
Cytokine responsiveness
Why is it that cytokine responsiveness is less in progenitor cells than their ancestors(stem cells)?
What will be the benefit of such reduction in responsiveness?

Maybe this is well-known, but I hadn't heard of it before. This sounds like a a rule that is far more complex in practice than in this question. Can you point out a citation/textbook in which you found this comment?

@AJK it's present in G.K. Pal physiology 2nd edition, pg.no-59

Could you add the quote to your question? I can't access that textbook.

@AJK it's present in the form of a table.

My answer assumes you are asking about in-vivo effects of cytokine responsiveness.
It has to do with the regulation of the differentiation process. Cytokine responsiveness depends on other factors like cell-cell signaling. To be sure that the differentiation occurs in the right place, the progenitor cells need a signal feedback from the surrounding context (the actual tissue where the cells will differentiate). If the feedback matches, they differentiate.
Stem cells on the contrary, are physically distant from that context, so they lack all the feebacks needed and do not respond to cytokines stimulation as the progenitors do.
Here's some literature about it:

Developmental changes in progenitor cell responsiveness to cytokines.
Mechanisms regulating lineage diversity during mammalian cerebral cortical neurogenesis and gliogenesis.
Signal transduction pathways involved in the lineage-differentiation of NSCs: can the knowledge gained from blood be used in the brain?
Enhanced responsiveness of committed macrophage precursors to macrophage-type colony-stimulating factor (CSF-1) induced in vitro by interferons alpha + beta 1.

However, note that the whole process is still largely unclear and it may vary for different cell types, so consider my answer as a generalization of the concept.


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Why nerve fibre is infatiguable?( is my conjecture correct?)
According to this:

A nerve fibre cannot be fatigued, even if it is stimulated for a long time. This property of infatiguability is due to absolute refractory period.

How is refractory period related to infatiguability?

My attempt: If there were no absolute refractory period, then there will not be closure of Na+ ions into cell, so there will be temporary deficiency of Na+ at that location, now if a new action potential arrives at that point then , due to lack of Na+ there will not be further conduction of it.
Is my conjecture correct?

What exactly is your question? Is it why nerves don't get tired, or whether your conjecture is correct?

Is my conjecture correct?

Then it seems my awnser isn't what your looking for,  but the conjecture is not  quite right. It isnt a lack of ions, but rather the sodium gates are inactivated (and cannot open) that causes a absolute refractory period.

I really don't understand the reason for down vote.

If you study the electrical function of the nerve, it does exhibit attenuation to repeated signals, and there are various electrical stabilization times for the stasis within and outside the nerve to reach a balance after stimulation. ou should read about nerve disorders and nerve fatigure research to get an idea of how they malfunction. this is not recent but it could be interesting: http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.1906.sp001147/pdf

One can imagine that each action potential causes a small amount of $\ce{Na+}$ goes inside the cell, and a small amount $\ce{K+}$ goes outside the cell, thus weakening the electrochemical gradient of both ions. If each action potential has (approximately) the same flux of $\ce{Na+}$ and $\ce{K+}$ then higher frequency of action potentials means more flux, thus a quicker depletion of the electrochemical gradients. The absolute refractory means there is a maximum firing frequency.
Thus the Sodium-Potassium pump only needs to be able to "recharge"  the maximal possible depletion of ion's gradients. If there was no absolute refractory period then theoretically the action potential frequency could be faster than the Sodium-Potassium pump can keep up. A abnormally fast firing rate in theory could deplete the potassium gradient and sodium gradient thus would result in a fatigued neuron.
Edited to add in reference to the conjecture:
Absolute refractory periods are cause by sodium gate inactivation, thus no matter how much current one adds the sodium gates will not open until sodium inactivation ends. However, over long periods of time (in seconds) and in the absences of a ionic pump, the lack of sodium (and potassium) gradients will cause fatigue.
However, "fatigued" neurons may not act like one expects.

Hopefully, the edit clarifies.

You mean lack of gradient? because Brayn Krauss comment on this question says so https://biology.stackexchange.com/questions/62826/what-is-the-energy-cost-of-an-action-potential

Yes I do mean lack of gradeint. I will edit for clarity when I return to my desktop.

How do you define the side effects of fatigue neuron?

@LéoLéopoldHertz준영  thats a complicated question, and the linked paper gives some possible side-effects such as hyper-excitablility. It's counter-intuivite so I left it out, and gave a link for the more interested reader. Perhaps a separate question would be good?

@xelo747 No, I do not think so. It is part of the topic here. Please, add a section about it in your answer stating some of the factors.

Nerve fibres cannot be fatigued even when stimulated continuously because the nerve fibres primarily conduct impulses that do not involve any type of energy expenditure

Can you elaborate on this? We're looking for fully-fledged answers with detailed explanations, and with supporting references.

Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers in the help center.

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Why can mitochondria make only 34 molecules (rather than 61 molecules) of ATP ？
Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from the oxidation in the electron transfer system of NADH and FADH2 generated by oxidation of glucose in glycolysis and the tricarboxylic acid cycle?
The electron transfer system oxidizes 10 mol of NADH and 2 mol of FADH2 obtained from glycolyses and the tricarboxylic acid cycle, and up to 34 mol of ATP can be obtained by the electron transfer system alone. Complexes I and II take energy from NADH and FADH2, and complexes I, III, and IV are also proton pumps that pump hydrogen ions against a concentration gradient. The reactions carried out by the four enzymes, known as complexes I–IV, and their Gibbs free energies are as follows;

Complex I: (NADH + H+ + CoQ → NAD+ + CoQH2 — ΔG˚′(1) = -71 kJ/mol)×10
Complex Ⅱ： (FADH2 + succinic acid + CoQ → FAD + CoQH2 + Fumaric acid — ΔG˚′(2) =-2.9 kJ/mol)×2
Complex Ⅲ：(CoQH2 + 2 cyt c(Fe3+) → CoQ + 2
cyt c(Fe2+) + 2H+ — ΔG˚′(3) =   -41 kJ/moll)×12
Complex Ⅳ：(4 cyt
c(Fe2+) + O2 + 4H+ → 4 cyt c(Fe3+) + 2H2O — ΔG˚′(4) =  -110 kJ/mol)×6

Therefore, the ‘net’ reaction, from complex I–IV, is as follows:
10 NADH + 2 FADH2 + 6 O2+ 2 Succinic acid → 12 H2O + 10 NAD + 2 FAD + 2 Fumaric acid — ΔG˚′ (total)
Here,
ΔGo' (total)= 10ΔGo'(1) +  2Go'(2) + 12ΔGo'(3) +  6ΔGo'(4)
= 10*(-71) +  2*(-2.9) + 12*(-41) +  6*(-110) kJ/mol
= -1867.8  kJ/mol
The following reactions then occurs in complex V using the above ΔG˚′ (total);
ADP + Pi → ATP , ΔGo'(5)=  -30.5 kJ/mol
Simply considering abovementioned only,  the amount of ATP that can be generated from the energy derived from a single molecule of glucose entering the electron transfer system via NADH or FADH2 is as follows;
-1867.8/-30.5 =61.2 ATPs
So, my question is as folilows;

Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from a single molecule of glucose in the electron transfer system?

I would like to ask this question especially from the perspective of Gibbs energy balance (in terms of energy loss).
Related

https://chemistry.stackexchange.com/questions/72457/why-delta-g-nfe-and-not-f-integraldne/176835#176835
How many molecules of ATP are actually produced in aerobic respiration?

The fundamental flaw in the poster’s logic is the implicit supposition that if a mitochondrial (or other) oxidation reaction has a standard Gibbs Free Energy change of -x kJ/mol, all of that can be used to drive the reaction ADP + Pi → ATP; and that one can just divide x by 30.5 to find how much ATP is produced.
One cannot.
One needs to consider the actual physico-chemical reactions of the oxidations and the subsequent phosphorylations of ADP. When you do this you will find that much of the free energy of the oxidation reactions is not used to drive a chemical reaction, but is converted into (‘lost’, in the terms of the poster) heat energy.
Even if one considers the simplest situation, ‘substrate level’ phosphorylations — reactions in which the oxidation of NAD+ is coupled directly to the synthesis of ATP or GTP — there is no logical reason why the free energy change should be zero. The oxidation reaction may well have a –ΔG˚′ of greater absolute magnitude than the +ΔG˚′ required to synthesize NTP, and the difference will be released as heat. This is indeed the case for the succinyl-CoA synthetase reaction which generates GTP in the tricarboxylic acid cycle.
However the mitochondrial oxidation reactions are not coupled directly to generation of ATP. They are used to pump protons across a membrane, and to generate a membrane potential, which is the basis of the proton-motive force used to drive ATP synthetase and synthesize ATP. There is no reason to expect that all the free energy from the oxidation reactions will be conserved as a proton gradient and membrane potential, and good reason to suppose that it will not.

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Where are interneurons in Autonomic Nervous System?
According to  the following, it implies that preganglionic neurons are interneurons.

Interneuron called preganglionic neuron whose cell body is situated in the "intermediolateral" column of spinal cord( also called 'lateral column').1

From this:

The interneuron (connector neuron) of somatic system has cell body in the dorsal horn and terminates in the ventral horn, while that of ANS has cell body in the intermediolateral horn and terminates in the autonomic ganglia....In the ANS, there are two efferent neuron chains between CNS and the effector organ: first efferent neuron (pre-ganglionic neuron) has its cell body in CNS while the second efferent neuron (post-ganglionic neuron) has its cell body out-side the CNS in the ganglion.

But this source implies quite opposite:

The spinal sympathetic interneurons that most directly influence the activity of sympathetic preganglionic neurons after spinal cord injury....

So which one is correct?

Please read Dot 2,3,4 on right column of that page, then it implies same as of first link.

