texts: Why would evolution favor blue as a color in bugs?

texts: This question arose when I saw a metallic blue - black bug some while ago. I can't remember the species name now, but a quick google search will show that such bugs do exist. I'm down with green and black - camouflage, right? But what is the case for blue color? What kind of an advantage does it provide so that they have survived to this date?


texts: Definition of a Katal (unit of enzyme activity)

texts:
I am very confused about what one 'Katal' actually is. From Wikipedia,

  "The katal is not used to express the rate of a reaction; that is expressed in units of concentration per second (or moles per liter per second). Rather, it is used to express catalytic activity which is a property of the catalyst. The katal is invariant of the measurement procedure, but the numerical quantity value is not and depends on the experimental conditions. Therefore, in order to define the quantity of a catalyst, the rate of conversion of a defined chemical reaction is specified as mols reacted per second. One katal of trypsin, for example, is that amount of trypsin which breaks a mole of peptide bonds per second under specified conditions."

So if a Katal is a specific AMOUNT of trypsin, then why is it expressed in units of moles per second. This is not dimensionally consistent! An 'amount' could be expressed as moles or mass, but certainly not as moles per second which is like a rate of reaction multiplied by volume...? The units and definition just seem to be all wrong.

If I were to take it that the Katal is the amount of enzyme catalysing one mole of a reaction per second, then this would mean that an enzyme with a smaller number of Katals of activity would actually be more active because less of it is required to catalyse one mole of the reaction per second?


texts: How do I compare the variance of a distribution of species in one area versus another?

texts:
It's possible that this question is better suited for stack overflow, but I think the ecologists on this site might be better equipped to answer it.

I'm trying to study two geographically-isolated populations of the same species. Inspecting the distributions, I see that both are bimodal (there's some seasonality to their occurrence), but the peaks in one population are much higher and much narrower (i.e., the variance of the local peaks is smaller).

What sort of statistical test would be appropriate to determine whether these differences are significant?


texts: What is the convention for indicating genomic primer sites?

texts:
What is the most common notation for indicating genomic binding sites of primers relative to an ORF?

For instance, if I want to indicate a primer like so:

...tccgccGCCCGTCCACACCCGCCGCCagctcaccATGGATGATGATATCGCCGCGCTCGT...
         [ Primer           ]        [ Hs ACTB coding sequence   ]

Should the location of this primer be indicated as -8 or -28 (from ACTB start codon) or something else?


texts: Does the species of snake that eats Amphidromous inversus have chiral dimorphism?

texts: From what I read at Schilthuizen and Davison (2005), Amphidromous inversus is a species of snail that occurs in 2 forms that are nearly mirror images of each other occurring in nearly equal proportions. I don't see any way that could be evolutionary stable if it was only eaten by snakes with a symmetrical jaw because then the snake species would evolve to be ambidextrous and then the snails would lose the selection pressure for being the rarer form but retain the selection pressure for the more common form. I can't find the information anywhere on the internet of what the snake species that eats that species of snail looks like. Have observations shown that that species of snake has a chiral jaw and occurs in 2 forms that are mirror images of each other in nearly equal proportions?


texts:
Can methylation of a promoter induce gene expression in some rare cases?

I've read somewhere that methylation of an intron can induce gene expression (eg. Igf2). How is that even possible?

Thank you in advance!


texts:
I understand that the function of melanin is to protect individuals from sunlight, and that people living in sun exposed areas are darker due to increased production of melanin. But why is the melanin pigment black in color? Wouldn't it have been more useful if melanin was white?

From my understanding, black absorbs more sunlight than white, so if melanin is black, it will tend to absorb more heat (which isn't a good thing in areas with a lot of sun exposure). This will lead to production of more melanin (tanning).

Instead, evolutionarily wouldn't it have made more sense if melanin were white, since not only would the pigment protect the person from sun exposure, but also prevent more sunlight from being absorbed?


texts: Why People have skin color between fair and dark?

texts: According to Mendel's laws traits do not show any blending. So according to his laws people only with fair or dark skin should exist. Do the alleles in this case blend? And why?


texts: Ka/Ks (dN/dS) analysis module for Python?

texts:
From this wiki article:

  In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the number
  of Nonsynonymous substitutions per non-synonymous site (Ka) to the
  number of synonymous substitutions per synonymous site (Ks), which can
  be used as an indicator of selective pressure acting on a
  protein-coding gene.

Question:

Are there any modules/packages available in Python for doing Ka/Ks analysis? I wish to carry out whole gene Ka/Ks analysis and then maybe "codon level" Ka/Ks analysis (i.e. within gene via sliding window).


texts: Could anyone please explain to me, why the nail which is nailed in a coconut tree is not raised from ground level, when the tree is growing up?


texts: Cloning problem. Digestion test at the end of the cloning is always negative

texts:
I have a problem with my cloning, I'm trying to clone a 483 pb in a pSecTag vector with restriction sites HindIII and BamHI. Here are the procedures I'm doing:

•   I introduce the restriction sites BamHI and HindIII into my insert by PCR with Pfu (blunt end polymerase) and gel purified it.
•   I clone my insert in a pJET1.2/blunt vector. I get enough colonies and I tested few of them with an internal insert primer and a vector prime via PCR. The results are positive.

The problem came when I digest my insert from pJET and try to clone it in a pSecTag vector.

•   I digest my insert and the vector with HindIII and BamHI in Buffer Red during 1.5h at 37ºC (fermentas). I purify the insert and the vector from the gel and checked that all fragments run at the correct size on a gel. All correct.

•   I do the ligation (T4 DNA ligase) using a 5:1 Insert:vector and less tham 100ng of total DNA. The ligation (20ul) is performance at 22ºC for 30 minutes.
I get few or not transformant colonies. When I get colonies, I tested them by PCR:

**
•   With internal primers, the result are positive

With a primer for the vector the result is negative.
The strangest thing is that when I use pJET primers that do not anneal in the pSecTag I get positive results.**

For transformation i'm using chemocompetent DH5-alpha, with a heat-shock of 42°C at 45 seconds. I tested the bacteria with a plasmid before using them.

I change condition several times but always obtain the same result. I follow all the protocols but I don’t get my construction.

Anybody knows where the problem is? Thank you.


texts: Are there any sustained efforts to model existing ecosystems?

texts:
Are there any ongoing, sustained efforts to obtain enough data about an ecosystem or part of one to build a viable computer simulation of it? All I can find (e.g. in Brazil or by google) appear to be sandboxes for demonstration or experimental purposes.
What I envision is a true model that can predict the future development of an existing system, and of course run simulations to predict the impact of certain external changes: Deforestation, temperature and precipitation patterns, introduction of non-native species etc.
Such a model would require a fairly detailed and complete biological inventory as well as detailed knowledge of the species' interactions, and a detailed map of the physical and chemical makeup of the location or region (water, ground, atmosphere, radiation). This would obviously be a vast undertaking, but with the potential of tremendous insights. Last not least, such a model would be a tremendous planning tool.
Are there any projects attempting this?


texts: What is the name of this species which I found in an Epipremnum (Money Plant)?

texts: I found a very rare specie (at least from my knowledge of species and research) today in a money plant (Epipremnum plant) in my kitchen garden. This caterpillar was on it. Please help me with the name of this species and any information about it.


texts: What causes Pseudomonas fragi to smell sweet?

texts:
I am working with Pseudomonas fragi and I could not help but notice that it smells sweet, which probably explains its species name 'fragi' from 'fragum', strawberry in Latin.

Does anybody know what causes this bacterium to smell sweet? It must be some volatile compound that they release in the air? Why would they do that? Do other bacteria release odorant molecules? If so, why?


texts:
I am sorry if this question is too general, and does not have any concrete answer.

I was explaining to my non-biology-background friend about plasmids and how they are picked up by bacteria from the remains of other dead bacteria during stressful conditions. This is when this question arose:

Why would bacteria pick up plasmids released from the dead bacteria, as this means that these plasmids either did not help it survive in those conditions, or could have in fact been the cause of their death? This also lead to the question of whether plasmids can be lethal? (I believe there could be, for example plasmids which are translated into proteins which are endonucleases which would probably kill the bacteria, yet I am not sure).

Moreover, if this sort of plasmids exists, then why could we not engineer them specifically and use them as medicine as an “antibiotic”?


texts: What's the difference between mutation and substitution rates?

texts:
The Wikipedia section on substitution rates (shown below) isn't clear to me. What's the precise definition and difference between mutation and substitution rates, and how do they relate to each other?

  Substitution Rates

  Many sites in an organism's genome may admit mutations with small fitness effects. These sites are typically called neutral sites. Theoretically mutations under no selection become fixed between organisms at precisely the mutation rate. Fixed synonymous mutations, i.e. synonymous substitutions, are changes to the sequence of a gene that do not change the protein produced by that gene. They are often used as estimates of that mutation rate, despite the fact that some synonymous mutations have fitness effects. As an example, mutation rates have been directly inferred from the whole genome sequences of experimentally evolved replicate lines of Escherichia coli B.

Further context behind this question here.


texts: What is the correct nomenclature for expressing a genotype where a recombination event may occur?

texts:
Given an example punnett square:
 -------------------------
 | x   | A-b     | Y     |
 -------------------------
 | a-B | A-b/a-B | a-B/Y |
 -------------------------
 | A-b | A-b/A-b | A-b/Y |
 -------------------------
 | a-b | A-b/a-b | a-b/Y |
 -------------------------

What is the correct nomenclature to express the genotype prior to putting it into a punnett square? The parent's genotype looks like a-B/A-b x A-b/Y except I want to show that a recombination event can occur, yielding the third row in the punnett square table.
This is relation to my previous question about how to calculate recombination frequencies.


texts:
On the left, is my histology book, on the right there's qoura (the internet).
My histology textbook says that "unlike glycoproteins, proteoglycans have attached GAGs which often comprise a greater mass than the polypeptide core"

What I found on qoura is "The carbohydrate content of proteoglycans (10-15%) is far less than glycoproteins is (50-60%)"

I tried googling the question but couldn't find the answer so which of these is correct ?


texts: Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?

texts:
The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl.

