evolutionary reason behind sharing the same path for food and air?

While it might make more logical sense to have separate passageways for air and food/water, this did not happen in evolutionary history due to the peculiarities of lung development. Vertebrate lungs develop as an outpouching of the gut tube, which itself has a very long evolutionary history (probably homologous among all deuterostomes).

In the image below, the trachea has budded off the esophagus. Further lung development will involve the differentiation of main, secondary, and tertiary bronchi as well as the alveoli, etc.

Additional images and description at http://www.uoguelph.ca/zoology/devobio/210labs/lung1.html

Air-filled organs like lungs and swim bladders actually have a broad distribution going way down into fishes. Human (and other mammalian) lungs are likely homologous with ancestral air-filled organs of fishes. We can't be certain, but there is no reason to think that mammalian lungs are a de novo evolutionary innovation. So our airway and food-ways are tied together developmentally and are constrained by evolutionary history.

As for breathing and eating (swallowing) at the same time, most mammals can do this, and baby humans can as well.

Like most anatomical systems that seem as though they could have evolved better, this system works most of the time and has worked well enough for hundreds of millions of years.


Biostatistics: Pollen dispersal directionality

(This isn't an answer, but hopefully it will help get it past the experimental design into just solving the equation.)

Where did you get that α0 was not determined from their data? On p. 10 (256), they state, "The prevailing direction of effective pollen dispersal within neighbourhoods (a0) that gave the best ﬁt of the model was 91 degrees from north (nearly due east)."

The best-fit δ parameter value of 0.56 (which determines the size of the effect of the angle between the male tree and the wind) is also determined by their model (table 1, model 9) based on their sample set.

This math is too much for me to solve, but here is how I would go about getting through the experimental setup to just solving the math equation:

Since you're only looking for the effect of wind/directionality, you would set the tree height and distance between trees to be equal. So βd and γh would remain constant and cancel out when you solve for a.

Then you want to determine what angles would give you the highest and lowest pollen counts. Set a0 to wind direction and aj to the angle between a0 and the half disk. The highest pollen count would happen at aj = a0. The lowest pollen counts would happen at aj = (a0-180) or (a0-π or whatever unit of angle is appropriate. Stupid trig.).

With those settings, it should be possible to determine the values of ϕ where aj = a0 and where aj = a0-180.

Then you can get the proportion of pollen grain falls into each disk by finding the ratio of ϕj(a0-180) / ϕj(a0).

Assumptions:
1) There's a linear correlation between ϕ, "the mating success (i.e. fertility) of each outcross male in the neighbourhood" and the distribution of pollen grain dispersal.

2) That a0 ("The prevailing direction of effective pollen dispersal within neighbourhoods") is entirely due to wind. Here I could see terrain being a factor, which would make the effect of wind xδ, such that x<1. If this were the case, the calculated ratio of high pollen / low pollen would be higher than actual.


Laetrile/Amygdalin has been claimed to be a suitable treatment for 'cancer' (which is a summary term for an extremely heterogeneous class of diseases). Even though laetrile/amygdalin in these claims is often called a vitamin, it in fact is not a vitamin as the molecule is not essential for the metabolism (Greenberg (1980)).

The claimed effects of laetrile/amygdalin are not only based on supplementing the molecule to balance a putative deficiency (with the false assumption that it is in fact necessary), though. Both other putative mechanisms are based on reactions that form HCN/cyanide: the enzyme $\beta$-Glucosidase breaks down laetrile/amygdalin and this reaction releases HCN. The argument now is that tumour cells have higher levels of $\beta$-Glucosidase which leads to accumulation of cyanide in tumour cells - with the effect of killing the tumour cells selectively. This would be great... if healthy and tumour cells actually had different levels of the enzyme. Unfortunately, they seem to have similarly low levels of $\beta$-Glucosidase (Greenberg (1980)). Even more problematic, Greenberg (1980) also reports elevated levels of $\beta$-Glucosidase in the liver and small intestine ... and you would not really want to release cyanide there.

There is a second mechanism, though: The enzyme $\beta$-Glucuronidase is claimed to be at higher levels in cancer tissue than in healthy tissues (leading to the same desirable effect described above). But again, there does not seem to be a difference in enzyme levels between healthy and cancer tissues (Dorr and Paxinos (1977)), and even more: $\beta$-Glucuronidase does not even break down the molecule as laetrile/amygdalin has a glucoside bond - so there is not even any cyanide release in that case (Holzbecher et al. (1984)).

Additionally, there is no clinical evidence that laetrile/amygdalin is an appropriate treatment for any form of cancer. This topic has been reviewed substantially (see Milazzo et al. (2006) for a review and this fairly recent Cochrane review by Milazzo and Horneber (2015)) and none of the studies included and analysed indicate any positive effect of laetrile/amygdalin. On the contrary, the in vivo cyanide formation after laetrile/amygdalin uptake makes the treatment very dangerous as it can lead to cyanide poisoning (and death, eventually) - especially after oral uptake due to higher $\beta$-Glucosidase concentrations in the digestive system. The authors of the Cochrane review therefore conclude that

  The claims that laetrile or amygdalin have beneficial effects for cancer patients are not currently supported by sound clinical data. There is a considerable risk of serious adverse effects from cyanide poisoning after laetrile or amygdalin, especially after oral ingestion. The risk–benefit balance of laetrile or amygdalin as a treatment for cancer is therefore unambiguously negative.


Does coloring affect the perception of depth?

Yes, color and shading can certainly affect depth perception, as explained by wikipedia:

  Aerial perspective – Due to light scattering by the atmosphere, objects that are a great distance away have lower luminance contrast and lower color saturation. Due to this, images seem blurry the farther they are away from a person's point of view. In computer graphics, this is often called "distance fog." The foreground has high contrast; the background has low contrast. Objects differing only in their contrast with a background appear to be at different depths. The color of distant objects are also shifted toward the blue end of the spectrum (e.g., distant mountains). Some painters, notably Cézanne, employ "warm" pigments (red, yellow and orange) to bring features forward towards the viewer, and "cool" ones (blue, violet, and blue-green) to indicate the part of a form that curves away from the picture plane.

Here are a few examples:

The above is Manet's "Luncheon on the Grass" - and if you look at it briefly it seems the bathing woman is sort of hovering amidst the trio instead of rinsing herself off in the background. This is because the warmer colors flanked by more saturated greens in the grass around her "pull" her forward into the same space as the rest of the painting. Here, scale is one of the major cues that she should be in the background.

Above is Cezanne's "The Bay" and is an excellent example of how warmer colors (reds, yellows, oranges) are used to add depth when contrasted with cool colors (blues, greens, violets). The image works very well, and that's partially because of the colors chosen. You can almost draw a diagonal line between the warm and cool portions of the painting.

  I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to "blue" is closer than "black"?

Well, there are many differences between the two! The daytime sky has numerous reference points - the horizon, mountains, clouds, airplanes, nearby buildings, etc. I would bet the reference points are the number one reason you perceive the daytime sky to be closer, as our brain is constantly taking them into account without us thinking about it. There are other cues, too: The daytime sky has a gradient to it - that is, the blue of the sky differs due to the curve of the atmosphere, and gradients increase depth perception with more saturated colors being perceived as closer (as opposed to the edges of the daytime sky, which are often less saturated).

The night sky, on the other hand, is pretty much solid black (if you live in suburban or urban areas). The lack of a gradient or other colors immediately robs the observer of some depth perception, and because of the inky blackness of night the other reference points - the horizon, nearby structures, airplanes, clouds, etc. - can practically disappear, robbing the observer of additional depth perception.


What insect is this with 'horn' at the side?

That is a treehopper. Order Hemptera, family Membracidae. I looked on a site for membracids of Malaysia, and could not bring it to species-level. But I am confident that it is a membracid. This family is characterized by sometimes bizarre protrusions of the pronotum.
https://en.wikipedia.org/wiki/Treehopper


What is the body density of insects on average?

A recent studya measured the volumes (using a 3D scanner) and masses of 113 different insect species. They found the following relationship between the mass of the insects and their volumes ($V[mm^3]$ and $m[mg]$):

$\ln (V) = 1.019 \ln (m) + 1.46$

$\Leftrightarrow V = 4.30596 m^{1.019}$

Thus, since $\rho = \frac m V$

$\rho(m) = \frac m {4.30596 m^{1.019}} = \frac {0.232236} {m^{0.019}}
 $

Figure: Scatter plot of the measured masses and volumes

Reference:

a Kühsel, S., Brückner, A., Schmelzle, S., Heethoff, M. and Blüthgen, N. (2016), Surface area–volume ratios in insects. Insect Science. doi:10.1111/1744-7917.12362


What are the structual differences between DNA and RNA?

DNA and RNA are similar, but different molecules. Both are made up of nucleic acids attached to a backbone made of phosphate and a sugar forming a nucleotide. DNA uses the nucleic acids Guanine, Cytosine, Adenine, and Thymine, while RNA replaces Thymine with Uridine.

The nucleic acids can form pairs due to hydrogen bonding, which allows the DNA/RNA to store information, if one strand has a C, the other must have a G and vice versa. Same applies for A and T.

While both molecules are capable of forming double helices by hydrogen bonding between G and C or A and T/U, the types of helix tend to be different. DNA prefers to form what is known as a B type helix, while RNA prefers the A type.

The left most helix is A type, the middle is B type, and the right helix is Z type, a highly unusual form found only under certain conditions.