It sort of depends on your definition of interneuron. Many school-level textbooks suggest that any neuron that has neurons both pre and post synaptically are interneurons. Therefore both the preganglionic neuron and the spinal sympathetic interneurons could be considered interneurons. This means that all neurons in the brain are interneurons and vastly oversimplifies the CNS.
I would argue that it's probably more helpful to think of the preganglionic neurons as "projecting" neurons, as they come down the spinal cord. The post-ganglionic neuron is more like a motor neuron.
Edit: I answered a similar question in more detail here: Is the bipolar neuron of the retina considered a sensory neuron?

So, what's the extra neuron in link 3?

Most likely a small, localised interneuron, residing solely within a confined region of the spinal cord. Edit, it will receive input from nearby neurons and send output to other nearby neurons.

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Seeing with one eye, why intensity doesn't get half?
Today I just closed one eye(for finding blind spot), and as usual some of the visual field is lost, but I wonder why is not intensity of light(brightness) reduced to half?
Shouldn't it be since our brain is now getting only half impulses?
Does our brain instantly reduces the threshold of rods and cones when one of the eye is closed?

Never experienced, but removing one earphone surely reduces sound intensity that is perceived.

Consider two tuning forks are being vibrated one at each ear, now removing one will certainly reduce the intensity of that same frequency.

Okay , take this example, put one ear in water bath and let other in the air. ask someone to make some noise, now remove the ear, the noise will be increased.

This is actually a very interesting question! (Binocular neurons will change their activity when you close one eye by definition.)

Think of eyes as cameras producing an image at a given framerate. If you have 2 cameras and shut 1 of them off, that doesn't change the amount of light incoming to the other camera.
Your question is one of signal interpretation rather than receiving signals and adding them. Given that the 2 cameras have different perspectives, adding their respective pixels makes no sense. Instead, the dual images (if both cameras are on) are post-processed for spatial reference relevant to perspective.
In the case where a camera is shut off, then the spatial reference becomes a null picture and the post-processing can be skipped.
(For reference, if you took incoming data from both eyes and added them, the result would be an incoherent and largely unusable mess)

Experiment 2
Aim: Effect of intensity on two eyes
Requirement : Two eyes, a dark transparent glass, an object to glance.
Procedure :
1)Sit in a lit room
2)Look at fan with only right eye
3) Look at fan with only left eye through dark glass.
4) Look from both eyes( keep dark glass in front of left eye)
Observation : Brighter in only right eye, darker in only left and medium brightness with both eyes.
Result: Intensity do add when are different. Or more correctly they rather average out.
In your actual experiment, the intensities in two eyes just averaged out, that was mathematicaly equal to single eye.
Theory:
Three principle

1) Brightness is transferred via frequency principle. Greater the intensity of light, greater the frequency of AP transmitted.
2) [Action Potential ][1]

Action Potential has a fixed depolarising potential.

3) Each spatial point, in space, of vision, is represented on a single spatial point in occipital cortex.

Two action potential caused by same image pixel reach their representative point on occipital cortex area 17.
They are then sent to visual associative Area 18 for matching.

“Fusion” of the Visual Images from
  the Two Eyes
To make the visual perceptions more meaningful, the
  visual images in the two eyes normally fuse with each
  other on “corresponding points” of the two retinas.
  The visual cortex plays an important role in fusion. It
  was pointed out earlier in the chapter that corresponding points of the two retinas transmit visual signals to
  different neuronal layers of the lateral geniculate
  body, and these signals in turn are relayed to parallel
  neurons in the visual cortex
  Source: Guyton and Hall, chapter 51.

Same impulses from same spatial point are sent to same interneuron.
The action potential cannot rise further.(Principle 1 above)
This fused signal reaches next neuron for further processing. Intensity is judged.
Same amplitude as of one eye reached, so same intensity was percieved by even two eyes.
If fused signal is of intermediate frequency, intermediate brightness is observed.


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What is the mechanism by which lamins regulate gene expression?
The heterochromatin is generally localized at the nuclear periphery (also near nuclear lamina), whereas active genes are preferentially found in the nuclear interior.
Children with Hutchinson-Gilford syndrome have a mutation in a LMNA gene, which codes lamin A and C, therefore, mutation in a LMNA gene causes overexpression of genes near nuclear lamina, this shows that nuclear lamina has something to do with gene expression regulation.
What is the mechanism by which lamins regulate gene expression?

Based only on your description, it would seem that lamins repress expression. Thus it would make sense that they're associated with hetero- as opposed to euchromatin.

@canadianer: Yes, they repress expression, if there's no mutation in LMNA gene and nuclear lamina is located near heterochromatin, I just don't know why.

Euchromatin is actively transcribed. It wouldn't make sense to localise it near something that presumably represses transcription.

@canadianer: But how does nuclear lamina repress gene expression?

So you want to know the mechanism by which lamins regulate gene expression?

@canadianer: Yes, that's what I want to know.

If someone wants to build an answer here, this article listed is where it's at. The fact is, we're at the frontier of understanding this, and so it's not a comprehensive mechanism, yet.
/e I'd also look here, the article is 2013, where the above is 2015, however:

So my answer was deleted because it "didn't answer your question."  Except that it did.  The article linked here, Gene expression, chromosome position and lamin A/C mutations, is an entire paper devoted to what we knew as of 2011 about lamins and gene expression, with references.  Your question was not a simple question, and article details how lamins are involved in gene expression.
I shall quote it here in order to "answer your question", and perhaps the moderators will see fit to not delete the post this time.  If said moderators think I should write a review of a review to facilitate your understanding, then I obviously have not understood the meaning for this board.
I don't have enough rep to leave a comment on anything other than my own answer, which seems to have been the appropriate way to link to the paper.  I figured an answer to your question would still be useful.
I would recommend reading the entire article as it is very useful in understanding additional indirect hypotheses for lamins controlling gene expression.

The Lamina as a Regulator of Gene Expression
In most cells, a dense heterochromatin network is visualized as electron dense material adjacent to the inner nuclear membrane and the nuclear lamina. The dense network is typically considered to reflect the association of transcriptionally inactive genes with the nuclear lamina. Specifically, this heterochromatin is thought to reflect a repressed gene state and suggests that the nuclear membrane and lamina may play an active role in gene repression.5 Lamin A/C and its binding partners can interact with DNA, histones, transcription factors and chromatin.6 Lamin-associated domains (LADs) are cis-acting sequences thought to range in size from ∼0.1–10 Mb, and these domains are thought to regulate the interaction of chromatin with the nuclear lamina; generally LADs are considered to be transcriptionally repressive.7 The precise sequences that define LADs have been elusive but nonetheless the LAD concept implies that the lamina and the genome interact in a specific manner. Therefore, it follows that one mechanism by which LMNA mutations may confer pathology is by altering the interaction between the lamina and chromatin. Consistent with this, LMNA mutant cells have altered chromosome territories.4 Meaburn and colleagues first examined chromosome localization in proliferating LMNA mutant fibroblasts and found that it resembled the chromosome organization associated with quiescent or senescent fibroblasts. They suggested that mutations in LMNA produced structural disruption to the lamina inducing a chromatin organization that may resemble an inappropriate cell cycle state. The presence of LADs and the fact that mutations in LMNA associate with altered nuclear architecture suggest that the nuclear lamina plays a vital role in both scaffolding chromatin and regulating chromatin organization. In this model, it is possible that distinct LMNA mutations may alter distinct regions of the genome leading to mutation specific profiles of altered gene expression.

An answer usually and preferably contains an answer that specifically targets the question. This question is really quite broad, and I understand it's hard to write a concise answer. However, it's best not to just link an article, or paste an entire abstract. You might want to get rid of the fluff and answer the question and only the question.


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How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?
No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds simple, but it sort of has me baffled.

Western blot: No. Need a known antigen and so, since we don't know what we're after, this won't work.
Total protein gel: Collect cell lysates from different cell populations that are in different parts of the cell cycle, run it on a gel and observe any cyclic expression. This seems sort of ok but I feel like there are a few problems with it: 1) identifying the cell populations that are in the different cycle stages; 2) other proteins of same/similar size that cannot be differentiated.
Some sort of RNAi, knockdown, etc.: Like the western blot, we don't know what we're dealing with and so can't target anything.
Pulldown assay with mass spec: I don't know a lot about it aside from that it looks at protein-protein interactions. Unsure if it would be appropriate here.

As far as a model, I was thinking either yeast or some immortalized mammalian cell line.

One can fairly easily do genome-wide knockdown experiments nowadays, so don't discount RNAi/siRNA right off the bat. Which tool(s) you pick is going to be dependent on the model you're using. If it's yeast, you have many validated tools at your disposal, including mutants/knockouts for every single gene in the S. cerevisiae genome,  two-hybrid systems for looking at protein-protein interactions, reporter constructs that indicate by fluorescence or enzymatic activity when the gene of interest is being expressed, and others.

For yeast, people used to rely on mutants/knockouts which are supposedly easy to produce using HR, compared to other organisms. For animal cells people extensively use high throughput RNAi/CRISPR-Cas screens to identify the functions of a gene. If you have the protein sequence then you can express it and raise antibodies against it. With the antibodies, you can Co-IP-MS for identifying protein-protein interactions and ChIP-Seq (for TFs) or CLIP-RNAseq (for RBPs) to identify protein-DNA and protein-RNA interaction respectively. Overall, your question is quite broad. You should narrow it down.