When the phosphate group is condensed with glycerol to make a phospholipid, is the hydroxyl from the glycerol molecule taken or the hydroxyl from the phosphate group taken?

I believe it's related to the difference of electronegativity of oxygen and phosphorus which causes unequal sharing of electrons between atoms, thus making a hydroxyl from one side easier to get taken off than the hydroxyl from the other side is.


texts:
I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time to ask questions or go over examples. One topic is transition/transversion ratio, and I'm not 100% sure I'm understanding it. Do you just compare the first symbol of string 1 to the first symbol of string 2? What if the two symbols you're comparing are the same? Do you just ignore it? Let's say string 1 is ACGATG and string 2 is TCAGTG. Would the ratio be 2/1?

Here are the comparisons I made.
Transitions: G-->A, A-->G,
Transversions: A-->T,
Neither: C-->C, T-->T, G-->G

Is this correct or am I completely on the wrong path?


texts: What is the standard electrode potential of human blood?

texts:
Healthy humans have a pH of around 7.4 (slightly basic.) But if you hooked up the blood as a battery how much electric voltage would one generate, what is the standard electrode potential?

This seems to me like it should be important for stuff such as transporting ions across the cell membrane.

If I think about it this question basically comes down to if things like iron tend to dissolve $\ce{Fe -> Fe^{2+} + 2e^-}$ (SEP of 0.44)  or precipitate $\ce{Fe^{2+} + 2e^-->Fe}$ in human blood.

Because of important chemicals like haemoglobin I think the SEP should be around 0.44 but differs depending upon whether cells are absorbing oxygen from it or recharging it with oxygen. Maybe this would even vary depending on whether heavy exercise is happening.


texts: What is the biochemical reason for mental fatigue?

texts: Is it known exactly why the brain needs sleep? What's dropping low / going high when we experience mental fatigue? I can see why low glucose could result in mental fatigue, are other reasons known?


texts: Why are probionts not considered cellular life?

texts:
I am currently studying Prescott's Microbiology, 10th edition, by Willey, Sherwood, and Woolverton. Chapter 1.2 Microbes Have Evolved and Diversified for Billions of Years presents the following figure:

The authors then ask the question: Why are the probionts pictures above not considered cellular life?

I'm unsure of why the probionts are not considered to be cellular life. If I'm not mistaken, the probionts contained ribozymes, no? This means that they have the capacity to catalyse their own reproduction. And, according to the figure, later probionts also consisted of proteins, so I'm presuming that catalysis and reproduction were not issues here.

I would greatly appreciate it if people would please take the time to clarify this.


texts:
Can anyone explain why inside plasmid mapping software the annotations are layered under each other, I am confused as to why there are essentially two layers within the map, for example in the image below.

The bottom red layer is annotated as "DsRed2" and the top yellow is "LacZ-DsRed2 fusion expressed in E. coli". Does this mean that the red layer is inserted into the original LacZ gene or some sort of mutagensis...? Any explanation would be real helpful.

Second Plasmid design

Third Plasmid


texts: Is it possible to separate the binding and catalysis of an enzyme in two steps?

texts:
Is it possible to do the following:

Enzyme E binds to its substrate S without catalysis;
Add a controllable stimulus, such as light, adding or removing chemicals;
The enzymatic reaction is triggered by the stimulus.

The word controllable means I can add the stimulus at any time I want. Before I add the stimulus, the enzyme keeps binding to the substrate specifically but no reaction takes place.

This is what I mean by separating binding and catalysis in two steps.

In the case of allosteric regulation, some chemicals will inhibit the activity of an enzyme. For example, ATP will inhibit the activity of phosphofructokinase 1 (PFK1). But I'm not sure whether this allosteric inhibition also hinders PFK1's binding to the substrate, which does'nt satisfy my description above.


texts: I saw this flower in Pulau Ubin in Singapore. Can anyone identify the species of this flower?


texts: How can some enzymes work faster than the diffusion rates of the molecules it catalyzes allow?

texts:
Quoting Wikipedia: "Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible." Which are those enzymes and how can they be so fast?

One example is catalase which Lionel Milgrom discusses in Water Journal no. 7.


texts: By what mechanism is Streptococcus bovis acting as a risk factor for colorectal cancer?

texts: Streptococcus bovis bacteremia/endocarditis is considered a risk factor for colorectal cancer. What pathophysiological mechanism may link the two together?


texts: Are there histones present in the cytoplasm?

texts:
In this paper the authors depleted core histone heterodimers H3-H4 at 90 % from the cytoplasm of Xenopus oocytes. They state that their concentration is in the order of 6 uM.

My question is, are histones found in cytoplasm besides the nucleus location? (ignoring the newly sythesized ones), and if so, is there any known function?


texts: What are the major steps of follicular B cell development

texts:
This is a learning objective in my curriculum, and after having spent two hours trying to answer it for myself using official course resources (many of which are online, but some of which are behind paywalls and so may be inaccessible to other community members), it's clear to me that I need some assistance.

So I would just like to know what is the latest understanding of the major steps of follicular B cell development in mouse and human.


texts:
In Rieke et al, Spikes, p. 31, I found this instructive picture showing and explaining phase-locking.

I take it for granted, that phase-locking is possible only upto a maximal stimulus frequency (well below the maximal firing rate of the neuron). Beyond this, phase-locking must break down: the neuron cannot follow the stimulus anymore.

My questions are:

Does this maximal frequency count as a characteristic of a neuron (type of neuron), and what is its name?
Are there typical values of this frequency, e.g. as a fraction of the maximal firing rate of the neuron?
Does the breakdown of phase-locking typically occur suddenly (as a phase transition) or gradually?
What happens beyond? Does the neuron follow a virtual stimulus of 1/n of the original frequency (which would be in phase with the original stimulus)? Or does chaotic firing take over?


texts: Are unilaterally deaf people able to determine where sound comes from?

texts:
My question is on people deafened in one ear, but normal hearing in the other.

Time and level differences between the two ears are only part of how the human body can localize the source of the sound. So what other factors are there and are they enough to help accurately determine the location of the sound for unilaterally deaf people ?


texts: Is a minimum size/complexity necessary for an organism to exhibit territoriality?

texts:
A follow-up to Is territoriality only the domain of the male of a species?

I've seen a large butterfly chase a different kind of butterfly around - it may, or may not have been territoriality. Is there a minimum scale of size, sentience(?) an organism must attain to exhibit territoriality?


texts: How do you biologists draw a protein when you write a paper?

texts:
The following is one example of protein structure diagram that I want to put in my research paper. I took this from

Koniev, O. & Wagner, A. “Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation.” Chem. Soc. Rev. 44, 5495–5551 Jan. 2015, DOI: 10.1039/C5CS00048C

As a Chemist, the only drawing tool I have used so far is ChemDraw and it does not provide such protein structure; The only protein diagram it provides is a Y-shaped IgG. How do you biologists draw such convoluted proteins when writing a paper? Do you use a specialized software for this?


texts: Are there comprehensive species descriptions on most species?

texts:
I was having a browse through Wikipedia and noticed how even the rarest, hardest to find species of bird have comprehensive articles and comprehensive descriptions, but other species like the 1400 Andrena species have next-to-no information.

I tried to do a search for resources on individual species of Andrena bees but found very little - at best a short description and the name of the entomologist who described it. Is there a place I could go to find comprehensive resources on these bees? If not, why are the available resources on these species much less comprehensive than those on other species?


texts: Why do stranded marine mammals die so quickly?

texts:
Mammals have lungs, so do marine mammals. Nevertheless some marine mammals seem to die rather quickly when they strand on a beach.

As they have lungs and can breath while on land, why do they die so quickly? Not being in water only restricts them from food.

Do they maybe try to get back into the water so rudely that they get hurt by rocks and/or break bones? Pressure difference doesn't seem to be a problem as they can jump out of the water as well.

I was wondering after reading this article on stranded pilot whales that got spot but died rather quickly after.


texts: What regulates these two methods of splicing?

texts:
Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can intergenic trans splicing can do this starting from multiple gene sites?

What regulates these two "non linear" gene combination, transcript-splicing processes?


texts:
Wikipedia, and Space.SE seem to indicate humans become infertile in space due to the increased exposure to cosmic rays. Knowing as we do that Antarctica is holey, and subject to increased radiation (atleast UV if not broad-spectrum), I find myself wondering whether any studies on fertility were ever conducted on that continent.

So ... Are there any studies on the fertility levels of humans/mammals as a function of their stay at Antarctica?


texts: Does self replicating RNA occur in nature?

texts: Do self replicating, independent RNA strands occur in nature? They are often used in laboratory experiments but I have not heard of any wild populations. I mean independent of other organisms and able to reproduce on their own in the environment. I.e., not just viruses or transcription RNA.


texts: Why do people dying of immune deficiency diseases appear sick?

texts:
Please forgive the obviously silly appearance of this question, and/or of the tenor which may come across as flippant or dismissive of real world suffering. My intention is none of the above.

As a layperson, I have always understood that the expression of our various colds/flus etc, while frequently mis-understood as being caused by the virus, are actually just manifestations of our own immunity fighting same.  In other words, all the snot, and fever and inflammation are not caused *by the virus, they are a reaction *to the virus, as we fight it off.

My question then is why do people with AIDS (or similar immunity destroying affliction) appear sick?  If they have weak or non-existent immune systems, following the above logic, would one expect to see them passing away while looking entirely healthy?


texts: What kind of owl does this moth look like?

texts:
I found this moth and I noticed that it looked like an owl to me and remembered something about how some moths camouflages look like predictors?  What kind of moth this is and what owl does this moth resemble? Would this moth be a newer species than other moths because it came after the owl? The wing span is 5.5 inches across. The eyes of the wing are transparent allowing light to pass through like reflecting eyes.

North American Great Horned Owl


texts: What kind of big bird is this seen walking around Taipei?

texts:
I've seen this humorous sign warning drivers to keep an eye out for birds many times, but today I finally realized what it's talking about!

