text:
Why do you get prion diseases from eating animal brains but not other parts of the animal?
Eating animal brains is considered a delicacy in parts of China. We know that eating animal brains can lead to prion related diseases.
Prions are misfolded proteins that are potentially infectious. But the whole body of an animal is full of proteins. What makes the brain special? (or specially infectious?)
My question is: Why do you get prion diseases from eating animal brains but not other parts of the animal?

Because the proteins that are susceptible to what we characterize as prion disease is mostly specific to the brain / nervous system. Research is still being conducted regarding why these proteins and not others.

Thanks - could you expand that into an answer?

The notion that you get prion diseases like BSE only by consumption of brain is not correct. Any part of the infected animal that contains nervous system tissue or lymphatic tissue can be infectious, although I guess this is dose-related.
Quote from OIE, "BSE. General disease information sheet" ([1]):

The risk linked with consumption is addressed by the requirement for
  routine removal of all visible nervous and lymphatic tissue (Specified
  Risk Materials (SRMs)) from carcasses during the processing of
  cattle as well as the removal of any suspect animals from the human
  food chain.
Appropriate handling of nervous and lymphatic tissue tissues from
  BSE-suspect animals in abattoirs and laboratories is indicated to
  avoid accidental exposure (ocular or oronasal). Milk and milk products
  are considered safe.

[1] http://www.oie.int/fileadmin/Home/eng/Media_Center/docs/pdf/Disease_cards/BSE-EN.pdf
The OIE is the animal equivalent of the WHO.


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What is the direction of the processing of light by the (human) retina and how does it happen?
Quoting Textbook of Medical Physiology by Guyton and Hall, 2016, page 647,

...the functional components of the retina, which are arranged in layers from the outside to the inside as follows:
(1) pigmented layer, (2) layer of rods and cones projecting to the pigment, (3) outer nuclear layer containing the cell bodies of
   the rods and cones, (4) outer plexiform layer, (5) inner nuclear layer, (6) inner plexiform layer, (7) ganglionic layer, (8) layer of optic nerve fibers, and (9) inner limiting membrane.
After light passes through the lens system of the eye and then through the vitreous humor, it enters the retina from the inside of the eye (see Figure 51-1); that is, it passes first through the ganglion cells and then through the plexiform and nuclear layers before it finally reaches the layer of rods and cones located all the way on the outer edge of the retina. This distance is a thickness of several hundred micrometers; visual acuity is decreased by this passage through such nonhomogeneous tissue. However, in the central foveal region of the retina, as discussed subsequently, the inside layers are pulled aside to decrease this loss of acuity.

I have attached Figure 51-1 for people who would like to see it.
My questions are: How does light travel to the inner parts of the retina first even when there are so many impeding layers preceding it? Why does it not stimulate the photoreceptors first? What is the pathway of the light after it travels to the the innermost retinal layer? Are the photoreceptors the first to be stimulated by the light?

As can be understood, I am quite confused, so if the framing of any question is reflective of erroneous understanding, kindly let me know. All help appreciated.

Short answer
Photoreceptors are the only cells in the retina that directly detect light; they can detect light through the other layers because those layers are so thin and effectively transparent: light passes right through to the photoreceptors.
Longer answer
The retina is fairly thin, and the bipolar/RGC layers don't contain much pigment. Have you ever looked at a thin slice of tissue under a microscope? You can do this and focus to different layers because single layers of cells are fairly translucent (remember they contain a lot of water): most light passes right through them. Some cells, such as red blood cells or photosynthetic plant cells, are harder to see through, but that's only because they are full of pigments.
The reason the photoreceptors respond to light in a way that can be detected biologically is that they contain special photosensitive pigments. In rods, this pigment is called rhodopsin and it is composed of a protein and a molecule of retinal. Most other cells in the retina don't have any such photoreceptors (there is a special class of retinal ganglion cells that is an exception, see for example here - these cells have a pigment melanopsin and contribute to light detection for circadian rhythms rather than vision).
Other cells in the retina respond to light only because they are sensitive to neurotransmitters released by photoreceptor cells and other retinal cells.
As far as why this is the arrangement, with photoreceptors in the back, it's really just a fluke of evolution and evidence that evolution and not design is the best explanation for diversity in biology. Eyes have evolved more than once in animals, however, and cephalopods like squid do not have their retinas arranged this way; in squid the photoreceptors are the most superficial layer.
Because the retina is so thin, this arrangement doesn't provide a large enough disadvantage to be selected against given the complexity in changing the organization. One exception to the thinness, however, is in the blind spot. The blind spot exists because all of the axons from the retinal ganglion cells have to exit the retina someplace. They exit in a big bundle, and there can't be any photoreceptors where that bundle is, so there is a spot where you cannot see. However, the position of the spot is not in the center of your vision, and that part of the visual field is usually covered by the other eye

The Müller cells act as light guides that differentiate among wavelengths of light and make sure that both rods and cones receive their optimum wavelengths without much loss. Since Müller cells span the whole thickness of the retina from the retinal ganglion cells (RGCs) to the the beginning of the photoreceptors, they act as optical fibres allowing the light to pass unhindered through the rest of the retina to the photoreceptors.
Refer to this publication for more details - Labin, A. M., Safuri, S. K., Ribak, E. N., & Perlman, I. (2014). Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision. Nature communications, 5(1), 1-9.

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Why are C4 plants mainly tropical plants?
Why is it that most C4 plants are tropical plants?
As far as I am aware the C4 cycle does not prevent water loss; so having it exist in tropical areas does not serve these plants any good other than preventing photo-respiration. Hence I do not understand why it is solely found in tropical plants and not plants from other areas as photo-respiration is a problem not limited to tropical areas
Reference:
http://lifeofplant.blogspot.sg/2011/10/c4-and-cam-photosynthesis.html?m=1

See c4 cycle occurs in bundle sheath cells which are impermeable to gases. And rubisco affinity for O2 is increased with temp. Tropical regions have high temperatures
So therefore co2 is given to rubisco in these gas impermeable cells in the form of maleic acid in order to reduce photorespiration

This is not my field, so the following is based solely on a brief reading of Internet sources.
The Wikipedia entry on C4 carbon fixation states:

When grown in the same environment, at 30°C, C3 grasses lose approximately 833 molecules of water per CO2 molecule that is fixed, whereas C4 grasses lose only 277.

However it does not explain why this is so.
In contrast, the section in Berg et al. focuses on the energy losses caused by photorespiration and makes the following initial point:

…the oxygenase activity of rubisco increases more rapidly with temperature than does its carboxylase activity. How then do plants, such as sugar cane, that grow in hot climates prevent very high rates of wasteful photorespiration?

The answer to this (didactic) question is the C4 pathway (as described in full in that text), but the answer to the question posted here  is that “tropical plants employ the C4 pathway because of this increased wastage of energy through photorespiration at the higher temperatures in which they live.”

Thank you. This response pretty much sums up my question

Now I think of it,  maybe the increased rate of carbon dioxide uptake due to increased light intensity in tropical areas also play a part

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text:
Can plants yield two more molecules of ATP from glycolysis?
Since 2 ATP are used to convert glucose to glyceraldehyde 3-phosphate in glycolysis, can plants bypass this step of ATP investment since they produce glyceraldehyde 3-phosphate directly from the Calvin cycle?
If yes,  what would be the final yield of ATP.
If not,  why not?

Plants produce ATP in the ‘light reaction’ of photosynthesis.
The purpose of the Calvin cycle (the ‘dark reactions’) is to produce glucose, for which it uses some of this ATP to provide the energy to make carbon–carbon bonds.
Glycolyis in plants functions to produce ATP from reserve carbohydrate etc. when ATP is not available from photosynthesis, or in tissues, that do not have sufficient ATP from photosynthesis.

So this question makes no physiological sense†, as it is based on a misunderstanding of the purposes of the differ metabolic reactions in plants. The answer is not that it cannot happen, but that it would not happen — the regulatory mechanisms that prevent futile cycling of pathways would come into operation.
† It is analogous to saying that the liver can perform gluconeogenesis, and so can produce glyceraldehyde 3-phosphate. So can the liver bypass this step...

Isn't the dark reaction of photosynthesis the Calvin cycle?  From my understanding, the Calvin cycle uses most if not all the atp produced from the light dependent reaction to fix phosphate and reduction of PGA to G3P,  which is the final product of the Calvin cycle

@user35897 — whoops! Too busy thinking about the structure to get the detail right. Thanks for pointing this out.


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Is this answer about the limiting factor correct?

The graph shows the result of adding both phosphorus and nitrogen to different algae populations. I have a hard time figuring out why the correct answer is C, I thought that  groups 4 and 5 would have nitrogen as a limiting factor because adding it increases their growth. Help me please.

Welcome to Biology.SE. Please avoid posting text as images. Images are not searcheable and the format can be unpleasant. While it is easy to read in your case, nobody needs to know that you have 48% of battery left! Also, it may give a feeling that you're not putting much effort in the posting a nice question and this is probably why you got a down vote (the down vote was not from me). Also, "Help me please" makes it feel like your begging for help which is never really welcome on SE sites. You might want to edit all that.

I agree with you, and think that there is a mistake in the "Correct answer". The interpretation in the "Explanation" seems to be correct though ("Algae at locations 4 and 5 exhibited growth in response to fertilization with nitrogen."), so I think that there is a typo/mistake in the "correct answer". The answer should be D.
Normally within ecology (and especially in reference to nutrients, such as  nitrogen and phosphorus), limiting factor refers to the substance/nutrient that is in short supply within a particular environment, and is therefore limiting the potential growth of organisms. For examples, see any ecological textbook or Blumenthal et al (2001) (as an article example, picked at random). The concept of limiting factors is related to Liebig's_law, which states that growth of organisms is determined by the scarcest resource, and not the total level of resources.
When performing a couple of searches now, I see some instances though where the term limiting factor is used on the opposite way, in reference to toxic substances. One example of this is Imadi et al (2016), where monomeric aluminum reduces root growth due to aluminum toxicity. This is not the most common use of the term though.