DNA is almost always found as a double stranded molecule, and is primarily responsible for storing the information for making proteins and RNA and regulatory functions in cells. RNA is made by copying information from DNA through a process known as transcription and performs a variety of roles. Messenger RNA, or mRNA, carries information from DNA to ribosomes where it is used to build proteins through translation. Transfer RNA, or tRNA, carries amino acids to ribosomes to build proteins. The ribosome itself is made of RNA, known as rRNA, with proteins to help it function. Even through RNA is usually made up of only 1 strand, it can fold up and form complex shapes, such as the characteristic tRNA structure shown below. Some RNA molecules can even act as catalysts, carrying out chemical reactions such as cutting up other RNAs. These catalytic RNAs are known as ribozymes.


Does vaccination make the immune system "lazy"?

Contrary to many beliefs our immune system needs no "training". It is permanently active and confronted with dozens to hundreds of antigens in our food, from dust we inhale and so on. This all happens to protect our body from the environment and the immune system is pretty efficient with that and certainly it is not getting lazy.

By vaccinating against a certain disease, you generate immunogenic memory against this disease. When you then get exposed to the disease, this memory helps to speed up the immunogenic reaction against the disease - ideally you are not getting sick, in some cases the progression of the disease is much milder.

Further reading:

Wikipedia on adaptive immunity
The front line of host defense from Janeway at the NCBI Bookshelf


Is it possible for two people to repopulate earth?

Well, mathematically it might be possible. But, I would rather worry about the low amount of genetic diversity that the growing population would have, which would make it extremely sensitive to external stresses.

To repopulate earth from such a small pool of genetic material, one would need an organism that is much more sturdy as compared to humans in extreme conditions, multiplies fast and is much more prone to mutations that actually convert to a phenotypic significance so as to increase the genetic diversity of the total population.


Two mice heterozygote and black are reproduced. Find the probability of getting the filium dark and heterozygote

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


V1-V5 are different (sub) regions of the visual cortex itself.

via http://www.tecsyn.com

The layers L1-L5 (some regions have a layer 6) refer to the different cellular strata in the depth dimension of the cortical mass.  This stratification occurs to some extent or another in various areas.  Different sections of the cortex, e.g., the primary motor cortex have a predominant level 5 (for the pyramidal tract).  Something like the visual cortex has more cells in layers 4 and 6.

 From http://www.unige.ch/cyberdocuments/theses2003/RivaraC-B/images/fig.2.jpg

Layers 2 and 3 tend to carry interconnections between different areas of the cortex, and the topmost layer is generally less dense.


Which sequence characteristics influence the transcription efficiency of T7 polymerase?

By far the most important part is the very beginning of the transcript, especially the positions +1 and +2. The conservered consensus sequence in class III T7 promoters is GGGAGA, any changes in the first two nucleotides severely reduce the transcription efficiency. Changes at positions +3 to +6 have much smaller effects.

Additionally, changes that put many AU base pairs in that region (e.g. GGUUU) seem to affect the trancription efficiency negatively.

Other sequences that are problematic anywhere, not only in the beginning are long stretches of uridines or adenines. Sequences with eight or more uridines or adenines can cause the polymerase to slip, which results in transcripts with more uridines or adenines than in the template.

These characteristics are detailed in the paper from Milligan and Uhlenbeck from 1989.

Milligan, J. F. & Uhlenbeck, O. C. Synthesis of small RNAs using T7 RNA polymerase. Meth. Enzymol. 180, 51–62 (1989).


Why are cell lines frozen in vapor phase?

The storage itself can be done both in the liquid and also in the vapor phase in the liquid nitrogen. Both have their advantages and disadvantages. In my experience there are two main reasons why storage in the vapor phase (although there may be temperature fluctuations when the nitrogen gets low) is recommended.

First, you avoid cross contaminations of your cells lines with mycoplasma (and possible other contaminants) which can get transferred into the liquid nitrogen phase and then into your other cultures. This is not a theoretical danger, but pretty real. See the papers in the reference below.

Then liquid nitrogen will enter your cryotubes (which is also the cause for contaminations). If you use tubes which are not explicitly made for this kind of storage (which is not a problem for the vapor phase storage) then the liquid nitrogen which made it into the tube will expand upon thawing and can cause your tube to explode. This can cause injuries. For more details see here and here.

References:

Risk of contamination of germplasm during cryopreservation and
cryobanking in IVF units.
Microbial contamination of embryos and semen during long term
banking in liquid nitrogen


Does opening the lid of the spectrophotometer affect my results?

It depends on the construction of the spectrophotometer, the wavelength of light you're detecting, and the sensitivity/accuracy that you're demanding of the result.

In the past I have used spectrophotometers which were completely missing their sample lid, with no appreciable detriment to the result. Several things were in my favor, though. The light path from the sample to the detector was suitably collumated, such that any light that wasn't coming from the sample was blocked. I was attempting to detect far UV wavelengths (e.g 260 nm), for which there is little to no ambient source - attempting to detect a wavelength at the peak of a fluorescent light wouldn't have been as successful. I also didn't need highly accurate results, and I was able to dilute my sample such that it fell within a region (~50% absorbance) that is least sensitive to small changes in the amount of light being received.

In your case? If you can retake your measurement "properly", then I'd recommend doing so. If not, you can run some tests (like user aaaaaaa suggests) with some other similar sample, seeing if the absorption readings for that wavelength are affected by having the lid open.


Hydrogen peroxide decomposition and catalase uses

Manganese(IV)oxide can be used as a catalyst to speed up the decomposition of hydrogen peroxide


How does cytochrome c oxidase inhibition cause cell death?

Inhibition is rarely binary - it's almost always subjected to stoichiometric effects. So the answer could be either option, depending on the amount of the inhibitor present in the system. If there is a huge amount of the inhibitor in the cell, it may more or less completely ablate ATP production by the ETC.

On the other hand, if there isn't enough of the inhibitor to shut down all cytochrome C oxidase, you'd only see a reduction in the amount of ATP produced by the ETC (which could still be sufficient to kill the cell).

It also depends on the type of inhibition taking place. Is it reversible or does it bind permanently? Does it degrade quickly? These aspects are also important to consider.


From the Tree of Life page for Mammalia:

All of these groups of animals are mammals, including extinct triconodonts and multituberculates. Among living mammals are monotremes (most notably the platypus), marsupials (kangaroos and opossums), and eutherians. Eutherians are placental mammals, so all eutherians are placental mammals, but not all mammals are eutherians.

Both armadillos and pangolins are eutherian mammals, so both are mammals and both are placentals. "Difference Between" is quite incorrect.


In addition to Remi.b's answer, it should be noted that the phage Phi X 174 is the only organism in your list which significantly deviates from Chargaff's Rule (by more than 1-2 percentage points for the A-T pair). While sampling errors are indeed more likely in organisms with small genomes, there is in fact another factor in play here.

This is because Chargaff's Rule only applies to double-stranded DNA, due to the complementary base pairing that occurs between A-T and C-G. Since Phi X 174 is in fact a single-stranded + sense bacteriophage, Chargaff's Rule is inapplicable to it, since it does not obey the standard Watson-Crick base pairing that is the molecular basis of Chargaff's Rule. In fact, the Wikipedia article from which you obtained the chart states this as well:

  The following table is a representative sample of Erwin Chargaff's 1952 data, listing the base composition of DNA from various organisms and support both of Chargaff's rules. An organism such as φX174 with significant variation from A/T and G/C equal to one, is indicative of single stranded DNA.


The beta-form of DNA and the alpha-form of DNA are based on the pucker on the sugar ribose. As DNA doesn't have a 2'-OH, it can obtain both conformations.

RNA does not have this luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus constraining the RNA to adopt the A-form. Incidentally this steric limitation is also why RNA structures are more stable (see https://biology.stackexchange.com/a/769/389)


This is probably a crape myrtle, a plant from the Genus Lagerstroemia.

Here is another photo for comparison:

And here another photo, showing the whole tree:


Have there been any experiments that duplicate chromosome copies from 23*2 to 23*3 or 23*4?

It's an idea that doesn't hold much promise.
Individuals who show diploid/tetraploid mosaicism present "failure to thrive and multiple minor anomalies." according to:

Alonso L et al (2002) Tetraploid/diploid mosaicism: case report and review of the literature. Annales de Genetique 45 177-180

On the other hand, complete tetraploidy is apparently lethal:

Nakamura, Y. et al. (2003) A Tetraploid Liveborn Neonate: Cytogenetic and Autopsy Findings. Archives of Pathology & Laboratory Medicine 127:1612-1614.
Abstract
Cytogenetic and autopsy findings of a nonmosaic tetraploid male neonate, alive until shortly after birth at 37 weeks' gestation, are described. Oligohydramnios, intrauterine growth retardation, cranial abnormalities, and Dandy-Walker malformation were noted prenatally. Autopsy findings included cleft lip and palate; overlapping fingers; low-set ears; simian creases; hypoplastic external genitalia with undescended testes; Dandy-Walker malformation; slightly dilated lateral and third ventricles; hypoplasia of the cerebrum, pons, medulla, pituitary gland, thymus, lung, adrenal gland, and kidney; large ventricular septal defect; and enteric cyst behind the urinary bladder. The placenta was hypoplastic and showed no remarkable abnormalities, except for mild syncytial knots. Chromosome analyses of amniotic fluid cells at 31 weeks' gestation and the umbilical cord blood cells at delivery revealed a 92,XXYY karyotype. G-, C-, Q-, and N-banding heteromorphic studies demonstrated duplication of paternal chromosomes 1, 3, and 15, and maternal chromosome 22. In addition, the results of an analysis with 16 CA repeat polymorphic markers were consistent with duplicated inheritance of 1 paternal and 1 maternal haploid sets to the tetraploid patient. Therefore, it is most likely that the tetraploidy was caused by a cytoplasmic cleavage failure at the first mitotic division.

full text available here.