This is a large bird and I've seen it all around Taipei in gardens and green areas. It's not shy of people unless you get too close.

I'd guess it's about 30 cm tall when standing upright, but it often is bend down looking for things to eat. It takes one step at a time, sometimes very slowly, and it's head moves out-of-synch with its body as it hunts for food. I am not sure if it can fly, I've only seen it on the ground, and I've never heard it make a sound.

It's various shades of brown and tan, and just like the cartoon on the sign it has long feathers projecting backwards from its head. That can be seen in the center top of the photo montage.

Any idea what kind of bird this is?

These are cell-phone photos from the closest I could get without it getting nervous.

"Life imitates Art far more than Art imitates Life" Oscar Wilde


texts: How often do retrotransposons jump in human cells?

texts: If I followed the life of a typical cell in my body, how many retrotransposon jumps would I observe per day? I'm only interested in a rough order-of-magnitude estimate: should I think of it as a common event that happens basically all the time in most of my cells, or is it a rare event that happens only occasionally in my body?


texts:
My eyes are very sensitive to flashing lights - for example I'm always the first person to notice that a fluorescent tube is about to fail because I see it flickering when other people can't.

When I'm driving at night, I perceive LED rear lights on cars as being a series of unconnected dots when I scan my eyes quickly across the scene. Evidently, many, if not all, LEDs are actually flashing at a high rate which most people don't perceive.

It almost seems as though I have a higher "refresh rate" than most people. How unusual am I? What is the physiology of it?

EDIT: I suppose what I find most fascinating is that at times when I see a trail of flashes, the spacing between them is remarkably consistent. This implies to me that there is an incredibly accurate timing mechanism somewhere in my visual system that is taking "snapshots" with clockwork regularity - probably between 50 and 100 samples per second. I'd like an insight into this "clock" and why mine seems to be faster than anyone I've ever met.

This similar to what I perceive:


texts: What happens during the fermentation process of the eco-enzyme?

texts:
introduction about the eco-enzyme
I have tried to make several ones at home, no matter what I am using, lemon or pineapple peels with brown or white sugar, the final products all show the similar brown colour.
It seems to me that no matter what type of fruit peel or sugar used as the material, would all lead to a similar brown colour.

So I am curious about:
Why the colour of the final product is different from normal homemade fermentative fruit or vegetable?
Are the microbes  involved in fermentation have some difference between the both? Is this because of the difference between enzymes that are produced by bacteria?

I have tried to find the appropriate and availible resource about microorganisms that may take part in the fermenting process of fruit and vegetables, but I am still not sure which one would take part in which step of the eco-enzyme.
(In my observation, some white tiny spots and big speckles began to float on the the surface of the liquid after a week, before opening the container to release gas and make it become aerobic).

What could be the role of fruit peels aside from being the source of microbes,if it will also produce enzymes to influence the chemical reaction?

Is the eco-enzyme really an enzyme?


texts: How to supply oxygen to a culture vessel?

texts:
I'm reading this paper:
https://www.jstage.jst.go.jp/article/jpsa/51/3/51_0130043/_pdf

From day 17 of the culture period until hatching, pure oxygen was supplied at a flow rate of approximately 500 ml/h through the previously installed plastic tube.

What kind of hardware is used to achieve this ? I would like to test this method, but I don't have access to laboratory equipment ( meaning .. I'm not going to buy expensive equipment for this hobby project..)

I'm used to incubate eggs inside an incubator, and day 17 is approximately the day when they start chirping, and sometimes hatching, so it's my understanding that at this point the chick starts to use its lungs, and breaks the shell in search of oxygen.

Also I don't understand the airflow in this setup: when I supply 500 ml/h of oxygen, where does the displaced gas go ?


texts: How can site-directed mutagenesis be used to suppress the production of anti-antibodies?

texts:
In a previous post of mine, I asked how to supress the creation of anti-antibodies in vivo. In the answer, it was mentioned that site-directed mutagenesis could be used. Currently, I can't find mcuh on how to do so... How does this work?

Update: As people want to know where this idea is coming from, here is the link to my previous question about it.. look in the answer for more info:

How to inhibit formation of specific antibodies (to antisera)?


texts:
N. Shubin's Your Inner Fish makes the point several times that there is a lot of functional similarity between some seemingly remote gene cousins. If that needed reinforcing we have the spider-goat, whose milk contains spider's silk, and a knock-in mouse whose vision resembles that of humans.

The last two examples are interesting because, as I recall, nothing beyond the gene insertion (already a feat) had to be done to confer the extra/new capability. The machinery at the cellular level (for the mouse to perceive a new color or for the goat to somehow process the milk) already existed.

My question is whether it might not be possible in theory to create a mammal with the ability to photosynthesize? If this is a polygenic trait perhaps it would be accomplished in multiple stages. I realize an answer here would be highly speculative but a careful answer might cast some light on the process of conferring new traits/abilities in this way.

While I see no obvious benefit of creating a photosynthesizing mouse, at least the food bills for their maintenance might be low. This sounds like a joke but it's not a trivial benefit.

Thanks for any insights.


texts: Why people like to see pornographic scenes, but do not feel the same about eating scenes?

texts:
This question may seem funny, but I think biology must have good answers.
I think no more explanation is needed.

I really thought about this and searched for an answer, but there is nothing yet.
If you know some thing about or have some thing which may lead to good answer(s) please express.

Also, do animals portray the same behavior in such situations?


texts: What happens to the cell during post-hypothermia?

texts: A friend of mine said that the cell membrane somehow changes after rewarming from hypothermia and that the body does not recognize it's own cells, thus leads the immune system to attack it self. Is this true? And do anyone know how/why the cell changes?


texts: How does the pancreatic beta-cell know how much insulin to secrete in response to glucose?

texts:
How do $\ce\beta$-cells know how much glucose is in the blood?

I know that when glucose enters a beta cell it triggers the cell to produce insulin. $\ce\beta$-cells trap glucose by converting it into glucose-6-phosphate, this means $\ce\beta$-cells actually consumes glucose.

So my question is: how do $\ce\beta$-cells decide when to stop producing insulin? (To do that the cells must know the level of glucose in blood, right?)


texts: Recently while cleaning my garden, I saw this worm like creature which resembles a leech but is humongous in size if I compare that with commonly found leeches in my area, Kolkata, West Bengal, India. I did not see something like this before so, I captured a snap of this creature and posting it here to know more about it if someone can give me a hint.


texts: What are the functions of magnetic bacteria?

texts: I'm trying to understand why are bacteria "equipped" with magnetosomes ("intracellular organelles in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field") and why and for what do they need such organelles.


texts: Any nerves/fibers in foot similar to ulnar nerve in elbow?

texts:
I just noticed that when I gently run my fingers along the top of my right foot, I get the same exact "funnybone" sensation in my toes that I get when I hit the ulnar nerve in my elbow.

So I ask: are there similar nerves/fibrous structures running along the top of your foot as whatever is going on in your elbow with the ulnar nerve?

Not medical advice; just curious about the anatomy here.


texts: Is a neurostimulation implant for the soft-palate component of obstructive sleep apnea plausible?

texts:
There are currently ongoing clinical trials for neurostimulation implants designed to keep the tongue from blocking the airway in obstructive sleep apnea.  The nerves for this are in the neck and surgically accessible.

Where are the nerves that control the soft-palate, and would it be plausible to implant a similar device for them (given years of development obviously)?


texts: Why don't breast enlargements leave any marks of surgery on breasts?

texts: If we get stitches, we get marks left on the skin, but there are no marks for breast enlargements. I saw a YouTube video about a breast enlargement wherein a doctor makes a cut. Where does the cut mark go after surgery?


texts: What are gram negative and positive bacteria?

texts:
I've just finished a course of double antibiotics for Helicobacter pylori in my stomach.  I looked up H. pylori and found that it was a gram-negative bacterium.  I looked up gram-negative and didn't understand the definition.  I assume that if there are gram-negative bacteria then there are also gram-positive ones.  Can someone explain the terms gram-negative and gram-positive in basic, layman's terms?

Thanks,

Sachin


texts: Why there is unusually big leaves on a single tree branch

texts:
I have a freshly planted katsura tree - in general it has leaves that are 1-2 inches in diameter.

But one single branch has grown disproportionally longer than others and leaves on this branch are up to 4 inches in diameter

Why is that? Should I trim it?


texts:
As far as i know hemispherectomy is a rare procedure when individual will going to have half brain removed in very young age. Because brain has quite remarkeble neuroplasticity patient usually will survived only with half of brain.

My questions is?

How much brain can be removed to not to negatively influence brain activity?
Does anatomy hemispherectomy alter secretion of glands for example pineal gland?


texts: Doubt on genomic code for nucleosome positioning?

texts:
I was reading "A genomic code for nucleosome positioning" (by Eran Segal et al). And I am having 2 doubts.

The figure(b) in this image from the paper shows the graph of fraction (3-bp moving average) of AA/TA/TT dinucleotides of nucleosome dna sequence they analysed statistically as far as I understand.
What is 3-bp moving average here?
I also don't understand how they chose 0th position (the so called dyad).
Also what does it mean to have oscillations (correlation?) in this graph?

UPDATE : I am adding some supplementary information related to finding the dinucleotide fractions. Still I don't understand why is the fraction found so?


texts: How to quantitatively measure work done by a biological system?

texts:
Thermodynamic efficiency can be expressed as the ratio of Work done(W) to Energy invested (Q).

Thermodynamic efficiency= W/Q

How can one measure work done by a biological system?


texts:
Most cases of sex chromosomal abnormalities in humans have a case of learning disability or less developed cognitive abilities. Wikipedia says:

When additional X and/or Y chromosomes are present in 48,XXXY, 48,XXYY, or 49,XXXXY, developmental delays and cognitive difficulties can be more severe and mild intellectual disability may be present

So, the question is simply this: How is cognitive ability linked to the presence of sex chromosomes?


texts: Do kids under a certain age not hear the warning beeps that smoke detectors make when they are running out of battery power?

texts:
I've always been very annoyed by those regular single beeps that smoke detectors start doing increasingly often as the batteries start to run out, to warn (and annoy) the user to replace the batteries. They drive me insane.