You might want to mention Liebig's Law of the Minimum here (https://en.wikipedia.org/wiki/Liebig%27s_law_of_the_minimum).

@arboviral Good call - now added.


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How do memory cells(B-cells) encounter pathogens?
From what I understand, once the infection is handled, some of the B cells capable of producing the correct antigens are stored for the long-term in the lymph nodes.
They will start multiplying again upon encountering the pathogen again.
What I don't understand is how can these cells, that should be in relatively small numbers, can effectively encounter the pathogen ? Do all pathogens travel to the lymph nodes? Do the memory B cells travel out and encounter pathogens?

Great Question.
Location:
Memory B cells are highly abundant in the human spleen, and they make up 45% of the total B cell population in this organ. There is evidence to indicate that human memory B cells might mostly reside in the spleen, and some memory B cells recirculate in the blood [1].
Activation:
Memory B cells circulate throughout the body in a quiescent state until specific antigen is re-encountered and triggers a potent secondary immune response [2].T cell help is a strict requirement for the reactivation of memory B cells that are specific for monomeric protein antigens [3].
Sources:

Hauser, Anja E., and Uta E. Höpken. "B cell localization and migration in health and disease." Molecular Biology of B Cells (Second Edition). 2015. 187-214.
Firestein, Gary S., et al. Kelley's Textbook of Rheumatology E-Book. Elsevier Health Sciences, 2012.
Janeway, Charles A., et al. "Immunobiology: the immune system in health and disease." (2005).


text:
Why are the posterior and anterior inferior temporal cortex called area TEO and area TE respectively?
I don't understand why you would call them that. How did these names originate/where did these names come from?

Was able to add some more information on the "TE" terminology after you accepted the answer, just a FYI if you are interested.

Thanks I see now, it's a lot clearer now that I know it has no meaning.

These are very old names for primate cortical areas, originally from the anatomist Constantin von Economo and also used by von Bonin and Bailey (1947) (where the TEO region name seems to originate).
Like Brodmann areas these regions were defined by cytoarchitecture well before most functions were determined.
I discovered another work that I can access from 1935, Rose (1935) that is quite helpful for the TE terminology. From Rose it is clear that von Economo labeled areas in the temporal lobe TA, TB, TC, etc. up to TH. So they seem to be simply "temporal"+letters of the alphabet. Rose refers to "Area temporalis propria" as area TE, comprised of Brodmann areas 21 and 20; Rose calls Brodmann 21 "TE1" and Brodmann 20 "TE2" which are separated based on the size of layer 3 pyramidal cells.
As far as the TEO terminology, Boussaoud et al (1991) write:

In their study of  the cytoarchitecture of  macaque cortex, von Bonin and Bailey ('47) labeled this region with a question mark on their section drawings but showed a photomicrograph through the region that they labeled  “TEO.”

This is the best evidence I can find that the TEO name a) originated with von Bonin and Bailey, and b) that the further origin or meaning of the name is unclear; it's just a label on a photomicrograph that wasn't even used in the drawings by those authors who instead used a ?. I suspect further authors preferred the TEO terminology rather than confusingly referring to "area ?" and yet they felt like giving credit to von Bonin and Bailey for their work on the macaque cortex.
It's unclear to me whether TEO is meant to be an acronym; "temporal" is part of the name, but whether O stands for a word (perhaps occipital, as it is toward the occipital lobe?) or if it is actually the number 0, or a non-English word (possibly German or Latin?). However, when more modern neuroscientists refer to area TE and area TEO, they are simply intending to refer to "area TE and area TEO in the von Economo/von Bonin & Bailey terminology."
Other terminology, such as referring to posterior or anterior inferior temporal cortex, may seem more descriptive but there isn't anything inherently wrong with referring to the older names as long as people know what area you refer to. TE and TEO are clear, short names that have been used for decades, whereas inventing a new acronym like PIT or AIT would be unfamiliar at this point.
References
Boussaoud, D., Desimone, R., & Ungerleider, L. G. (1991). Visual topography of area TEO in the macaque. Journal of Comparative Neurology, 306(4), 554-575.
Rose, M. (1935). Cytoarchitektonik und Myeloarchitektonik der Großhirnrinde. Handbuch der Neurologie, 1, 588-778.
von Bonin, G., & Bailey, P. (1947). The neocortex of Macaca mulatta.(Illinois Monogr. med. Sci., 5, No. 4.).
von Economo, C. F., & Koskinas, G. N. (1925). Die cytoarchitektonik der hirnrinde des erwachsenen menschen. J. Springer.


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V(D)J recombination on homologous chromosome
V(D)J recombination is known to recombine IG locus of a B cell. Is anything known about how the recombinations on two homologous chromosomes are connected? For example, are the selected V(D)J couples(triples) the same on both homologues?

I did not understand the selected V(D)J couples(triples) the same on both homologues part, but if you are asking about it's mechanism, then Wikipedia, this paper and this article are places to start.

There are two alleles (variants of the same genetic region) for the Ig and TCR loci, one on each chromosome. The cell will try first with one allele to obtain a productive arrangement, and then with the other. If the cell fails on both alleles, the cell undergoes apoptosis. If at least one allele has a productive arrangement, the cells move on to selection.
Groups are still uncertain, however, how the cell chooses which allele to initiate recombination on, and ruled out parental imprinting as a culprit last year (1).
To be certain, the regions are the same, though not the same sequence. However, mechanisms during recombination ensure that recombination events among individual cells result in robust junctional diversity and a suitably diverse repertoire of immature antibody or TCR sequences (example).
In activated B cells, however, class switching and somatic hypermutation can result in gross changes to the Ig locus not seen in immature or pro-B cells.

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text:
Trying to understand reduction of color dimension in colorblind case
I understand that dichromats have one of their cone missing/not functioning. And as for Monochromats, 2 or all of their 3 cones are missing/not functioning. And I read from Wikipedia - Color Blindness :

Dichromacy occurs when one of the cone pigments is missing and color is reduced to two dimensions.

and

Monochromacy occurs when two or all three of the cone pigments are missing and color and lightness vision is reduced to one dimension.

Since in the description they relate the cones with Red, Blue, Green (RGB) a lot, eventhough I'm fully aware that relation of cones and RGB is most likely for historical reason . I'd like to assume in this reduction from 3-dimensional into less dimensional colorspace dimension written in Wikipedia based on RGB colorspace.
This is original RGB colorspace in 3-Dimension

Question 1 : How exactly reduction from 3-dimensional to 2-dimensional or even 1-dimensional in colorblind case happen ? For example in Protanopia, would they lose the Red axis ? So only Blue and Green axis left ? (Any reference will be appreciated).
I also read this question If people with colorblindness lack one type of cone cells, shouldn't they be unable to recognize one particular color?. And it's written that Dichromats can match any color they see with some mixture of just two primary colors. Cones do not literally interpret colors. The three cones work together to encode a signal.
Question 2 : If cones don't really interpret any color in human color vision system. Is it wise that losing cone means reduce from 3-dimensional color into 2-dimensional by completely erase the corresponding color axis to the cone ?
[UPDATE]
For Question 1 :
Taken from the book Visual Transduction and Non-Visual Light Perception (p308),
Univariance, Monochromacy, Dichromacy, and Trichromacy

If only one photoreceptor type operates, vision is monochromatic or reduced to a single dimension

If only two cone photoreceptors operate, vision is dichromatic or reduced to two dimensions

and

Most observers
  with normal color vision have three classes of cone photoreceptor and are therefore trichromatic.

So, I'm sure in my Question 1, they really refer to Young–Helmholtz Trichromatic theory. A theory when human color vision possess 3 types of cones thus they have three dimensions of color vision.
However, I still need some opinion related to Question 2. Any comments will be appreciated.

Let's start with a quick overview of the different types of dichromats in man:

Protanopes have no functional red cones. Red appears as black. Certain shades of orange, yellow, and green all appear as yellow.
Deuteranopes have no functional green cones. They tend to see reds as brownish-yellow and greens as beige.
Tritanopes have blue-yellow color blindness and lack blue cone cells. Blue appears green and yellow appears violet or light grey.

Now color vision can be modeled with the Hering model, where there are two opponent channels, namely red-green and blue-yellow. These opponent channels determine color vision. Because of these two limbs, color space is often represented as triangles, rather than cubes as in your post. Fig. 1 shows the color space in trichromats. In Fig. 2 the same is shown, alongside the three types of dichromatic deficiencies.

Fig. 1. Color space in trichromats. source: Lighting Analysis

Fig. 2. Triangles in trichromatic and dichromatic vision. source: Chartlr.

Thanks! I'm aware of this triangle 2D representation. I believe this is adaptation of colorblindness taken from CIE 1931 color space. I believe color vision can also be represented by Helmholtz trichromatic theory which has 3 primary color, exactly like RGB. What I want to confirm is the reduction of 3-dimensional space into 2 (or 1) dimensional space in colorblind. I'm open to any possibility that the RGB 3D diagram above is wrong. I'm not sure is it RGB or which other 'color dimension' they meant, since it's not exactly written there.

It depends on the definition of dimension, but yes, you could say you loose one.


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What are the principles of stem cell engineering?
Suppose you want to convert the skin cell into a pluripotent stem cell. I know there are a few genes that were identified for this purpose (a recent Nobel Prize). But apart from finding such genes, it also seems to involve maintaining the right environment, such that some critical receptor doesn't get triggered and alter the entire expression. It also seem to involve ensuring gene expression stability after the change has occurred. Could someone add to this? What are the broad paradigm ideas in stem cell engineering?