I've actually been involved in a hunt for checkpoint proteins in diatoms (a type of eukaryotic algae), the cyclin family has been greatly expanded in these organisms and we were trying to figure what these extra cyclins were sensing/signalling[1].
In a nutshell, the first author looked at different conditions which were likely to affect cyclin expression. Most of these conditions prevented cell division (e.g. lack of nutrients, G2/M chemical inhibitors or light) and samples were taken before and after the blocking conditions were removed. Afterwards mRNA's were quantified of suspected cell cycle genes. As the checkpoint genes' mRNA and protein cycles extremely transiently this took some doing. Cyclins that reacted to the conditions were characterised using complementation assays and other techniques.
Afterwards yeast two hybrid assays were used to identify interacting proteins to build up the network[2]. In general, these experiments were not that straightforward and messing with essential genes causes a lot of trouble but it still nothing compared to the original yeast cyclin work where they were slogging through mountains of temperature sensitive mutants defective in their cell cycle (see the work of Lee Hartwell and Paul Nurse who got the Nobel prize for this in 2001 with Tim Hunt).


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Can DNA be considered as a fractal antenna?
I was reading about the consequences of using mobile phones and came across the statement that mobile phones are a potential source of cancers because DNA is a kind of a fractal antenna. The reason put forward for this was that it shares with mobile phone antennae the properties of self-similarity and electric conductivity.
The scientific paper which is the source of this statement appears to be: Blank and Goodman, “DNA is a fractal antenna in electromagnetic fields” Int J. Radiation Biology, 87:4, 409–415, DOI:10.3109/09553002.2011.538130. Is anyone able clarify this assertion and explain whether or not the arguments in the paper support it.

Where did you "meet" said statement?

@BenBolker why bogus? this is my question

@BenBolker See also this comment: http://www.tandfonline.com/doi/full/10.3109/09553002.2011.626490

I have revised the question so that it is clear that the main question is the validity or not of the arguments in the source paper, which is cited. If someone is able to argue in support them they no doubt will be able to explain what a fractal antenna is and how this could cause DNA damage. I for one would be interested to know.

See my associated question https://biology.stackexchange.com/questions/91078/what-is-the-antenna-gain-of-two-pieces-of-sars-cov-2-retrotranscribed-dna . It was deleted because I initially mentioned a disapproved reference that I later removed but the moderators did not undelete the question. I will post i Physics SE if it isn't unlocked.

I looked at the original paper, Blank and Goodman "DNA is a fractal antenna in electromagnetic fields" Int J Radiation Biology, 87:4, 409-415, DOI:10.3109/09553002.2011.538130.
To be honest I can't give concrete reasons to doubt it, but here are a few things that raise my suspicions:

it is a review article that relies heavily on self-citation (15/50 citations are authored or co-authored by the two authors of this paper, including most of the primary experimental references)
in my judgement "responding to many different frequencies" and "having structures on several different scales" (Table 1) is not particularly strong evidence to support the conjecture that DNA acts as a fractal antenna; I would be much more convinced by an analysis based on physics rather than analogy (this comment on the paper by Foster reviews the physics of fractal antennas and its application to DNA and concludes that "Loose and implausible conjectures about DNA as a fractal antenna do not substitute for careful discussion of these matters"; I don't find the authors' rebuttal particularly convincing)
the authors cite epidemiological evidence that non-ionizing/low-frequency radiation causes cancer: according to the US NIH's National Cancer Institute, this evidence is weak. (However, one of the authors of this paper is a contrarian on this subject and believes that the mainstream view is wrong, for a variety of reasons.) (See Are low-intensity radio-waves carcinogenic? for more discussion on Biology.SE.)
the paper uses very disparate lines of evidence (not necessarily a bad thing, but in this case it feels haphazard): in particular, the authors discuss both low-frequency and ionizing radiation (this is part of their "DNA is sensitive to many different frequencies" argument, but ionizing radiation operates in a very different way)
it is highly speculative in places (e.g. "EMF is believed to have been an important driving force in evolution", p. 413, no reference; the authors go on to attribute the faster evolution of eukaryotes to the fact that their DNA structures are more fractal)
at least one of the references cited (de Pomerai et al. Nature 2000) was retracted in 2006 (5 years before the current paper was published)

What I can say in favor of the authors is that exploring the mechanisms by which low-frequency electromagnetic fields/radiation (ELF) affect cellular biology is indeed interesting; many of the epidemiological studies, while finding very weak effects, have also downplayed risk because so little is known about mechanisms of operation. If we could come up with a rigorous mechanistic understanding of ELF effects, that would be scientifically worthwhile.

See also the comment on this article: http://www.tandfonline.com/doi/full/10.3109/09553002.2011.626490

thx, incorporated in my answer

Well done Ben for taking the time to handle a complex subject!

many thousands, perhaps millions of people have been incorporated into studies of cancer rate Vs mobile phone use since mobile phones started warming folk's ears in 1995, so the topic went a phase of intense study in the 2000's as folk were suspicious that phones could actually cause cell damage. Actually, the many studies surprising found that the cancer rates were inconcluseively low and non-detectable. Also the conductivity of DNA is not like an antenna, it is probably 100 times less, and that conductivity may serve to protect it anyway, by giving oxidative charge a path of escape.


text:
Can someone identify this tree from the Pacific Northwest?
A tree at my house in Seattle, Washington, USA has these leaves. Can someone tell me what it is?

Do you have a photo of the flowers?

It looks similar to a Cotinus coggygria, which is a shrub that we call a Smokebush in the UK. But given your location, it could be Cotinus obovatus, known as American smoketree.
See http://dendro.cnre.vt.edu/dendrology/syllabus/factsheet.cfm?ID=415
The leaves will start green and progressively change colour to deep reds in the autumn with sprays of pink-purple flowers in the summer that from a distance look like smoke, hence the name.
Here are some images I have found on the web.

http://www.cirrusimage.com/tree_American_smoke.htm

http://allthedirtongardening.blogspot.co.uk/2012/08/smoke-tree-smoke-bush-coninus.html

Hello Martin, could you explain why you think it is Cotinus  sp, ideally with links to references and images. You may also like to read this and find many sample responses to some highly received species-id questions here.

I think this may be a Chokecherry. Prunus virginiana 'Canada Red'
Found this on a Washington nursery website so it would make sense that it would be planted in your region. I am inclined to think it is closer to this species than a smoke bush based off what I can see from the flower in the photograph.

Possibly, although the leaves appear to be smooth-edged, rather than serrated

That's a good point. I would have rather left a comment because not 100% sure, but didn't have enough reputation.


text:
Could AI be applied to protein folding?
Two years later, there is a follow up question to the one asked here: How do we know if the folding@home project results are right?
Since we are quite sure F@H is working right and following this article's statement:

Similar techniques could be applied to protein folding, reducing energy consumption, or searching for revolutionary new drugs and materials.

...I would like to ask if AI stuff, like deep learning, neural networks and the rest of today's buzz words could be applied to molecular dynamics, especially in the protein folding field?

Yes, and no :-)
In the meantime many protein structures can be predicted quite accurately - even those for which no reference fold had been known before.
In this case the important buzz word is "big data": co-mutations (of charged amino acids) that can be found when sequencing many independent genomes. (... which indirectly bypasses the emphasis on dynamics for protein folding)
Editorial: 2017, Science: http://www.sciencemag.org/news/2017/01/hundreds-elusive-protein-structures-pinned-down-genome-data
Perspective: Soding et al. , 2017, Science ( http://science.sciencemag.org/content/355/6322/248 )
Research article: Ovchinnikov et al. 2017, Science ( https://www.bakerlab.org/wp-content/uploads/2017/01/ovchinnikov_science_2017.pdf )


text:
NMR spectroscopy detection methods for proteins
I've stumbled upon a table comparing the sensitivities of different detection methods in NMR spectroscopy: "Direct", "DEPT" and "Inverse", where "Inverse" seems to be the most sensitive.

What exactly are those different methods are and how do they differ?

In most cases when you perform NMR experiments on proteins you detect the signal on the protons. Even if you're looking at other nuclei, in the end you transfer the magnetization to a proton and detect that signal. This is simply the most sensitive method due to the high gyromagnetic ratio of 1H, and this is the method that is labeled "inverse" in your figure. This is pretty much the default way to measure heteronuclear spectra.
Direct detection means that you directly observe the less sensitive nucleus like 13C. This has certain advantages especially for large proteins where you often have to deuterate the protons to be able to measure anything useful.
DEPT is a type of experiment where magnetization is transferred from the directly attached protons to the heteronucleus. This increases the sensitivity and allows to distinguish CH and CH3 groups from CH2 groups


text:
Why must gene entrapping constructs be integrated into introns and not exons?
Homework Question:
In enhancer trapping, reporter transgenes are integrated randomly into the fly genome and their expression identifies enhancers and thereby genes expressed in particular patterns. In mice, a similar technique for gene identification is employed called “gene trapping.” In gene trapping, an exon encoding a reporter protein such as GFP (see below) is integrated into random locations in ES cell chromosomes (when DNA constructs are introduced into mouse ES cells, most recombination events are into random sites; homologous recombination is relatively rare). ES cell lines with randomly integrated transgenes are used to generate mice.

Where in the genome must a gene trapping construct integrate in order for ES cells to express GFP?
Answer:

My Question:
Why can't the construct simply be knocked into the coding DNA sequence of the mouse genome? Why does it have to be integrated into an intron?

I don't know that they must integrate into an intron. It seems perfectly reasonable that they could also integrate into an exon, as long as the reporter is in-frame. There is obviously an element of chance in that, and so the advantage of integration within an intron is that splicing will ensure that the reporter is translated correctly. Intragenic regions are also more abundant in the genome and so insertion is more likely. They discuss the advantage of this design in the original paper:
Gossler A, Joyner AL, Rossant J, Skarnes WC. 1989. Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science 244:463-465.

...ES cells permit selection for rare-occurring integration events, which allowed us... to design and use a "gene trap" vector. The vector contains the lacZ gene, lacking a promoter and translation initiation signal, inserted in frame into the homeobox exon of the En-2 gene such that a splice acceptor is placed at the 5' end of lacZ. Integration of the construct into introns of genes in the correct orientation should create a spliced lacZ fusion transcript and a functional fusion protein when the reading frame is maintained. Evidence for this came from experiments in which a construct lacking the 5' En-2 splice acceptor yielded 12-fold fewer lacZ-expressing transformants than the construct carrying the splice acceptor.