Meaning of "stripped" in "stripped antibody-depleted sera"

I believe this is a failure of editing, and the meaning in this paper of "stripped" cannot be determined without correspondence with an author.  "Stripped" is an informal term for either removal of some substance or treatment with a material such as charcoal which affects many substances. Normally in papers "stripped" is qualified (at least initially) to indicate the type of treatment.  Here it could plausibly refer to antibodies, folic acid, or any number of other things.  It may be an artifact of draft editing that was meant to replace "stripped" with "antibody depleted" as a more precise term.  I suggest writing the corresponding author.


You probably mean genomic and non-genomic DNA - Plasmids are small rings of non-genomic double-stranded DNA in Bacteria. They replicate mostly indepently of the genomic DNA can can occur from a few to several hundred copies per cell. See the illustration from the Wikipedia:


It has a cytoskeleton, a network of fibers stretched across the cell which it can shorten and expand (by adding or subtracting actin monomers which build them) in a coordinated manner to more-less arbitrary change shape.

According to this paper, on surfaces they generally can adhere to it using membrane protein structures, thus the locomotion occurs due to friction.

To swim, they generate bumps near the front end of the cell and move them towards the back, similarly to how a swimmer uses hands.


Is there a scale suitable for continuous tracking and recording of plant weight?

maybe this company  https://www.industrial-needs.com/scales-and-balances/recording-scales.htm

Our scale software allows a real-time measurement on a computer and
depending on the weighing data, they can also be saved with a date
stamp as a TXT file on the computer


How do you turn a minimal CIF description into a complete one?

Not quite as ideal as I had hoped, but it works:

Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere.  Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return

If it complains it's not found, the CCP4 bin directory may not be in your PATH environment variable.  You can get around this by specifing the full path to the program, e.g.: c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe (may vary with version)

Say "Y" or "A" at the _DOC: prompt for some more files, "N" if you don't care (I generally don't)
At the --> prompts, specify:

the input file, e.g.: file_l: ABC.cif
the monomer: mon: ABC
output file name: file_o: ABC_out

Leave a prompt blank and hit return to start processing.

If it runs successfully it might look something like this:

C:\Users\Nick>libcheck

  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/

  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: libcheck.bat
 _DOC:n

 #
 #      Keywords:
 #
 #FILE_L:   < >  - additional library, " " means without this file
 #MON:      < >  - give info about this monomer
 ... (shortened) ...
 #SRCH: <N>/Y/0  - Y - global search, 0 - for MON from PDB_file
 #                 (only with NODIST = N)

 #---  type "keyword   parameters" and/or ---
 #---  press key "CR" to run program      ---
 -->file_l: ABC.cif
 -->mon: ABC
 -->file_o: ABC_out
 -->
 MON   : ABC
 -------------
 Output file   :ABC_comp
 Input user lib:ABC.cif
 _chem_comp.name "DRUG INTERMEDIATE"

          17          55
 "DRUG INTERMEDIATE"

 -------------
 Keywords:
 HFLAG : Y
 COOR  : N
 LCOOR : Y
 SRCH  : 0
 REF   : Y
 NODIST: Y
 ERROR ==> In the loop containing the item_chem_comp.three_letter_code
 ERROR ==> The number of expected items and the number existing items do not match
 ERROR ==> The number of expected items is    7
  NUMBER OF MONOMERS IN THE LIBRARY          :     1
                with complete description    :     0
  NUMBER OF MODIFICATIONS                    :     0
  NUMBER OF LINKS                            :     0
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  I am reading library. Please wait.
      - monomer"s description
  WARNING : monomer:ABC      - has the minimal description.
  now monomer:ABC      - has complete description.
  I will check it.
 * CIFile  : ABC_out_ABC.cif
 * PDBfile : ABC_out_ABC.pdb
 * Plotfile: ABC_out_ABC.ps
  I am writing new description to
  file: ABC_out.lib

C:\Users\Nick>

It yields the following output files:

(file_o): looks like a CIF file with lots of whitespace and records stripped out
(file_o).lib: the desired, complete definition file
(file_o)_(mon).cif: an even more minimal CIF file with only XYZ coords
(file_o)_(mon).pdb: a PDB file
(file_o)_(mon).ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes.  Can convert it to the easier-to-use PDF format using this http://www.ps2pdf.com/convert.htm, or other tools.


Is there a scientific proof that smoking spoils face skin?

This page is pretty complete with examples and references.

In summary a lot of the evidence is empirical - you look at smokers and the quality of their skin and compare to non-smokers and the differences are statistically significant and reproducible.  It seems as if this is old work, dating from the 1970s.

So in many cases these are only observed correlations.  But they are pretty strongly agreed upon by medical people.  Given the fact that we still don't know exactly what causes cancer, I think this is not an unusual level of explanation for medical conditions.

As you can see some theories would include direct effects of the smoke and some indirect effects.

  It is not certain exactly how smoking causes early ageing of the facial skin. Theories include:

  Heat from the cigarette directly burning the skin
  Changes in the elastic fibres of the skin
  Narrowing of blood vessels (vasoconstriction), which reduces blood supply to the skin and can cause changes in skin elastic fibres and
  loss of collagen
  Reducing Vitamin A levels and moisture of the skin


Measuring reverse transcriptase activity in E. coli

the devil is in the details here - the logic is okay, but there is no experiment here. Too many unanswered questions.

Are you doing anything specific to see optimize RT activity?

How are you preventing your GFP mRNA from being turned into protein, producing much larger signal than you will ever see from RT activity?

Once its integrated into the chromosome, how will this gene be expressed when it has been suppressed in all these other stages?

How do you know that the plasmid isn't just being incorporated into the chromosome by some other means?

Where is the RT coming from ?  E coli doesn't have the gene. this experiment is very likely to give no results.

When/how does this RT work?  If its some sort of phage RT ( i don't know if there are such things) any sort of viral RT will probably kill the cell the way normally it would.

so many questions before this could work - need to do some homework here.


What does NaOH do for the plating of Bacillus subtilis?

I think NaOH is added to bring up pH not to get too acidic. I feel autoclaving LB or LB-agar for 2 hours is too long. During autoclaving, some components are gradually degraded.


Do we actually get more sick (flu/cold) during winter?

The combination of these two reports from the CDC give information about the comparative prevalence of flu infection in the winter (September '12- May '13) and summer (May '13 - September '13). I'm going to assume that 2012-2013 was a fairly representative year as far as the level of detail of "do we get sick more in the winter" goes. Particularly striking are the graphs linked to in both documents of the number of flu-infected respiratory specimens per week:

Winter (infected specimens out of 311,000 tested):

Summer (infected specimens out of 52,000 tested):

Together these two figures cover data Sept '12 - Sept '13. Note the difference in scale on the vertical axis. Forgive me if I don't run any statistical tests, but I think you can spot the trend.

The sum of all the Winter cases represents 23% of the 311,333 specimens tested from Sept '12 to May '13, and the sum of all the bars in the Summer figure represents 3.9% of the 52,150 respiratory specimens tested from May '13-Sept '13.

Still left to answer: Why is this the case? In my preliminary research it seems like we still don't fully know the answer to this one; I'll leave someone else to speculate.

Edit: Some tentative answers to why is there a seasonal flu outbreak:

This review (1) does a nice job of laying out some of the current ideas about the cause of the seasonal flu. One interesting note is that seasonal flu is a phenomenon of temperate climates: in tropical regions flu outbreaks occur on a much less regular periodic schedule. Some possible causes mentioned by the authors (paraphrased from the article):

It takes time for virus to mutate enough to be infectious again to people who were already infected with it.
The efficacy of the immune system may vary seasonally, say, due to changes in daylight hours/vitamin D and melatonin levels (which have been shown to affect immune system function in hamsters)
Flu is transmitted better in more crowded conditions + in winter people are more crowded together. This is a popular explanation, but the authors claim that it has not been satisfactorily tested. It has been argued convincingly that the 1918 flu epidemic was exacerbated by the crowded condition of army barracks in WWI (see citation in paper).
Indoor heating encourages air recirculation, which allows virus to persist in the air around you longer.
Viruses survive/persist better in cold, dry conditions. This may allow them to spread in the atmosphere longer during the winter, and be more easily transmitted from person to person via "bioaerosols" (sneezes).

Ultimately, as I said before, we don't really know yet. Reading that list you can imagine several ways in which a few of those factors are not at all causal and are rather just strongly correlated with the "true" cause of flu seasonality.

(1): Lofgren et al. Influenza Seasonality: Underlying Causes and Modeling Theories. (2007). J. Virol. 81(11): 5429-5436. doi:10.1128/JVI.01680-06


Why do we urinate more when we are nervous?

I found an interesting article that dealt with anxiety and micturition. There are no proven or accepted view on this. There are a few theories as to how this happens.

I am quoting it:

  There are several beliefs for what causes frequent urination from anxiety, and the likelihood is that all of these factors play a role:

  Muscle Tension – This is one of the most likely causes of frequent urination. When you have anxiety, your muscles get very tense. This tension puts pressure on your bladder, which in turn makes you feel like you need to urinate more than you would otherwise.

  Evolutionary Adaptation – Another theory is that there is an evolutionary reason that frequent urination would be advantageous. Remember, anxiety is the misfiring of your healthy fight/flight system. In times of fear, urination may keep the body lighter by losing extra weight, making it easier to flee.

  Light Overload – It's also possible that, because anxiety is a misfiring of the fight/flight system, your body may simply be lightly overloaded. The fear is not intense enough to cause immediate urination, but it may make it harder for you to feel like you can hold it back.
  Also, those with anxiety are more prone to focusing on different sensations unintentionally. There are often times when you may feel the need to urinate slightly but your body has no problem ignoring the feeling and holding it back. With anxiety, it's possible that your brain is focused on the sensation, potentially causing you to feel like you need to urinate more than you do.