The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation

Current reprogramming technology, pioneered by Takahashi and Yamanaka
  1, was built on several seminal advances in the field of
  developmental biology. First, nuclear transfer experiments
  demonstrated that a somatic cell nucleus could be epigenetically reset
  to an early developmental state [2]. Second, cell culture conditions
  were developed that allowed for the isolation and culture of
  pluripotent cells, termed embryonic stem (ES) cells, from the inner
  cell mass of the human and mouse blastocyst [3,4]. Finally, study of
  these cells and of early embryonic development led to the
  identification of factors that were ultimately able to reprogram mouse
  embryonic fibroblasts (MEFs) to the iPS cell state when ectopically
  expressed, albeit at low frequency.
Reprogramming of somatic cells is a multistep process that culminates
  in the expression of pluripotency genes such as Nanog. Although
  morphological changes occur at early and intermediate stages of
  reprogramming, pluripotency gene expression is only induced during the
  late stage and indicates faithful reprogramming.
The core reprogramming cocktail, consisting of the transcription
  factors Oct4, Sox2 and Klf4 can be augmented by the
  addition of factors that enhance the efficiency of iPS cell
  generation

Its a multistep process in which much research is still needed,

The frequency with which somatic cells convert to iPS cells is
  typically below 1%. Therefore, much effort has gone into improving
  reprogramming.

specially to increase efficiency of iPS cell generation

The ability of cells to pass through the cell cycle has also been
  shown to be an important determinant of reprogramming efficiency.
  Knockdown or gene deletion of p53, p21 or proteins expressed from the
  Ink4/Arf locus allows cells undergoing reprogramming to avoid the
  activation of cell cycle checkpoints and cellular senescence, leading
  to greater iPS cell formation [21],24-27].

Gene expression changes during reprogramming

First and foremost, stem cell therapies are cell therapies that, in the US, are regulated by such agencies as FACT (foundation for the accreditation cell therapies), CAP (college of American pathologists) and the FDA (food & drug administration). Manufacturing must be compliant under GTP (good tissue practice) and GMP (good manufacturing practice) standards. Even the labeling of products is moving to the harmonized system ISBT128, managed by ICCBBA (International Council for Commonality in Blood Banking Automation). The take-home point here is that everything is tightly regulated, and produced under rigorous standards of safety, conformity and documentation. Not everyone is FACT accredited, but the benefits are becoming of increasing importance, especially to insurance providers (ref). The therapies are costly to manufacture, to be certain. The two FDA-approved CAR-T immunotherapies YESCARTA and Kymriah run around $500,000.
So you have a number of types of stem cell therapy. Bone marrow transplantation is considered a stem cell therapy, and then you have therapies that involve human embryonic stem cells (hESC) and human induced pluripotent stem cells (hiPSC).
In terms of hiPSC, groups have been successful both in culturing with transcription factors such as Oct4, Sox2, Klf2 and so forth, and in using sendai virus to deliver these transcription factors directly within the cell (thermofisher's Cytotune®-iPS Sendai Reprogramming Kit, youtube video).
We can also see, however, that stem cells can be obtained elsewhere and don't necessarily need to be induced. You can source hESC from embryos and cord blood, and hematopoietic stem cells (HSC) can be mobilized from the marrow with a drug cocktail (like plerixafor and GM-CSF) and harvested with apheresis.
So just for a real-world example of what you're thinking: Papers on the production of glucose sensitive insulin-secreting ß cells from hESC using carefully controlled culture conditions have been published (ref), and companies have taken advantage of this technology. Subdural implants using this system are in clinical trials right now. They produce the ß cells from hESC by controlling the cultures:

Source: 1,2
The transcription factors along the bottom of the figure, which I've pasted together from two sources, shows what transcription factors should be active at that stage. The identity of the final product can be surmised from a combination of what transcription factors should and should not be active. It's also important to realize that there will be off-target cells, but that the process should be validated to ensure on-target cells stay within an acceptable range as defined during pre-clinical development.
Manufacturers would also need to test for the purity, sterility, endotoxin and potency of their cells. Potency assays have become something of a prerogative for the FDA, since anyone can produce a cell, but how can they say it's effective or does what it's marketed to do? An example potency assay might be two cultures, one with glucose and one without, does one secrete more insulin than the other? You'd pick this assay because the proposed mechanism of action for ß cells is they respond to glucose, and secrete insulin.
For sterility, they sell some good kits like BacT alert aerobic and anaerobic test bottles, mycoplasma testing kits, you can also do culture plates and gram stain. Products that don't exhibit 100% sterility can't be infused, and so it generally follows that exceptional releases can be made for many other issues by a physician, but contamination will stop a cell therapy product dead in its tracks.
You're also right in that cell therapies which involve a gene modification step need to look at such things as transduction efficiency, live virus titer, expression of molecules related to the transduction and so forth. The sendovirus kit referenced above is a fair pick because as they demonstrate, after several passages the non-integrating virus titer is negligible. For human administration, in the CAR-T space, the FDA has required that studies where CAR-T have been infused follow patients for 15 years after treatment to study the effect of infusing virally-transduced vectors. I don't think that there's a clear answer as to whether the virus is an issue. You're also right, however, that it's necessary to test the stability of the transduced gene(s) , especially through passaging, holding and cryopreservation. All of this is nicely outlined here.


text:
Do all transmembrane proteins contain channels or tunnels?
In my book, there is written something like this.
The integral proteins pass into the lipid bilayer to different depths and establish hydrophobic bonds with lipid molecules. Some of the integral proteins run throughout the lipid bilayer. They are called tunnel proteins OR transmembrane proteins.
My question is do all the transmembrane proteins have to have channel or tunnel for transport of materials?

https://www.ncbi.nlm.nih.gov/books/NBK26878/ Might help dude. Anyway it is quite easy to find something about it and if you dont do a little searching about it nobody will have attempt to answer it.

You know idk what you mean by the material stuff but i think the right answer is just no !

The substances .

What could it be other than this?

I was asking if all the transmembrane proteins have to be tunnel proteins as it was written in my book . And I think that's not right .

When you search Pubmed for "transmembrane proteins" you get 78328 hits.  "Tunnel protein" gets 2312.

@swbarnes2 that doesn't mean that they aren't interchangeable terms. For example, polytopic proteins and multi-pass proteins might return different numbers but mean the same thing. There is a lot of redundant jargon in this field!

It doesn't mean that they are.  When I checked a few of the abstracts in the pubmed search, they were mostly about the "exit tunnel" of the bacterial ribosome.  None were about transmembrane proteins.

@swbarnes2 I must say, I haven't read anything that suggests tunnel proteins and transmembrane proteins are interchangeable terms.

Transmembrane proteins don't all have tunnels.

Do all the transmembrane proteins have to have channel or tunnel for transport of materials?

Calling transmembrane proteins tunnel proteins is very misleading. There are a wide range of functions carried out by transmembrane proteins. I'd say the most famous example that don't include a tunnel are the GPCRs that have 7 transmembrane segments. These are used for passing information across a membrane by acting as a receptor to a molecule on one side causing a conformational change which causes an action on the other side of the membrane.
How many transmembrane proteins do have tunnels?
Here is a link to all the GO annotation held by UniProt on transmembrane proteins. There are 10s of millions of results including, but certainly not limited to tunnels and channels.
In the human proteome, there are 831 transmembrane proteins tagged with G-PCR (7TM proteins without a tunnel).
The "Transport" keyword, which probably has some sort of tunnel, is present in 1106 transmembrane proteins.
In total there are around 5200 human transmembrane proteins in the human proteome.


text:
Log-tranformation and GWAS
Before doing any GWAS (genome-wide association study) it is necessary to check for the normality of the phenotypic distribution. If the phenotype is normally distributed only once it is log-transformed, what phenotypic data do I have to use while doing the GWAS? The non-transformed one or the log-transformed?

How is the significance computed? If the computation assumes that the response variable is normally distributed (which is likely the case), then you need it to be normally distributed (hence log-transformed in your case).

Related https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869493/

Yes, use the log-transformed phenotype. if you want to use a normally distributed error term, and this will only occur if the phenotype is log-transformed, then you must log-transform the phenotype.
The phenotype should be distributed in the same manner as the error term in your regression model of the GWAS.
$pheno = \beta_1 X_D + \beta_2 X_A +\epsilon$
$\epsilon = \mathcal{N}(x | \mu,\sigma)$
Following the central limit theorem, most of phenotypes are normally distributed.  However, there are cases where a Bernoulli distribution is correct, and a logistic style regression should be used.


text:
What is the response vector in the fMRI GLM model?
In fMRI, univariate analysis typically makes use of the general linear model (GLM), where the relation between experimental condition and BOLD activity is estimated with a linear regression model for each voxel separately ("mass univariate model"). However, I found it surprisingly hard to find out what the response vector $Y$ contains. I am aware that it is some measure of the blood oxygenation level dependent signal (BOLD signal) - but what is measured exactly, i.e. what are the units? Is it the oxy/deoxy ratio, or is it another property?

Short answer
The units aren't important, and are typically normalized.
Longer answer
The name "BOLD" is actually very instructive: Blood Oxygenation Level Dependent contrast (or signal). BOLD is not directly measuring anything like oxygenated/deoxygenated ratio, or we would probably call it something more similar to that: oxy/deoxy ratio.
Instead, "BOLD" is just the MRI image you get when you set up the scanner properties in a way that happens to be influenced by the oxygenation level of blood. Oxygenation level is far from the only contributor to the BOLD signal, but experimentally you try to factor out any influences that are time-varying but not interesting, and you ignore baseline levels that don't change.
fMRI works because the transverse relaxation time T2 of water in blood depends on oxygenation of the blood. From the original paper showing BOLD contrast in a rat brain Ogawa et al. 1990:

At the 7-T field strength used in this study, T2 varies from 50 msec at 100% oxygenation to 4 msec at 0% oxygenation. The venous blood signal becomes very weak when the T2 value becomes comparable to or shorter than the echo time of the signal acquisition. At 60% oxygenation level, the estimated T2 value is 18 msec, similar to the echo time used in this report.