Lately, I've been observing how a bunch of kids seem to sit in a room and just ignore those beeps completely, even after I point it out and ask them to really listen. They can't hear them. I seriously believe that they just don't physically hear them. Kind of like those dog whistles.

Is this backed up by science? Do kids under a certain age literally not hear those "low battery" warning beeps? Is this maybe per design, even? If so, why? Isn't it important that as many humans as possible are annoyed by this so that they replace the old batteries with new ASAP?

It's really frustrating to me when they don't even hear it, but I hear it very well. I hate it so much.


texts: What enables azacitidine to incorporate into both DNA and RNA?

texts: I did a mini-project on the drug azacitidine for my pharmacology class, and I learned that azacitidine has the ability to incorporate into both DNA and RNA. I think this is really unique because a similar drug, decitabine, is exclusively incorporated into DNA. Are there any specific physical/structural characteristics of azacitidine that allow it to affect the structure and function of DNA/RNA? Any help would be greatly appreciated!


texts: Is it possible to build a hive for bumblebee or hornet

texts: People commonly build hives for honey bees and it works . Is it also possible to build a hive for a bumblebees or hornets ? Should it have any special shape or form or is it just impossible ?


texts: How much energy is used to construct a pound of fat tissue?

texts:
A widely cited figure is a pound of fat contains 3500 calories of energy in fatty acids.

However, a pound of fat also contains adipose cells, arranged in adipose tissue, connective tissue etc.

When a human breaks down fat to use as energy, from what I understand it doesn't break down the fat cells, just liberates the triglycerides stored inside those cells.

Those fat cells, and connective tissue took energy to assemble as well.

How much energy is used to create a pound of fat tissue?

Let's assume that all the cells and the triglyceride stored inside them are created from scratch.


texts: Carrying out a BlastP on ORF and achieving hits but 2 have the exact same score, evalue and query cover?

texts: I'm working on a project in my university and we were all given different sequences to work off of. I am meant to compare my blastN to my blastP result. However, when I carried out my blasP I got many hits but the top 2 hits had 100 percent cover, 100 percent identity and 0.0 evalue. I am meant to work off of one of the species I achieved from blastp to compare to blastN. How do I know which one to compare to see what's most significant to my blastn species? I have to continue on and use clustalw and phylogeny after so I need to be sure.


texts: Where can I find a picture of the inflorescence of Epipremnum aureum (golden pothos)?

texts:
Epipremnum aureum (golden pothos) is a very popular house plant - attractive and almost impossible to kill.

Also, it is a flowering plant with flowers produced in a spathe up to 23 cm (9 in) long, according to Wikipedia.

I have been trying to find further documentation of these flowers, in particular a picture, without success. Can anyone help?

(Google image search produces some stock photos that claim to show E. aureum flowers but I am skeptical about these.)


texts:
Context: I have seen promoters used to have gene therapy viruses target specific cells, so I am referring to that apparent function of theirs.
As an example I have seen GFAP promoters used for targeting astrocytes (I have seen this in many more papers but this is the first one I found on google).
I am curious what the purpose of the EF1-alpha promoter in a lentil/retro/Adeno-Associated virus for gene expression is?
It would seem that it is often used for targeting embryonic stem cells, but then I had also seen else where that "The Lenti-X Expression System (EF1α Version) enables you to produce exceptionally high titers of recombinant lentivirus for expression of any cDNA in any cell type susceptible to lentiviral transduction." This made me think that perhaps since this promoter 'targets' stem cells which later turn into any type of cell, that this quote meant that the EF1-alpha promoter can be used to indiscriminately target cells? Is this true?
Please forgive any incorrect assumptions on my part, I am a novice in this field.


texts: Can the word phalanx also be used to describe the finger bone plus the soft parts around the bone?

texts: I was talking in an SE chatroom about fingers, and not being a native English speaker, I had to look up the word used for the part of a finger from the tip to the closest knuckle. I came across the word "phalanges", but the Wikipedia article specifically refered to this as phalanx bones, i.e. just the bone and not everything around it. Can this term also be used to describe the bone plus all of the softer parts around it like the muscles, blood vessels, skin and nail? If not, is there a more commonly accepted biological term for the bone plus the soft tissue around it?


texts: What happens to neutrophils in whole blood stored for transfusion?

texts:
The lifetime of neutrophils is normally quite short, 3-5 days in vivo (link).  On the other hand, whole blood can be stored for a fairly long time, up to 35 days (link).

What happens to neutrophils in whole blood for transfusion that was stored for more than 5 days?


texts: How would a herbivore's digestive tract differ from a human's? What are parts (organs, tissues, etc.) or enzymes that can't be found in one but is in the other? Also, is it correct to say that a herbivore's digestive tract would be more complex than a human's because herbivore diets tend to  contain a lot of complex carbohydrates to digest?


texts: What would cause a single white eyelash?

texts: I couldn't find a paper who could give me the explanation. Unfortunately, according to my search, it seems there are not many reported case, particularly for the younger population (<30). Would stress cause this?


texts: Why is the total length of Introns greater than the total length of exons?

texts:
I have just been reading that typically the total length of the Exons of a split gene is very much smaller than to total number of its Introns.
Could anyone please explain why this is the case if its correct, why are some genes composed of more non coding DNA(intron) than coding DNA.
Thanks


texts: Why do you need to calculate the lane normalisation factor when doing western blot data analysis?

texts:
I am learning about western blot data quantification from some online resources. I have read about methods to normalise the data.
I have seen in a number of resources, such as this handbook and this video when normalising western blot data, they use a lane normalisation factor. For example, if using a total protein stain to normalise the integrated density of your target protein bands, they first obtain the integrated density of all the lanes stained with the total protein stain. Then they find the lane with the highest integrated density value. For each lane, its integrated density value is divided by the highest integrated density value - the resulting value being the normalisation factor of the lane.
Then when doing the normalisation, for each lane, the integrated density of the protein band of interest is divided by the lane normalisation factor.
However, I am not sure what is the reasoning behind calculating the lane normalisation factor. Why can you not just divide the integrated density of your protein band of interest by the integrated density of the total protein stain region for each lane?
Any insights are appreciated.


texts: What does the empty space in the bamboo stem do?

texts: Is the empty space inside a bamboo stem a xylem? And why is the space so large?


texts: Can the human body enter "Power Save" mode?

texts:
Once a year, I am fasting for 24 hours. No food or drink at all for whole 24 hours.

Recently I thought about what is happening to me during those 24 hours, and realized there might be something strange going on. I will try to describe the things I find strange:

I do not feel thirst or hunger at all. Not even after 20 hours.
I still urinate after 10, 15, and 20 hours, and unlike what I would expect from not drinking, the color is not very dark. (actually, same as when I drink normally)
I can still perform energy consuming tasks after 20 hours without eating or drinking anything. I'm not talking about running in the park or lifting weights, but I can walk, do house chores etc, and only after 20 hours or so the body starts to "protest" in the form of headache.

All of the above led me to think that maybe when knowing it's going to be deprived of energy, the body enters "Power Save" mode, allowing it to function as usual under those conditions? (to a limit of course, but still - I would expect hunger, thirst, and headaches to appear few hours into fasting)


texts: Can you help me to ID this tortoise? It was walking around near to my house and then my mom found it, so we'd like to know more info. Its Straight Carapace Length is about 5+ inches. Found it in mid-Mexico (Guanajuato state). Most part of the year we have a warm weather.


texts:
Who (and in which article) was the first to reformulate Hamilton's rule using the letters $B$ and $C$?. See below comments on this reformulation.

Hamilton, in his 1964's article gave a mathematical formulation to explain the direction of social traits. Below is its formulation. Note: Hamilton used quite a complicated formulation, I hope I am not misunderstanding its meaning. Please let me know if it is the case.

$$R\cdot\frac{dw(x,y,z)}{dx}>\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual draw from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again).

Most often this formula is expressed in the following form:

$$RB>C$$

$B$ and $C$ are called cost and benefit of the social trait. I believe that $B$ and $C$ are often not understood as a consequence of a change of the social trait but rather as a cost and benefit of carrying the social trait (compare to not carrying it).


texts: Is there any way to differentiate between a contractile and a non contractile vacuole by observation alone in any given organism

texts:
I have read about distinguishing them using osmotic experiments in books and here as well.
But is there any thing common (on a biochemistry level) from which I can tell if a vacuole is contractile or non contractile irrespective of the organism taken and only by observing?


texts:
Can Cannabidiol be used to steady shaky or nervous hand for precision work like surgery?

I have used it for shooting pool/billiards and I'm not sure if it is a placebo or it is helping? but I am more steady.

I have seen where Cannabidiol helps this man with Parkinson's stop shacking.
https://www.youtube.com/watch?v=rAdDdTZuNA8


texts: ID of a pair of similar-looking birds in NT, Australia

texts:
I spotted these two birds in Yellow Water, Kakadu NP. They were not in each other's vicinity, so it's not a pair in the sense that they were mates (not that I can tell at least :-).

Their appearance is quite similar, so I'm expecting they are the same species of bird. They look like egrets to me, which are common water fowl in the wetlands of Kakadu. However, they may in fact be different species altogether. One has these speckles on the wings, the other one doesn't, by the looks of it.

Can anyone help me ID these birds?