  Finally, anxiety can also change your body chemistry, altering your digestion and changing the way you process nutrients. That may cause more water to pass through your body.

Source:http://www.calmclinic.com/anxiety/signs/urination-problems


First off this is called genetic mosaicism and indeed mitotic recombination is a contribution factor.

Mitotic crossover events involve the exchange, by homologous recombination, of regions of chromosomes. 60% of homologous recombination events might occur during G1 and 40% of those event occurs after chromosomes are replicated (see this paper). For twin spotting to occur, you need the homologous recombination to happen on replicated chromosomes (i.e. you need 4 chromatids).

For you question on twin spotting. The following picture illustrates well what are the outcomes of homologous recombination involving two alleles and replicated chromosomes (each line being a chromatid).

If the cell is heterozygous (normal phenotype) for the two recessive alleles, here called y and sn (respectively the "yellow" and "singed bristles" alleles), then two recombination scenarios are possible and differs based on where the recombination occurred. Note that y+ and sn+ are the wild-type alleles and carrying those alleles do not provoke a particular phenotype. The phenotype of the resulting daughter cells are:

Twin spots: Yellow but not singed spots (y/sn+) and singed but not yellow spots (y+/sn) for recombination after the y/sn locus
Single yellow spots: Yellow but not singed spots (y/sn+) and no spots (y+/sn+) for recombination between y and sn

Here the actual picture of what happens:

Therefore this should make clear why daughter cells can show phenotypes that differ from the original parent cell, i.e. the combination of alleles (especially for recessive ones) changes after mitotic crossover events. The twin spot phenotype in Drosophila melanogaster is an excellent example for illustrating that.


Do mammals and birds have a common warm-blooded ancestor?

Welcome to Biology.SE.

Did you say warm-blooded?

The term warm-blood is very unclear. The correct terms are endo-, exo-, poikilo- and homeo- therm. In short…

Source of heat

endo = inside
exo = outside

Variation in inside temperature

Poikilo = varies
homeo = does not vary

Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. A fun example also are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur homeo-endo-therm individuals. Hope that makes sense to you.

By warm-blooded I will assume you meant endotherm.

MRCA of mammals and birds (and other things)

The Most Recent Common Ancestor (MRCA) lived 301.7 millions years ago (see on tolweb and on OneZoom). This MRCA was exotherm. In consequence, birds and mammals endothermy are an example of convergent evolution (even if they are not using exactly the same mechanisms).

References to go further into the evolution of endothermy in birds and mammals

Grigg et al. 2004
Hillenius and Ruben 2004
Ruben 1995


Can white eggs be considered as non-vegetarian?

Of course eggs are not vegetarian. Eggs are, well, the eggs of chickens (usually). Chickens are animals so their eggs are animal matter as well. Whether or not the egg has been fertilized is completely irrelevant, eggs are chicken just as much as drumsticks are.

The color of the egg has nothing at all to do with it. All eggs are, by definition, animal cells. Basically, the chicken's egg is the equivalent to the human ovum. In both humans and chickens, the female will regularly produce eggs and discard them. In the case of a human woman this is the monthly period. When an egg is not fertilized, it is discarded along with some cells of the wall of the uterus. Similarly, in chickens, the female produces and lays eggs. If an egg has been fertilized, it can grow into a new chicken. If it has not been fertilized, it cannot become a new chicken but is most certainly still an animal cell.

So yes, eggs are most certainly animal, not plant or any other kind of matter. Whether or not you should eat them is up to your own moral guidelines to decide. While they are animal tissue, no animal has been killed to obtain them and no harm comes to the chicken if we harvest them.


What does the 'V' stand for in ECG electrode names?

Short answer
V stands for voltage.

Background
The various leads in an ECG montage are shown below:

ECG electrodes. Source: American Heart Association

I am not an expert in ECGs, but as far as I can see, RA, LA and LL are return electrodes as they are situated far away from the heart. In other words, they act as reference electrodes. RL is the ground, basically to correct for baseline shifts. This leaves the V electrodes, which are the chest leads, or precordial leads, and are situated right above where the action is, i.e., the heart. The ECG is determined between the V electrodes and a distant reference, with a ground added. The V electrodes are the active electrodes, picking up the signal. The others are references and a ground only.


I guess you meant the population size stability.

It is considered that the biosystems will increase their capacity of adaptation when evolving in very fluctuating environments. I believe the population stability is embedded in the adaptability of individuals.

There is a measurement about it, evolvability, when the environment changes, the faster the population adapted to the new environment, the higher evolvability it has. This means that if the population has higher evolvability then the population may be more stable to environmental variation.

Even so, there might be plenty of underlying mechanisms to enable a certain population stability. I recently read a paper about two mechanism: phenotypic switching and sensing machinery, which are common in bacteria and fungi. Please refer to Edo Kussell and Stanislas Leibler's science paper (2005).

As the organism increase its complexity, biosystems invented many more tools to make the individual survival from disasters. Such as human's intelligence. Well it would be an endless issue.


Things are not fundamentally tasty or disgusting. A dung fly loves that taste of dungs while I personally prefer the taste of an apple and my dog prefers the taste of duck fat. A classic example is the gene family TAS2R and the evolution of bitter taste in rodents and primates.

Predator (incl. herbivores) evolves as to like the taste of what he should be eating (Carlsson et al., 2009). Preys (incl. plants) can eventually play out with their taste though, trying to either taste bad to avoid specific predators or taste good to attract specific predators that may disseminate their seeds. I have failed to find evidence that plants can deceive animals at being more tasty than nourishing but you might still want to have a look at Dethier (1980), Sorensen (1983) and Goff and Klee (2006).

One could therefore expect an evolutionary race (red queen) between preys and predators upon how they taste. It would likely be a rather complex race as most species have several predators and several species they prey upon. However, such race on taste would work only if plants can deceive animals which I failed to find evidence for. Arms race for toxic compounds relating to evolution of taste in animals are very much known though (Edger et al., 2015).


What are the ways to test for protein in the canine urine?

After some research, I could primarily find two tests for testing the protein content in dog urine.

1) The Urinalysis dipstick test (reference) which has a chance of giving false positive results (reference). Here is the link to a lab test done using the dipstick method and the results that the researchers got.

A sample Dipstick (reference)

2) The second test would be the benzethonium chloride test (reference).

  This test precipitates the protein and increases the turbidity of the
  sample. The turbidity is proportional to the protein concentration.
  This technique is very sensitive and can yield accurate results in
  samples with very low protein concentrations (< 20 mg/dL).

A lab study done using this procedure to precipitate protein (reference).

  The urine sample is best read within 30 minutes of collection
  otherwise certain factors (like crystals, bacteria and cells) may
  alter their composition (dissolve or multiply) over time. If you
  collect a urine sample at home, please drop it off at your veterinary
  clinic as soon as possible (reference).

Reasons for excess protein if present in the urine of your pet is listed in this article.


Will meat rot in alcohol below freezing?

A chemist's perspective:

Ethanol and water are miscible, meaning they are perfectly soluble in one another in all proportions. So given enough time, the alcohol will likely seep into the tissues and cells of the meat, and some water will seep out into the surrounding alcohol bath. The liquids might not equilibrate very well on a reasonable time scale, that is, the bath surrounding the meat could remain mostly alcohol with some water, and the tissues of the meat could contain more water than alcohol. This is because the biological barriers of the meat interfere with the diffusion of the fluids to reach a mixture of equilibrium proportions. However, in theory, cell membranes are permeable to ethanol, so given enough time soaking we might build up a useful concentration of ethanol within the meat.

Note that it doesn't matter so much what happens outside the meat - being bathed in a substance that remains a liquid below 0 °C won't necessarily stop the meat itself (well, the aqueous solutions within it) from freezing. That is why the considerations of solubility and permeability are crucial. As I said, for ethanol we have perfect solubility with water (miscibility), and possibly sufficient ability to diffuse throughout the organic catacombs of our meat. So, assuming ethanol can sufficiently perfuse the tissues and enter the cells, what would happen?

Water has a higher freezing point (not "freezing rate") than ethanol (0 °C > -114 °C). When you mix some ethanol into water, the freezing point of the solution will be lower than the freezing point of the pure water. The freezing point of pure water is depressed by the addition of ethanol. Here is some data on the freezing point of water solutions with different amounts of added ethanol:

(Note that the freezing point at 100% ethanol seems to be -111 °C according to this data; this should technically be freezing point of pure ethanol itself, so we would expect it to be the -114 °C figure I quoted earlier. But that small discrepancy between this experimental data and the traditionally accepted number will not affect our analysis.)

So, as you lower the temperature, the water-ethanol solution in the meat will begin to freeze. It will freeze at some temperature lower than normal because of the ethanol present. Note that the normal freezing point of water in meat is already going to be lower than 0 °C due to all of solutes inherent in such a biological system (ions, sugars, metabolites, maybe a few stray amino acids, etc). As it freezes, the water will freeze first and leave the ethanol behind.

So, inside the meat, you will see the meat freeze at slightly lower than normal, with some liquid remaining in the tissues which would be the ethanol. Outside the meat, in the bath of ethanol which has drawn some water out of the meat, you will see that water forming ice on top of the liquid, which will become purer and purer ethanol as the water freezes out of it. The process I just described is fractional freezing, and you may be interested to know it is how "ice beers" (Keystone Ice, Natty Ice, etc) are made more alcoholic.