In other words, if you produce gradient-echo images with an echo time of 18 ms, the images you get show very different signal levels at 100% vs 60% oxygenation. Depending on the strength of your magnet, you can tune this time to go after the differences you want to see.
There is no straightforward way to compare images recorded in different conditions (i.e., different scanners, different parameters) on any useful scale of measurement. Instead, people typically report relative values, either in time or space. For this reason, you often see BOLD signals expressed as a % change or in terms of standard deviation (i.e., z-scores).
Ultimately, for fitting a general linear model it doesn't matter: you can freely scale a dependent variable without changing the structure of the model fit, all you influence is the interpretation of the magnitudes of the intercept and coefficients.
References

Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proceedings of the National Academy of Sciences, 87(24), 9868-9872.

Hi Bryan, my question w.r.t to units was to clarify what the response vector is quantifying, and I am aware that scaling does not affect the strength of the relationships between response and regressors quantified in the GLM - so I am not quite sure still about the original question: Are you saying that the response vector quantifies changes in properties of the magnetic field?

@Pegah It's measuring a radio signal from magnetically excited hydrogen atoms. However, it takes a lot of signal processing to go from that radio signal to a 3-dimensional image. See https://en.wikipedia.org/wiki/Physics_of_magnetic_resonance_imaging


text:
Does the brain consume more energy when a person is stressed or anxious
When a person is anxious or stressed or suffering from chronic depression, it is observed that the person is usually tired.
Is there there a connection between fatigue and racing thoughts/obsessions.
Also I want to know what damage can anxiety do to brain and body over time.

The tiredness associated with depression/stress is not due to the 'brain power' increasing but due to a change in what parts of the brain are active and/or disrupted sleep. Anxiety can cause issues to the brain and body over time.
Brain power is relatively constant
For the average adult in resting state the brain consumes about 20% of the body's energy. It has been shown that the brain requires about as much energy at night when you are asleep as during the day. The increase of energy for 'hard thinking' is about 8% which is very little compared to the baseline usage (leg muscles can have a 300-400% increase when walking compared to sitting).
See this paper for more analysis.
Tiredness and Mental Health
Depression affects neurotransmitters associated with alertness and reward systems thus making you feel less awake, less motivated, and more tired even if you might have sufficient sleep. However depression and anxiety often also lead to disrupted sleep (trouble falling asleep, nightmares/poor quality sleep, waking up too early etc). This would lead to a feeling of constant fatigue. Unfortunately, the feeling of fatigue can also worsen feelings of depression and anxiety though it is often not the root cause of depression.
Effects of Anxiety Over Time
Repeated activation of the stress response (a cascade of stress hormones colloquially known as the 'fight-or-flight' response) takes a toll on the body. Research suggests that chronic stress contributes to high blood pressure, cardiovascular disease, and causes brain changes (including differences in the volume of gray matter versus white matter, as well as the size and connectivity of the amygdala paper) that may contribute to anxiety, depression, and addiction. Preliminary research also suggests that chronic stress may also contribute to obesity, both through direct mechanisms (causing people to eat more) or indirectly (decreasing sleep and exercise). Chronic stress keeps levels of cortisol in the body high.
Source
Another important factor is the effect of stress on the cortisol levels.
Stress leads to an increased release of the steroid hormon cortisol, which can lead to reduced bone formation, favoring long-term development of osteoporosis (progressive bone disease) source.
It transports potassium out of cells in exchange for an equal number of sodium ions. This can trigger the hyperkalemia of metabolic shock from surgery. Cortisol also reduces calcium absorption in the intestine source. Cortisol down-regulates the synthesis of collagen source.
Sustained stress can lead to high levels of circulating cortisol (regarded as one of the more important of the several "stress hormones"). Such levels may result in an allostatic load,which can lead to various physical modifications in the body's regulatory networks source.


text:
Low cost cell free expression system
I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like amino acids etc.. ($$$).  I need this to be ultra cheap as this will be a side show until I can show something for my efforts. I prefer a cell free workflow because of the quick turnaround from template to protein and ease of purification. My backup plan is just to add a tag at the end of my constructs but I would prefer to avoid this.
Any suggestions would be much appreciated.
Thanks

There is nothing like a cheap cell free translation system if you buy it, as these systems needed a lot of optimization in the development (I once worked for a company who developed such systems). If you want it cheap, go for a tagged protein where the tag can be cleaved.

What kind of scale do you need? If you need some milligrams that might already rule out cell-free expression completely. Afaik cell-free expression systems are only used where normal expression is really not an option (to incorporate non-natural amino acids, when no purification is possible, for small peptides perhaps, radiolabels, that sort of stuff).

@VonBeche Really small quantities in terms of amounts and say 100AA in terms of size. I would use this platform to try and engineer protein linker. I read that you can turn around a protein quickly and I will fail a LOT. I would want to take advantage of non-natural amino acids for smFRET to get a feel for the dynamic motion.

It sounds like you want to try a lot of new things at once (although I don't know which techniques you have up and running). Also, keep in mind that building good linkers shouldn't be that hard and therefore they are scientifically not that interesting. I'd expect that a standard linker would work. If it doesn't work, scale up to a few more. Because the usual lack of secondary structure in a linker usually there's not that much to engineer. If you really want to, just try a standard one vs polyproline or something like that.

@VonBeche I was hoping to make a disordered linker that can pass information between domains bound at each end. So I am looking for something more sophisticated than just a polyG peptide sequence.

Could you post an example in nature or someone that did something similar previously? It sounds very interesting, but I don't understand how that would work.

@VonBeche This is sort of what I am looking to do [The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains. J. Biol. Chem. 292, 14765–14774 (2017)].


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Does this leaf belong to carissa macrocarpa?
I have a picture of a leaf and I am trying to find it's scientific name. The closer I got is Carissa Macrocarpa based on thorns alignment. If I am wrong, I need help in identifying correct species.. Thank you very much in advance!
Edit: Adding some more images

Can you give more pictures (e.g. the thorns you mention, and of course any flowers, the overall growth habit - tree, shrub etc) and location?

Hi Bryan, I added few more images.

I think you are close with your ID, certainly down to the genus.  However, all the pictures I can find of C. macrocarpa have leaves which are slightly more peaked/acute, and have a tiny little spine-like structure at the end.  Also, it looks like the thorns are bifurcated, but your specimen has simple spines.  Since this plant is used in landscaping, there are various cultivars available which may combine characteristics of the cannonical species.  You might need to find a key to this genus to be sure.

Try to find a key for Carissa for your area if this is a "wild" plant, not landscape specimen.  I found several by googling.

Thanks Bryan, that suggestion helped! It is highly likely that this specie is Carissa carandas which I found out grows in and around my locality.

Put it as an answer then with a little info about how you decided. It’s perfectly OK to answer your own question. Thanks for posting the question, I actually knew that plant indirectly from when I grew up in Southern California, where it was used as a landscape plant (and hurt a lot if a child tried to hide in a hedge of it!)

This plant seems to be Carissa carandas. With the thorns placements besides leaves, I was sure that this plant belonged to genus Carissa. Taking advice from Bryan Hanson, I searched for the plants in the same genus in my locality(Hyderabad, India). The white flowers and their rosy stalk made it easier for me to search. I found out that this is a common plant in country side and is used in many dishes. Thanks Bryan for pointing me in the correct direction.


text:
Why warfarin is given as racemic mixture?
Warfarin is administered as a racemic mixture of S- and R- warfarin.
S- warfarin is 3 to 5 times more potent than R- warfarin.
So, what's the logic behind giving a mixture of it? Isn't administration of only one form gives more predictable results?

In general, it's more difficult to produce a specific stereoisomer of a compound than it is to produce the racemate. Producing a pure S- or R- sample of a particular compound requires either enantioselective synthesis, or racemic synthesis followed by a purification step such as chiral chromatography. This tends to be expensive - especially for an older drug like warfarin where it would likely imply either chiral purification (throw away half your product) or redesigning the synthesis to be chiral.
For some drugs it makes sense to do this - some reasons might include adverse effects of the undesired stereoisomer, or taking a drug that's about to go off-patent and re-branding an enantiopure preparation for further patent protection. I think the latter is what happened with Citalopram -> Escitalopram (Lexapro) although this is speculation.
Most likely in the case of warfarin there is no strong argument for producing a pure enantiomer. It has been off-patent for a while, there likely aren't major adverse effects related to the less potent isomer, and most likely economics dictate that producing and selling the racemate is cheaper / more profitable than retooling to produce and sell an enantiopure version. That latter option would only make sense if they could sell the pure S-warfarin for enough to recoup the development / purification costs, and this is unlikely for a drug with such a long history of use in its racemic form.

Another "evergreening" example is omeprazole --> esomeprazole

I wasn't even aware that esomeprazole was a thing :)


text:
How many colors can colorblind people really see compared to normal color vision?
A person with normal vision, it seems, can see 7,000,000 colors.
How many can a colorblind person see?
I'm not as much interested in the exact number, or the technicalities that might exist due to different types of color blindness (let's just consider the most prevalent colorblindness, which is red-green I think) but I'm more interested in how low or what percentage would that number be w.r.t. to the normal vision? Is it like half, or only 10%, or much closer like 90%?
This is sort of a follow up of this question. If 3 cone cells can see between 7,000,000 colors, how many would 2 see?


text:
What's the amount of blood passing through heart every second at Max Heart Rate?
How many mL of blood passes through the heart every second at maximum heart rate?
Is there any formula to calculate the amount of blood flowing through the heart per sec at say for example 70% of the max heart rate?
I didn't ask
Let's assume that the person in question is a fit 23 yo Caucasian male(if there are differences for various ethnicities)

· Heart Beat Rate

The normal heart has a rate of 72 beats per minute, but in infants the
  rate may be as high as 120 beats, and in children about 90 beats, per
  minute.