Where: Yellow Water Region in Kakadu NP, Northern Territory, Australia;
Size: Not too big, my guess is about 20 to 40 cm from beak to tip of the tail (about a foot or so);
When: Southern hemisphere's spring, early September; the end of the dry season;
Time of day: afternoon.


texts:
Could someone help me understand a few concepts related to apical dominance
1) why auxin is a dominant over other hormones?
2) how exactly the mechanism of apical dominance works?


texts:
This picture shows the development inside a bird egg:

This shows the connection of the embryo to the yolk sac.  Does this mean birds have navels?  And if so, what happens to the umbilical cord once the bird hatches?


texts: Why can't cell division happen the other way around?

texts:
Mitosis in eukaryotes happen in this order: DNA replicates and then the cell divides. Why doesn't it happen in reverse order (i.e., cell divides and then replicates the DNA)?
I am talking about diploid cells.
Why has evolution favoured the first way?


texts: Analytical Methods for Estimating Probability of Fixation

texts:
The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to remember the methods that exists and what are their assumptions.

For example some use $P=2s$, this obviously cannot be right for be values of s, neither for deleterious mutations, and therefore, this approximation seems to make sens only for big population size. Haldane developed a method to calculate the probability of fixation based on the assumption that the fecundity follows a binomial distribution. Kimura used diffusion equation to approximate the probability to fixation. There might exist other solutions. I don't think I ever seen an equation that allows for varying dominance effect $h$.

Can you make a summary of the methods you know for calculating the probability of fixation? Don't forget to highlight the assumptions. A comparison between the accuracy of the different methods would be great as well.


texts: Do identical twins have the same fingerprint?

texts: When there is every thing same from their genes to their phenotype so then why they don't have same fingerprints?


texts: If humans had cellulase would they be able to digest grass?

texts: Cellulase is an enzyme capable of breaking cellulose. If humans were able to produce cellulase in our stomach would we be able to digest grass? If not, what more things would we need in order to digest grass?


texts: Free software for measuring parts of an image?

texts: Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? Would the software be able to export these data to a spreadsheet?


texts: How much time does HIV live outside the body?

texts:
I'm wondering HIV viability outside the body of an infected person, for example in a knife that contains blood of an infected person, with N virus cells. (N could be for example, 1000).
Some virus might live more than others, then I'm asking the half-life of it.


texts: I just learned that ATP can not be stored in excess and is only made by the body when it is needed. What makes ATP, like glucose and fat is what is stored under the skin or wherever. Now why cant the body just produce ATP and store it for heavy, heavy exercise when it would advantageous for it to be ready rather than it going through the production phase and then used. When I say ATP storage I mean in large amounts.


texts: There has been a warning about E. coli contaminated water in South Florida. Now I'm wondering are there empirical data or historic cases which show a correlation between E.coli levels in tap water and risk of infection in the population drinking this water. Which pathogens, that could be transmitted through tap water, are common in this area?


texts:
I am a bit confused.
During Meiosis, DNA is replicated to form a cell with half the DNA and likely to have variations.
But since the replication process of meiosis and mitosis are the same, why do DNA in different cells of an individual organism not have variations? Or do they have variations that are just not expressed?


texts: The ability to taste PTC is due to a single dominant allele "T". You sampled 215 evolution students, and determined that 150 could detect the bitter taste of PTC and 65 could not. Assuming this trait is in Hardy-Weinberg equilibrium in this population and that there are only two alleles, calculate the number of heterozygotes for this trait there are in the population.


texts: Are there any real life instances of kidney organoid transplants in human?

texts:
Googling the terms "kidney organoid", "artificial kidney" etc. shows quite a huge amount of research papers regarding studies about kidney organoid synthesis from pluripotent stem cells and transplantation attempts.
But what I did not found (& my questions) are:

Are there any instances of successfully development and transplantation of kidney organoids in human beings? (yes/no)

If yes, then is it available as a therapeutic method? (yes/no)


texts:
if the adjective of the noun BACTERIUM is 'bacterial' and that of VIRUS is 'viral', what is the adjective for (BACTERIO)PHAGE? Is 'phagial' accepted?
Thank you


texts: NADP and NADPH in in vitro metabolisme test

texts:
I did an in vitro metabolism test using chicken liver S9 as the source of the enzyme. I did two different of method experiment. one was using NADP and second was using NADPH as the co-factor. my compound was fipronil, and I expect it to be metabolised become Fipronil sulfone (through oxidation reaction). The results, when I use NADP, fipronil sulfone formed was very low concentration, but in contrast, when using NADPH, I got high amount of fipronil sulfone.
what is the different using NADP and NADPH in this experiment?
Thank you for sharing the informatio.
Kind regards

Alex


texts: I know that microbes are not capable of sexual reproduction, thus sorting them into species according to "groups that can interbreed and generate fertile offspring" should not apply.


texts: Why are turtles classified as reptiles and not amphibians?

texts: I understand that turtles are reptiles because like all reptiles, they have scales on their body. But turtles (specifically sea turtles) live on both land and water, very much like amphibians. Also, don't sea turtles have more of a moist skin unlike reptiles? So is there any anatomical difference which makes turtles different from amphibians?


texts: How to get only perfect matches with blastn?

texts:
I have installed Blast locally and I've configured the nucleotide database to use. I want to search some sequences (from a .fastafile) in this genome. So I used blastn:

blastn -db NewDb -query input.fasta -out blast.txt

Then I added some options to require a 100% identity and no gaps:

blastn -db NewDb -query input.fasta -perc_identity 100 -ungapped -out blast.txt

But I still have some results where only a subpart of the string is matching the genome:

BLASTN 2.2.29+

[…]

Database: […].fasta
           20 sequences; N total letters

Query= Mutant M :

Length=226
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  chrom19                                                               435   3e-122
  chrom2                                                                429   1e-120

> chrom19
Length=W

 Score =   435 bits (226),  Expect = 3e-122
 Identities = 226/226 (100%), Gaps = 0/226 (0%)
 Strand=Plus/Plus

[…]

> chrom2
Length=Y

 Score =   429 bits (223),  Expect = 1e-120
 Identities = 223/223 (100%), Gaps = 0/223 (0%)
 Strand=Plus/Plus

[…]

Both results have an identity score of 100%, but the second result only use 223 of the 226 bases from the input sequence.

What parameters can I use with blastn to get only perfect matches, with 100% identity and all the nucleotide bases from the input sequence used?


texts: Identifying a thin, black, worm-like creature with a hammer-shaped head

texts:
I came across the creature shown in the photo below yesterday evening while walking the dogs. At first, I thought it was an earthworm, but a flashlight revealed it to be something I had never seen before.

It is approximately 12 inches (300 mm) in length and about 1/3 of an inch (10 mm) in diameter at its maximum. It is pitch black and very shiny—like piano black. It moves very slowly, using a snake-like motion. It had a very strange head, like a hammerhead shark.

I live in Durban, South Africa, if that helps to narrow down the possibilities.

Can anyone help in identifying this creature?


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

texts: I know that one way is to use the reagent sticks and the refractometer, but this is inaccurate. Is protein distinguishable when using a microscope? Is it time sensitive(i.e. have to test it right away)?


texts: How to find the concentration of an enzyme?

texts:
I need to know the concentration of pectinase enzyme (sigma aldrich) which has stated 5KU, 5U/mg protein (lowry) and lot result 20U/mg protein in the label of the enzyme bottle. This is all it has mentioned. How do I calculate the concentration from this information?

hey everyone, sorry for not been straight forward with the question. I'm asking for U/ml.I think I can find it if the label has mentioned the total volume of enzyme solution. Then I know how much mg in 5KU which is 5000/5=1000mg which I can easily get mg/ml or U/ml which is more appropriate. But the question is pointless if it hasn't mentioned the total volume. Thanks for the replies.

PS My supervisor asked me to prepare a standard graph of enzyme concentration (U/ml) against absorbance(O.D value) for DNS assay instead of a Galacturonic acid standard/glucose standard.(galacturonic acid is not available so he thinks it is better to you this graph than a standard glucose graph)

PS I checked the bottle again.On the bottom side of the bottle it has stated 10 ml.


texts: Why are oceans said to have "low productivity" in terms of photosynthesis?

texts: 80% of the world's photosynthesis takes place in the ocean. Despite this, oceans are also said to have low productivity - they cover 75% of the earth's surface, but out of the annual 170 billion tonnes of dry weight fixed by photosynthesis, they contribute to only 55 billion tonnes. Are not these two facts, which I have come across separately, contradictory? If oceans fix 80% of the total $\ce{CO2}$ fixed by photosynthesis on earth and release 80% of the total $\ce{O2}$ released by photosynthesis on earth, they should have accounted for 80% of the dry weight produced as well. Is there any way to reconcile these facts? In any case, if 80% photosynthesis occurs in oceans, that hardly seems low productivity - then why are oceans said to have low primary productivity (a host of reasons are also given for this - that light is not available at all depths in oceans, etc.)? A large amount of photosynthesis taking place should mean a large productivity!


texts: Is there any research on how accurately people can follow a beat?

texts:
I'm currently helping develop a rhythm game, and as part of the scoring system, I'd like to make scores and ranks based more on accurate pattern recognition rather than hitting notes very exactly on time as is the case for many games of this variety.

In many cases, the margin of error for the best judgment in rhythm games is so small that it seems to be a matter of chance more than skill that a certain judgment is counted between "excellent" and "good" (for example, one game has the margin as small as ±0.011 s).

Of course, some people are better at hitting notes accurately than others either naturally or through practice, but I would like to find some actual research into what the base neurological limitations to rhythmic precision are and to what degree practice can actually improve it.

As a baseline benchmark for the best judgment, I was thinking of looking for some research into how accurately people can follow the tick of a metronome - for example, by measuring the average deviation of somebody tapping a button to a regular beat after about 100 beats or so when they've gotten used to it.

A Google search didn't return anything useful, probably because the search terms draw up so much other, irrelevant content. Is there any prior research on this subject? If so, where can I find it? If not, how could I conduct such an experiment myself?


texts: Let's take the Influenzavirus as an example, and I have 5 of it. Would all 5 viruses have the same RNA with the same base order? Or would the RNA base order differ from eachother?


texts:
I was wondering which kind of plants would survive longest without CO2 : plants with fatty, thick leaves or plants with thinner, less fatty leaves?
And can we conclude that the plant species that are more dependent on CO2 levels, would benefit from the greenhouse effect?


texts: What is the equation and mechanism of Hopkins-Cole Test reaction?

texts:
The Hopkins-Cole reaction or glyoxylic acid reaction, is a chemical test used for qualitative detecting of tryptophan in protein solutions.

tryptophan + glyoxylic acid + sulfuric acid  >  violet product

I know the chemical formulas of reactants, but I could not find the product formula and a mechanism for the reaction.


texts: What happens to lipoprotein lipase after a sugar only diet?

texts:
Insulin increases the activity of lipoprotein lipase thay allows cells to take in lipids from chylomicrons in the blood.