Now, if the proportions of ethanol and water are just right, something interesting happens. Instead of the water freezing first and precipitating out of the ethanol, a special eutectic solution is formed that freezes all at once. (Perhaps you've heard of fractional distillation and azeotropes, the the boiling point analogue to fractional freezing and eutectic mixtures). On the graph above, the eutectic mixture is achieved at the very minimum value, around -118 °C. Note that freezing point of the eutectic mixture is lower than the freezing point of pure ethanol alone. Unfortunately, for the specific case of water and ethanol, reaching that special point of bonus freezing point depression requires the solution to be almost completely ethanol (about 93%). That would be the holy grail of lowering the freezing point of your meat, but it's likely not feasible to replace that much water with ethanol throughout the meat.

So, in conclusion: It's what happens inside the meat that counts. If you bathe meat in ethanol, a useful amount of ethanol may permeate the meat. The freezing point of the meat (rather, the aqueous solution within it) will be lowered the more ethanol perfuses it. In theory, you could even drop that freezing point below that of ethanol itself, but it would require replacing nearly all of the water with ethanol.


How does the human body extract energy from ethanol?

Preamble

The question suggests unfamiliarity with the nature of biochemical oxidations and their relation to energy transfer in biology. The naïve reader is recommended to consult a text for a coverage of this subject: all I feel is appropriate here is a general summary followed by a brief indication of the key reactions.

General principles of energetic value of and biological oxidation of foodstuffs

The energy available from the oxidation of foodstuffs such as starch, fat and alcohol may be represented as the thermodynamic Gibbs Free Energy change (ΔG) in their complete oxidation.
This value can be determined chemically by bomb calorimetry in which the oxidation is done directly by oxygen and the energy produced is in the form of heat.
In biological oxidations the immediate oxidant is a molecule (an enzyme cofactor) such as NAD+ (or NADP+ or FAD), and *part of the Gibbs Free Energy change is translated into chemical energy in formation of the reduced compound — NADH etc. Only some is lost as heat*; but enough to give an overall negative ΔG, that causes the reaction to proceed.
The reduced coenzymes can be used to produce ATP by oxidative phosphorylation (involving oxidation by oxygen) or in reductive processes such as the synthesis of fatty acids, depending on the organism’s energy requirements.
Likewise, the molecular intermediates produced in the course of the biological oxidation (e.g. acetate) can be oxidized completely by oxygen (the terminal electron acceptor of the electron transport chain) to carbon dioxide and water (with production of more NADH in the tricarboxylic acid cycle, and hence more ATP), or can be converted to other metabolic intermediates or used as the precursors of other molecules, including storage molecules.
If the organism has a sufficient supply of energy (ATP) already, surplus intake of foodstuffs will lead to the deposition of energy reserves.

The case of ethanol

The question rightly states that ethanol is converted to acetaldehyde and then to acetic acid, but fails to include the oxidant, NAD+, which is an essential participant in the biological reactions:

[ADH: alcohol dehydrogenase; ALDH: aldehyde dehydrogenase ]

Thus, two molecules of NADH are produced, providing either ATP or reducing power.

The question assumes that after conversion of the acetate to acetyl-CoA it will be oxidized in the tricarboxylic acid cycle*. However in a fed subject with sufficient energy the cycle is suppressed and the acetyl-CoA will be converted to malonyl-CoA, the precursor of fatty acid synthesis. These processes require both reducing power (NADPH, which can be obtained from NADH) and ATP (ditto):

*The quotation states that “acetic acid is excreted in the urine…”. I have no knowledge of what proportion of ethanol is disposed of in this way, but I would imagine it is small — certainly not enough to prevent beer belly. However this is not the main reason why “catabolism of alcohol” does not “go(es) all the way to completion”.

Postscript

The biochemistry above is covered in Section 30.5 of Berg et al., entitled “Ethanol alters energy metabolism in the liver” (freely available to read online). This explains in more detail why the acetate is not metabolized in the tricarboxylic acid cycle. It does not discuss fatty acid synthesis, as the emphasis is on the more immediate pathological consequences of excess intake of alcohol.


At what age do babies begin to synthesize their own antibodies?

In the graph above the darker blue line refers to the antibodies the baby receives from the mother in utero, as you mentioned in your question.

As you can see, the red line indicates that babies begin to produce low levels of their own antibodies between 3 and 6 months before birth.  However, these are IgM antibodies, immature 'rough draft' versions.  These have much lower affinity for antigens then their mature IgG counterparts which are the classically thought of antibody.

Levels of an infant's own IgG start to rise after birth, however don't reach a reasonable level until after the child is roughly 1 year old.  Maternal antibodies start to tail off at around 3 months leaving a period highlighted in blue on the graph where infants are particularly prone to getting infections.


Do all Gram negative bacteria cause septic shock?

all Gram negative bacteria can potentially cause septic shock, but septic shock is not limited to Gram negative cell wall lipopolysaccharides. Any infectious agent can cause septic shock, including gram positive and gram negative bacteria, fungi and even viruses (this is quite evident in the recent Ebola outbreak).[1]

The causative agents for sepsis/septic shock have evolved. Originally strongly considered to be related to Gram-negative bacteria, that is no longer the case. About 25 years ago, sepsis was considered to be a response to endotoxin thought to be relatively specific for Gram-negative bacteria. That Gram-negative bacteria were the most common causes of sepsis[2] resulted in trials that focused on  specific therapies for G negative endotoxins.

It is now recognized that sepsis may occur from bacterial, fungal and viral organisms. More recent epidemiology studies reveal that Gram-positive bacteria have become the most common cause of sepsis in the past 25 years. According to the most recent estimates in sepsis, there are approximately 200,000 cases of Gram-positive sepsis each year, compared with approximately 150,000 cases of Gram-negative sepsis.[3]

Fungal causes of sepsis have also grown at a rapid pace. Why this occurs may be two-fold: a general increase in nosocomial (hospital acquired) cases of sepsis, and more effective treatment of bacterial infections, thus promoting fungal infections to a more leading role. The increase of fungal nosocomial infections has also shifted away from the common Candida albicans organism to the more recalcitrant torulopsis, glabrata and krusei subspecies.[4]

So while the Gram negative Lipopolysaccharide or “endotoxin” is unique to Gram negative bacteria, cell components of Gram positive bacteria have been identified that appear to be biologically equivalent to endotoxin in stimulating the inflammatory response associated with sepsis and septic shock. These include a peptidoglycan layer outside the cell membrane of Gram positive bacteria as well as non-peptidoglycan polymers (such as the teichoic acids). They have been shown to stimulate the release of cytokines, specifically tumor necrosis factor and interleukin-1.[5]

[1] How Ebola Kills You: It's Not The Virus
[2] Septic shock in humans. Advances in the understanding of pathogenesis, cardiovascular dysfunction, and therapy
[3] The epidemiology of sepsis in the United States from 1979 through 2000.
[4] Nosocomial bloodstream infections. Secular trends in rates, mortality, and contribution to total hospital deaths.
[5] Sepsis and Septic Shock
Sepsis, severe sepsis and septic shock: changes in incidence, pathogens and outcomes


Why are stem cell therapies more preferred (theoretically) over current measures?

Stem cell therapy was never going to replace surgery, and it isn't supposed to. We just don't have the tools to move stuff around inside the patient without breaking the skin.

Stem cells therapies offer replacement parts for organs that can't regenerate themselves. For example, after a heart attack the heart often forms a scar where heart tissue has been injured or died. The scar often doesn't conduct electrical signals properly or doesn't beat at all, both of which are a problem for a heart. The scar can't be surgically removed, because there's nothing to replace it with. Stem cell therapy would provide new heart muscle to replace the damaged tissue.

There are of course exceptions, some stem cell therapies are injected and left to 'settle' in the right tissues. That kind of therapy generally doesn't replace a surgery either, because that kind of problem can't be fixed with surgery at all.


Which of the cell types commonly found in mammals has the greatest number of mitochondria?

It's commonly believed that it's muscle cells that have the largest amount of mitochondria, and for good reason.  Muscle cells are continually used to move the body, so they have the most mitochondria because of the large energy requirement.  If you want to be more specific, the muscle cells of a marathon runner have even more since the muscle cells involved in running need to be able to do a lot of aerobic respiration.  Another example is the cells in the heart; the amount of mitochondria makes up 40% of the cell.

The truth is, retinal cells with photoreceptors most likely have the most (80% of the cell volume) since they need to reset the potassium/sodium pump to keep the action potential in the nerves the same.

If you're curious, the cells with the least amount of mitochondria are skin cells and erythrocytes (red blood cells) since skin is just a protective barrier and red blood cells don't need to exert any effort or energy to move.

Sources:

http://hyperphysics.phy-astr.gsu.edu/hbase/biology/mitochondria.html
http://www.ncbi.nlm.nih.gov/pubmed/12511073


What is the difference between gene and CDS annotations?

CDS is based on ORF prediction and unless the protein product is known it is classified as an mRNA for a hypothetical protein (Refseq id: XM_*).

As Devon Ryan said sometimes UTR ends are not accurately annotated. If you are interested in finding the 3' end of 5'UTR then the problem is basically to find the translation start site. You can have a look at ribosome profiling experiments or try doing eIF2 CLIP-RNAseq (I don't think it has been done); peptide sequences may not be of help because N-terminal region in many cases, gets clipped.

If you are interested in finding the 5' end of 5'UTR then the problem is relatively simple. You just need to do a 5'-RACE followed by Sanger sequencing (this would work in most cases or you can do a deep-RNAseq).

There are official GTF files that provide the most reliable annotations. For human I would recommend GENCODE.

In the annotations the term Gene denotes the entire DNA region that is responsible for all of its RNA products (splice variants, alternate start/termination etc). Other features include Transcript, Exon, CDS, UTR and in some cases translation start site is separately annotated. CDS comprises of just the protein coding region.

You should read more about the GTF/GFF annotation format.


Are there any fungi that can digest humic acids?