Lets say the heart beats at an average pace of 70 bpm (beats per minute)
(~100.000 times a day)

· Cardiac Output
Volume of blood pumped by the heart in a minute.
CO = HR X SV (heart rate multiplied by the stroke volume)
Cardiac output is the volume of blood being pumped by the heart in a minute. It is equal to the heart rate multiplied by the stroke volume. So if there are 70 beats per minute, and 70 ml blood is ejected with each beat of the heart, the cardiac output is 4900 ml/minute. This value is typical for an average adult at rest, although cardiac output may reach up to 30 liters/ minute during extreme exercise.
So for an average adult at rest the estimate is around 5 litres of blood per minute (~1.33 gallons)

· Cardiac Outout / second
There are 60 seconds in a minute so simply :
divide amount pumped per minute by 60
0,083̅3̅  L of blood per second
(83,33 mL of blood per second)
But this is just an average with specific variables defined... so maybe you have to take into account other factors that may vary this value.

· Factors Affecting Cardiac Output

Factors affecting cardiac output in a healthy but untrained individual
  could be:
Increase/ decreased in heart rate
Change of posture
Sympathetic nervous system activity
Parasympathetic nervous system activity can also affect cardiac output.

Heart rate can vary by a factor of approximately 3, between 60 and 180
  beats per minute, whilst stroke volume can vary between 70 and 120 ml,
  a factor of only 1.5.

You can read more here & here

How's the SV like at high rates?


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Do mutagens ever increase the "rate of evolution"?
There are a lot of sci-fi plots where mutagens, especially radiation, cause some organism to evolve at an accelerated rate. Obviously evolution does not occur within a single organism and most of the authors behind these works are more concerned with finding a justification for a desired plot rather than adhering to known science. Nonetheless, I'm curious to know if there is any well-known case where such a scenario is true. (To get one obvious reply out of the way, all evolution that we've observed on Earth occurs in the presence of the background radiation experienced on Earth. Also, although mutagens by definition increase the rate of mutation, those mutations can of course be harmful, so the question is whether the effective "rate of evolution" can be increased rather than the rate of mutation.)
Is there any well-known case where introducing mutagens can increase the "rate of evolution" in an experimental evolution study?
By "rate of evolution", I'm informally referring to either the amount of time or the number of generations that pass before some beneficial mutation occurs and is selected for. For example, in the E. Coli strains from Lenski's E. coli evolution experiments, are there any known cases where a mutagen reduces the amount of time or the number of generations required for a non-citrate-metabolizing E. coli strain to acquire the ability to metabolize citrate?

The Ames test comes to mind, though it’s specifically designed to detect beneficial mutations in response to a mutagen.

Yes, although what you mean by increasing the rate of evolution is a little vague. Plant breeders regularly use mutagens of various types to increase the mutation rate. The mutants are then screened for useful traits, and useful mutants are cross-bred with existing lines.

Chemical mutagens like EMS and DMS, radiation and transposons are used
  to generate mutants with desirable traits to be bred with other
  cultivars – a process known as Mutation Breeding. Classical plant
  breeders also generate genetic diversity within a species by
  exploiting a process called somaclonal variation, which occurs in
  plants produced from tissue culture, particularly plants derived from
  callus. Induced polyploidy, and the addition or removal of chromosomes
  using a technique called chromosome engineering may also be used.

Wikipedia: Plant breeding

Do mutagens ever increase the “rate of evolution”? [..] By "rate of evolution", I'm informally referring to either the amount of time or the number of generations that pass before some beneficial mutation occurs and is selected for

This is a very unusual definition of "rate of evolution" but I'm happy to consider it if you want.
If more mutations happen per generation, then it takes less time for a beneficial mutation to happen. So yes!
By rate of evolution, some people may like to refer to the rate at which neutral mutations fix (fixation=reaching a frequency of 1 in the population). If $\mu$ is the mutation rate, then $2N\mu$ mutations are produced each generation (assuming diploidy), and a fraction $\frac{1}{2N}$ of them fix (as they are neutral), this means that the rate of fixation is $\frac{2N\mu}{2N} = \mu$. So, again increasing the mutation rate increases the rate of fixation of neutral mutations. It is actually true also for deleterious and beneficial mutations but the computation is a little more complicated.
Note however, that there is a point after which the mutation rate is so high, that your population might be drawn to exctinction. This is called a mutational meltdown. Mutational meltdown is unlikely to happen unless the population size is already small to start with and/or the mutation rate is really really high.

But OP seems to be looking for a documented case where the rate of fixation of advantageous mutations (a combination of mutation rate, strength of selection, and population size) has been shown to increase in an environment with a higher overall mutation rate ...

Perhaps you can also comment about mutation-selection balance. I guess that would be a relevant factor here.


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How were genes located before the development of bioinformatics?
I would like to know the detailed procedure of how scientists in earlier time were able to locate genes like how we were able to locate Huntington gene in 1983?

Could you clarify what you mean by  earlier time, are you asking how the Huntington's was located or before it was located, and in what organism? And what precisely do you think bioinformatics has to do with it? What research have you done yourself to find the answer, and why don't you start your title with a capital letter like almost everyone else and run a spelling check if English is not your first language.

The detailed procedure of how scientists located the huntingtin gene spans at least a decade and includes multiple papers, and so your question seems rather broad. It was mapped to chromosome 4 in 1983 but the full ORF, with CAG repeats, wasn't identified until 1993.

Your question is also broad in that different techniques were often used for different genes. See this answer for a very brief summary of how the insulin gene was discovered.

The earliest genome maps were constructed from Escherichia coli by abusing conjugation of special Hfr-mutants. I'm assuming you are somewhat familiar with bacterial conjugation - the process of transferring genetic material between bacterial cells.
Usually, only mobile plasmids are transferred. They carry the necessary tra-genes for the construction of the sex-pilus, replication and transfer system. They also need the oriT-site (origin of transfer), at which transfer is initiated. A famous mobile plasmid is the F-plasmid.
Some mutant cells integrated the F-plasmid into their main chromosome via recombination. Thus, they are able to transfer their whole genome to a recipient cell. These strains are called Hfr-strains (high frequency of recombination) and they were used intensely in early genome mapping.
They discovered, that it takes roughly 100 minutes for a Hfr strain to transfer its entire genome to another cell. By interrupting conjugation (e.g. by vigorous shaking) the transfer was interruped and the genome could be divided into sections by transfer time (10min, 20min, 30min and so on).
The function of the genes (or genome sections) was revealed by mating Hfr strains with defective mutants. If the mutant was unable to grow on saccharose for example, several conjugation experiments with different mating times were conducted. When a mutant was able to grow on saccharose again after mating, the transfer time was checked. If the strain was able to grow again after 30 minutes of conjugation, but not after 20, they knew the genes necessary for saccharose growth lay in the 20 - 30 min region.
It took a painstaking amount of experiments with a wide range of mutants to construct the first map of E. coli genes, but it was achieved before even the nucleotide sequences were known.

Just to complement Pythagyros.
Sequencing and bioinformatics were already around in 1983, actually Frederick Sanger and colleagues published their automated method of sequencing (Sanger sequencing) in 1977. They published the complete sequence of the bacteriophage φX174.
Other methods of DNA sequencing had been around since the first one in 1970 established by Ray Wu.


text:
Many black people I've met have bigger lips than white people, why?
I noticed that many black-ish people I've met have bigger lips than the white-ish people I've met. However, not all black-ish people have big lips.
Is there any explanations in terms of natural selection, geographic localisation, common ancestors, or something else that could explain why a subset of dark skin people have bigger lips on average than pale skin people?
Edit: This question is different from the other one because the answer talks about the nose and its function (air temperature) linked to the environmental factors. I don't see how this applies to lips.

May be just coincidence?

Regard this one as a comment

I prefer to cite some text form this website instead of providing the link only (as it could be removed).

In general, this pattern can be observed across the planet with the
  size of lips and nose decreasing as we move away from the equator
  towards the poles. So what could the reason be?
For someone living in hot climatic conditions, cooling down the body
  is critical for their survival. Our body has many cooling mechanisms
  and one of them is simply disseminating heat when it comes in contact
  with colder air (simple thermodynamics). This however requires larger
  surface area so that more heat can be disseminated.
Given that a significant portion of breathing also happens through the
  mouth (especially when exposed to heat), lips are pretty much like the
  gateway for colder air being inhaled and exhaled. So, the larger the
  lips, the more heat that can be disseminated. Thus, people living in
  hotter climatic conditions gradually evolved to have bigger lips.
The opposite is true for people in colder climates. They get a
  survival advantage if they are able to retain as much heat as possible
  and so they gradually evolved to have smaller lips thus limiting the
  amount of heat that can escape when cold air brushes past their lips
  while inhaling and exhaling.

Notably, there was no scientific source provided for this claim, however intuitively this could make sense.

(This is an extended comment rather than an answer.)
One important thing to note is that depending on where you live, the "black-ish people you've met" may not be at all representative of black people worldwide. For example, if you live in the Western Hemisphere, then the large majority of the black people who live in your country are probably descended from Africans who lived in the so-called "Slave Coast of West Africa", which roughly comprised the modern-day nations between Sierra Leone and Nigeria. For example, here is a photograph of a present-day resident of Ghana (where many descendants of modern-day black inhabitants of the Western Hemisphere lived), and here is a photograph of a present-day resident of Eritrea. They look very different.


text:
Why does drinking milk lead to increased fractures?
Milk has always been associated with strong bones due to the high amount of protein and calcium in it. Yet reading it up on wikipedia,

A study published in The BMJ that followed more than 45,000 men and 61,000 women in Sweden age 39 and older had similar results. Milk consumption in adults was associated with no protection for men, and an increased risk of fractures in women. The risk of any bone fracture increased 16 percent in women who drank three or more glasses daily, and the risk of a broken hip increased 60 percent. It was also associated with an increased risk of death in both sexes.