Exonal insertions by gene traps have been reported:
Song G, Li Q, Long Y, Gu Q, Hackett PB, Cui Z. 2012. Effective Gene Trapping Mediated by Sleeping Beauty Transposon. PLS One 7.

Insertion of a trapping cassette into an exon or an intron of transcriptional active loci can generate a fusion transcript that contains the upstream exon and the reporter/selectable marker.
...
Eighteen transposition events were obtained from distinct cell colonies. Blasting the human genome in the NCBI and ENSEMBL database... indicated that seventeen of them landed in an intron and one of them integrated in an exon at active genomic loci. These data are in consistence with the fact that exons and introns comprise 1.5% and 24% of human genome, respectively.

See here for further reading.


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How much time can a human survive only drinking water and eating sugar?
If a person only drinks water and eats glucose, how long could they survive before getting any symptoms? When would the damage become irreversible? When would that person die from lack of minerals, proteins and vitamins? Also, can this "process" be sped up by drinking distilled (pure) water?

You may want to look at so called "Muselmann" created in german concentration camps, becasue their diet consisted of nothing but carbohydrates(vegetable broth and bread) and water.  Protein deficiency seems to be the most important factor.

According to WP, symptoms of vitamin C deficiency (scurvy) will appear after 1 month.

@John Actually there's at least one study I'm familiar with where a 27yo male fasted for 382 days with no ill effects (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2495396/). He had vitamin and nutrient supplements but no protein. I'm pretty sure the cause of death will be related to a vitamin deficiency.

What about vitamin deficiencies that weaken your immune system and tend to lead to death from infection? Would those count?

Almost a duplicate of https://biology.stackexchange.com/questions/8279/how-long-human-can-survive-with-just-drinking-water-everyday (but without the sugar)

The type of sugar matters a lot in this case, since muscovado, jaggery or other non-centrifugal cane sugars contain vitamins and minerals (https://en.wikipedia.org/wiki/Muscovado#Nutrition).

@arboviral fasting does not mean zero calories, you have to look at the type of fasting, many are only a restriction on on one type of food or to a specific calorie count. You also need to look at the patient, for a 800lb patient has a much larger reservoir.   If a normal person did not eat for 300 days they would be dead, your body would literally run out of calories to operate.

@john Agreed, but in this particular case it seems the only calories taken were those forming part of the glucose tolerance tests required during fasting. The patient was 456lb at the start but OP didn't give any restrictions on starting weight. It is an unusual case, but that's why they wrote it up as a paper (and presumably why it was entered into the Guinness book of records). The full text is available at the link I posted above.

Depending on the weight of an individual, about 3 weeks or longer. Sugar will not ward off starvation.


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Metabolic significance of aspartate transaminase in mammalian liver
Aspartate transaminase (aspartate aminotransferase) is an enzyme that is abundant in hepatocytes and catalyses the reaction:

(Modified from https://en.wikipedia.org/wiki/Aspartate_transaminase)
There is ample literature available on its diagnostic use in liver disease (where it goes by the abbreviation AST) but much less on its metabolic role. (There is a SE question on its role in gluconeogenesis.)
It seems to me that the roles of aspartate transaminase in metabolism are as follows:

to convert aspartate to oxaloacetate so that it can be used in the citric acid cycle,
to generate aspartate from oxaloacetate and glutamate (in the reverse reaction) for supplying the urea cycle.

However, in the equation above, α-ketoglutarate is 1-carbon longer than its product, oxaloacetate. Therefore I would think that more energy can be extracted from α-ketoglutarate than from oxaloacetate.
So what is the benefit of converting α-ketoglutarate into oxaloacetate if there is a loss of potential for generating energy?

I have edited your question in the light of your explanation. The edits may seem extensive, but the SE philosophy is to try to rescue questions if possible, and I am keen on increasing the representation of biochemical questions. I will provide an answer in due course. If I have misrepresented you, do say. I would note that we avoid non-standard abbreviations such as AST in science (rather than clinical testing) and that all the acids are ionized at physiological pH (as in the formulae) so we refer to the ion (which is also shorter). And they are cycles, not circuits.

@David Thanks for the very nice edit. You have cleared up my questions. Perhaps the significance of the amino acid transferase-mediated input to the TCA cycle is not so much to get energy from the amino acids, but rather to get amino acids of various lengths. Is this understanding correct?

I've answered the question now. Amino transferases are to transfer amino groups, not to generate energy or to alter carbon skeletons.

Summary
The primary metabolic function of aspartate transaminase, like other transaminases is to transfer nitrogen, in the form of amino groups, between 2-oxo acids. These reactions are readily reversible, and so can function in both directions, i.e. in the context of both amino acid synthesis and degradation.
In the liver aspartate transaminase and alanine transaminase are especially important for feeding nitrogen into the urea cycle for disposal as urea. Alanine transaminase transfers amino groups to glutamate, from which ammonium ions are liberated. Carbamoyl phosphate, formed from the ammonia, and aspartate, produced by transamination catalysed by aspartate transaminase, are the nitrogen inputs to the urea cycle. Thus, the poster’s second postulate is correct.
However the poster’s first postulate is incorrect. Aspartate transaminase is not concerned with energy generation, and the demands of the urea cycle ensure that aspartate is normally a product, rather than a substrate, of the transamination in the liver. In certain situations aspartate does feed into the tricarboxylic cycle as oxaloacetate, produced by transamination as shown in the question. This is to replenish oxaloacetate removed for gluconeogenesis, but does not short-circuit the tricarboxylic acid cycle as the α-ketoglutarate consumed in the transamination is subsequently replenished from the glutamate produced.
The central role of glutamate in transamination
The diagram in the question shows an example of transamination, which is a reversible reaction between two amino acid / keto-acid pairs: the amino group of the first member of the pair replaces the keto group of the second member, with a reciprocal replacement of the amino group of the first member by the keto group of the second. In general this allows the distribution of nitrogen to different carbon skeletons to form a balanced distribution of amino acids for protein biosynthesis.
The poster’s question concerns aspartate transaminase, in which one of the pairs is aspartate/oxaloacetate; but before considering this particular enzyme in the context of the liver, I think it useful to emphasize the central role of the other pair — glutamate/α-ketoglutarate — in the uptake and disposal of ammonia. This is summarized in the diagram below:

It can be seen that the formation of glutamate from α-ketoglutarate is the entry point of ammonia into metabolism, and that transaminases allow glutamate to transfer its acquired amino group to produce a range of amino acids. In conditions where excess nitrogen must be removed, glutamate is formed from the transamination of α-ketoglutarate by other amino acids, typically with the liberation of ammonia. In aerobic organisms the α-ketoglutarate is available from the pool in the tricarboxylic acid cycle, but is regenerated and so does not drain this pool.
In simple organisms ammonia is released from the cell as such, but in many animals this is not possible and it must be converted to some other nitrogenous compound. In terrestrial mammals this is urea.
The mammalian liver and urea production
There is a cyclic sequence of reactions — the urea cycle — involved in the formation of urea, which occurs in the liver. It is important to realize that the two nitrogens in this compound, (NH2)2CO, come from two different molecular species.The first is the ammonium ion released by the reduction of glutamate, above, which reacts with carbon dioxide to form carbamoyl phosphate:

The second nitrogen input required for the urea cycle is aspartate, which is also formed from glutamate, but by transferring the amino group of glutamate to oxaloacetate in the aspartate transaminase reaction, but in the reverse direction from that shown in the question:

glutamate + oxaloacetate → aspartate + α-ketoglutarate

At first sight, this formation of aspartate would seem to drain oxaloacetate from the pool of the tricarboxylic acid (TCA) cycle. However the outline diagram below shows that carbon skeleton of aspartate is released from the urea cycle as fumarate. This is an intermediate in the tricarboxylic acid cycle, and regenerates oxaloacetate after conversion to malate.

Alanine transaminase
In the mammalian liver the main transaminase used to transfer amino groups into glutamate is alanine transaminase. This is because glucogenic amino acids produced from protein breakdown in the skeletal muscle are generally converted to alanine before transport to the liver through the blood.
Entry of aspartate into the tricarboxylic acid cycle
The primary role of the TCA cycle is to generate energy by the complete oxidation of the acetyl group of acetyl CoA, derived from fatty acids (especially in the liver) or pyruvate. Oxaloacetate is required for the acetyl group to enter the cycle, and must be regenerated at the end for the cycle to continue.  In the liver — especially in starvation — oxaloacetate from the TCA cycle can be converted to phosphoenol pyruvate for gluconeogenesis, providing essential glucose for the brain and nervous tissues (see this answer). This uses amino acids from the breakdown of muscle protein, as mentioned above, and is illustrated by the red arrows in the diagram below:

The TCA cycle also serves as a pool of certain intermediates that are starting points for biosynthetic pathways: e.g. oxaloacetate and α-ketoglutarate for the several amino acids, and succinyl CoA for porphyrins. When intermediates are drawn off for this purpose they must be replaced or the TCA cycle will come to a halt, and this is accomplished by input from other compounds such as pyruvate and aspartate, when they are available, in so-called anaplerotic reactions. In the case of aspartate, this is accomplished by the reaction catalysed by aspartate transaminase, in the direction shown in the diagram in the question (as pointed out by @user338907). It should be emphasized that this reaction alone could not maintain the TCA cycle, as it would remove α-ketoglutarate from it. The glutamate produced from this transamination must be converted back to α-ketoglutarate via glutamate dehydrogenase or transamination with some other aminoacid/oxoacid pair. Thus, it would be incorrect to think that α-ketoglutarate is being converted directly to oxaloacetate in these circumstances, forfeiting energy that could be generated from an oxidative conversion in the TCA cycle: the overall reaction is the conversion of (external) aspartate to oxaloacetate + ‘amino group’.
Literature
The topic of transaminases is dealt with in an organism/tissue-agnostic manner in most biochemical texts. I therefore suggest this review of the Urea Cycle that appeared in Biochemistry and Molecular Biology Education, and can be accessed without subscription.