According to Wikipedia, humic acid (HA) is a product of the biodegradation of dead organic matter. Shown below is a representative structure, but it important to understand that humic acid is a name given to a family of loosely related polymers of the products of biodegradation.

Although HA is resistant to further biodegradation, there are indeed fungi that are able to break it down further.

There is evidence that fungi can break down HA:

  Grinhut et al (2011) Mechanisms of Humic Acids Degradation by White Rot Fungi Explored Using 1H NMR Spectroscopy and FTICR Mass Spectrometry Env Sci & Technol 45, 2784-2754

This paper reports studies of the mechanism of HA degradation by Trametes and Phanerochaete fungi (Basidiomycetes). This degradative property is attributed to the secretion of non-specific oxidising enzymes: manganese peroxidase, lignin peroxidase and laccase. the authors report evidence for "oxidation, a decrease in the aromatic content, and indication of demethylation of the HA during biodegradation.

The paper is also a source of references to earlier work.

The indications are however that these fungi carry out this degradation in the presence of other nutrients, i.e they cannot utilise HA as a major carbon/energy source.


What will happen if a poisonous snake bites itself?

“The conventional wisdom is that they have circulating antibodies in
  their blood,” says Stephen Mackessy, Ph.D., a Professor of Biological
  Sciences at the University of Northern Colorado and an expert in
  venomous snakes. “This would protect them from their own venom, as
  well of venom from another snake in their own species.”

  Hypothetically, if a speckled rattlesnake bit another speckled
  rattlesnake, the immunity they’ve built from being exposed to low
  levels of their own venom—kept in glands behind their eyes and
  secreted when they bite—would protect them from a fatal wound. (Even
  though the glands are closed, they still contain blood vessels that
  allow the venom to circulate in their system, causing mild exposure,
  Mackessy says.) But a speckled rattlesnake that meets up with a cobra
  might have a different day entirely.

So in the case snake were to bite itself it wouldn't suffer as much from the poison compared to the actual bite it self-inflicted.


Is there any non-pathogenic gram negative bacteria?

As Canadianer already mentioned in the comments, the majority of bacteria (this includes gram-negative bacteria) are non-pathogenic.

I think a prime example is the human gut flora. You can find loads of bacterial species living in your gut without doing you any harm, if anything they are doing you a favour by breaking down food.

Here some examples of gram-negative genera:

Bacteroides
Escherichia

Most species within those genera are non-pathogenic, however, there are exceptions.


Balanced vs Maximized Codon Optimization

Codon usage optimization is still pretty much heurestic. The most common factor we think are important in E. Coli are:

optimization to highly expressed genes, i.e. maximization of codon adaptation index http://www.ncbi.nlm.nih.gov/pubmed/19359587/
keeping the optimal GC content http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107319
not introducing motifs that are somehow detrimental, e.g. restriction enzymes, or some dinucleotides http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642
adapting to available tRNA http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002
minimizing folding energy (in the first ca. 30 codons) and minimizing the amount of hairpins at the 5' end http://www.sciencedirect.com/science/article/pii/S0014579305010719
optimization of 'codon context' e.g. dicodons but also using nonoptimal codons between secondary structure for more accurate folding http://www.ncbi.nlm.nih.gov/pubmed/15772378
optimization of codon balance and also maybe the introduction of a 'ramp of slow codons' in the beginning of a gene to avoid 'traffic jams' of ribosomes later on. http://www.ncbi.nlm.nih.gov/pubmed/20403329

Most probably it's a mixture of all of those.

Disclaimer: We are working on a codon optimization strategy for e.coli/yeast/hela and it works in e. coli but is yet untested in human cells. If you want to take a long shot just shoot me a message and we could try it. Apart from this, I would also offer you to have a look at your sequence and see if there is anything 'strange' from the codon usage point of view and what I think what be the best optimization strategy.


What role does the eardrum and ossicles play in hearing, versus cilia?

Sounds are pressure waves in air, but the inner ear is a liquid-filled space. This presents an impedance matching problem where sound is reflected rather than transmitted.
The eardrum and inner ear bones perform this mechanical impedance matching/transduction of air-to-liquid sound. From Purves' Neuroscience:

Sounds impinging on the external ear are airborne; however, the environment within the inner ear, where the sound-induced vibrations are converted to neural impulses, is aqueous. The major function of the middle ear is to match relatively low-impedance airborne sounds to the higher-impedance fluid of the inner ear. The term “impedance” in this context describes a medium's resistance to movement. Normally, when sound travels from a low-impedance medium like air to a much higher-impedance medium like water, almost all (more than 99.9%) of the acoustical energy is reflected. The middle ear (see Figure 13.3) overcomes this problem and ensures transmission of the sound energy across the air-fluid boundary by boosting the pressure measured at the tympanic membrane almost 200-fold by the time it reaches the inner ear.

Some sources will refer to this as "amplification" which is correct in some ways (without it, sound would be too "weak" in the inner ear) but doesn't quite explain the whole problem.
Inner hair cells do the actual sensory transduction, converting vibrations into electrical signals when the "hairs" are stretched apart mechanically, causing a fragile "tip link" to pull on a physical channel, opening it and allowing ions to flow through. The cochlea is a frequency-analyzer, vibrating at different frequencies along its length and allowing different hair cells to respond maximally to different frequencies of sound.

As a side note, although you asked about vertebrates, aquatic vertebrates like fish don't have these middle ear bones, their hearing is quite different from the mammalian ears I am most familiar with. I'm not sure at all about hearing mechanisms in aquatic mammals that evolved from terrestrial ancestors, like whales and dolphins, but that might be a good subject of a later question.


How to integrate transcriptomics data with kinetic metabolic models?

I am assuming that in your model, the reactants and products (species) are metabolites and each reaction denotes conversion of one metabolite to another.

From transcriptomics, you will get the relative expression levels of different genes.
When you have two samples from different conditions you can calculate the differential expression.

A model can be as complex as you can make it but we can start with simple assumptions. As you said, enzymes are assumed to be constant with respect to metabolites and are not dynamically changing. I also guess that you are not considering genes other than enzymes to be affecting the metabolic reactions (you might actually want to consider the solute transporters). Also, you are assuming Michaelis-Menten kinetics for all reactions.

In that case your Vmax (i.e. maximum rate of a reaction) would be kcat × E0 where kcat is the turnover number and E0 is the total amount of enzyme.

E0 can be approximated using the transcriptomics data. However, transcriptomics data is relative and not absolute. If you need absolute quantification, you must have at least one reference whose absolute mRNA copy number is known. Another issue is that the ratio of protein and mRNA expression would not be the same for all genes and it is basically the amount of active protein you need to know. So proteomics would be one step closer.

When you are comparing two conditions, you can use the differential expression (fold change values) to adjust the parameters between the two conditions. For e.g. if you know that phosphofructokinase is 2 fold downregulated in diabetes (compared to healthy case) then you can reduce the Vmax of the corresponding reaction by 2 fold in your diabetes model. However, it all would make sense only if the parameters of your "healthy" model are reasonably close to the biological reality.

Moreover, you still need to know kcat. It cannot be obtained from high throughput studies. You may have to either make some guesses or check out papers/databases. Also, your rate is not always Vmax. To estimate the dynamic rate you must know KM too (when the substrate is in excess you can ignore KM). BRENDA may have some information about these constants for different enzymes.

At a very crude level, you can remove the reactions whose corresponding enzymes have zero expression.

These are some articles on integration of transcriptomics data with FBA (not kinetic models):

Blazier and Papin (2012)
Machado and Herrgård (2014)
Guo and Feng (2016)

Machado and Herrgård actually claim that integration of transcriptomics data does not improve their model predictions:

  Also, it is observed that for many conditions, the predictions
  obtained by simple flux balance analysis using growth maximization and
  parsimony criteria are as good or better than those obtained using
  methods that incorporate transcriptomic data.


After fat is burned from one part of the body, is fat moved around the body?

Fat burning is a generalized procedure so there is no such a thing that some part of body loses fat and other part gains it.

Targeted Fat Loss still is a myth.


Ways to measure effectiveness of a gene therapy trial?

If all you cared about was genomic integration, then your best bet would be some kind of sequencing. If you sequence the modified region and the flanking regions you could be sure that the new sequence was present in the genome.

It would probably be more interesting to look at how the new genes affect the cell. For example you could look at differences between protein expression in modified and unmodified cells. For that you could use RNAseq.


How are Raunkiær's plant life forms viewed today?

Oreotrephes, it all depends on the needs. Reproductive schemas don't exclude shape schemas. There has been, however, a shift to cladistics in classification, which means to give scientific names ONLY to monophyletic groups, i.e. groups that include all the descendants of a single ancestor - and only its descendants. But we still use tree/shrub distinction and epiphytes, for instance, but that's to describe the ecology of species, helping identify them, not to classify them on these grounds alone.


Could plasmids and conjugation mechanisms be used against antibiotic-resistant bacteria?

If we assume all of these things could be practically done at least at some point in the future, here are the problems I see with the suggestions, and why they might not work (others may spot additional ones).
1 Translocation of a sabotaging 'agent' via the conjugation apparatus.
This basically already exists, look up the various secretion systems of bacteria. In particular, the Type 6 Secretion System does exactly this (though with a somewhat limited target range).
The first paragraph on wiki summarises:

The type VI secretion system (T6SS) is molecular machine used by a wide range of Gram-negative bacterial species to transport proteins from the interior (cytoplasm or cytosol) of a bacterial cell across the cellular envelope into an adjacent target cell.