My question is:
Why did this happen? Can someone explain the biological reason of this observation?
Even though milk really does provide large amount of calcium and proteins yet isn't is contradictory that the fracture rates increase?
This is the aforementioned study.
Michaëlsson, K.; et al. (2014). "Milk intake and risk of mortality and fractures in women and men: cohort studies". The BMJ. 349: g6015. doi:10.1136/bmj.g6015.

The authors suggest a reason in their abstract:

Given the observational study designs with the inherent possibility of residual confounding and reverse causation phenomena, a cautious interpretation of the results is recommended.

There are variables they haven't measured that lead to the observed patterns. A simple one is that the respondees to the initial survey are self-selected (they return the survey). What if milk-drinkers are more likely to respond? Even if the base rate of fractures remains the same, then there will be an apparent association of fracture with milk consumption.
They also discuss physiological reasons, which is the subject of a different answer.

And: As far as I see, this is only one obeservational study which shows this results. I would be very careful to draw conclusions from this study unless this has been replicated, to say the least.

This paper should be in the BMJ christmas issue instead of in October issue.


text:
Gene located on Which strand? Want reference.
Update: Initially my question (below) was appropriately marked as duplicate/overlapping  with two other questions; This and this ; among them a specific part of an answer of the second duplicate/overlap ; appropriately answer my question.

The convention is that in indicating any sequence feature† in a protein-coding gene on double-stranded DNA, a single strand‡ is represented — the one from which the amino sequence could be read using the genetic code (conceptually, with T substituted for U). Like any other nucleic acid sequence§, it is always written in the 5ʹ to 3ʹ direction in the same manner as the mRNA transcribed from it, without this being explicitly stated.

But what it does not mention (but I'm still looking for); is whether there is a standard and universal documentation for this particular convention (IUPAC/ IUBMB/ ICBN/ ICZN/ anything such); because "conventions" are human-made rules, and without "declared, universally followed, and accessible" documentation; the conventions does not make a sense.  It rather feels like a rumor or viral phenomenon.  I visited the IUPAC and IUBMB website home pages but I could not locate the documentation from there. Also google keyword search did not found the helpful.
So I specify my question that I want to get the standard/ official source of this convention. I would be highly grateful if anyone kindly mention the source hyperlink.

My Initial Question
I'm stuck at a very basic convention on notation on reading Gene sequence. *Specially when a  book (or question paper or anything) does not mention whether a  nucleic acid (usually DNA), uses a single stranded DNA
The problem appears because similar region of the 2 opposite strands of a DNA can contain different gene, i.e.

(So it is possible that if we note a stretch from gene-1 with its complementary sequence, that complementary sequence could be confused with gene-2.)
In some cases, a sequence to a stretch of nucleic acid, indeed mean the sequence directly.
For example; In the wikipedia image about Reading Frame (Permalink)

the 5'to 3'Left to Right indicates the sequence of the template strand directly whereas
But at the more and more "interior chapters" I've seen a rather complicated and indirect notation (although I could not found  clear mention of a convention anywhere in books or web)... when they mean a sequence of a stretch of a gene (or a regulatory sequence), they writes the "nontemplate" or "sense-strand" sequence of the respective gene.
In the Wikipedia image on TATA Transcription Box (Permalink);

it must be a sequence from the nontemplate strand because if it was the template strand,  the "Promoter" location on the "template" strand must be on 3' side otherwise RNA polymerase would not be able to synthesize the nontemplate strand mRNA strand from 5' to 3' time-order. But it would become impossible to infer for me if the given sequence lacked labelling for relative locations of promoters and structural genes.
Now my question is If an article  provides me a single stranded  "Gene Sequence"; How can I infer it is directly the sequence of the mentioned gene stretch or it is the complementary ("sense") strand of the gene? What is the convention about it?

I have cited this as a possible duplicate of the What direction is a sequence in databases written? but my answer to  that covers just part of the question. I think the rest is covered in Terminology of the sequences of promoters in relation to DNA strands. If the poster doesn't agree, perhaps he can explain what is not covered.

You should post a new question if you have, well, a new question.

Sure, Thanks for the advice. Would  I need to revert my current edits?

@canadianer i am dwindling if new question may also overlap/duplicate. I've initially put a comment on said answer to add that document; but to also ask the same question to other visitors I kept the update here.

Okay I'm submitting a new separate question as @canadianer said. But if any user want to submit the addition into their existing post, they may please feel free to do proceed and mark the new question as duplicate. It is upon community.

I have posted my question here https://biology.stackexchange.com/questions/76643/want-reference-for-a-convention . Now question management decisions (keep/delete) are upon community.

Assume that you are given the gene in the "forward direction"; the one where the starting ATG is on the left, that the sequence you are looking at is what the single stranded RNA will be.

Not clear... say of fig.1; gene 1 (lower strand) will be "forward" if I read it as 3'...CGTACCGGTTAA..5'. Would I tell it "Sequence of Gene1"? Or would I have to write its complementary strand as "sequence of gene 1"?

I see more than one ATG in my question. Which specific ATG you are telling about?

In the context of a gene, I mean the ATG that is the actual start of translation. In figure 1, it would just be wrong to call those reading frames if the sequence is the reverse complement of the real RNA.

In real life, no one is going to give you data in the form of figure 1.


text:
We know archea and eukarya are more closely related but endosymbiotic theory says eukarya have evolved from prokaryotes, justify the statements?
I am confused if eukaryotes have evolved from prokaryotes then how are they more closely related to archea?

I'm voting to close this question as off-topic because it is based on a false premise.

I think it is better to clarify a student's misunderstandings. at least the student recognised "something is going wrong", from their perspective.

Actually endosymbiotic theory (we should write "Endosymbiotic theory of origin of eukaryotic organelles") suggests a theory about only the eukaryotic organelles (mainly Plastid-family and Mitochondrion).
I'll divide my answer into 3 parts:
# Theory of archaeal origin of the eukaryotic host.
* 1. How Archaea (Archaebacteria) and Eukaryotes shared a closest common ancestor
# Endosymbiotic theory of origin of Eukaryotic cell organelle.
* 2. How mitochondria originated?
* 3. How plastid was originated?
Please keep in mind, in origin and evolution of eukaryotes, origin of the host cell (and the nuclear genome) is a different event; and origin of eukaryotic organelles mitochondria and plastid is another different event.
Theory of archaeal origin of eukaryotic host
1. How Archaebacteria (archaea) and precursor of eukaryotes evolved from their nearest common ancestor.
It has been established (First by Carl Woese, mainly based on her prolonged researches on  rRNA sequences) (PDF) (REFERENCE-1 *) that Eukaryotic "host cell" (with the nuclear genome) shares the closest common ancestor with Archaebacteria, not the eubacteria.
Further reading: Relationships of Eukaryotes and archaea

Fig-1: Here the horizontal axis is the time axis.
(The small black balls here indicating many other possible extinct lineages (hypothetical, just todemonstrate how evolution works) )
On other hand, After the group bacteria (eubacteria) developed (better to say the precursor of bacteria further diversified, bacterial groups like proteobacteria and cyanobacteria developed. For bacterial phylogeny, see Wikipedia (image)
Endosymbiotic theory:
Now endosymbiotic theory tells that the origin of some eukaryotic organelles (at least Mitochondria and Plastid) were different and distant taxa from the eukaryotic cessls, and they came from outside and entered into the cell and formed symbiotic relation; and the endosymbionts gradually lost their free-living ability, were gradually became part of host cell. The peculiarity of this "Endosymbiosis" phenomenomenon in evolution is that; not only the "parent" taxa; but another "distant taxa" merge from side of the lineage. The concept is not only confusing but it was so shocking that when H. Margulis first proposed this hypothesis, the idea was rejected. Later on, genome-based research proven that the origin of mitochondria (and as we will see, plastids); were originated from mutualistic- symbiosis.
2. How mitochondria evolved in eukaryotes?
It has been suggested, the "precursor" of eukaryotes (which was descendant of closest-common ancestor with archaebacteria), the host cell, engulfed some aerobic eubacteria (perhaps allied to proteobacteria) those aerobic eubacteria gave rise to mitochondria. These derived protists were unable to photosynthesise. This endosymbiosis is very much similar to previous one.

Fig 2a: origin of the organelle mitochondria.
So our evolutionary tree now look like

Fig 2b: Origin of mitochondria in eukaryotes, placed in evolutionary tree.
The white balls here represent living and contemporary groups.
(Just like previous picture the extinct groups are hypothetical and representitive; but the relative positionsof clades for proteobacteria and cyanonbacteria is actual, and taken from from Prescott's microbiology **)
(A common example of intracellular endosymbiosis will help us to understand the theory-  we can still see such intracellular symbiosis in rhizobial bacteria colonising plant root/tissue; where we get both intracellular stage and culturable extracellular phase)
3. How Plastids evolved then?
From this group of protists, a certain group again engulfed a sort of eubacteria (allied to cyanobacteria). The cyanobacteria gave rise to plastids  , and photosynthetic protists.
There are disputes about whether plastid and mitochondra evolved simultaneously or at an interval. According to T. Cavalier smith they originated simultaneously, but according to other newer sources like this  and  this   , mitochondria appeared first.

Fig.3.a. one lineage eukaryote that already formed mitochondria, forming another association with a photosynthetic eubacteria.
It is not clear to me whether all eukaryotes (protists and their derivative higher plants, fungi and animals) had a plastid containing ancestor; or at least some non-photosynthetic protists came before origin of chloroplast (However just to mention, some of photosynthetic protists again evolved progeny with lacked  photosynthetic ability due to retrogressive evolution (degradation) of plastid, such as Helicosporidium sp. etc )
So our final evolutionary tree looks like

Fig.3b. Chloroplast originated similar way from eubacteria (bacteria)

REFERENCES:
BOOKS
* 1. : Molecular Biology, Author: R. F. Weaver, ED-5; Publisher: McGraw-Hill.

: Cell Biology: Concepts and Experiments. Author: Gerald Karp, ED6, Publisher: Wiley.