Thanks for the great answer.  Your answer seems to extend to the next question, I'm preparing a new thread of questions on this.
The main point of the new question is: as long as we use transaminases, we can just use members of the citric acid cycle (alpha ketoglutarate, or sucinyl CoA) that were on the TCA-cyclethere originally; what is the significance of introducing amino acids from the outside, since it does not seem to increase the number of "molecules that will become OAA".

@BlueVarious — Could you do some reading before posting  more questions. Mammalian metabolism is quite complex and relates to the role of different tissues in different physiological conditions, and should be approached by looking at pathways as a whole and how they interact.

As for the question I was preparing, it appears that a significant portion of the answer is contained in your response to this question. Perhaps a little paraphrasing based on your answer would create a answer to the new question.

Maybe this is it.　https://i.sstatic.net/HJNGI.png

@user338907 — I see you've deleted your comment, but on reflection it is particularly relevant to an answer to a question about aspartate transaminase. And, of course, aspartate transaminase can be considered anaplerotic in conjunction with glutamate dehydrogenase (or another transaminase) to regenerate αKG. So I need to modify my answer again. Not a bad thing if it results in something more generally useful. My answer was based on undergraduate lectures I had to give ca. 30 years ago on a subject which was not in my research area. I could do it better now, but it's a little too late.


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Comparative evolutionary study: is amino acid or nucleotide comparison more useful?
I am a high school student and am currently learning about evolutionary relationship study in biology.
My teacher said that a comparative study of amino acid sequences is more useful than a comparative study of nucleotide sequences, because the genetic code is degenerate in nature — several codons may code for the same amino acid.
However, I just do not understand the logic.
Since several codons may code for the same amino acid, I (as a math person) consider the conversion of a nucleotide sequence to an amino acid sequence as a non-injective function, and thus is information-losing.
(Analogy: consider the function $f(x)=x^2$. Imagine that you have a number, and you plug it into $f(x)$ to get $1$ as the output. You would never know if the original number is $1$ or $-1$.)
Therefore I arrive at the exact opposite conclusion. Is my conclusion correct or not, and why?

I have corrected your misuse of Genetic Code leaving only the single correct instance of use (and tidied your question a little). I have explained this in the first part of my answer and given some more references.

I have provided you with a well documented answer. (Your teacher is right in most circumstances.) Please read it and let me know if there is anything you don't follow in the biology. We (or at lest I) cannot help you with the maths, so consider my suggestion that you — as a mathematician — find the flaw in your logic, and perhaps let us know when you have done so. This is a real-world example of the dangers of simplistic application of mathematical logic, so it worth your attention.

@David I think I need more time to understand as it is a bit complicated to me. Please be patient.

No hurry.  In fact it might be better to ask the question on a Maths site. One difficulty for you will be lack of familiarity with the sequence comparison algorithms. Because these algorithms compare sequences on a letter-by-letter basis, when they compare DNA they are not using the information of the genetic code, which would involve comparison in groups of three. There must be other examples where mathematical transformations driven by external considerations produce a more useful form of data.

The Answer
It is correct that the product of the conceptual translation of a nucleotide sequence into an amino acid sequence results in the loss of certain information present in the former. An obvious example is that the amino acid sequences of the same protein in two individuals may be identical, but there may be silent mutations in the DNA, and these can be useful in tracing ancestry. The one part of Crick’s Central Dogma about which there can be no argument is that you cannot go from protein to DNA because the information for the nucleotide sequence is not present in the protein, with or without the genetic code.
However…
An amino acid sequence contains information that is not present in the gene from which it originates, if we just consider the sequence as mathematical sequence of symbols. And, with 20 letters instead of 4, this new information has a different (and greater) complexity. The mistake is an unspoken assumption that the information of the genetic code is inherent in the nucleotide sequence. It is not. Yes, if we have the information of the genetic code, then the nucleotide sequence also has the information of the amino acid sequence, but that is not the practical question at issue.
So (addressing the poster) in the majority of practical instances your school teacher is correct. I am not a mathematician, so I cannot be sure what is the flaw of your argument. Perhaps it is the fact that only a subsection of the information can be used in the sequence comparison, perhaps the fact that you are talking three symbols from a set of four in your non-injective function to produce one symbol from a set of 20, or perhaps it is the biology. That’s something for you to work out. But if your conclusions are wrong (which they are) there must be a flaw in your logic)
The Question at Issue
The practical question at issue is:

Which is more suitable for determining the evolutionary relatedness of
  two organisms — a pairwise comparison of the amino acid sequences of a functionally
  similar protein (e.g. cytochrome c) or of the nucleotide sequences of the corresponding gene?

The general answer is:

It depends on the relatedness of the organisms, but, except for very
  close kinship (e.g. humans and neanderthals) or certain specialized
  problems, the answer is likely to be the amino acid sequences.

How can this be?

In relationship to the evolutionary distance between organisms, it
  is necessary to consider the different rates at which nucleotides and
  amino acids mutate, and the constraints on what mutations are likely
  to occur. If the rate of mutation is too fast there will be a time
  difference after which it will be difficult or impossible to
  calculate their evolutionary divergence accurately and ultimately even
  to detect any relationship between them.

Nucleotides mutate more rapidly than amino acids, and in practice comparison of nucleotide sequences is less useful than comparison of amino acid sequences for longer timespans.

Because of the degeneracy of the genetic code (the fact that an amino acid can be encoded by more than one triplet of nucleotides) it is possible for one or even two nucleotides to mutate without affecting the amino acid sequence. (And the similarity between sequences is computed from a letter-by-letter comparison.)
Statistics is not my forté, but in a general sense, because there are only four bases, 25% identity between two nucleotide sequences would be expected to occur by chance, whereas two amino acid sequences that are 25% identical would be statistically significantly similar because there are 20 amino acids. (Only 5% identity would arise by chance.)

There is a further aspect of divergence of amino acid sequence that is useful for evolutionary comparison, and this is that the nature of the mutation of amino acids is far more constrained than that of nucleotides. Admittedly purine-to-purine or pyrimidine-to-pyrimidine mutations are more frequent than purine/pyrimidine mutations, but amino acid mutations are often constrained by the role the amino acid plays in a protein. However one can construct empirical matrices of the likelihood of different amino acid mutations to obtain a more subtle and accurate estimate of relatedness.
What this means in practice is that instead of having to use a scoring system for comparisons of amino acid sequences that is either 1 for identity or 0 for non-identity, one can use a scoring system that gives ‘half marks’ (as it were) for structural/functional similarity. Thus, two amino acid sequences having 5% identity in pairwise comparison could be shown to be related because  of an overall higher ‘similarity’ score.
Appendix 1: Sequence Comparison
It is important to realize that however much information resides in nucleotide or amino acid sequences, only the information that is actually used in the practical methods of determining evolutionary differences is relevant. These methods involve computer programs that compare sequences according to mathematical algorithms to answer the question of how similar two (or more) sequences are. So, regardless of the fact that the amino acid sequence is generally computed from the gene sequence, the question is “should I imput nucleotide or amino acid sequences into the program to get the best comparison?”. It is in this context that the remarks above about rate of change and likelihood of interconversions should be taken.
To quote from an article by one of the pioneers in sequence comparison, W. R. Pearson:

“Protein (and translated-DNA) similarity searches are much more sensitive than DNA:DNA searches. DNA:DNA alignments have between 5–10-fold shorter evolutionary look-back time than protein:protein or translated DNA:protein alignments. DNA:DNA alignments rarely detect homology after more than 200–400 million years of divergence; protein:protein alignments routinely detect homology in sequences that last shared a common ancestor more than 2.5 billion years ago (e.g. humans to bacteria). Moreover, DNA:DNA alignment statistics are less accurate than protein:protein statistics; while protein:protein alignments with expectation values < 0.001 can reliably be used to infer homology, DNA:DNA expecation values < 10−6 often occur by chance, and 10−10 is a more widely accepted threshold for homology based on DNA:DNA searches.”

There are Wikipedia articles about sequence alignment, and about the use of BLOSUM and PAM matrices. The section on sequence alignment in Berg et al. online — which involves amino acid, rather than nucleotide sequences — may also be of interest.
Appendix 2: Terminology and Definitions
As the term, Genetic Code, was misused in the unedited version of the question — and is widely misused in the press — I thought that a glossary of terms might be helpful
DNA (from which the genome and its constituent genes are constructed) are linear polymers of 4 nucleotides. The order of these is called the nucleotide sequence, or, because the only the purine or pyrimidine base varies between nucleotides, the base sequence.
Proteins are linear polymers of 20* amino acids. The order of these is called the amino acid sequence.
The Genetic Code is a cipher — and can be represented as a table showing the correspondence between 64 triplets of three nucleotides and the 20 amino acids and three stop signals when these nucleotides are part of the translatable part of a gene. The genetic code is highly — but not absolutely — conserved between organisms (and differs for proteins encoded by mitochondrial DNA).
In NO circumstances can the word Genetic Code be used as a synonym of Genome, although this is abused by even the scientific press, and is difficult for computer programmers to come to terms with, working as they do in a field where the noun ‘code’ is used for the product of encoding instructions.
*The genetic code has a certain plasticity and two additional amino acids can be encoded by termination codons in certain circumstances.

In your referenced answer you say, "An amino acid sequence contains information that is not present in the gene from which it originates, if we just consider the sequence as mathematical sequence of symbols. And, with 20 letters instead of 4, this new information has a different (and greater) complexity. The mistake is an unspoken assumption that the information of the genetic code is inherent in the nucleotide sequence." Please explain this in more detail. Having a larger alphabet does not imply greater complexity nor that proteins contain information not written into them by DNA.