If a person takes a sugar only meal like drinking coke, insulin is released. Will this insulin activate the lipoprotein lipase despite the lack of chylomicron synthesis due to lack of fat in the diet?

Could activation of the enzyme without adequate substrate be of any harm?


texts: Could bone marrow transplants help make xenotransplants viable?

texts:
So the immune system doesn't calibrate (for want of a better euphemism) to recognize it's own cells until fairly well along in fetal development & the major components of the immune system (antibodies, white blood cells, etc) are all produced by the bone marrow.

Those are the known details that cause me to wonder if this (below) might not be a viable approach.

Introduce the patients cells to a pig fetus before it's immune system has been set & it will be born with an immune system that recognizes both it's own cells & the patients cells as it's own.
Kill the patients own marrow (as per a normal bone marrow transplant) & transplant the pigs bone marrow into him giving him an immune system that recognizes both his cells & the pigs as it's own.

If my understanding is correct you should then be able to transplant any other organs from the pig into the patient without any tissue rejection issues.
I am only interested in the science so (any legal & moral issues aside) are there any major factors I'm unaware of to suggest this approach is a non-starter?

See Xeno: The Promise of Transplanting Animal Organs into Humans By David K. C. Cooper M.D., Robert P. Lanza M.D. Published 23 March 2000 by Oxford University Press, specifically the section on "The Induction of Chimerism Before Birth" from page 117 onward in this link.
That talks about my suggested first step (though in reverse), creating a human with immunity to cell rejection of a donor animals cells, which isn't much use to anyone who's already been born.
So I flipped the idea.

A Thymus transplant might be needed as well.


texts: What is the role of TATA box in transcriptional regulation?

texts: I know what is the TATA box, but I wish to know whether it has specific roles in transcriptional regulation.


texts: Robertsonian translocation on the same chromosome

texts: is there any big difference between Robert-son-i-an translocation between two 13 chromosomes comparing to a translocation between 13 and 14 chromosomes


texts: Why can't we see in low light if staring long enough?

texts:
For me it seems reasonable that if I kept my gaze on a fixed point in a room with low light, a progressively brighter and better picture would appear before my eyes, just like a camera can see in the dark if the shutter speed is really slow, e.g. 4 seconds exposure. Why can't our brain do this trick as well (accumulate visual information over time)? Or is it a limitation of the eyes?

edit:

To further clarify what I'm after; I will show a concrete example from the world of photography (images taken from this website).

Here is an example where we have a series of underexposed images - this would be what the brain receives:

Now, combining all of them with a simple add-operation reveals one image that has normal exposure.

This seems like a simple trick for our powerful brain - surely it can add incoming signals?


texts: How to determine if twins are identical or fraternal if only one is alive?

texts:
I had a twin brother who died at birth. I've missed him all my life, and have been curious to know if we were identical or fraternal.

Is there a test to determine whether we were identical or fraternal?


texts: Inheritance patterns in individuals with triploidy

texts:
If you search on the genetics of Down's Syndrome, you'll find plenty of results explaining the genetic mechanisms which can result in triploidy. However, I can't find any information on the inheritance combinations of triploidy - i.e. what are the possible genetic outcomes in the event that an individual with triploidy should reproduce.

It might seem unlikely, which is presumably why it's glossed over. However, I'm just curious about it from an academic standpoint.

So: how does one calculate the inheritance probabilities for a trait associated with triploidy, and what are the outcomes?


texts: Effect of pupil responses on the electroretinogram

texts:
The electroretinogram (ERG) is a measure of electrical activity of the retina. It is typically recorded from the cornea with a wire electrode or gold-foil electrode. Generally, the the ERG is considered to reflect the retinal processing of a light stimulus, typically a photoreceptor response followed by secondary neuronal activity and electrical activity evoked by supportive Muller cells.

I am wondering if the pupil response will add signal on top of the ERG? Firstly, there is the direct pupil response, which causes the pupil to constrict when the eye is subjected to bright light. Pupil constriction may, perhaps, induce electromyogram (EMG) activity when the smooth sphincter muscle around the pupil contracts, which in turn could theoretically contaminate the ERG. Secondly, there is neuronal activity involved in constricting the pupil, as light is processed in the retina by ganglion cells that in turn drive the pupil reflex. Furthermore, there is the consensual pupil response as well. This response causes the contralateral pupil to constrict when the ipsilateral eye is subjected to bright light. The consensual response is mediated by efferent input from the brain following stimulation of the other eye and causes both eyes to restrict. Hence, neural input arrives in the contralateral retina from the brain. This activity is not directly related to the processing of the light stimulus and may disturb the ERG proper when ERGs are recorded with a flash and both eyes are open.

So my question is

Does a pupil-mediated EMG affects the ERG signal?
Does neuronal activity involved in the pupil reflex affect the ERG, for example the  efferent input involved in the consensual response?

I have had no luck after extensive searches in text books, Scopus, Pubmed, Google, Google Scholar.


texts: Sensory-motor pathway from visceral organs

texts:
Does anyone know is which nerves carries the transmission of sensory-motor impulses from the visceral organs? Is it splanchnic nerves?
There is conflicting evidence in the literature. On the one hand, many sources told that splanchnic nerves belong to the sympathetic nervous system. On the other hand, there is information that sensory-motor impulses from the visceral organs travel along the splanchnic nerves. And there is a slight contradiction, because sensory-motor impulses usually go not in to to the sympathetic trunk, but to the dorsal ganglia. But the splanchic nerves connect just with the sympathetic trunk, and not with the dorsal ganglia.

For example, in this study:
https://www.ncbi.nlm.nih.gov/pubmed/22209656

sensory transmission pathways have been found to go to the spinal cord through the dorsal ganglia, which, to my knowledge, are not associated with splanchic nerves.


texts: How is a T lymphocyte specific to an antigen but not specific to an epitope?

texts:
In my immunology notes, it states that B lymphocytes (and other APCs) capture and present antigens to T lymphocytes that is specific for an antigen, but that the T cells do not necessarily recognise the same epitope. How can a cell be specific to an antigen but not to the epitope presenting on the surface of the antigen?

I've been in the process of discussing this with a friend and trying to make sense of Janeway's immunobiology and we've come to the theory that the APC recognises the antigen and takes it up, breaks it down and presents the epitope via the MHC where it is then recognised by the T cell. Am I right in saying that the antigen is broken down into many fragments that act as epitopes but each clonal expansion of T cells can only recognise the various epitopes of one antigen?


texts:
I saw this plant during the summer in Yorkshire, in the north of England. It was found near in a lowland area not too far from a river, but not in a boggy / marshy place. I’ve also seen them ok roadside verges as well.
I think it’s possibly related to a Lily, but I’m not sure at all about that.
Does anyone know what species this might be?


texts: Cerebral/Cerebellar Cortex versus Deep Nuclei

texts:
I have troubles using the terms Cortex & Deep Nuclei, and 'Nuclei' in general. From what I understand, a brain has '3 matter types in accordance to anatomical locations'

Superficial Grey matter - This is called the 'Cortex (Cerebral or Cerebellar Cortex)'

Middle White Matter
This is called 'Cerebral/Cerebellar White Matter' separating the cortex and deep nuclei

Deep Grey Matter, deep to the cortex -This is called 'Deep Nuclei' (for e.g.: Basal Nuclei of the Cerebrum, and four deep Cerebellar Nuclei (dentate, globose, emboliform, and fastigial))

Quote from the book that helps me to jump into this conclusion or summary:

  'The brain, like the spinal cord, is composed of gray and white
  matter. Gray matter - the seat of the neurosomas, dendrites, and
  synapses - forms a surface layer called the CORTEX over the cerebrum &
  cerebellum, and deeper masses called NUCLEI surrounded by white
  matter... (Saladin 2015, Unity of Form & Function, McGrawHill)

Thank you!


texts:
According to my understanding, vomiting happens when the body wants to get rid of something that we have ingested or put in our mouths to get it out of the body.

So why is it that when something smells really bad our bodies make us vomit even if we have not ingested the food, or not even put it in our mouth yet? Is this something psychological?

Thanks!


texts: What is an "end-to-end fusion" in the context of telomerase?

texts:
Telomerase is said to prevent "end-to-end fusion" of chromosomes.

My question is threefold:

What is an "end-to-end fusion"?
How does Telomerase prevent end-to-end fusions?
Why do end-to-end fusions cause problems in cells?


texts: Bone conduction . Different from the normal hearing phenomena in humans?

texts:
Bone conduction, is it something different from the normal phenomena of listening through the ears. I checked on some literature . Is it so that Bone conduction has very less to do with the ears and more to do with vibrations of the bones in the skull. Maybe I am mistaken . Please anyone can present a simple picture here and maybe some text to refer .
Thanks !


texts: Acrosomal enzymes and the female reproductive tract

texts: My textbook wrote that the reason why acrosomal enzymes are so securely contained within the sperm (thus needing capacitation to facilitate their release) is to prevent any premature release in the male reproductive tract. If they were released, they would start digesting the male organs. However, wouldn’t this apply in the female reproductive tract too, once capacitation has occurred? Does the female reproductive tract have some sort of protection against this? (I’m assuming that the sperm has been capacitated but has not fertilized the egg yet.)


texts: I have read that bacteria "thrive" in warm places. Naturally, I am very interested in why this is the case. Humans for instance thrive also in relatively warm conditions if it's too cold or too warm we die. However why would this also apply to bacteria?


texts: Could a mammal convert ingested dissolved CO2 to usable energy?

texts:
I'm trying to find out if it's possible that a mammal could orally ingest dissolved CO2 and convert it to energy for body heat, organ function, etc.