The reason this wouldn't work is that bacteria have already evolved to deal with such mechanisms, and one we engineer is unlikely to fare much differently.
You can take it from me (as my PhD concerns exactly this!) that changing what the secretion systems translocate, while possible, is very difficult.
2 Phony conjugation
Antibiotics tend to be small molecules. They bind and dock with enzymes or substrates in order to inhibit some kind of activity typically, e.g. cell wall synthesis in the case of Beta-lactam antibiotics such as penicillin. I'm not sure how you imagine it would "tear a hole in the bacterium" really?
Related to the T6SS, are R-type Pyocins, which are co-opted bacteriophages that sort of do this. It requires no conjugation, and the currently proposed mechanism is that they either deliver a payload of toxins or molecules in to the cell by puncturing the exterior, or they simple create a pore in the membrane causing cellular depolarisation and death. As with phage and antibiotics however, these mechanisms can have resistance evolved against them.

As an additional point, unless you could somehow guarantee that the conjugations were sabotaged or ineffectual in some way, promoting conjugation artificially is almost certainly going to aid the spread of resistance and virulence determinants, actually worsening the situation.

3 A suicide plasmid
It is not trivial to 'confer significant advantages' on a cell. Most plasmids are maintained by amelorating a significant disadvantage that is often supplied artificially, e.g. auxotrophy or antibiotic selection. Given the 'choice' bacteria tend to kick out the plasmids unless they simply cannot afford to live without it. Maintaining the replicon is an expensive process in terms of cellular metabolism and resource utilisation.
'In the wild' the weaponised plasmid would likely not persist long enough to be translocated in to any target of interest in a significant enough proportion to have a real effect. The key is that and of these ideas mentioned cannot simply kill a single target cell, as they will not have an appreciable effect on the population. The bacteria will recombine or straight up remove the plasmid if it's in any way deleterious or even neutral to them, until they've 'corrected' the problem.
Addiction modules and toxin-antitoxin systems are common to see in natural plasmids, as with the other ideas mentioned. Bacteria can recombine out the 'poison' though, and eventually over time lose the plasmids. If the toxin is encoded on the chromosome, it's a little more robust.
4 Bad plasmids
See addiction modules and toxin-antitoxin systems above.
I'm afraid in general I think you're underestimating evolution!


RNA-seq data usually provides a snapshot in time of the transcriptome of that which is being sequenced. Single-cell sequencing is possible, but less common than RNA-seq on a sample (containing many cells).

You are correct that RNA-seq provides one with knowledge of RNA sequences, like AUGGUCAUCAG and so on. However, one will not necessarily have information about all possible RNA sequences from a particular species. Performing RNA-seq on the same cell type of a species at two different time points, or two different cell types at the same time point, may result in different profiles for the RNA sequences you get back. It depends on which parts of the genome are being expressed by the cells in a sample at the time of RNA extraction.

The data one gets back from RNA sequencing depends on the technology and company used. Typically, RNA-seq involves using a reverse transcription step so that the sequence data you get back is actually reported as the cDNA version of your original mRNA transcripts. Usually one gets a (very large) file of sequencing 'reads'. One can either then 'assemble' these directly to form a snapshot of the transcriptome or one can map them to a known reference genome. One of the main benefits of RNA-seq is that we learn not just what the sequences of the RNA molecules are, but also their relative abundances within the sample. Knowledge of this can be particularly useful in testing or developing a large range of biological hypotheses.


Why is muscle force more dependent on cross-sectional area than on fiber length?

Here is a thought experiment that might help. Consider a single muscle fiber as being like a rope. Granted, a rope won't shorten on its own, but if you think of an isometric muscle contraction, then it's closer to what is happening when a single fiber contracts.

Now think about two situations:

You double the length of the rope. Does the total force that the rope can hold get larger, smaller, or stay basically the same?
You halve the length of the rope by doubling it up (so two ropes instead of one). Does the force that the rope can hold get larger, smaller, or stay basically the same.

So lining up more fibers in series is like making a longer and longer rope. It's still basically as strong (or weak) as a single rope. But when you bundle more ropes, increasing the cross-sectional area, the overall force that they can hold increases.

I'm not sure why a thought experiment needs citations, but here you go:

The canonical source for discussion of muscle fiber architecture is Gans C. 1982. Fiber architecture and muscle function. Exerc Sport Sci Rev 10:160–207.


[ For the sake of answering a question that is long unanswered ]

  Can two hammerhead ribozymes simultaneously cleave each other?

Yes, in principle they can.

  two hammerhead ribozymes simultaneously cleave each other when both
  are expressed, but have these ribozymes cleave a target transcript
  when expressed alone.

This may be realized only when ribosomes have higher affinity for each other than for the target. As you said in the comment, inserting few mismatches in the ribozyme-target interaction may work. You may need to notice that since the two ribozymes are complementary to each other but cleave the same target, the target sequences will form a set of two mutually complementary regions. If separated well enough, there may not be much of a problem. From your design strategy I guess that UTRs are the best place to keep the ribozyme target sequence. If you keep both the target sequences in the 3'UTR (lets say), then they may form a hairpin structure, which may interfere in the targeting. So you can insert mismatches that also destabilize the possible hairpin.

  Has it ever been shown in the literature that a hammerhead ribozyme
  was able to cleave the flanking arms of another ribozyme?

Not yet. Self cleaving examples are there but not mutually cleaving ones.


What can cause the bloating in high protein diet of Whey proteins?

The cause of the swelling is lack of lymphatic carriage capability of proteins to the muscles, because of systemic conditions affecting the circulation of proteins through your lymphatic system.
There will be edema extracellularly because of insufficient carriage of proteins through lymphatic system.

My schematic drawing about the fluid movement between these spaces

I started to think why some people do not observe so much swelling.
I discussed with a few and come to conclusion that the main difference between those people who did not have noticeable swelling was that that they did lymphatic system massage by maximising abdominal breathing after taking whey proteins (before training and after training).
I think it sounds sensible to some extent.
Those people also included lymphatic system massage in their recovery after training.
One video here Lymphatic Drainage for Abdomen and Trunk.
So another reason what may cause the swelling is insufficient drainage of lymphatic system.

The swelling does not happen to the same extent in all people.
Some people swell much after one intake of protein drink.
Some people also do not have to do lymphatic massage.

My conjecture: The reason to this is most probably one glue-gene-group.
Those people who have this genome have other systemic diseases that causes the lymphatic drainage have high proportion of proteins already:

for instance, uncontrolled asthma patients, who are circulating lysed DNAs of lymphocytes from small bronchial tree through the lymphatic circulation

Lymphatic circulation is the system which circulates the proteins to the muscles.
After absorption from the digestive tract, lymphatic circulation carries proteins systemically.
However, since there is already a high proportion of proteins, lymphatic circulation cannot take much more proteins to carry.
Our body has to remove toxic wastes before it can build new materials.
Catabolism then conquers anabolism in some situations.


Lack of A/B-antigen equivalent to Rhesus disease

So it turns out it can occur. It's called Hemolytic Disease of the Newborn (ABO), and according to the article (the relevant citations are a book and some journals to which I do not have access), it is very rare, and severe cases are even more rare. Apparently anti-A and anti-B antibodies are typically of the IgM isotype, which cannot cross the placental barrier. However, occasionally IgG is produced, which can cross.

This is what causes the hemolysis in the fetus - if the mother is type O, and the baby is either A or B, the mother is exposed to unknown antigen and produces antibodies. If they happen to class-switch to IgG, they can cross the placenta and, if in large enough quantities, cause the opsonization and lysis of red blood cells.


Why squirrel behaviour varies greatly throughout India?

Given that you're dealing with fairly smart mammals with a short lifespan and limited distance migration, it seems likely that you're dealing with strong local selection effects that are going to be reflected in all three layers:

Learned behaviors from observing other squirrels and their own interactions with humans.
Epigenetic effects tied to things like maternal stress
Differences in the frequency of genetic tendencies towards caution / aggression, etc.

Now, what would the source of those differences be? I don't know if anybody's studied these particular cases, but there's some pretty strong candidate hypotheses for a starting point:

In West Bengal, you're dealing with high-density non-touristy areas (especially Howrah, right on the edge of Kolkata). The squirrels there are likely in constant conflict with humans who do not want to be sharing their food, which will select strongly for aversion to humans.  Humans might well be poisoning them as a means of control too, which could explain the picky eating.
In tourist spots anywhere, the squirrels are probably getting fed well by humans either intentionally or accidentally (e.g., careless children), whcih will select strongly for attraction/aggression toward humans.  I'll bet you'd see this in Victoria Memorial too, for all that it's right next door to Howrah.
In Uttarakhand, which is a much lower density state than West Bengal (189/km^2 vs. 1029/km^2), you're probably seeing much more of the default state of interaction, without a strong selection in either direction.


How are drug metabolism and detection related?

Short answer: Yes.

Diazepine is a ring-structure that forms the basis for the class of drugs called benzodiazepines. This class includes long acting and short acting agents. If you're actually talking about diazepam, it's one of the long acting agents, which means the half-life of the metabolite in your body (and it's detection) is long.

The National Highway Traffic Safety Administration has good reasons to want to collect samples of various drugs non-invasively, and, indeed, they're headed toward saliva for screening. A neat little item called a Drugwipe can pick up traces of diazepam from not only saliva and sweat, but from surfaces people have touched.*

The real kicker, though, is hair, from any part of your body. Drug use(including diazepam) can be  detected in hair for months after (even single) use, and many employers are now going for hair sample testing to screen for drug use.

*Saliva and Sweat Testing With Drugwipe®.


What is this bizarre looking animal we found in the forest? Bug identification

That is the caterpillar of a lobster moth (Stauropus fagi), family Notodotidae. It is mimicking a scorpion to help protect it from predation. An amazing insect.


Why isn't phosphorus or nitrogen a limiting nutrient for animals?