@S.McGrew — I think it speaks for itself. The poster is concerned with a theoretical informational problem (of his own making). I explain how he has forgotten the additional information required if one performs the conceptual translation of a nucleotide sequence into amino acids. The practical explanation of why protein sequences are used for evolutionary comparisons over periods longer than a particular time is different. It is just that the same number of mutations produce smaller changes in proteins than DNA. For comparison within a species or between closely-related species DNA is better.

You seem to be stating that a protein (encoded by DNA) contains more information than the DNA that encodes it.  Ts certainly not self-evident and, according to my understanding, incorrect.

@S.McGrew — No. I am saying that a string (in computer terminology) composed of the four characters ATGC has less mathematical complexity than a string containing the 20 different letters of the alphabet minus B, J, O and Z. Although it is possible to derive the latter from the former this does not violate the second law of thermodynamics (as applied to information) because 1. The knowledge of which One of the six reading frames to select has to be invoked (I don’t think I mentioned this) 2. A hash table (a description of the Genetic Code in programming terms) has to be used.

The "structure" of a protein encoded by DNA is of course different from the "structure" of the DNA  encoding it,  but the Kolmogorov  complexity pf the two is identical.  There is no new information in the protein, unless you are asserting that mutations occur spontaneously in proteins and are then inheritable.

@S.McGrew — Again, I am saying nothing about mutations and real proteins. Perhaps mathematical is not the right word. The poster talked about gain and loss of information. In his terms I demonstrate in a qualitative sense how the conceptual translation of 64 codons into 20 amino acids might result in a net gain, rather than a net loss, in information. Karl Kjer deals with the broader real world problem.

Sorry to be obnoxious, but IMHO you stated, but did not demonstrate,  any net gain.  A code consisting of 4 characters in four-character words does not inherently contain more or less information than a 20- character code consisting of words of arbitrary length.  Measures of complexity are well understood in information theory, and contradict the statement.

This has turned into a conversation and illustrates well the purpose of the StackExchange model. I haven't even looked at my answer again properly. I don't do chat on principle, but I have had an idea for another approach for addressing this question and will either extend my answer or add a new one in the next few days. It's an old question, so it has to take its turn.

Each has its own utility, depending on the time-frame you are looking at. For evolutionary studies, you need variation, but not so much variation that one substitution at the same position overwrites a previous substitution. So if you are looking at deep splits, over hundreds of millions of years, it may be that amino acids are more reliable. But you are correct in that since they are functionally more important than silent substitutions (nucleotide changes that don't change the amino acid), it is possible to have amino acids converge on the same state, independently. Nucleotides do this too. Both require statistical models (maximum likelihood) that accommodate the possibility of multiple changes at the same site. If you are looking at recent evolutionary splits, there may not be enough (or any) amino acid changes to compare, so in this case, nucleotides would be better. You would not measure continental drift with a stopwatch, or a 100-meter dash with radiometric dating.


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Meaning of a negative value for non-fiber, non-sugar carbohydrate based on a nutrition label
One of the questions for my lab is to find the non-fiber, non-sugar carbohydrate per serving of an onion. Now the total carbohydrate for this onion is 11 g, the total sugars for the onion is 9 g, and the total fiber is 3 g.
11-9-3 = -1 g of non-fiber, non-sugar carbs for this onion and this is not making any sense to me.

Welcome to Biology.SE! That could be due to rounding (e.g. more precise values might have been: 11.4 g total, 2.5 g fiber, 8.5 g sugars).  Are you restricted to using those specific labels or can you find a better source of nutritional information? —— Also, please note that homework questions should be tagged — I encourage you to take the time to go through the [tour] and the help pages starting with [Ask] questions effectively on this site. Thanks!

i am restricted to these nutritional labels sir

I got an answer faster on bodybuilding.com than i did here. WOW

Nutritional facts are rounded to the nearest unit use for measuring it, It is also only an estimation so combine errors in measurement and rounding error and it fairly easy to be off by that much.But honestly you should be asking this on the culinary stack.

@user55078 - That's not at all a surprise. Bodybuilders are rather heavily focused on many aspects of nutrition.

The values on the nutrition label from the question (11 g total carbs, 9 g sugars, 3 g fiber) could be actually explained by rounding:

Total carbohydrates: 11.45 (rounded to 11)

Sugars: 8.55 g (rounded to 9 g)
Fiber: 2.55 g (rounded to 3 g)

...which would mean there are additional 0.35 grams of non-sugar, non-fiber carbohydrates...
...BUT...
...using such a label with only rounded values (and students not knowing the exact values), does not make it possible for students to calculate the amount of non-sugar, non-fiber carbohydrates.
So, another explanation is that there is an error in either total carbohydrates (11 g - too low) or in sugars (9 g - too high; more likely 6 g), according to NutritionData for 150 grams of raw onion:

Total carbohydrates: 14 g

Sugars: 6.4 g
Fiber: 2.6 g

In either case, it seems they have used a nutrition label that is inappropriate to ask a question about the amount of non-sugar, non-fiber carbohydrates in raw onion.

The individual values in the OP's onion label are not out of line with the U.S. Department of Agriculture's reference data.  There are two of the latter, one for "Onions, raw" and one for "Onions, sweet, raw".  Their figures would lead to expecting carbohydrates of 13.8g or 11.2g, respectively, for a 148g sample.
The negative difference can be explained by simple rounding error. If the measured carbs, fiber, and sugar values were actually 11.49, 2.51, and 8.51 g then the label values would be rounded to those shown on the label, yet the difference of the measured values would be a positive value: 0.47 g.


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Identification of larva on cat fur
I found this larva (assuming it is a larva) when my cat jumped off my bed, I'm assuming she just picked it up outside. However, I'm not quite sure what it is or if it should be a concern she had it on her. When it moved, the tip of the "head" looked black and it did have "feet" like a caterpillar. If it helps, I live near middle TN and the approximate size was about an inch long. I took some pictures found below, if anyone has any information on it, thank you!

Made a small correction. Larvae is the Latin plural from the singular larva, which is what you are referring to.


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What is the status of the telomeres in HeLa cells?
I read several times about the hypothesis, also reported on Wikipedia, that ageing is linked to the length of the telomeres. Each time the chromosomes are duplicated during a cell split the telomeres lose a little bit of their length and their ability to drive further duplications declines.
But now I read the story of Henrietta Lacks. Her cancerous cells where harvested 70 years ago and they have been used to create thousands of cell lines. Since she was 30 years old when the cancer was discovered those cells now might be 100 years old. The real age is probably less because most of them were frozen from time to time, but on the other hand they are cancerous cells duplicating at a frantic pace.
I read from this answer that cancer cells can activate telomerase and restore the telomeres, but is it still happening after so many years? In all the cultivations in vitro did were they always provided with the right nutrients to produce telomerase?
Is there a study on the status of the telomeres in those cells? Are they really "eternal" in practice or the definition of eternal is still in theory?

Wow.  I looked this up on PubMed and there are 906 results for HeLa telomerase.  Not all are real, but there's some data to work with here.
I've been reluctant to rely on Russian charity with the Cold War in full swing, so there are a lot of leads I won't follow in the abstracts that came up: Ivankovic, 2007 says "surprisingly, found that the fraction of cells that divided 0-1 time over 6 days in culture have several times higher endogenous telomerase activity than the fastest dividing fraction. Additionally, the non-growing fraction regains an overall high labeling index and low SA-beta-Gal activity when subcultured again."  Varshney, 2014 wrote that "The overexpression of telomerase is not proportionate to telomere length in cancer cells, suggesting that the immortalizing phenotype can be mediated through other factors in addition to telomere length."  Taji, 2017 reports that autophagy reduces the telomerase activity in HeLa cells.  But TERT induces autophagy according to Roh, 2018, which describes the involvement of hexokinase 2 and glucose metabolism and more importantly is actually published in the sense of public.
Anyway, I eventually happened upon Nakashima, 2013 (open access) which says "the telomerase inhibitor BIBR1532 acts together with TEL patch mutations to inhibit the growth of HeLa cell lines and ... apoptosis is a prominent mechanism of death of these cells."  (Without the inhibitor the cells seem to just make more telomerase until it works without the patch)  I'm rather amazed that a veteran "cancer survivor" so to speak like HeLa will still undergo apoptosis if it runs into a telomere problem, but there it is!

What is unclear to me is why HeLa cells are that particular? My understanding is that the permanent based on (supposedly) the telomerase mechanism exists in all cancer cells, as well as in stem cells that are today cultivated. So why are HeLa's cells that important? Because they were the first to be cultivated?

First, I will address your misconception. You can interpret the telomere length of a typical somatic cell as its upper limit of remaining replication-cycles and therefore as an indicator of its age. This describes the fate of a cell, however, the age of a person should be seen as something else; when you are 20 years old, your cells don't have shorter telomeres than when you were half that age. Aging as a person is a complex topic with compound gradual influences e.g. loss of epigenetic memory, i.e. DNA and histone states, worsening of proteome health, i.e. worsening of protein homeostasis that eventually leads to cells not being able to cope with the required protein turnover leading to functionally ineffective proteins and accumulation of waste. DNA damage also plays a role.
To your actual question: HeLa cells can regenerate their telomeres with telomerases. This means that different HeLa cells within a flask will have telomers at different lengths. Most of your bodies cells do not have telomerase activity as it represents a huge risk for cancer. HeLa cells are enteral at least in the sense, that the cell-line will probably be conserved as long as there are humans or it is deliberately destroyed for political reasons. However, individual cells are not immortal, e.g. might die to external damage or mutations.

Thank you for the answer. But I still have a doubt. Those cells line are eternal by observation (because someone observed that at least few cells in the line have full length telomeres after thousands of duplications) or in theory.