Unfortunately, most of the scientific sources I've been able to find talk instead of CO2 gas inhaled by mammals. All the sources speaking to orally ingested dissolved CO2 begin their argument with the assumption that all of it is converted to (and expelled as) gas in the digestive tract, but they never bother to prove that or cite anything.

It seems like this would rarely be observed in nature, and therefor not really be studied or documented, so I'm curious what degree of chemical or biological certainty there is about this, and what research has been done.


texts: I was just wondering if any animals (are smart enough to) enhance the flavor of their food by, for example, mixing ingredients or seasoning or letting it cure in some ways. In the first episode of Life (on Netflix), they show a monkey who dries some oily nuts for a week but that's just to make it easier to break the shell. But do any animals prepare their food in any way similar to human cooking?


texts: Passing virus/diseases immunity to newborn

texts:
From my understanding, our white blood cells 'learn' to fight off viruses and other pathogens that make us sick (or that they encounter because of vaccination) so that the subsequent encounters with same strain will not make us as sick; our immune system is able to fend off much better.

Newborns are protected with mother's antibodies via placenta and breast milk. My question is, can immunity be passed from mother to child via hereditary mechanisms, or does the child have a completely fresh set of 'default' defenses? Is that the reason why we get sick so easily when young?


texts: How does zoo and laboratory animal feeding work?

texts: What steps are taken to ensure those animals are fed adequately? When dealing with larger populations of animals, how is it ensured that all of those animals received food during a certain time period, and not fed multiple times by different people working different shifts? Is there a procedure in place for identifying and treating animals with over and under nutrition?


texts: Parasympathetic effects on digestive tract - motility versus absorption

texts:
The parasympathetic nervous system's purpose is often referred to as "rest and digest." As part of this purpose, parasympathetic innervation increases motility in the digestive tract to move food through. However at the same time, slowing gastric motility and peristalsis is important for absorbing nutrients, which is accomplished by enterogastrones like secretin.
So on one hand, the PSNS promotes more motility to move things through the digestive tract. On the other, certain hormones are released in response to the presence of food that slow down motility for better absorption.

If one of the main purposes of the PSNS is to promote digestion (and thus I would subsequently think absorption), why does it cause increased motility, which gives less time for digestion and absorption?
Is it important during digestion to sometimes increase or decrease motility? If so, how does it related to the PSNS and SNS in terms of when either happens?


texts: Why do we need to put phosphate fertilizers along with rhizobium?

texts: Isn't phosphorous a macro nutrient? So it should be present in the soil in sufficient quantities... but still we add phosphate. Why?


texts: How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees, what features would it have? Would it be highly reliable, well resolved etc? What other features are important to aim to maximise when it comes to improving phylogenetic trees?


texts: I've noticed on my dahlia plants that sometimes there's a flower which looks completely different then the rest . Either color or structural.  I dig these bulbs up each fall and keep inside to replant.  So my question is are these simply mutations, or caused by environmental factors or? I would assume the dna should be identical to the mother plant ? Thanks


texts: Where are newly discovered medicines tested

texts: When a medicine is prepared by a biologist,then where does he first test on? And how does he know that this is the exact combination for a disease to get cured? Does he test that medicine on a human or specific sample of blood? I'm an engineering student but still I'm curious to know.


texts: Where and how is information about pathogen immunity stored in a cell?

texts: If all of the DNA is being used, then how would the cell be able to store new information about pathogens in DNA? It's like a full hard drive that can't hold any more. So does the cell just compress the information about the pathogens and then just adjust the existing information about pathogens?


texts: I picked an apple from the ground, it was wet with dew and a woodlouse was stuck to it, with its back against the apple. When it got loose, it started flexing its "tail" like this for a while. Why?


texts:
I recently camped at Harriman State Park in Southern New York, in early October.  Upon returning home, I noticed that I had a passenger with me.

The caterpillar in question is an almost translucent, pale green color with a single reddish stripe running down the center of the back.  It is approximately 1.5 inches long, with a reddish face as well.

I tried using a caterpillar identification book, but the closest one I could find also had a split tail, which this one does not.


texts: In what fluid does the sperm swim in the oviduct?

texts:
We know that after sexual intercourse, sperm enters the female body and continues to pass through the oviduct by swimming. "Swimming" implies the presence of fluid.

I want to know what that fluid is called. Also could you please tell me the color of that fluid? Is it yellow/off-white?


texts: Are there tools for automatically parsing glycan names into tree structures?

texts:
My colleague and I are working on a project involving data produced at a glycan microarray facility. The array data that came back to us were a list of glycan names (in IUPAC condensed format). We would like to parse the list of 610 names into the graphical representation of the glycan.

To clarify, I wanted to take a list of glycans, written in the IUPAC condensed nomenclature, and return an image for each glycan. Here, each image would be the "graph" representation (nodes + edges). Ideally, I would like to be able to write a Python script to get this done, so we wouldn't have to do this by hand.

Is this possible? If so, what tools are available to get this done?

Thank you!


texts: What are the issues with excessive tandem repeats in replication?

texts: Why is it that tandem repeats like CAGCAGCAG cause primer-template misalignment and diseases like Huntingtons disease? By my understanding, too many such repeats can cause strands to form hairpins and loops that fail to be replicated in the template strand, causing deletions. Is this correct?


texts:
As I am not related to biology, I would appreciate if you can keep your answers as simple as possible.

My question is about the influence of alcohol on the brain. As far as I know, drinking alcohol is killing cells in the brain. But is it linear? E.g. if I have 1.0 per mil and it kills 1000 cells will 2.0 per mil kill 2000 cells?

(An equation would be nice)

Thanks


texts: what is the meaning of VIP-cre::LSL-TOM::SOMGFP(GIN) mice?

texts:
I am reading the following paper and the researchers use

  "VIP-cre::LSL-TOM::SOM-GFP(GIN)"

mice (page 4) for multi cell patch clamp and

  "VIP-cre::LSL-TOM and SOM-cre::LSL-TOM"

mice injected with AAV1 for two photon calcium imaging.

I have tried to look it up in the web.
I understand, for instance, that AAV1 is an engineered virus, and that CaMKII is a promotor, that TOM is a red fluorescent protein, GCaMPis created from fusion of green fluorescent protein with other peptides etc.

However, I have a dificulty in putting together the pieces and understending the whole meaning of "VIP-cre::LSL-TOM::SOMGFP(GIN)" (and the other mice types memtiond).

For example:

Take a VIP-Cre mouse. Does it mean that every VIP neuron in this mouse contains a Cre sequence in it's DNA?
What about other neurons, can they contain Cre also?
When they inject AAV1 virus to VIP-cre::LSL-TOM mice, does this mean that all neurons get the virus? including the VIP and SOM neurons?
Say I have an "VIP-cre::LSL-TOM::SOM-GFP(GIN)" mouse. I understand that VIP cells will be colored red and SOM cells will be colored green. So, why the VIP cells need the Cre promoter and the SOM cells don't?

I'll be greatfull if you could answer some of these questions, of refer me to a suitable reference. I looked a lot but the references that I find are lab references with technical details and numbers. I didn't find anything specific for this mice types that contains explanations.

Thank you!!


texts: How does temperature affect sex drive in humans?

texts:
I've ran into a science journalism piece which reported on a NBER study fidning that lower human fertility following hot temperatures over 80 degrees Farhenheit. They attributed this effect to possible mediation by lower sex drive in higher temperatures, although other mediating biological effects leading to this decrease fertility were also mentioned

  "Temperature extremes could affect coital frequency," researchers said. "It could affect hormone levels and sex drives. Alternatively, high temperatures may adversely affect reproductive health or semen quality on the male side, or ovulation on the female side."

Besides the obvious fact that temperature extremes would be unsuitable for any human activity, is there more direct evidence that subtle (as in a few degrees) temperature differences significantly affect sex drive in humans?


texts:
I understand that too much close reading will strain the ciliary muscles of the eyes. But what about small fonts? The contraction of the ciliary muscles is dependent on the distance not font size.

In other words, it is better to read from a closer monitor with bigger font or from a further monitor with smaller font?


texts: How is it known that Homo sapiens and Homo neanderthalensis interbred?

texts:
Many recent articles maintain that a small percentages of Neanderthal genes (up to 2%) are found in modern non-African people. (I believe that currently there is insufficient genetic material from older hominids, such as H. erectus, to decode a genome).

My question is: how is it known the “Neanderthal genes” found in modern humans got there by way of interbreeding? What distinguishes those genes from genes that both species inherited from a common ancestor? After all, Neanderthals and H. Sapiens are over 99% genetically identical. How is it determined that gene A is found in both because it was from H. erectus, from which both evolved; but gene B was not already present in H. sapiens, so it must have arisen through interbreeding?


texts: If CO2 only makes up about 0.04% of the earth’s atmosphere how do trees and organisms in the ocean produce oxygen to 10% of the earth’s atmosphere?


texts: Why is coconut oil healthier when it has so much saturated fat?

texts:
I noticed that coconut oil has ~96% saturated fat, and I was under the assumption that saturated fats = bad for health.

Why is it that coconut oil is healthier to alternatives with much less saturated fat?


texts: Does male or female DNA contain more information?

texts: I wonder if the male or the female DNA contains more or less information than the other?


texts: Sickle cell anemia is autosomal recessive. Then Why is it an example of codominant alleles? I thought a person with sickle cell trait is heterozygous because one of his/her alleles is recessive and the other one is dominant which is not codominant.


texts: Why do the deoxyribonucleotides use T and ribonucleotides use U?

texts:
We all know deoxyribonucleotides form DNA while ribonucleotides form RNA, DNA is double stranded while RNA is single stranded, and RNA can transcribe from DNA. We also know that DNA use A, G, C, T, while RNA use A, G, C, U and that it's the DNA that stores genetics information, not RNA.