Phosphorus

Your suggestion that if we are meeting our calorific requirement we will be getting enough is true for phosphorus.
Most foods contain lots of phosphorus. The maximum dietary requirement occurs during adolescent growth, estimated at 1250 mg per day. Assuming a calorie intake of 2500 kcal we can calculate a 2500 kcal equivalent phosphorus content for various foods:

skimmed milk contains 7,400 mg phosphorus per 2500 kcal

roasted chicken breast contains 7,500 mg phosphorus per 2500 kcal

cooked white rice contains 3840 mg per 2500 kcal

(Calculations are based upon values obtained via this site.)

Nitrogen

Our requirement for nitrogen is met by our protein intake: inadequate protein intake manifests as kwashiorkor which is essentially due to a dietary deficiency of essential amino acids. In other words, the only way to achieve a nitrogen-deficient diet is to not eat protein, and this would not be alleviated by any inorganic source of nitrogen, even if we could consume enough of such a N source.


Why is the "worm" body shape so prevalent in Eumetazoa?

Is it just the body plan of the ancestral bilaterian and therefore remained prevalent due to absence of selective pressure against it?

Pretty much.

You can see some animals which precede the emergence of this plan, like sponges. They apparently do alright, so there's nothing precluding different body plans. However sponges also have a fairly limited niche, and perhaps there's a good reason. Similar things can be said for other non-bilaterians like jellyfish.

One could speculate that the "tall-donut" shape is the key innovation. When food moves in only one direction, it is much easier for the digestive tract to specialize and digest food much more efficiently in stages. Animals, after all, are things that survive by eating things and digesting them - the faster they can digest, the faster they can eat, the better they can survive.

Animals which have no separate anus seem to have more trouble eating things and digesting them: It's slower, and they can't eat as varied a diet.

A worm, being essentially a long tube, is a simple way of accomplishing accomplishing the one-way GI tract. If you think in an evo-devo sense, it also doesn't take a lot to progress from a "basket" to a tube (the two layers after gastrulation just have to meet, fuse, and form a second hole). If you consider the so-called higher animals, like humans, cats and dogs "worms", then we can stop there. Otherwise, we can remark that the "worm" shape also allows easy movement in water and on soil by wriggling.

Past the "pure worm" you can see a large variety of body plans, such as among arthropods, but they're really just worms with a few specialized segments, including, say, humans. This does have a fundamental reason: During early development, patterning of the body (deciding which organ or limb will grow where) relies on Hox genes, which are typically top-level transcription factors that determine a segment's identity. So the "worm" also happens to be a nice developmental "base" from which more complicated embryos can develop.

  is it a neutral adaptation? Or is it actually a positive one?

This is very hard to answer:

There are necessarily many confounds, and we cannot easily find two animals which are otherwise the same, but one is a worm and the other is not. We cannot artificially generate such animals yet either.
The obvious way to infer fitness is to look at whether the trait came to dominate the population. But with since body plan establishment is something that did not evolve independently many times, it is hard to say whether it dominated due to a genuine fitness advantage or purely out of being fixed. Perhaps there are other, yet more efficient body plans, but they have not yet arisen due to random chance.


Do mutated c-sis oncogenes only affect cell growth?

Cancer is not a disease like the flu or E. bola, where there is a single quick and easy cause for the disease which you can locate and describe in a single sentence.  Cancer consists of malignant cell growth, it is true, but why are the cells growing out of control?
The fact is that there is not one single cause.  At some point along the way, some cell experience a mutation to some gene which resulted in a slightly higher rate of proliferation than normal.  However, this in and of itself is not even enough to produce a tumour.  It simply gives the cells a higher number of daughter cells, and consequently, a higher risk of having more mutations.
At some point, one of those daughter cells acquires a mutation which results in higher levels yet of proliferation, or a mutation which encourages angiogenesis, or (in the case of epithelial cells, for instance) a mutation which allows the cell to escape typical anoikis pathways and perhaps perforate its basement membrane without dying.
Even the process of metastasis requires multiple mutations to happen, and yet if a tumour does not metastasize, it is typically regarded as benign.  The point is, cancer is not caused by a single mutation to an oncogene or otherwise.  It is caused by an accumulation of mutations which permit the cells to proliferate much faster than normal, to recruit the body's resources, and to live in tissues all around the body.
In the case of the particular gene that you mentioned, the exact role of the c-sis oncogene in cancer prevention is still unclear; in fact, according to the OMIM page,

The protein product of the c-sis gene has not been identified.

...though the gene is very similar to platelet derived growth factor genes, some of which have been identified as mitogenic factors.  Theoretically, therefore, it is possible that a mutation to the c-sis results in excessive mitogenic stimulation, resulting in an increase in cell division and proliferation.  But that last sentence is speculation, not hard science.
TL; DR:
We don't know, but it's possible c-sis encourages faster cell division.

Sources:

Platelet-derived growth factor, beta polypeptide; PDGFB on OMIM.org
Josephs SF, Guo C, Ratner L, Wong-Staal F. 1984. Human-proto-oncogene nucleotide sequences corresponding to the transforming region of simian sarcoma virus. Science 223(4635): 487-491.


Why do neurones use chemical signalling at synaptic junctions?

This is the coolest part. Those synapses are the reason the brain is so complex! Basically you've got the first part right, the neurones are quicker and they transmit messages from one end to the other. The other thing you have to do is analyse and calculate. Signals from multiple neurones feed into a single neurone using a chemical synapse. Similarly the converse is true, a single neurone can feed multiple synapses. So when we for example walk, receptors monitoring our balance can feed this to our conscious and unconscious mind, but I'm grossly simplifying this. What our brain does is take hundreds and thousands of ports of information, with where the chemical synapse is and the type of synapse and the receptors and a million other things just slightly changing the information until it's perfect and then send that information a million ways however it likes.

The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude, however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc. Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.

Does that make sense?


Does THC excretion increase if urine volume increases?

This question asks about the urinary excretion of THC. Before answering the question I think you're getting at, I'll first note that cannabinoids (of which THC is one) are primarily metabolized by hepatic cytochromes rather than being excreted directly. This article is a classical pharmacokinetic paper on the topic if you’re able to access it; this one is a more recent general review accessible on Pubmed Central.

Cannabinoid metabolites are excreted both renally (via kidneys) and in the feces, so I’ll understand your question to refer to the renally excreted portion. When considering renal excretion of any substance we think in terms of glomerular filtration rate, which refers to the volume of blood filtered through the glomerular capillaries per unit time, often estimated as creatinine clearance. The question then boils down to:

  Does excess hydration increase GFR?

And the basic answer is: no. The  kidneys control both volume and osmolality more distally, i.e. after the event of glomerular filtration.1

In the scenario you posit – drinking a lot of dilute fluid – osmoreceptors in the hypothalamus will sense the decreased plasma osmolality and suppress ADH (antidiuretic hormone, a.k.a. arginine vasopressin), the hormone that acts on the distal nephron to control water reabsorption. If ADH is completely suppressed, the kidneys can produce up to 25 L/day of urine with an osmolality as low as 60 mOsm/kg.2,3 This huge volume of urine, however, reflects water homeostasis achieved at the distal tubule rather than increased glomerular filtration. It does not correlate with increased excretion of THC metabolites or anything else at the level of the glomerulus.

Notes and References

1. If this makes no sense to you, you may want to check out this basic introduction to renal physiology that is available online. The referenced textbook in #3 below is more comprehensive but requires a library or purchase for access.

2. "Normal" urine osm ~300-800 mOsm/kg; plasma Osm ~280-290 mOsm/kg.

3. Christopher Lote. (2012). Principles of Renal Physiology. Springer New York.

P.S. If the question you really wanted to ask was, "Will drinking lots of water make my tox screen negative faster?".... I'm not answering that question. For reasons largely unrelated to the discussion here (but see references in paragraph #1), I suggest assuming that THC metabolites will be forever detectable via tox screen. ;-)


Can any one explain me the structural difference between Proteins and Peptides?

In terms of structure: both are composed of amino acids.

A peptide is when at least two amino acid are linked together.
A protein is composed of multiple amino acids and have a secondary, tertiary and even quaternary structure.

In terms of function: larger molecules have more complex functions.

Peptides can act as a intracellular or extracellular ligands which will activate a signal.

Proteins have a large array of functions (enzymatic, structural, receptors etc)

This article explains in more details the differences in proteins structure and functions:https://en.wikibooks.org/wiki/Structural_Biochemistry/Proteins


Mechanism of Tear Gas (chloropicrin/Trichloro methane)

The general belief is that these agents are irritants which do not have a very specific effect.  That is to say that there is no specific cell or biological function that they set off, but that they irritate the cells, so the cells respond by putting up general defenses to insulate themselves from the noxious chemicals.

Mucous and tears wash away the compounds.  I'm sure there are all sorts of things going on, but its hard to be more specific.  For instance, onions have many sulfhydryl (-SH) compounds,  many many of them.  In particular propanethial s-oxide causes the tears we get when we cut an onion. This compound is very reactive and reacts with all sorts of proteins and disrupts the membrane, etc.  Its perhaps an example of a specific irritant that is so reactive that it creates tears.

An example of a specific reaction would perhaps be capsaicin.  There is a specific protein that is a heat receptor and the chemical capsaicin activates it, causing the feeling of heat/warmth.

Tear gas and mustard gas appear to fall into the former category, which are chemicals so reactive that they just tear into the cell, damaging all sorts of things in there.


Mathematical relationship between membrane conductance and conduction velocity?

The conduction velocity is inversely proportional to the membrane time constant $\tau_m$ and proportional to the length constant $\lambda$. Membrane time constant is proportional to membrane resistance (inverse of membrane conductance), and the length constant is proportional to the square root of membrane resistance.