@FluidCode Both and neither. Cell lines are considered immortal when they are able to replicate indefinitely in a lab. That doesn't mean they will exist forever, doesn't mean that particular dishes of the cells can't accumulate mutations that make them no longer capable of dividing indefinitely, etc. From the perspective of telomeres only, all you need is to know both empirically and theoretically is that the telomeres do not get any shorter over time to say that telomere length will not be a limiting factor in replication.


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Why doesn’t a basic side chain (R group) of an amino acid form a peptide bond in protein biosynthesis?
Why doesn’t a basic side chain (R group) of an amino acid form a peptide bond in protein biosynthesis?
Consider lysine, for example, why can’t its side-chain amino group, –(CH2)4–NH2, form a peptide bond with the carboxyl group of the other amino acid? Is it due to orientation alone are their other properties involved?

Welcome to SE Biology. I have edited your question. Please do not make statements about "nobody being able to tell you something". It is untrue, irrelevant and appears to be an attempt to draw attention to your question. If nobody is able to tell you I suggest you try to find out for yourself. If you read the Help on asking questions you will see you should show your research when posting. Do you know about protein synthesis on ribosomes and their peptidyl transferase activity? Research this first and then ask for help if you still need it.

Possible duplicate of Why don't amino acids get linked in the functional groups of acidic and basic amino acids?


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Relative rates of migration of circular, linear and supercoiled DNA in agarous gel electrophoresis
I have read the supercoiled plasmid DNA migrates fastest when subjected to agarose gel electrophoresis and this makes sense to me because it is small and experiences the least friction because of its supercoiled structure.
Linear DNA migrates faster than the circular form. I didn't understand why exactly. Shouldn't the circular one be considered to be smaller than the linear, and thus quicker?

First let me supply an illustration of the situation described in the question, together with a reference.

Although you can see this sort of thing, just by searching for “plasmid migration on agarose gel”, this is one of my own from the last millennium (plasmid pBR322), appearing in a text from the last millennium, Adams et al. The Biochemistry of the Nucleic Acids (11th ed).
The poster’s attempt to rationalize the results, though expressing the quandary, is marred by the loose use of the word small, and the absence of any statement as to why ‘small’ pieces of DNA should migrate more rapidly.
The different forms of the plasmid have exactly the same molecular mass, so what is meant by small? My own initial way of looking at this is to consider the agarose gel as a mesh or sieve through which the molecules must pass, so that the larger the volume they occupy in space, the less likely they are to pass through the ‘holes’ in the mesh. The volume that they occupy in space might be regarded as that generated by rotating them from their midpoint in three dimensions. On this basis the supercoils, in which the DNA is collapsed into a short fat pseudo-linear shape should occupy the least volume in space, and the long thin linear the greatest. The diameter of the circle should place it somewhere between the other two.
So, we reach the same conclusion as the poster: the faster migration of the ‘linears’ than the nicked circles does not fit this simple model. In the text accompanying the figure I wrote “…a result that is a little unexpected” without attempting to explain it.
Am I able to explain this somewhat unexpected result now? An internet search produces either hand-waving or evasion (I stand to be corrected on this), so that I can only imagine that the result has something to do with the linear molecules having a greater chance of their ends being directed to the holes in the ‘mesh’ than the nicked circles, because of the open nature of the latter. One can perhaps imagine an hour-glass shaped portion of the sphere for the rotation of the linears that allows the ends to be directed at the holes.
More waving of hands? Perhaps. But the main point is that the physical explanation for the migration of molecules of different shapes during electrophoresis is more complex than a mere biologist might have hoped.


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What determines the length to which hair grows?
Correct me if i am wrong, if we cut 2mm from eyebrow hair, it will grow 2mm and then stop growing, or if we cut 5mm, then it will grow only 5mm. My question is, does hair know how long to grow ?

Probably easier to understand if you look at the answer for a dogs coat. https://en.wikipedia.org/wiki/Coat_(dog)#Genetic_basis_of_length_and_texture Short answer is it is controlled by gene expression.

Individual hairs fall out after they grow for a certain amount of time. If you cut off 2mm of hair, those hairs will grow to what would be their maximum length (had you not cut them), then fall out and are replaced by uncut hairs that grow to maximum length.


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Why does azithromycin not affect human mitochondria?
Drugs like tetracyclines, macrolides and aminoglycosides bind to prokaryotic ribosomes. It is interesting that our body too having mitochondria, which have prokaryotic ribosomes, there is little(?) effect seen. It can not be ruled out that the effect may be lesser due to them being organelles. Azithromycin's effect on parasites like Toxoplasma and Plasmodium is due to its effect on the plastid that these Apicomplexans have (Castro-Filice et al. 2014).

Azithromycin is a macrolide, but it also inhibits bacterial protein synthesis. I'm not sure if its effects are studied but aminoglycosides like streptomycin are known to cause mitochondrial toxicity.  The overall toxicity would depend on the pharmacokinetics. I did look up some articles that do say that azithromycin has an effect on Toxoplasma. Added a reference for you. As per the reference, azithromycin seems to be acting via many different mechanisms. It seems macrolides in general, have different pharmacological effects.

those drugs target the bacterial ribosomes, but not human ribosomes. Even though the mitochondria have 'bacterial' DNA-origins, I'm fairly certain that they don't express bacterial ribosomes. The genes the originate from the mitochondrion are transcribed to RNA and then translated by eukaryotic (i.e. human) ribosomes

@Vance L Albaugh, human cells have two kinds of ribosomes: those in the cytosol which translate nuclear mRNAs and those in the mitochondria which translate mitochondrial mRNAs.  The latter are derived from the bacterium which became the mitochondrion.

the ribosomes of bacteria are NOT the same as the ribosomes of the mitochondria, even though mitochondrial ribosomes have a distant prokaryotic ancestor - which is why drugs like tetracyclines (etc) that target bacterial ribosomes do not effect human mitochondrial ribosomes...Here is a link to a open access manuscript that discusses the differences in human, bacterial and mitochondrial ribosomes... http://onlinelibrary.wiley.com/doi/10.1080/15216540310001626610/abstract;jsessionid=28D286AFDEAEC35928908AAACDFFFB31.f02t03

There are two general points that should be appreciated in relation to this question:

Your statement that mitochondria “have prokaryotic ribosomes” is a misleading simplification. Although mitochondria and plastids are thought to be derived from eubacteria — and their ribosomes have some similarities  in antibiotic sensitivity — the structures of their large rRNAs differ (as indeed do those of their small rRNAs and their ribosomal proteins). This is important because the large rRNA (the equivalent of 23S rRNA in E.coli) is the target of many antibiotics, including the macrolide antibiotics, of which azithromycin is a member.
Experiments in vitro have shown that human mitochondrial ribosomes are not sensitive to some of the macrolide antibiotics that inhibit eubacterial ribosomes, whereas those of some lower eukaryotes are.

Therefore it should not be particularly surprising that macrolide antibiotics do not affect human mitochondria, or that they do affect Toxiplasma etc., the ribosomes in the apicoplasts of which are sensitive to these antibiotics in vitro — presumably because of their rRNA structure in the specific target region.
An answer to the question in your title would seem to require an explanation of the molecular basis of these different sensitivities. It is thought (although not, I gather, definitely proved) that this is the identity of the base at the position equivalent to 2058 of E.coli 23S rRNA: those ribosomes that are sensitive to the antibiotics have the base A in that position, whereas those that are resistant have the base G.
References
Böttger, E.C. et al.(2001) EMBO Reports vol 21, pp. 318–323. Structural basis for selectivity and toxicity of ribosomal antibiotics.
Greber, B.J. et al.(2014) Nature vol 515, pp. 283–286. The complete structure of the large subunit of the mammalian mitochondrial ribosome.

The endosymbiotic theory states that eukaryotic mitochondria were once freely-living bacteria that somehow migrated into the cell and began a symbiotic relationship.
However, just because the mitochondria within human cells have prokaryotic origins, these are distant relationships that are exceedingly old. The ribosomes of current day bacteria (on which some classes of antibiotics target) are NOT the same as the ribosomes of the mitochondria. The structures and physical properties of the mitochondrial ribosomes, as well as many of the genes within the mitochondrial DNA are significantly different than their previous prokaryotic ancestors. Here is a link to a open access manuscript that discusses some of the differences in human, bacterial and mitochondrial ribosomes.

but still, how does it explain azithro targeting apicoplast ribosomes in human mitochondria? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085955/


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Should there be separate Ramachandran plots for an amino acid in different contexts?
I understand the nomenclature of the phi and the psi angles of the alpha-Carbon atoms in protein stucture, but I am confused by the Ramachandran plot. Each alpha-Carbon atom (magenta) makes two peptide linkages and has two corresponding neighbouring alpha-Carbons (cyan) and side-chains. I would expect the psi and phi values to depend on the interactions of these side-chains, so I would expect that for a single amino acid one would need a separate graph for every possible combination of neighbouring amino acids.

I am not clear whether this the case. The following graph (1) from Harper, Biochemistry, is for “many non-glycine residues from many proteins”. So, suppose a set of phi and psi is allowed for a right-handed helix (a value or data set taken from the plot) does it mean that it is allowed for any amino acid with any other amino acid? I woud expect an alanine adacent to an alanine to have a different interaction to an alanine adjacent to a bulky amino acid such as isoleucine.

I have also seen plots for specific amino acid and their allowed angles, such as that for proline (2), above. This suggests that the neighbours are not being taken into account. If this is so, why not?

I have edited your question to remove the various erroneous assertions and focus on the key point of interest. The question of whether the plots are for one or several amino acids is trivial — they are for many. The more pertinent question is why there are not different plots for amino acids with different neighbours, or, indeed, whether the different positions represent these different neighbours. This is answered by @VonBeche. (You may think it presumptious to alter your question in this way, but the idea of SE is, as you will be aware, to produce an archive of useful questions and answers.)