My question is: how does the lost oxygen atom on deoxyribonucleotides 2' site of the sugar (turning it into a ribonucleotide), make such a large difference in function? It just an oxygen atom. Why don't they just all use U or all use T?

Why deoxyribose for DNA and ribose for RNA?
This answer may solve the question why is DNA double strand, RNA single strand, but it doesnt explain why does RNA uses U instead of T.


texts: Real-time PCR delay in Cq due to insertion SNP in primer

texts:
I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR.
I am most interested in how much there is a delay in Cq (treshold cycle value) if compared to perfectly matched primer. But if you do not have Cq data, I also collect "Yes or No" answers, saying, whether there was amplification or no amplification.

I am interested specifically in insertion or deletion mismatches. (For substitution mismatches, there is a lot of data.)

I will appreciate any published or unpublished evidence.


texts:
This happened in LaGrange GA. We heard some crawling around behind one of the faux-wood shutters on our front porch. So I eased it back and saw this:

If you can't make out the scale, the furry part was about 3 inches long. I didn't want him hanging out right there so I took the shutter off and tried to carry it to the woods but he jumped off. I videoed this:

https://photos.app.goo.gl/NsAFrcry8nJmykzQ7

He definitely had trouble flying but he didn't seem to be sick. He didn't look like a baby to me but I'm not familiar. Any idea what his problem was? He's currently either in the holly bush right next to the house or made his way to the woods in the back yard. I've heard horror storied about rabies so I avoided direct contact the best I could considering how cool this was to see one this close.


texts: How is silica transported to the leaves of genus Dendrocnide trees to form stinging needles for toxin delivery?

texts:
I just read the NYTimes' This Tree’s Leaves Look Soft and Inviting. Please Don’t Touch Them. which mentions the genus Dendrocnide and that Wikipedia section begins with:

Contact with the leaves or twigs causes the hollow, silica-tipped hairs to break off, penetrate the skin and inject the toxins.10 The hairs cause an extremely painful stinging sensation that could last from several hours to 1–2 days, recurring to a lessening degree for several months or more whenever the area is touched, exposed to water, or subjected to temperature change. The injured area becomes covered with small, red spots joining together to form a red, swollen welt. The hairs are also believed to be released to the air when the plant is cut or cleared in large areas. Workers without respiratory protection have reported sneezing, runny noses, mild nasal bleeding and throat irritation while cutting or clearing.
10Hurley, Marina. "'The worst kind of pain you can imagine' – what it's like to be stung by a stinging tree". The Conversation. Retrieved 2020-03-08.

and that article says:

The stinging hair structure is complex and consists of a tip, shaft and bulb composed of silica, calcium carbonate and calcium phosphate.

Reference 5 in Neurotoxic peptides from the venom of the giant Australian stinging tree (open access in Science) is Stinging hair morphology and wall biomineralization across five plant families: Conserved morphology versus divergent cell wall composition and this article contains a lot of information, for example following Figure 2:

Biomineralization
Notable differences were found in the mineralization of stinging hairs. Three zones of the stinging hairs could be distinguished based on their mineralization patterns. The tip regions were generally strongly mineralized with highly concentrated silica or calcium phosphate, except for Cnidoscolus stinging trichomes, which were completely nonmineralized. The shafts were usually mineralized with calcium carbonate, but in some cases with calcium phosphate or silica besides calcium carbonate. Trichome bases showed more irregular mineralization, mainly with calcium carbonate and often additional silica deposits (Fig. 2K, L), or they were not yet completely mineralized (Fig. 2M).

This article primarily addresses structure and morphology, but I'm interested in how silica actually makes its way into a leaf structure. Unlike calcium and phosphorous, neither elemental silicon nor SiO2 readily dissolve in water, so I'd like to ask the following:
Question: Presumably it comes from minerals in the soil, but is it transported as particles of silica, or molecules of SiO2, or by other chemical forms containing silicon and reformed as silica on site, or something else?


texts: Is there evidence for higher human genetic diversity prior to the alleged Toba Catastrophe genetic bottleneck?

texts:
I've been reading on the Toba Catastrophe theory and that it supposedly caused a genetic bottleneck in humans some 70k years ago, which raised a question that I couldn't find an answer to by searching the internet.

According to wikipedia:

  It is supported by genetic evidence suggesting that today's humans are
  descended from a very small population of between 1,000 and 10,000
  breeding pairs that existed about 70,000 years ago

My question is regarding this evidence.

Is it a case of simply observing expansion of genetic diversity form a projected point of low genetic diversity and pinning it on the event that is most likely to have caused it?

Or is there genetic evidence, obtained from sequencing DNA from humans from say 80k and 60k years ago that proves genetic diversity 80k years ago was indeed higher and abruptly dropped due to that exact catastrophic event?

The former seems kinda possible, because as severe as the eruption might have been, most of the people back then were in Africa, which is on the other side of the planet, and the estimated global impact doesn't seem to be anywhere nearly as severe as to cause the extinction of a substantial amount of the human population.

I think the human, as a more intelligent omnivore, should be somewhat more resilient to such catastrophes than any large herbivore or apex predator. Yet there is no information on such species being largely affected by that event, although there are a few species that appear have been affected.

Furthermore, there appears to be evidence that human populations were not completely extinct even in areas as close as southern India.

Last but not least:

  genetic analysis of Alu sequences across the entire human genome has
  shown that the effective human population size was less than 26,000 at
  1.2 million years ago; possible explanations for the low population size of human ancestors may include repeated population bottlenecks or
  periodic replacement events from competing Homo subspecies

and

  A study by Chad Yost and colleagues of cores from Lake Malawi dating
  to the period of the Toba supereruption showed no evidence of a
  volcanic winter, and they argue that there was no effect on African
  humans.[51] In the view of John Hawks, the study confirms evidence
  from a variety of studies that the eruption did not have a major
  climatic effect or any effect on human numbers

Which further goes to add substance to my suspicion that the Toba event, as unlikely as it may be as a cause, was simply picked as the most convenient / least unlikely candidate.

So, in short:

Is it known for an evidence supported fact that this particular eruption caused an abrupt drop in genetic diversity and a genetic bottleneck, and if so, reference to said evidence will be appreciated, or is it merely the most plausible candidate to explain an observable genetic diversity expansion from a projected fairly recent initial condition of low genetic diversity?

Or to put it even shorter, is there evidence that humans were more genetically diverse prior to said event?


texts:
How do delete a single gene encoded in an operon on a plasmid using E. coli? Could you use the same principle as when knocking out a gene from the bacterial chromosome which is e.g. suicide vector-derived allelic replacement through homologous recombination?

Thanks for your response.


texts: Can a postsynaptic neuron 'shut itself off?

texts: I am an amateur interested in neuroscience and was curious whether there is a process by which a neuron or group of neurons would close their receptors and stop receiving signals from specific synapses for a temporary period?


texts: What's the difference between the spindle assembly checkpoint (SAC) and mitotic checkpoint complex (MCC)?

texts: Are the SAC and MCC two separate complexes? Does the SAC activate the MCC? Thanks


texts: Why is marginal reconstruction "more correct" than joint reconstruction in some cases?

texts:
When reconstructing the ancestral states on a phylogenetic tree given the states at the tips, there are a number of methods for performing the reconstruction. This question is about marginal and joint maximum likelihood reconstruction.

To quote the wiki, marginal reconstrucion "is akin to a greedy algorithm that makes the locally optimal choice at each stage of the optimization problem", while joint reconstruction "find(s) the joint combination of ancestral character states throughout the tree which jointly maximizes the likelihood of the data"

Pupko et al. (2000) describe an algorithm for performing joint reconstruction.

I have a question about a paragraph in the discussion of this paper, where they discuss the differences in the results between the joint and marginal reconstructions.

  Deciding which is ‘‘ more  correct ’’ depends  on  the  question
  asked.  For instance, if one wishes to count the number of threonine-
  to-methionine replacements over the entire tree, then the joint
  reconstruction should be used to obtain this number (2,  in  our
  case,  on  the  branch  connecting  node  24  to node 3 and the branch
  connecting node 32 to node 33). However,  if  one  wishes  to
  synthesize  the  hypothetical cytochrome b sequence  of  the  ancestor
  of  Cetartiodactyla,  then  one  should  use  the  marginal
  reconstruction approach. We emphasize that both methods compute op-
  timal reconstructions by using all of the available data.
  Discrepancies originate not from misuse of information, but from the
  difference in the nature of the probabilistic questions asked

I don't understand why you would use marginal reconstruction for estimating the ancestral state at one node, or how the question you ask affects which method you should use. There is only one true ancestral state, I would think that the correct method for any question is the one that most accurately estimates the true ancestral state. Can someone shed some light on why the marginal reconstruction method is preferable in this situation?


texts: Why is high fructose corn syrup unhealthy?

texts: I understand that high fructose corn syrup was found to have detrimental effects on peoples' health. Why is this so?


texts: How does the human stomach handle a mix of digested and undigested food?

texts:
As I understand it, the stomach digests the bolus into chyme and then passes the latter on to the small intestine. This process takes between 40 minutes and a few hours.

However, what happens when the processing of the bolus is not completely finished and new food arrives in the stomach?

Will the stomach pass on all the food, including the only partially digested "new food" to the small intestine when the time for digesting the first load is up? Or will it keep all of the food until all of it is completely processed? Or does it have some way of allowing only the processed parts to pass on and keeping the unfinished parts behind, like a gate control?


texts: How were we able to determine the age of the first cell?

texts:
I heard in episode 20 of Youtube channel CrashCourse's biology series that every living organism descended from a single microorganism 3.8 billion years old. I'm astonished by that figure. Even though it leaves a good 100 million years of wiggle room.

As a mathematician I happen to have a fair background in physics so I have been able to grasp the concept of carbon dating and a few other techniques, none of which seem to me to explain how this was determined. What trace could we possibly have of such an organism ? I can't imagine a team finding a fossilised cell and shouting "We've found the first cell !".

Might it have something to do with a well determined evolutionary rate conjectured to be constant and leading back to that particular time ?