** 3. : Prescott, Harley, Klein's Microbiology; Edited by Willey, Sherwood, Wolverton, Ed7, MackGraw-Hill.
Papers and Reviews

Bacterial evolution, Author : Woese; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC373105/ ; PDF: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC373105/pdf/microrev00049-0051.pdf
Endosymbiotic theories for eukaryote origin. Authors: Martin, Garg, Zimroski; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571569/ , Pdf: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571569/pdf/rstb20140330.pdf


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Is this sentence about RER correct on Wikipedia?
While studying about Endoplasmic Reticulum on Wikipedia, I came across this sentence

A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol. This special complex forms when a free ribosome begins translating the mRNA of a protein destined for the secretory pathway.

To my knowledge, most proteins are synthesized and modified post-translation in association with RER. Then why is protein destined for secretory pathway mentioned?

Your knowledge is defective. Read the article and search for associated articles. You may even find something in the archive here.

As stated in a comment, your understanding of protein translation in eukaryotes is not accurate. In order to provide a concrete reference that isn't wikipedia, I'll quote here from Biochemistry (2nd ed) by Voet and Voet (1995 / John Wiley & Sons) pg. 307:

Cytologists have long noted two classes of eukaryotic ribosomes, those free in the cytosol, and those bound to the ER so as to form the rough endoplasmic reticulum (RER ...) Both classes of ribosomes are nonetheless structurally identical; they differ only in the nature of the polypeptide they are synthesizing. Free ribosomes synthesize mostly soluble and mitochondrial proteins, wheras membrane-bound ribosomes manufacture transmembrane proteins and proteins destined for secretion, operation within the ER, or incorporation into lysosomes ... These latter proteins initially appear in the RER

Pretty succinct and thorough description.
The wikipedia text you quoted is a bit shallow (on its own) and somewhat incomplete, but essentially correct. The RER isn't solely associated with synthesis of proteins destined for secretion, but this is one of the classes of proteins synthesized in association with the RER. It would be more accurate to say that proteins destined for transmembrane insertion, secretion, or certain other kind of 'special handling' are synthesized in association with the RER rather than free in the cytosol.
The details of how, for example, these different classes are targeted to the RER are fascinating but somewhat beyond the scope of the question. Well explained in the referenced text, though, if you're interested.


text:
Any known values of density for spinal cord (pig or human)?
Need to know the density of spinal cord tissue to evaluate the shear modulus from ultrasound elastography (shear wave velocity) measurements, but need the density of the tissue to compute this.
I am a physicist by trade so unaware of whether white and gray matter have homogeneous properties in the CNS as a whole or whether they are different in the brain and spinal cord.
Could do with density (g cm^-3 or equivalent) of white matter, gray matter or of the cord as a whole.
Also if there are any sources so i can cite this this would be most useful.


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Can gene-gene interactions result in gene expression?
I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge.
The format of the input data is shown in the image.
Now according to what I studied, a Gene Expression Matrix has its rows represent genes, columns represent samples such as tissues or experimental conditions and the numbers in each cell refer to the expression level of a particular gene in the particular sample.
And that Gene Expression is the process in which information from a gene is synthesized to obtain Gene Products. The process of Gene Expression is that it undergoes a transcription process where a transcription factor attaches itself to the gene and then results in the formation of gene product.
But the input data apparently shows gene-gene interactions.
As a result of this I am extremely confused.
Any kind of help would be greatly appreciated. Thanks.

Let us continue this discussion in chat.

I don't know anything about your algorithms. But i will try to explain your the format of data that was given to you. I don't know your background in Biology, so i will assume it is not your expertise field and will make some simplifications of the subject.
What is gene expression?
To understand what is a gene expression, you need to understand what is a gene:

A gene is a sequence in the DNA (composed of 4 bases A,T,C and G) that can be transcribed by a protein, in your context we will say it always start with a start codon (a codon is a triplet of DNA bases) and stop with a stop codon. It is usually around a thousand bases long. The transcription will give you a RNA, and that RNA can be translated (note the difference with transcribed) into a whole new protein.

Now the gene Expression is a measure of the amount of RNA from the gene you are looking for. In a cell you can have around 10000-100000 copies of that RNA; the raw count is not really stable as you can have extract two cells or three and it will change your "expression". Most of the time we normalize the count by the count of a bunch of known genes called housekeeping genes. The particularity of these genes is that their expression is quite stable.

The figures you have are a ratio between RNA copies of your gene of interest and RNA copies of a stable gene (in term of expression).

What does G1(-/-) and wt mean?
Usually when we (biologist) call a sample wt it means wild type, in other words, a normal individual. G1(-/-) means that this sample is from an individual with the G1 gene inactive (could be obtained by genetic modification).
What is a gene-gene interaction?
An example of interaction first: let's imagine a gene coding for an enhancer (booster) of transcription. the presence of this gene allow another gene to be expressed in the cell, if this gene isn't present or isn't transcribed, the other gene won't be expressed either.
How can we see interaction there?
Let's look at line one, the control (normal individual), We see that G4 (column) is almost unexpressed (0.07). In normal conditions, this gene is not expressed. Now let's look at mutant G1(-/-) and G6(-/-), we see the expression of G4 is rising (0.37;0.23) compared to the control (wt).
We can suppose than G1 and G6 are acting as inhibitors of the G4 gene.

The short answer is yes, of course there are gene-gene interactions.  I'm not sure what the point of the experiment would be if there were not.


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What is structural RNA?
In genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Fungi/Saccharomyces_cerevisiae_uid128/) there are an archive .frn (nucleotide sequences of structural RNAs in fasta format), and  I want to know the differences between structural RNAs and genes.
Are the nucleotide sequences of structural RNAs a coding region?
My goal is separate the coding region from the non coding region of a given complete genome.
I'm physicist so, I apologize if my question is pretty simple.

@David I guess "structural RNA" is not a standard term. I won't even expect biologists to be sure about what it could mean.

@WYSIWYG — Inspection of one file with extension .fm gives names for some of these structural RNAs, such as Pro tRNA, 15S ribosomal RNA. I assume the poster has read this. I would have expected him to try to find out what a tRNA and a ribosomal RNA actually was. If he is not prepared to put the effort into reading about molecular biology he is wasting his (and our) time.

To be very brief: A gene is a sequence of DNA or RNA, which is hereditary and has a biological function. In the Saccharomyces cerevisiae genome you posted, every gene is a DNA sequence. The function of most genes is to be transcribed  to messenger RNA (mRNA), which is then translated to a protein. "Coding" DNA refers to DNA which eventually has its sequence translated into protein
Structural RNAs are encoded by genes but not translated to protein, and thus are not coding regions. They are made up of RNA, but function more like proteins. When they enable reactions, like enzymes, they are called Ribozymes. The most well known ones are the Ribosomes, which are an essential part of protein biosynthesis. Others form special structures which help molecules recognize each other. tRNAs are needed for the ribosome to recognize the right amino acids.
As David said, this is very basic molecular biology and gene regulation/expression in eukaryotes can get quite complex. The wikipedia articles provide a good introduction and the Berg biochemistry book he linked is excellent further reading. If you want to know more about yeast genomes, you can check out https://www.yeastgenome.org/. It provides a whole lot of information regarding the amount of coding/noncoding regions and their function. There is also a graphical genome browser, where you can view each region in detail and compare it with your own findings.

Coding DNA refers specifically to regions that are translated into protein. Non-coding RNA like tRNA or rRNA are by definition not part of coding regions.

i approved the edit but i am not sure if it is okay to change key concept of another user's answer.

molecular biology terminologies tend to be tricky and sometimes usage vary from person to person.


text:
What is the conversion between r and FST?
From Schonman (2013):

...allele A can only invade under Hamilton’s condition  R=$F_{ST}$ > C/B.

From Harpending (2002):

The best general definition of the coefficient of relation $R_{XY}$ between individuals X and Y is (Bulmer, 1994) $R_{XY}$ = $F_{XY}$/$F_{XX}$, where $F_{XY}$ is the kinship between X and Y and $F_{XX}$ is the kinship of X with himself [..]
[..] $F_{ST}$ is just the coefficient of kinship between members of the same deme [..]
[..] $F_{Self} = \frac{(1 + F_{ST})}{2}$  [..]

This means, unless I am mistaken, that if I take Harpending's equation and substitute $F_{ST}$ for $F_{XY}$ and substitute 1/2(1+$F_{ST}$) for $F_{XX}$, I can calculate within-deme relatedness: 2*$F_{ST}$/(1+$F_{ST}$).
Yet Schonman says R=$F_{ST}$?
What am I doing wrong here?

The low attention your post received is likely related to its format. I've improved the format for the quotation and  the references. You probably want to improve the format for the equations. For example, "Fst" should be "$F_{ST}$" (by typing $F_{ST}$). Here is a tutorial for formatting math equations.

@Remi.b Is this question too difficult or too trivial?  Do you know the answer?

It is not an easy question. My first thoughts were that $F_{ST}$ depends upon the genetic diversity while $r$ (or $R$ as it is apparently called here) is not. So equating the two sounds hard. You first quote comes from the social evolution literature and Nash's work into the discussion just makes things unnecessarily complicated.

Sentences like FST is just the coefficient of kinship between members of the same deme sounds wrong to me because $F_{ST}$ depends upon the genetic diversity in the total population but it might be hard to give an opinion on an out-of-context quotation (I have not read the paper). Also, I am not used to work with he coefficient of relatedness (or of kinship; to me these two concepts are the same but I might be mistaken) and might gets a bit lost here.

@Remi.b What do you mean by Nash's work?  You're not used to using coefficient of relatedness (r)?  Isn't that measure very commonly used?  Could you read the paper?  It is rather short and I think you would be able to understand it because you are familiar with math formulations in evolutionary biology.

I was referring to John Nash who's work underlies Hamilton's work. I just meant social evolution stuff.