@David Oh no! this is absolutely fine. Well, it looks much better now. Thanks :)

The phi and psi dihedrals describe the dihedral on both sides of the c-alpha of a single amino acid, and do not involve any angles of the neighboring amino acid.
The Ramachandran plot is something generated from a set of protein structures, an empirical data set. The top graph represents the dihedrals found for all non-glycine residues in a set of structures. You can filter this for proline only, and you'd get the bottom graph. The top cloud of dihedrals represents those found in beta-sheets, and the bottom cloud those for alpha-helices. Sequence (the amino acid before or after) doesn't really matter that much for what's allowed (although we cannot directly deduce this from the data in those graphs).
If you look a little bit more into the structure of helices and sheets you'll also find out why that's the case. In beta sheets the sidechain of the +1 residue is pointing completely the other way, and also in helices there's little interaction between the sidechains of subsequent residues. Secondary structures are built using the amides, not with the sidechains.

The OP might also find it helpful to look at the diagram in the Wikipedia entry for dihedral angles to see that any alpha carbon atom (with its sidechain) whose dihedral angle one is considering is three atoms away from each of the neighbouring two (note) alpha carbon atoms, and thus the neighbouring residues need not be in close proximity.

I have +1'd your answer, but if the OP accepts my modification of his question, you may wish to modify your answer somewhat. Sorry for the inconvenience, but see my comments to his question.

Some further observations about Ramachandran plots in response to the question:

They were originally calculated. This was done by considering the minimum contact distances shown in the diagram (which is from Wikipedia, but based on that in J. Mol. Biol. (1963) 7, 95–99). The side-chains were not considered, except for the  Cβ of the central residue. In the case of a glycine side-chain that lacks a Cβ, different values are allowed. The original plot had ‘allowed’ regions enclosed by a solid line, with an ‘outer limit’ indicated by a broken line.
The diagram in Fig. 1 in the question, in contrast, is an experimental plot for amino acid residues (other than glycine) in  several proteins. Each point represents the dihedral angles for a single instance of an amino acid. Such plots based on very many amino acids are sometimes used as a check for possible errors in experimental values obtained for new proteins — see review by GJ  Kleywegt.
When plotting experimental values for very many proteins, the points would superimpose, making it impossible to see which regions were most densely populated. That is why in Fig. 2 in the question a coloured contour map is used to represent the density in particular regions. (More elaborate examples may be found.)
On the general plot of the type originally calculated (1) one often sees particular constrained areas marked for chains in which the same Φ/Ψ angles repeat at every position. These are for structures like α-helices, β-sheets etc. (see image below, taken from Wikipedia entry on Ramachandran Plot.)

The reason Fig. 1 of the question excludes glycine is that its lack of Cβ means it can occur in regions such as Lα, from which most (but not all) larger amino acids are excluded. Likewise, the plot for the imino acid, proline, is different from the other amino acids because of the constraints imposed by the proline ring.
Small, non-repeating hydrogen-bonded structural motifs in proteins may also impose constraints on allowed dihedral angles at certain positions in the motif. Such motifs may exert other constraints which influence the amino acids at particular positions.  One might possibly regard this as an influence of amino acid side-chain on allowed dihedral angles, although it is perhaps better to regard it as an influence of amino acids on the occurance of the motif as a whole.


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Absorption of pentoses in intestine
Why pentoses are absorbed by facilitated diffusion in intestine? Wouldn't it be futile because , when the pentose concentration is lower in intestine, the pentoses would diffuse back to the intestinal lumen? So does our body looses them? If not then what is preventing this backflow?

First, pentoses aren't a major source of nutrition, at least for humans. That said, pentose absorption works the same way a lot of nutrient absorption works: the "magic" of metabolism, with respect to diffusion.
Pentoses leave the intestinal lumen, entering the intestinal cells, where their concentration is lower. From there, they again travel via facilitated diffusion into the bloodstream, again because their concentration is lower in the bloodstream.
From there, we can expect one of two outcomes: either an equilibrium will eventually be reached(i.e., lumen==intestine==blood), or the bloodstream pentoses need to be metabolized into something else. Indeed, certain pentoses (specifically D-ribose; I'm not sure if others can end up in this pathway as well but it is a very common pentose) can be metabolized in the pentose phosphate pathway for anabolic purposes. Others may end up in proteoglycans.
Regardless of the metabolic pathway, the effect on the process you are wondering about is the same: the metabolites no longer "count" in terms of concentrations for diffusion. Because membranes are not permeable to everything, if they are not permeable to the products of metabolism there is no way for those products to "diffuse backwards."


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Dynamic instability of microtubule
Why is it said that , warmth facilitates assembly and cold facilitates disassembly of microtubule?
But till now what I  had learnt is that as temperature increases so the kinetic energy of molecules increases so does the order decreases.
So what is the reason behind the above phenomenon?

I would look at chemistry. Look for heat dependent reactions.

In the paper "Phase diagram of microtubules" Fygenson, 1994. it's evident that with increasing temperature the length of the aggregates is growing. But it of course depends on other additional parameteres like concentration and I assume the type of the protein - alpha and beta-tubulin.

thanks for showing interest, but I want reason for that graph.

There can be many reasons: simple Brownian dynamics is the best explanation I think.


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How do sarcomeres coordinate contraction?

As can be seen from the figure

if myosins from both sides apply equal force then how does muscle contract? And also how do actins resist tearing?
Is there any kind of  coordination between different sarcomeres? How does they achieve it? I know that acetylcholine is released in response to action potential so does the release of acetylcholine controlled in each individual sarcomere?
Or simply there is an increase in the number of myosins as the distance of each sarcomere increases from the neuromuscular junction?

Can you focus your question more narrowly? Clearly, muscles do contract, so is the question just "how do sarcomeres coordinate contractions?"

I am waiting for a more physics oriented explanation but until that arrives, Think of all this as a rubber band. If you mark off sections on it to represent sarcomeres, then stretch it, each "sarcomere" will stretch. Then if you let go of one end of the rubber band, every "sarcomere" will contract, and the rubber band will contract toward the held end. When this happened, every "sarcomere" was being pulled in both directions, but the forces were all transferred from one to section another, because one end of the band was unable to move. On the whole, the band contracted towards the fixed end

For the second one, Nerves innervate the muscle and activate muscle fibres as a whole. A muscle fibre is a larger unit containing many myofibrils which are sarcomeres attached in series. Which of muscle fibres get excited is a different story. But when a muscle fibre gets excites, the impulse travels along its sarcolemma and when it reaches the the t-tubules leads to release of calcium from the cisternae. Because the contraction is finally mediated by calcium, the process is sychronized

I'm answering question 1, I think it'd be better to post these questions separately.
Consider action and reaction: myosins (thick) filament is experiencing force F towards Z line.

If the muscle is acting on something that is movable (e.g. you're pulling on a drawer which isn't locked), the force F towards Z line is greater than the force that maintains your thick filaments in place, and they'll slide towards Z line. The speed at which they slide is limited by the rate at which myosin heads can detach once they have performed power-stroke.
If the drawer is locked, then force F cannot overcome the external force. This force however is normally lower than the force required to tear actin or z-line, it is limited by two molecular factors: myosin will stall and not effectuate power stroke under too strong an opposing force, and myosin heads  will detach after some time and relax the tension they have built up. This is how you get the maximum force under clamped conditions.


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Why the name hypopharynx?
Why the tongue (like structure) in cockroach (or other insects) is called hypopharynx? In humans I know it's the lower part of pharynx, not a structure. Isn't this anatomical name misleading? Are there other ambiguous terms like this?


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Pneumonia in children after abdominal operations
This textbook says:

Consequently,  young  children are prone to  suffer from pneumonia after abdominal operations, because they resist breathing (being abdominal) due to  pain.  As a result the secretions in the lungs tend to  accumulate,  which may become infected and cause  pneumonia.

Iam unable to find which secretions are they and how breathing removes them from lungs?
I thought it could be pleural effusion but unable to figure out the mechanism involved and how it gets infected if it remains there for long.

As an aside, it's not just young children that are susceptible to pneumonia after abdominal surgery, and the subsequent infections are almost always nosocomial. I had a very personal experience with that many years ago, in my late teens.

Mucus is always being secreted and removed by ciliated cells.

@GrahamChiu So do you think resisting breathing will lead to clog up of mucus?

Inadequate chest wall and diaphragm movement will lead to atelectasis, and an inability to clear secretions.

Abdominal surgery results in a painful wound that affects the abdominal muscles, which are important for coughing. The Lungs and respiratory tracts constantly secrete mucus that flows upwards to the Trachea then down the Oesophagus. The trachea is lined with a moist mucous-membrane layer composed of cells containing small hairlike projections called Cilia. The Cilia project into the channel (lumen) of the trachea to trap particles. The Cilia constantly move in a manner that pushes the mucus up to help clear the respiratory tract of pollutants, debris and bacteria. Here is a link to show the Cilia Movement:
https://www.britannica.com/science/cilium/media/117814/16442
Abdominal Surgery reduces the efficiency of the cough reflex due to abdominal wound pain, while the Anaesthetic results in an increase in mucus due to the upper respiratory tract trauma, with some anaesthetic drugs also increasing these secretions and suppressing Cilia movement. All that eventually results in secretions being produced at a higher rate than being evacuated leading them to accumulate and resulting in an increased risk of lung infection.

This is largely correct, though it could do with some references.

Pneumonia after abdominal surgery can develop due to:

Decreased breathing movements when lying in the bed
Anesthetics/sedation use that decrease the sensation of irritation in the lungs and hence coughing out mucus
Pain preventing coughing
Eventual mechanical ventilation, especially when the organism is not immune to hospital-acquired (nosocomial) organisms, especially staphylococci
Spread of bacteria from the gut to the lungs via the blood)
Eventual underlying lung disease

Source: Post-operative pneumonia (TeachMeSurgery)