I could maybe work out from Bulmer's definition that $R_{XY} = F_{XY}/F_{XX}$. However, this definition does not specify whether Y is drawn from the population or not. $F_{ST}$ only makes sense in structured populations. I suppose Y would mean an individual drawn at random from the total population, what do you think?

I am not sure I understand the concept of kinship of X with himself too.  How can this value differ from 1? (I might be too used to think in terms of probability of identity by descent to think this problem correctly)

According to the paper, kinship with himself is 0.5 in a sexual population.

I am very unsure but here are my thoughts...
We can work out from
$$R_{XY} = F_{XY}/F_{XX}$$
I do not really understand the concept of coefficient of kinship and the concept of coefficient of kinship with oneself but you say

According to the paper, kinship with himself is 0.5 in a sexual population

So, let's assume
$$R_{XY} = 2F_{XY}$$
Let's assume that the individual Y is drawn from anywhere in the total population. Again, I don't really understand the concept of coefficient of kinship but let's assume that $F_{XY}$ is the same as the probability of identity by descent between these two individuals, then in Nei (1973) terms, $F_{XY} = J_T = 1 - H_T$. Hence, $R_{XY} = 2\left(1 - H_T\right)$ or $H_T = 1-\frac{R_{XY}}{2}$
Given that
$$F_{ST} = 1 - \frac{H_S}{H_T}$$
it results that
$$H_T = \frac{H_S}{1-F_{ST}}$$
and therefore,
$$1-\frac{R_{XY}}{2} = \frac{H_S}{1-F_{ST}}$$
solving into
$$R_{XY} = \frac{ 1 - \frac{H_S}{1-F_{ST}}  }{2} = \frac{1-F_{ST} - H_T}{2(1-F_{ST})}$$
I would recommend you making some more reading on the coefficient of kinship to ensure that my interpretation here is correct.

Oh Remi, I apologize.  The thing is, in the paper, Harpending says that kinship with oneself is 0.5.  But later on in the paper, Harpending gives a different equation for kinship with oneself in a subdivided population.  That is the one I thought should be used, since $F_{ST}$ implies a subdivided population, right?  So, that is the one I used in phrasing my question above.

Ok.... see new answer then! I am not sure it is of any help though.

I am not very at ease with the concepts of coefficient of kinship but
if $F_{self} = F_{XX}$, then
$$R_{XY} = 2F_{XY}(1 + F_{ST})$$
Assuming that Y is a random individual from the total population and if $F_{XY}$ is the probability of identity by descent of haplotypes X and Y (which I am unsure because I don't really ), then $F_{XY} = H_T$ and hence
$$R_{XY} = 2H_T(1 + F_{ST})$$
But really I am very unsure about all that. Note also that the small calculation is based upon the equation $F_{Self}$ = 1/2(1 + $F_{ST}$, which I don't really understand! I would recommend you making some more reading on the coefficient of kinship to ensure that my interpretation here is correct.

$R_{XY}$=2$F_{XY}$/(1+$F_{ST}$), correct?

Is the original expression $F_{Self} = \frac{1}{2(1 + $F_{ST})}$ or $F_{Self} = \frac{1 + F_{ST}}{2}$? It is unclear from the format you are currently using in the question. I might have assumed the wrong one.

The original is the latter.

I tried to modify the format but I don’t think it worked.  I’m on my phone and won’t have a computer for the rest of the day.

The format is corrected now.


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Is this panspermia mechanism feasible?
One episode of Cosmos: A Spacetime Odyssey describes a mechanism by which microbes could travel between planetary systems. As a star's orbit takes it around the galaxy, it occasionally passes through dense interstellar clouds. Rocks thrown into space at that time from the surface of a microbe-harbouring planet could carry life to temporarily nearby planets of another planetary system, before cosmic radiation would sterilise such rocks.
It's an interesting idea for TV; but scientifically, how plausible is this mechanism? My main concern is whether the average number of "infected" planetary systems per passage through an interstellar cloud is estimable as non-negligible.
Note: the use of "panspermia" in the title refers only to the question of whether an occasional interstellar transfer of microbes is tenable, not whether Earth's life originated outside this planet. As I understand it, the mechanism described above is lithopanspermia.

Unfortunately I think this may fall neatly between the expertise of Space.SE and here, but I think the key variable here is the time for which such propagules would remain viable. I suspect the sheer time and distance likely to separate compatible planets would exceed this period by a very significant amount. However, if we can show extensive 'cross-pollination' of planets within our own system then that gives us better data to estimate this likelihood.

The theory is staggeringly improbable. However, so is life. The probability of life emerging from non-life is the basis of the misguided idea of intelligent design (a thinly veiled repackaging of creationism). Bear with me: the probability of life on Earth is 1. It is here, and this is the only observation of Earth we have. But the thought of complex life appearing out of some molecular soup by chance (abiogenesis) is also staggeringly improbable. But as I said, life is here. How did it get here? There are only three possibilities: Abiogenesis, divine creation, or from panspermia (which kicks the can down the road, because it had to have begun somewhere). God is no explanation at all, because even a mystical imaginary creator would have needed some mechanism besides waving a finger. So in terms of probability, both abiogenesis and panspermia would be astronomically improbable, but since life is here (probability of life is 1), then one of these two is the source of it. We have no hard evidence to choose between them.

You've missed the point of the question. I'm not asking whether panspermia should replace terran abiogenesis as an explanation for life on Earth (it probably shouldn't); I'm asking whether it's plausible to claim planetary systems "contaminate" each other in the manner Tyson discussed.

No, I have not missed the point. Since it is one of only two possibilities, AND we have no evidence between either, then it is plausible, because something happened here. My point is, that there is no way to answer questions that estimate probabilities that are extremely unlikely, and have no data to directly support them. Thus Tyson's discussion is plausible.


text:
Palm Tree Identification
I need help identifying this particular palm tree. Unfortunately, I don’t have many details to give, and I’m by no means one to say I’m even an amateur at plant identification. We are unsure of its origin and can only confirm it’s age by how long we’ve resided here in Hockessin, Delaware. The plant is over the age of 14, and it stands a little over 12 feet high. The foliage is composed of single green shoots coming from the head of the plant which descend gracefully and reorganize into what one without knowledge would say is bark. We are looking to purchase another tree of this species or a close relative; there was a recent loss of an identical tree which sat opposed to this one.

Probably not a palm, looks like something in the Agavaceae so for example, a yucca or joshua tree (though not that specifically).  Try searching your local nursery websites for "yuccas" or something similar.  Or show the picture to your local nursery/landscape person or horticulture expert (maybe county extension agent).

I'm not sure about the species, but the staking seems a little intense. Was the other tree staked the same way?

I notice the soil is sandy and there is Opuntia growing nearby.  Yucca and Opuntia like it dry typically, and warm.  I see you are outside Philadelphia PA USA, where there are very cold winters.  This must be a species of Yucca that can take the cold.

Appears to me to be a Yucca tree, from the family Asparagaceae, whereas palms are typically a member of Arecaceae.

After searching various sites about cold-hardy yuccas, and looking at images, I think you have Yucca rostrata or possibly a hybrid of it.  According to Wikipedia it can be grown in zone 5.  Your location is zone 7, but perhaps if the microhabitat is just right it can survive your winters (perhaps the sandy soil evident in the picture helps it survive, since sand drains well).  I suggest you look at the description of the plant and images online and compare it to your specimen to see how well it fits.


text:
Why shouldn't I clean microscope slides with a paper towel?
I've recently bought a microscope and been looking at a lot of bacteria and such, and have quickly run out of clean slides. I've seen videos and articles saying how you shouldn't clean microscope slides with a paper towel and to use an ultrasonic cleaner instead. I don't have access to an ultrasonic cleaner, so I am wondering what is wrong with cleaning them with a paper towel?
Also if anyone knows of any good liquid solutions for cleaning slides that information would much be appreciated.

The main reason to avoid paper towels, tissues, and etc. is that they shed lint (paper fibers) which will be left behind on your slide and eventually interfere with your prep. They look small to the naked eye, but they are not small compared to the prep on your slide.
The other issue with paper towels and etc. is that there might be some particulate matter in the paper that's hard enough to scratch glass or optical coatings. This is more of an issue for optics - especially coated ones - than for cheap microscope slides, but it's something to consider.
If you're not mounting permanent preps then ultrasonic cleaning is probably a bit of overkill - although I have a surplus sonicator and it does a great job on a lot of tasks. It's generally sufficient to rinse the slide with distilled or deionized water and then follow up with (clean) alcohol. Optical purists will say spectroscopy grade methanol, but for home use any reasonably pure MeOH, EtOH or iPrOH will probably do. The main concern, again, is leaving behind particulates or residues. You can allow the slides to air dry if you're using pure alcohol, or use a piece of lens tissue (lint free paper tissue) to help them dry faster. I've also used Kimwipes in a pinch, but they're not truly lint free so not ideal. They're still much better than a tissue or paper towel.

+1. Distilled water, a wipe with Kimwipes if needed, then EtOH is all I use in the lab. Keep your slides in the box they came with, don't expose them.

For reference, a 280-pack of 1-ply kimwipes on fishersci.com is 9 dollars plus shipping. Other purists will still say buy lens wipes, which are like 1200 for $95 on fisher, but I find kimwipes do the job.

Kimwipes do this job quite well, but generic lens paper is quite cheap too - I think I got ~400 sheets on amazon for ~$10 and it's decent quality. Doesn't matter for this kind of cleaning, but for actual optics (if you're even wiping) it can be very hepful.

Methanol is toxic and very volatile, so you shouldn't advise its use without also advising to use it under a chemical hood.


text:
Insect ID, found in shower, northeast USA

I want to know if this is the kind of critter that will lay eggs in the drain and then have larvae emerge from there. We had that a few years ago and it was nasty...

That is a silverfish (Order, Zygentoma). The most common species of household silverfish is Lepisma saccharina. Details can be found here. https://en.wikipedia.org/wiki/Silverfish
They are relatively harmless.